From 88881204ca4d0961c523d25abbf509020c63222e Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 6 Jul 2015 15:31:02 -0600 Subject: [PATCH 001/250] First commit rewriting Yellowstone testing suite --- tests/yellowstone/README | 14 +- tests/yellowstone/checkresults.py | 12 +- tests/yellowstone/runtests-mul.py | 320 ------------------ .../{runtests-ind.py => runtestsi.py} | 147 ++++---- tests/yellowstone/runtestsm.py | 128 +++++++ 5 files changed, 210 insertions(+), 411 deletions(-) delete mode 100755 tests/yellowstone/runtests-mul.py rename tests/yellowstone/{runtests-ind.py => runtestsi.py} (83%) create mode 100755 tests/yellowstone/runtestsm.py diff --git a/tests/yellowstone/README b/tests/yellowstone/README index e298557..c8078e4 100644 --- a/tests/yellowstone/README +++ b/tests/yellowstone/README @@ -3,14 +3,14 @@ compute system. The general order of operations is described below: 1) Run Tests - runtests-ind.py: Run any number of selected tests as individual jobs - submitted to the queue. This uses a single Specifier - for each PyReshaper job, and each job runs in parallel - with all of the other jobs. + runtestsi.py: Run any number of selected tests as individual jobs + submitted to the queue. This uses a single Specifier + for each PyReshaper job, and each job runs in parallel + with all of the other jobs. - runtests-mul.py: Run any number of selected tests as a single job submitted - to the queue. This uses a list of Specifiers for a single - MultiSpecReshaper job. + runtestsm.py: Run any number of selected tests as a single job submitted + to the queue. This uses a list of Specifiers for a single + MultiSpecReshaper job. 2) Check Test Results diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index d4f72e3..0a43e69 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -20,7 +20,7 @@ # Command-Line Interface Definition #============================================================================== def parse_cli(): - usage = 'usage: %prog [options] test_name1 test_name2 ...' + usage = 'usage: %prog [options] test_dir1 test_dir2 ...' parser = optparse.OptionParser(usage=usage) parser.add_option('-a', '--all', default=False, action='store_true', dest='all', @@ -134,8 +134,10 @@ def get_comparison_info(options, arguments, comm, testing_database): # Parse each test argument for test directories possible_test_dirs = [] if (options.all): - possible_test_dirs = glob.glob(os.path.join('*', 'ser', '*')) - possible_test_dirs.extend(glob.glob(os.path.join('*', 'par*', '*'))) + possible_test_dirs = glob.glob( + os.path.join('results', '*', 'ser', '*')) + possible_test_dirs.extend( + glob.glob(os.path.join('results', '*', 'par*', '*'))) else: possible_test_dirs = arguments @@ -163,7 +165,7 @@ def get_comparison_info(options, arguments, comm, testing_database): if (comm.rank == 0): print ' Test found in test info' new_results_dir = os.path.join( - cwd, test_name, run_type, ncformat, 'output') + cwd, 'results', test_name, run_type, ncformat, 'output') good_test = good_test and os.path.isdir(new_results_dir) if (comm.rank == 0): print ' New results dir found:', new_results_dir @@ -213,7 +215,7 @@ def get_comparison_info(options, arguments, comm, testing_database): if (comm.rank == 0): print ' Full test name:', full_test_name - log_dir = os.path.join(cwd, full_test_name) + log_dir = os.path.join(cwd, 'results', full_test_name) log_filename = os.path.join(log_dir, 'check-' + test_name + '.log') if (comm.rank == 0): print ' Log file will be:', log_filename diff --git a/tests/yellowstone/runtests-mul.py b/tests/yellowstone/runtests-mul.py deleted file mode 100755 index 8d22fd2..0000000 --- a/tests/yellowstone/runtests-mul.py +++ /dev/null @@ -1,320 +0,0 @@ -#!/usr/bin/env python -#============================================================================== -# -# multitest.py -# -# This script is written to make running the "Bake-Off" time-slice to -# time-series tests on Yellowstone easy and efficient. This allows code -# re-use for the various tests. -# -# This script requires the testinfo.json file be present in the same directory -# as the runtest script itself. -# -# This script runs MULTIPLE tests at a time. It uses the multi-spec -# reshaper, so every test is run sequentially (at the moment). -# -#============================================================================== -import optparse -import os -import sys -import shutil -import glob - -from subprocess import Popen, PIPE, STDOUT -import json - -#============================================================================== -# Command-Line Interface Definition -#============================================================================== -usage = 'usage: %prog [options] test_name1 test_name2 ...\n\n' \ - + ' This program is designed to run yellowstone-specific\n' \ - + ' tests of the PyReshaper. Each named test (or all tests if\n' \ - + ' the -a or --all option is used) will be given a run\n' \ - + ' directory in the current working directory with the same\n' \ - + ' name as the test itself. The run script will be placed\n' \ - + ' in the current working directory, as will be placed the\n' \ - + ' run output/error file. All output data files will be\n' \ - + ' placed in the output subdirectory.' -parser = optparse.OptionParser(usage=usage) -parser.add_option('-a', '--all', default=False, - action='store_true', dest='all', - help='True or False, indicating whether to run all tests ' - '[Default: False]') -parser.add_option('-c', '--code', default='STDD0002', - help='The name of the project code for charging in ' - 'parallel runs (ignored if running in serial) ' - '[Default: STDD0002]') -parser.add_option('-f', '--force', default=False, - action='store_true', dest='force', - help='True or False, indicating whether to force deleting ' - 'any existing test or run directories, if found ' - '[Default: False]') -parser.add_option('-i', '--test_info', default=None, - help='Location of the testinfo.json file ' - '[Default: None]') -parser.add_option('-l', '--list', default=False, - action='store_true', dest='list_tests', - help='True or False, indicating whether to list all tests, ' - 'instead of running tests. [Default: False]') -parser.add_option('-o', '--only', default=0, type='int', - help='Runs each test limited to the indicated number of ' - 'output files per processor. A value of 0 means ' - 'no limit (i.e., all output files) [Default: 0]') -parser.add_option('-p', '--processes', default=0, type='int', - help='The integer number of processes to request in parallel' - ' runs (0 means run in serial) [Default: 0]') -parser.add_option('-q', '--queue', default='economy', - help='The name of the queue to request in parallel runs ' - '(ignored if running in serial) ' - '[Default: economy]') -parser.add_option('-t', '--tiling', default=16, type='int', - help='The integer number of processes per node to request ' - 'in parallel runs (ignored if running in serial) ' - '[Default: 16]') -parser.add_option('-w', '--wtime', default=240, type='int', - help='The number of minutes to request for the wall clock ' - 'in parallel runs (ignored if running in serial) ' - '[Default: 240]') - -# Parse the CLI options and assemble the Reshaper inputs -(options, arguments) = parser.parse_args() - -#============================================================================== -# Initial pre-processing before running test -#============================================================================== - -# For convenience, pull out the useful option arguments -num_procs = options.processes -num_procs_per_node = options.tiling -queue_name = options.queue -project_code = options.code -output_limit = options.only - -wtime_hours = options.wtime / 60 -if (wtime_hours > 99): - wtime_hours = 99 - print 'Requested number of hours too large. Limiting to', wtime_hours, '.' -wtime_minutes = options.wtime % 60 -wtime_str = '%02d:%02d' % (wtime_hours, wtime_minutes) - -# See if there is a user-defined testinfo file, otherwise look for default -test_info_filename = '' -if (options.test_info == None): - runtest_dir = os.path.dirname(__file__) - test_info_filename = os.path.join(runtest_dir, 'testinfo.json') -else: - test_info_filename = os.path.abspath(options.test_info) - -# Try opening and reading the testinfo file -test_info = {} -try: - test_info_file = open(test_info_filename, 'r') - test_info = dict(json.load(test_info_file)) - test_info_file.close() -except: - err_msg = 'Problem reading and parsing test info file: ' \ - + str(test_info_filename) - raise ValueError(err_msg) - -# List tests only, if option is set -if (options.list_tests): - print 'Tests found in the Test Info file are:' - print - for test_name in test_info: - print ' ' + str(test_name) - sys.exit(0) - -# Determine which tests to run -test_names = arguments -if (options.all): - test_names = test_info.keys() -else: - for test_name in test_names: - if (test_name not in test_info): - print str(test_name) + ' not in testinfo file. Ignoring.' -print 'Tests to be run:', -for test_name in test_names: - print str(test_name), -print ' ' -print - -# Set the name of the job and script names -run_job_name = 'multirun' -run_script_name = run_job_name + '.sh' -python_script_name = run_job_name + '.py' - -#============================================================================== -# For each test, create the run directory and output dir -#============================================================================== - -output_dirs = {} -for test_name in test_names: - print 'Currently preparing test:', test_name - - # Create the test directory - test_dir = os.path.abspath(test_name) - if (num_procs > 0): - test_dir = os.path.join(test_dir, 'par' + str(num_procs)) - else: - test_dir = os.path.join(test_dir, 'ser') - - # Delete old directory, if forced - if (os.path.isdir(test_dir)): - if (options.force): - shutil.rmtree(test_dir, ignore_errors=True) - print ' Directory (' + test_dir + ') removed.' - else: - err_msg = ' Test directory (' + test_dir + ') already exists.' - raise RuntimeError(err_msg) - - # Make new test directory - os.makedirs(test_dir) - print ' Test directory (' + test_dir + ') created.' - - # Create the output subdirectory - output_dir = os.path.join(test_dir, 'output') - os.makedirs(output_dir) - output_dirs[test_name] = output_dir - print ' Output data directory (' + output_dir + ') created.' - print - -#============================================================================== -# Generate the bash run script -#============================================================================== - -run_script_str = ['#!/bin/bash'] - -# If necessary, add the parallel preamble -if (num_procs > 0): - run_script_str += [ - '#BSUB -n ' + str(num_procs), - '#BSUB -R "span[ptile=' + str(num_procs_per_node) + ']"', - '#BSUB -q ' + queue_name, - '#BSUB -a poe', - '#BSUB -x', - '#BSUB -o ' + run_job_name + '.%J.log', - '#BSUB -J ' + run_job_name, - '#BSUB -P ' + project_code, - '#BSUB -W ' + wtime_str, - '#', - 'export MP_TIMEOUT=14400', - 'export MP_PULSE=1800', - 'export MP_DEBUG_NOTIMEOUT=yes', - ''] - -# Now create the rest of the run script -run_script_str.extend(['', - '# NOTE: Your PYTHONPATH must be properly set before', - '# this script will run without error', - '', - '# Necessary modules to load', - 'module load python', - 'module load all-python-libs', - '']) - -# Generate the command line arguments -run_cmd_str = '' -if (num_procs > 0): - run_cmd_str += 'mpirun.lsf ' -run_cmd_str += 'python ' + python_script_name -run_script_str.append(run_cmd_str) -run_script_str.append('') - -# Open the run script file and write script -run_script_file = open(run_script_name, 'w') -run_script_file.write(os.linesep.join(run_script_str)) -run_script_file.close() - -#============================================================================== -# Generate the python script -#============================================================================== - -# Start the python script strings -python_script_str = [ - '#!/usr/bin/env python', - 'import glob', - '#', - '# PYTHONPATH must be set for this to work', - '#', - 'from pyreshaper import specification', - 'from pyreshaper import reshaper', - '', - 'spec_list = {}', - ''] - -# Define the Specifiers for each test -for test_name in test_names: - input_dir = str(test_info[test_name]['input_dir']) - input_file_list = [] - for input_glob in test_info[test_name]['input_globs']: - input_glob_str = str(input_glob) - full_input_glob = str(os.path.join(input_dir, input_glob)) - input_file_list.extend(glob.glob(full_input_glob)) - netcdf_format = str(test_info[test_name]['netcdf_format']) - output_prefix = str(os.path.join(output_dirs[test_name], - str(test_info[test_name]['output_prefix']))) - output_suffix = str(test_info[test_name]['output_suffix']) - time_variant_metadata = map(str, test_info[test_name]['metadata']) - - python_script_str.extend([ - 'spec = specification.create_specifier()', - 'spec.input_file_list = ' + repr(input_file_list), - 'spec.netcdf_format = ' + repr(netcdf_format), - 'spec.output_file_prefix = ' + repr(output_prefix), - 'spec.output_file_suffix = ' + repr(output_suffix), - 'spec.time_variant_metadata = ' + repr(time_variant_metadata), - 'spec_list[' + repr(str(test_name)) + '] = spec', - '']) - -# Now create the multi-spec reshaper and run -ser = str(num_procs == 0) -reshaper_params = 'spec_list, serial=' + ser + ', verbosity=2' -python_script_str.extend([ - 'rshpr = reshaper.create_reshaper(' + reshaper_params + ')', - 'rshpr.convert(output_limit=' + str(output_limit) + ')', - 'rshpr.print_diagnostics()' - '']) - -# Open the python script file and write script -python_script_file = open(python_script_name, 'w') -python_script_file.write(os.linesep.join(python_script_str)) -python_script_file.close() - -#============================================================================== -# Launch the job -#============================================================================== - -print 'Launching multitest job:', -if (num_procs == 0): - - # Launch the serial job as a subprocess - job = Popen(['bash', run_script_name], stdout=PIPE, stderr=STDOUT, - env=os.environ.copy()) - print 'PID:', str(job.pid) - sys.stdout.flush() - - # Wait for job to finish and grab job output - job_output = job.communicate()[0] - - # Write output to log file - log_file = open(run_job_name + '-ser.' + str(job.pid) + '.log', 'w') - log_file.write(job_output) - log_file.close() - -else: - - # Open up the run script for input to LSF's bsub - run_script_file = open(run_script_name, 'r') - - # Launch the parallel job with LSF bsub - job = Popen(['bsub'], stdout=PIPE, stderr=STDOUT, - stdin=run_script_file, env=os.environ.copy()) - - # Grab the bsub output - job_output = job.communicate()[0] - - # Close the script file and print submission info - run_script_file.close() - print job_output - -print diff --git a/tests/yellowstone/runtests-ind.py b/tests/yellowstone/runtestsi.py similarity index 83% rename from tests/yellowstone/runtests-ind.py rename to tests/yellowstone/runtestsi.py index cd21c52..b9812b9 100755 --- a/tests/yellowstone/runtests-ind.py +++ b/tests/yellowstone/runtestsi.py @@ -98,7 +98,7 @@ def parse_cli(): #============================================================================== # Find and generate the testing database #============================================================================== -def gen_testing_database(options): +def get_testing_database(options): # See if there is a user-defined testinfo file, otherwise look for default testing_database_filename = '' @@ -133,7 +133,7 @@ def gen_testing_database(options): #============================================================================== # Generate the list of tests to run #============================================================================== -def gen_tests_to_run(options, arguments, testing_database): +def get_tests_to_run(options, arguments, testing_database): # Determine which tests to run tests_to_run = arguments @@ -152,10 +152,41 @@ def gen_tests_to_run(options, arguments, testing_database): return tests_to_run +#============================================================================== +# Initialize the test for running +#============================================================================== +def get_test_dirname(options, test_name): + + # Create the test directory + test_dir = os.path.abspath(os.path.join('results', test_name)) + if (options.nodes > 0): + test_dir = os.path.join( + test_dir, 'par' + str(options.nodes) + 'x' + str(options.tiling)) + else: + test_dir = os.path.join(test_dir, 'ser') + test_dir = os.path.join(test_dir, options.ncformat) + + return test_dir + + +#============================================================================== +# Create the output directory +#============================================================================== +def create_dir(name, path): + # Create the output subdirectory + if os.path.isdir(path): + print ' ' + name.capitalize() + ' directory (' \ + + output_dir + ') already exists.' + else: + os.makedirs(path) + print ' ' + name.capitalize() + ' directory (' \ + + output_dir + ') created.' + + #============================================================================== # Generate the test run command #============================================================================== -def gen_run_command(options, test_name, output_dir, testing_database): +def create_run_command(options, test_name, output_dir, test_database): # Generate the command line run_args run_cmd = [] @@ -178,19 +209,19 @@ def gen_run_command(options, test_name, output_dir, testing_database): run_cmd.extend(['-f', format_str]) prefix_str = os.path.join( - output_dir, str(testing_database[test_name]['output_prefix'])) + output_dir, str(test_database[test_name]['output_prefix'])) run_cmd.extend(['-p', prefix_str]) - suffix_str = str(testing_database[test_name]['output_suffix']) + suffix_str = str(test_database[test_name]['output_suffix']) run_cmd.extend(['-s', suffix_str]) - for var_name in testing_database[test_name]['metadata']: + for var_name in test_database[test_name]['metadata']: run_cmd.extend(['-m', str(var_name)]) input_files_list = [] - for input_glob in testing_database[test_name]['input_globs']: + for input_glob in test_database[test_name]['input_globs']: full_input_glob = os.path.join( - str(testing_database[test_name]['input_dir']), input_glob) + str(test_database[test_name]['input_dir']), input_glob) #input_files_list.extend(glob.glob(full_input_glob)) input_files_list.append(full_input_glob) run_cmd.extend(input_files_list) @@ -199,9 +230,13 @@ def gen_run_command(options, test_name, output_dir, testing_database): #============================================================================== -# gen_submission_script - write bash run script as string +# create_run_script - write bash run script as string #============================================================================== -def gen_submission_script(options, test_name, run_command): +def create_run_script(options, test_name, test_dir, run_command): + + # Generate the run script name and path + run_script_filename = 'run-' + test_name + '.sh' + run_script_abspath = os.path.join(test_dir, run_script_filename) # Start creating the run scripts for each test run_script_list = ['#!/bin/bash'] @@ -249,76 +284,28 @@ def gen_submission_script(options, test_name, run_command): run_script_list.append(run_command) run_script_list.append('') - return run_script_list - - -#============================================================================== -# Initialize the test for running -#============================================================================== -def init_test(options, test_name, testing_database): - - print 'Currently preparing test:', test_name - - # Create the test directory - test_dir = os.path.abspath(test_name) - if (options.nodes > 0): - test_dir = os.path.join( - test_dir, 'par' + str(options.nodes) + 'x' + str(options.tiling)) - else: - test_dir = os.path.join(test_dir, 'ser') - test_dir = os.path.join(test_dir, options.ncformat) - - # Look for output directory...and make it - if (os.path.isdir(test_dir)): - print ' Test directory (' + test_dir + ') already exists.' - else: - os.makedirs(test_dir) - print ' Test directory (' + test_dir + ') created.' - - # Create the output subdirectory - output_dir = os.path.join(test_dir, 'output') - if os.path.isdir(output_dir): - print ' Output data directory (' + output_dir + ') already exists.' - else: - os.makedirs(output_dir) - print ' Output data directory (' + output_dir + ') created.' - - # Generate the run script - run_script_filename = 'run-' + test_name + '.sh' - run_script_abspath = os.path.join(test_dir, run_script_filename) - run_command = gen_run_command( - options, test_name, output_dir, testing_database) - run_script_list = gen_submission_script( - options, test_name, run_command) run_script_file = open(run_script_abspath, 'w') run_script_file.write(os.linesep.join(run_script_list)) run_script_file.close() print ' Run script written to', run_script_abspath - # Container for test info - test_info = {'name': test_name, - 'directory': test_dir, - 'output': output_dir, - 'script': run_script_abspath} - - return test_info + return run_script_abspath #============================================================================== # run_test - Run/Launch a test #============================================================================== -def run_test(test_info): +def run_test(test_name, test_dir, run_script): # Now launch the test cwd = os.getcwd() - os.chdir(test_info['directory']) + os.chdir(test_dir) print ' Launching test job:', if (options.nodes == 0): # Make the script executable - os.chmod(test_info['script'], - stat.S_IRWXU | stat.S_IRGRP | stat.S_IROTH) + os.chmod(run_script, stat.S_IRWXU | stat.S_IRGRP | stat.S_IROTH) # Launch the serial job as a subprocess - job = Popen([test_info['script']], stdout=PIPE, stderr=STDOUT, + job = Popen([run_script], stdout=PIPE, stderr=STDOUT, env=os.environ.copy()) print 'PID:', str(job.pid) sys.stdout.flush() @@ -327,13 +314,13 @@ def run_test(test_info): job_output = job.communicate()[0] # Write output to log file - log_file = open('reshaper-' + test_info['name'] + '.log', 'w') + log_file = open('reshaper-' + test_name + '.log', 'w') log_file.write(job_output) log_file.close() else: # Open up the run script for input to LSF's bsub - run_script_file = open(test_info['script'], 'r') + run_script_file = open(run_script, 'r') # Launch the parallel job with LSF bsub job = Popen(['bsub'], stdout=PIPE, stderr=STDOUT, @@ -352,23 +339,25 @@ def run_test(test_info): #============================================================================== -# For each test, initialize and run the test +# Command-Line Operation #============================================================================== -def run_tests(options, tests_to_run, testing_database): +if __name__ == '__main__': + options, arguments = parse_cli() + testing_database = get_testing_database(options) + tests_to_run = get_tests_to_run(options, arguments, testing_database) for test_name in tests_to_run: - test_info = init_test(options, test_name, testing_database) - run_test(test_info) + print 'Currently preparing test:', test_name + test_dir = get_test_dirname(options, test_name) + create_dir('test', test_dir) -#============================================================================== -# Main Execution Routine -#============================================================================== -def main(options, arguments): - testing_database = gen_testing_database(options) - tests_to_run = gen_tests_to_run(options, arguments, testing_database) - run_tests(options, tests_to_run, testing_database) + output_dir = os.path.join(test_dir, 'output') + create_dir('output', output_dir) + run_command = create_run_command( + options, test_name, output_dir, testing_database) -if __name__ == '__main__': - options, arguments = parse_cli() - main(options, arguments) + run_script = create_run_script( + options, test_name, test_dir, run_command) + + #run_test(test_name, test_dir, run_script) diff --git a/tests/yellowstone/runtestsm.py b/tests/yellowstone/runtestsm.py new file mode 100755 index 0000000..b5b4c66 --- /dev/null +++ b/tests/yellowstone/runtestsm.py @@ -0,0 +1,128 @@ +#!/usr/bin/env python +#============================================================================== +# +# runtestsm.py +# +# This script is written to make running the "Bake-Off" time-slice to +# time-series tests on Yellowstone easy and efficient. This allows code +# re-use for the various tests. +# +# This script requires the testinfo.json file be present in the same directory +# as the runtest script itself. +# +# This script runs MULTIPLE tests at one time through a single instance of +# the multi-specifier reshaper class. +# +#============================================================================== +import optparse +import os +import sys +import shutil +import glob + +from subprocess import Popen, PIPE, STDOUT +import json + +from runtestsi import * + + +#============================================================================== +# Generate the test run command +#============================================================================== +def create_run_command(options, python_script_name): + + # Generate the command line run_args + run_cmd = [] + if (options.nodes > 0): + run_cmd.append('mpirun.lsf') + run_cmd.extend(['python', python_script_name]) + + return ' '.join(run_cmd) + + +#============================================================================== +# Generate the python script +#============================================================================== +def create_python_script(options, test_name, output_dir, testing_database): + + # Start the python script strings + python_script_str = [ + '#!/usr/bin/env python', + 'import glob', + '#', + '# PYTHONPATH must be set for this to work', + '#', + 'from pyreshaper import specification', + 'from pyreshaper import reshaper', + '', + 'spec_list = {}', + ''] + + # Define the Specifiers for each test + input_dir = str(testing_database[test_name]['input_dir']) + input_file_list = [] + for input_glob in testing_database[test_name]['input_globs']: + input_glob_str = str(input_glob) + full_input_glob = str(os.path.join(input_dir, input_glob)) + input_file_list.extend(glob.glob(full_input_glob)) + netcdf_format = str(testing_database[test_name]['netcdf_format']) + output_prefix = str( + os.path.join(output_dir, + str(testing_database[test_name]['output_prefix']))) + output_suffix = str(testing_database[test_name]['output_suffix']) + time_variant_metadata = map( + str, testing_database[test_name]['metadata']) + + python_script_str.extend([ + 'spec = specification.create_specifier()', + 'spec.input_file_list = ' + repr(input_file_list), + 'spec.netcdf_format = ' + repr(netcdf_format), + 'spec.output_file_prefix = ' + repr(output_prefix), + 'spec.output_file_suffix = ' + repr(output_suffix), + 'spec.time_variant_metadata = ' + repr(time_variant_metadata), + 'spec_list[' + repr(str(test_name)) + '] = spec', + '']) + + # Now create the multi-spec reshaper and run + ser = str(num_procs == 0) + reshaper_params = 'spec_list, serial=' + ser + ', verbosity=2' + python_script_str.extend([ + 'rshpr = reshaper.create_reshaper(' + reshaper_params + ')', + 'rshpr.convert(output_limit=' + str(output_limit) + ')', + 'rshpr.print_diagnostics()' + '']) + + # Open the python script file and write script + python_script_name = 'run-' + test_name + '.py' + python_script_file = open(python_script_name, 'w') + python_script_file.write(os.linesep.join(python_script_str)) + python_script_file.close() + + return python_script_name + + +#============================================================================== +# Command-Line Operation +#============================================================================== +if __name__ == '__main__': + options, arguments = parse_cli() + testing_database = get_testing_database(options) + tests_to_run = get_tests_to_run(options, arguments, testing_database) + for test_name in tests_to_run: + print 'Currently preparing test:', test_name + + test_dir = get_test_dirname(options, test_name) + create_dir('test', test_dir) + + output_dir = os.path.join(test_dir, 'output') + create_dir('output', output_dir) + + python_script = create_python_script( + options, test_name, output_dir, testing_database) + + run_command = create_run_command(options, python_script) + + run_script = create_run_script( + options, test_name, test_dir, run_command) + + #run_test(test_name, test_dir, run_script) From 31caa43b7001dd0e384a937aacd9d791a0e3ab74 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 6 Jul 2015 15:36:49 -0600 Subject: [PATCH 002/250] Reorganizing Yellowstone tests directory --- tests/yellowstone/{postproc => }/getsizes.out | 0 tests/yellowstone/{postproc => }/getsizes.py | 0 tests/yellowstone/{postproc => }/mkplots.py | 3 ++- tests/yellowstone/utilities/__init__.py | 0 tests/yellowstone/{postproc => utilities}/plottools.py | 0 5 files changed, 2 insertions(+), 1 deletion(-) rename tests/yellowstone/{postproc => }/getsizes.out (100%) rename tests/yellowstone/{postproc => }/getsizes.py (100%) rename tests/yellowstone/{postproc => }/mkplots.py (99%) create mode 100644 tests/yellowstone/utilities/__init__.py rename tests/yellowstone/{postproc => utilities}/plottools.py (100%) diff --git a/tests/yellowstone/postproc/getsizes.out b/tests/yellowstone/getsizes.out similarity index 100% rename from tests/yellowstone/postproc/getsizes.out rename to tests/yellowstone/getsizes.out diff --git a/tests/yellowstone/postproc/getsizes.py b/tests/yellowstone/getsizes.py similarity index 100% rename from tests/yellowstone/postproc/getsizes.py rename to tests/yellowstone/getsizes.py diff --git a/tests/yellowstone/postproc/mkplots.py b/tests/yellowstone/mkplots.py similarity index 99% rename from tests/yellowstone/postproc/mkplots.py rename to tests/yellowstone/mkplots.py index 77b73a8..7eb5b41 100755 --- a/tests/yellowstone/postproc/mkplots.py +++ b/tests/yellowstone/mkplots.py @@ -21,7 +21,8 @@ #============================================================================== import optparse -import plottools as pt + +from utilities import plottools as pt #============================================================================== # Command-Line Interface Definition diff --git a/tests/yellowstone/utilities/__init__.py b/tests/yellowstone/utilities/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/yellowstone/postproc/plottools.py b/tests/yellowstone/utilities/plottools.py similarity index 100% rename from tests/yellowstone/postproc/plottools.py rename to tests/yellowstone/utilities/plottools.py From f98334937f536ba212035e490617565573b40c6f Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 6 Jul 2015 15:42:44 -0600 Subject: [PATCH 003/250] Creating stub to hold common testing routines --- tests/yellowstone/utilities/testtools.py | 8 ++++++++ 1 file changed, 8 insertions(+) create mode 100644 tests/yellowstone/utilities/testtools.py diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py new file mode 100644 index 0000000..bd3efe0 --- /dev/null +++ b/tests/yellowstone/utilities/testtools.py @@ -0,0 +1,8 @@ +#============================================================================== +# +# TestTools +# +# This is a collection of functions that are useful for running the PyReshaper +# tests on the Yellowstone compute system. +# +#============================================================================== From db02c07a100df81462b8e9ad41de56de71188614 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 6 Jul 2015 16:01:49 -0600 Subject: [PATCH 004/250] Starting testing database class --- tests/yellowstone/utilities/testtools.py | 30 ++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index bd3efe0..c77e9ce 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -6,3 +6,33 @@ # tests on the Yellowstone compute system. # #============================================================================== + + +class TestDatabase(object): + + def __init__(self, filename=None): + # See if there is a user-defined testinfo file, otherwise look for + # default + abspath = '' + if filename: + abspath = os.path.abspath(filename) + else: + this_dir = os.path.dirname(__file__) + abspath = os.path.join(this_dir, 'testinfo.json') + + # Try opening and reading the testinfo file + self._database = {} + try: + dbfile = open(filename, 'r') + self._database = dict(json.load(dbfile)) + dbfile.close() + except: + err_msg = 'Problem reading and parsing test info file: ' \ + + str(abspath) + raise ValueError(err_msg) + + def list_tests(self): + print 'Tests found in the Test Database are:' + print + for test_name in self._database: + print ' ' + str(test_name) From 45c087c3ea4dcb5ac4b1417e97d52e0037f50876 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 6 Jul 2015 16:02:31 -0600 Subject: [PATCH 005/250] Code comments only --- tests/yellowstone/utilities/testtools.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index c77e9ce..b6319b1 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -8,6 +8,9 @@ #============================================================================== +#============================================================================== +# TestDatabase Class +#============================================================================== class TestDatabase(object): def __init__(self, filename=None): From a65c3a1b0067c8128f3ca6a342fb068111c8972d Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Tue, 7 Jul 2015 16:19:44 -0600 Subject: [PATCH 006/250] Saving state. --- tests/yellowstone/utilities/testtools.py | 307 ++++++++++++++++++++++- 1 file changed, 295 insertions(+), 12 deletions(-) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index b6319b1..600a2e0 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -7,35 +7,318 @@ # #============================================================================== +# Builtin Modules +import glob + +# Third-Party Modules +import numpy as np +import Nio + +# Package Modules +from pyreshaper import specification + #============================================================================== -# TestDatabase Class +# Data Type Mapping & Sizes #============================================================================== -class TestDatabase(object): +__DTYPE_MAP = {'d': np.float64, 'f': np.float32, 'l': np.long, 'i': np.int32, + 'h': np.int16, 'b': np.int8, 'S1': np.character} + + +def __dtype_itemsize(tc): + dt = np.float + if tc in __DTYPE_MAP: + dt = __DTYPE_MAP(tc) + return np.dtype(dt).itemsize - def __init__(self, filename=None): - # See if there is a user-defined testinfo file, otherwise look for - # default - abspath = '' - if filename: - abspath = os.path.abspath(filename) + +def __shape_size(shp): + if (len(shp) > 0): + return reduce(lambda x, y: x * y, shp) + else: + return 1 + + +#============================================================================== +# Byte Size Conversion & Units +#============================================================================== +__BYTE_UNITS = ['Bytes', 'KB', 'MB', 'GB', 'PB'] + + +def __nbyte_str(n, exp=0): + if (n > 1024.): + return __nbyte_str(n / 1024., exp=exp + 1) + else: + if exp < len(__BYTE_UNITS): + units = __BYTE_UNITS[exp] + else: + n *= 1024.**(exp + 1 - len(__BYTE_UNITS)) + units = __BYTE_UNITS[-1] + return '%.4f %s' % (n, units) + + +#============================================================================== +# Test Database Class +#============================================================================== +class TestDB(object): + + def __init__(self, file_name=None): + """ + Constructor + + Parameters: + file_name (str): The name of the test database file. Defaults + to 'testinfo.json'. + + Raises: + ValueError: If the test database file cannot be opened and/or + read. + """ + # See if there is a user-defined testinfo file, + # otherwise look for default + abs_path = '' + if file_name: + abs_path = os.path.abs_path(file_name) else: this_dir = os.path.dirname(__file__) - abspath = os.path.join(this_dir, 'testinfo.json') + abs_path = os.path.join(this_dir, 'testinfo.json') # Try opening and reading the testinfo file self._database = {} try: - dbfile = open(filename, 'r') + dbfile = open(file_name, 'r') self._database = dict(json.load(dbfile)) dbfile.close() except: err_msg = 'Problem reading and parsing test info file: ' \ - + str(abspath) + + str(abs_path) raise ValueError(err_msg) - def list_tests(self): + # Reset the analysis state to False + self._analyzed = False + + def list(self): + """ + List the tests in the test database. + """ print 'Tests found in the Test Database are:' print for test_name in self._database: print ' ' + str(test_name) + return + + def create_specifier(self, test_name, ncfmt='netcdf4c', **kwargs): + """ + Create a Specifier object for the given named test. + + Parameters: + test_name (str): The string name of the test in the database + for which to construct the Specifier. + ncfmt (str): The NetCDF format string to be passed to the + Specifier. + kwargs (dict): A dictionary of additional options to be + sent to the Specifier. + + Returns: + Specifier: A Specifier instance with the information to run the + named test. + """ + + # Check types + if type(test_name) is not str: + err_msg = "Test name must be a string" + raise TypeError(err_msg) + if type(ncfmt) is not str: + err_msg = "NetCDF format must be a string" + raise TypeError(err_msg) + + # Check for the given test name + if test_name not in self._database: + err_msg = "Test '" + test_name + "' not found in database" + raise ValueError(err_msg) + + # Define the Specifier input + input_dir = str(self._database[test_name]['input_dir']) + infiles = [] + for input_glob in self._database[test_name]['input_globs']: + input_glob_str = str(input_glob) + full_input_glob = str(os.path.join(input_dir, input_glob)) + infiles.extend(glob.glob(full_input_glob)) + prefix = str( + os.path.join(output_dir, + str(self._database[test_name]['output_prefix']))) + suffix = str(self._database[test_name]['output_suffix']) + metadata = map(str, self._database[test_name]['metadata']) + + # Remove duplicate parameters from the kwargs dictionary + kwargs.pop('infiles', None) + kwargs.pop('prefix', None) + kwargs.pop('suffix', None) + kwargs.pop('metadata', None) + + # Return the Specifier + return specification.Specifier(infiles=infiles, ncfmt=ncfmt, + prefix=prefix, suffix=suffix, + metadata=metadata, **kwargs) + + def create_specifiers(self, test_list=[], ncfmt='netcdf4c', **kwargs): + """ + Create a dictionary of named Specifier objects for a list of tests. + + Parameters: + test_list (list): A list of string names of tests in the database + for which to construct Specifiers. + ncfmt (str): The NetCDF format string to be passed to the + Specifier. + kwargs (dict): A dictionary of additional options to be + sent to the Specifier. + + Returns: + Specifier: A Specifier instance with the information to run the + named test. + """ + + # Check types + if type(test_list) is not list: + err_msg = "Test list must be a list of string test names" + raise TypeError(err_msg) + test_types = [type(test_name) is str for test_name in test_list] + if not all(test_types): + err_msg = "Test list must be a list of string test names" + raise TypeError(err_msg) + + # Construct the list of specifiers + spec_list = [self.create_specifier(test_name, ncfmt, **kwargs) + for test_name in test_list] + + # Return a dictionary of named specifiers + return dict(zip(test_list, spec_list)) + + def analyze(self): + """ + Analyze the test database to determine test statistics + """ + + # If analysis has already been done, skip + if self._analyzed: + return + + # Initialize test statistics database + self._statistics = {} + + # Generate statistics for each test + for test_name in self._database: + + # Create a specifier for this test + spec = self.create_specifier(test_name, ncfmt='netcdf') + + # Validate the test information + spec.validate() + + # Sort the input files by name + spec.input_file_list.sort() + + # Open the first input file + infile = Nio.open_file(spec.input_file_list[0], 'r') + + # Get the name of the unlimited dimension (e.g., time) + tdim = None + for dim in infile.dimensions: + if infile.unlimited(dim): + tdim = dim + continue + + # Get the data dimensions + metadata_names = set(infile.dimensions.keys()) + + # Add the extra metadata variable names + metadata_names.update(set(spec.time_variant_metadata)) + + # Gather statistics for variables in dataset + self._statistics[test_name] = {} + for var_name in infile.variables.keys(): + self._statistics[test_name][var_name] = {} + var_obj = infile.variables[var_name] + + xshape = var_obj.shape + tlength = 1 + tvariant = False + if tdim in var_obj.dimensions: + xshape = list(xshape) + tindex = var_obj.dimensions.index(tdim) + tlength = xshape.pop(tindex) + xshape = tuple(xshape) + tvariant = True + self._statistics[test_name][var_name]['tvariant'] = tvariant + self._statistics[test_name][var_name]['xshape'] = xshape + self._statistics[test_name][var_name]['length'] = tlength + + xlen = __shape_size(xshape) + typecode = var_obj.typecode() + xsize = xlen * __dtype_itemsize(typecode) + self._statistics[test_name][var_name]['xsize'] = xsize + + if var_name in metadata_names: + self._statistics[test_name][var_name]['meta'] = True + else: + self._statistics[test_name][var_name]['meta'] = False + + # Close the first file + infile.close() + + # Loop over all input files and compute time-variant variable sizes + for file_name in spec.input_file_list[1:]: + + # Open the file + infile = Nio.open_file(file_name, 'r') + + # Get the number of time steps in the file + tlength = infile.dimensions[tdim] + + # Add the time length to each time-variant variable + for var_name in self._statistics[test_name]: + if self._statistics[test_name][var_name]['tvariant']: + self._statistics[test_name][ + var_name]['length'] += tlength + + # Close the file + infile.close() + + # Set the analyzed flag to Tru + self._analyzed = True + + def print_statistics(self): + """ + Print the statistics information determined from self analysis + """ + + # Perform self analysis, if needed + if not self._analyzed: + self.analyze() + + # Print the statistics information + for test_name in self._statistics: + print "Statistics for Test:", test_name + print + + test_stats = self._statistics[test_name] + num_vars = len(test_stats) + meta_mask = [test_stats[v]['meta'] for v in test_stats] + tvar_mask = [test_stats[v]['tvariant'] for v in test_stats] + + tser_mask = [not meta_mask[i] and tvar_mask[i] + for i in range(num_vars)] + imet_mask = [meta_mask[i] and not tvar_mask[i] + for i in range(num_vars)] + tmet_mask = [meta_mask[i] and tvar_mask[i] + for i in range(num_vars)] + lost_mask = [not meta_mask[i] and not tvar_mask[i] + for i in range(num_vars)] + + num_tser = sum(tser_mask) + print " Number of Time-Series Variables: ", num_tser + num_tmet = sum(tmet_mask) + print " Number of Time-Variant Metadata Variables: ", num_tmet + num_imet = sum(imet_mask) + print " Number of Time-Invariant Metadata Variables:", num_imet + num_lost = sum(lost_mask) From 7844a50c31da2f76d463cfdf1c846d870f536c0b Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 9 Jul 2015 08:09:22 -0600 Subject: [PATCH 007/250] Saving state. --- tests/yellowstone/utilities/testtools.py | 149 ++++++++++++++--------- 1 file changed, 94 insertions(+), 55 deletions(-) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index 600a2e0..9f6703a 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -19,41 +19,34 @@ #============================================================================== -# Data Type Mapping & Sizes +# Private Bytesize from Typecode Calculator #============================================================================== -__DTYPE_MAP = {'d': np.float64, 'f': np.float32, 'l': np.long, 'i': np.int32, - 'h': np.int16, 'b': np.int8, 'S1': np.character} - - -def __dtype_itemsize(tc): - dt = np.float - if tc in __DTYPE_MAP: - dt = __DTYPE_MAP(tc) - return np.dtype(dt).itemsize - - -def __shape_size(shp): - if (len(shp) > 0): - return reduce(lambda x, y: x * y, shp) - else: - return 1 +def __bytesize(tc): + DTYPE_MAP = {'d': np.float64, 'f': np.float32, 'l': np.long, 'i': np.int32, + 'h': np.int16, 'b': np.int8, 'S1': np.character} + return np.dtype(DTYPE_MAP.get(tc, np.float)).itemsize #============================================================================== -# Byte Size Conversion & Units +# Private Size from Shape Calculator #============================================================================== -__BYTE_UNITS = ['Bytes', 'KB', 'MB', 'GB', 'PB'] +def __shape2size(shp): + return 1 if len(shp) < 1 else reduce(lambda x, y: x * y, shp) +#============================================================================== +# Private Bytesize to Unit-string Converter +#============================================================================== def __nbyte_str(n, exp=0): + BYTE_UNITS = ['Bytes', 'KB', 'MB', 'GB', 'PB'] if (n > 1024.): return __nbyte_str(n / 1024., exp=exp + 1) else: - if exp < len(__BYTE_UNITS): - units = __BYTE_UNITS[exp] + if exp < len(BYTE_UNITS): + units = BYTE_UNITS[exp] else: - n *= 1024.**(exp + 1 - len(__BYTE_UNITS)) - units = __BYTE_UNITS[-1] + n *= 1024.**(exp + 1 - len(BYTE_UNITS)) + units = BYTE_UNITS[-1] return '%.4f %s' % (n, units) @@ -187,6 +180,10 @@ def create_specifiers(self, test_list=[], ncfmt='netcdf4c', **kwargs): err_msg = "Test list must be a list of string test names" raise TypeError(err_msg) + # If test list is empty, assume all tests + if len(test_list) == 0: + test_list = self._database.keys() + # Construct the list of specifiers spec_list = [self.create_specifier(test_name, ncfmt, **kwargs) for test_name in test_list] @@ -236,32 +233,36 @@ def analyze(self): # Gather statistics for variables in dataset self._statistics[test_name] = {} + self._statistics[test_name]['length'] = infile.dimensions[tdim] + self._statistics[test_name]['variables'] = {} for var_name in infile.variables.keys(): - self._statistics[test_name][var_name] = {} + self._statistics[test_name]['variables'][var_name] = {} var_obj = infile.variables[var_name] - xshape = var_obj.shape - tlength = 1 tvariant = False + xshape = var_obj.shape if tdim in var_obj.dimensions: - xshape = list(xshape) + xshape = list(shape) tindex = var_obj.dimensions.index(tdim) - tlength = xshape.pop(tindex) + xshape.pop(tindex) xshape = tuple(xshape) tvariant = True - self._statistics[test_name][var_name]['tvariant'] = tvariant - self._statistics[test_name][var_name]['xshape'] = xshape - self._statistics[test_name][var_name]['length'] = tlength + self._statistics[test_name]['variables'][ + var_name]['tvariant'] = tvariant + self._statistics[test_name]['variables'][ + var_name]['xshape'] = xshape - xlen = __shape_size(xshape) - typecode = var_obj.typecode() - xsize = xlen * __dtype_itemsize(typecode) - self._statistics[test_name][var_name]['xsize'] = xsize + xlen = __shape2size(xshape) + xsize = xlen * __bytesize(var_obj.typecode()) + self._statistics[test_name]['variables'][ + var_name]['xsize'] = xsize if var_name in metadata_names: - self._statistics[test_name][var_name]['meta'] = True + self._statistics[test_name][ + 'variables'][var_name]['meta'] = True else: - self._statistics[test_name][var_name]['meta'] = False + self._statistics[test_name]['variables'][ + var_name]['meta'] = False # Close the first file infile.close() @@ -272,14 +273,9 @@ def analyze(self): # Open the file infile = Nio.open_file(file_name, 'r') - # Get the number of time steps in the file - tlength = infile.dimensions[tdim] - - # Add the time length to each time-variant variable - for var_name in self._statistics[test_name]: - if self._statistics[test_name][var_name]['tvariant']: - self._statistics[test_name][ - var_name]['length'] += tlength + # And number of time steps to the test data + self._statistics[test_name][ + 'length'] += infile.dimensions[tdim] # Close the file infile.close() @@ -302,23 +298,66 @@ def print_statistics(self): print test_stats = self._statistics[test_name] - num_vars = len(test_stats) - meta_mask = [test_stats[v]['meta'] for v in test_stats] - tvar_mask = [test_stats[v]['tvariant'] for v in test_stats] + var_stats = test_stats['variables'] + num_steps = test_stats['length'] - tser_mask = [not meta_mask[i] and tvar_mask[i] + num_vars = len(var_stats) + meta_mask = [var_stats[v]['meta'] for v in var_stats] + tvar_mask = [var_stats[v]['tvariant'] for v in var_stats] + + timd_mask = [meta_mask[i] and not tvar_mask[i] for i in range(num_vars)] - imet_mask = [meta_mask[i] and not tvar_mask[i] + tvmd_mask = [meta_mask[i] and tvar_mask[i] for i in range(num_vars)] - tmet_mask = [meta_mask[i] and tvar_mask[i] + tser_mask = [not meta_mask[i] and tvar_mask[i] for i in range(num_vars)] lost_mask = [not meta_mask[i] and not tvar_mask[i] for i in range(num_vars)] num_tser = sum(tser_mask) print " Number of Time-Series Variables: ", num_tser - num_tmet = sum(tmet_mask) - print " Number of Time-Variant Metadata Variables: ", num_tmet - num_imet = sum(imet_mask) - print " Number of Time-Invariant Metadata Variables:", num_imet + num_tvmd = sum(tvmd_mask) + print " Number of Time-Variant Metadata Variables: ", num_tvmd + num_timd = sum(timd_mask) + print " Number of Time-Invariant Metadata Variables:", num_timd num_lost = sum(lost_mask) + if num_lost > 0: + print " WARNING:", num_lost, " unclassified variables" + print + + print " Number of Time Steps:", num_steps + + tvmd_shapes = set() + timd_shapes = set() + tser_shapes = set() + for name, stats in var_stats.items(): + if stats['meta']: + if stats['tvariant']: + tvmd_shapes.add(stats['xshape']) + else: + timd_shapes.add(stats['xshape']) + else: + tser_shapes.add(stats['xshape']) + + print " Time-Series Variable Shapes:" + print " ", " ".join(tser_shapes) + print " Time-Variant Metadata Shapes:" + print " ", " ".join(tvmd_shapes) + print " Time-Invariant Metadata Shapes:" + print " ", " ".join(timd_shapes) + print + + tser_xsize = sum([d['xsize'] + for d, m in zip(var_stats.values(), tser_mask)]) + tvmd_xsize = sum([d['xsize'] + for d, m in zip(var_stats.values(), tvmd_mask)]) + timd_xsize = sum([d['xsize'] + for d, m in zip(var_stats.values(), timd_mask)]) + + tser_bytesize = tser_xsize * num_steps + tvmd_bytesize = tvmd_xsize * num_steps + timd_bytesize = timd_xsize + + print " Time-Series Variable Total Size: ", __nbyte_str(tser_bytesize) + print " Time-Variant Metadata Total Size: ", __nbyte_str(tser_bytesize) + print " Time-Invariant Metadata Total Size:", __nbyte_str(tser_bytesize) From 014bb50e64adf02d92c52db851199395d2507632 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 9 Jul 2015 10:20:07 -0600 Subject: [PATCH 008/250] Adding the ability to the command-line tool to read a pickled Specifier --- bin/slice2series | 40 ++++++++++++++++++++++++++++++++-------- 1 file changed, 32 insertions(+), 8 deletions(-) diff --git a/bin/slice2series b/bin/slice2series index 3bea071..b0270a3 100755 --- a/bin/slice2series +++ b/bin/slice2series @@ -11,7 +11,11 @@ Copyright 2015, University Corporation for Atmospheric Research See the LICENSE.txt file for details """ +# Builtin Modules import optparse +import pickle + +# Package Modules from pyreshaper import specification from pyreshaper import reshaper @@ -57,6 +61,11 @@ def cli(): action='store_true', dest='overwrite', help='Whether to overwrite existing output files. ' '[Default: False]') + parser.add_option('--specfile', default=None, + help='Allows the user to use a Pickled Specifier (file) ' + 'as input to the script, instead of the command-' + 'line options and arguments.' + '[Default: None]') parser.add_option('-v', '--verbosity', default=1, type='int', help='Verbosity level for level of output. A value of 0 ' 'means no output, and a value greater than 0 means ' @@ -76,15 +85,30 @@ def cli(): #============================================================================== def main(options, input_file_list): - # Create the input object for the Reshaper - spec = specification.create_specifier() + # Check for a Specifier file + if options.specfile: + + # Try importing the file + try: + specfile = open(options.specfile, 'r') + spec = pickle.load(specfile) + specfile.close() + except: + err_msg = "Specifier File '" + str(options.specfile) + "' " + \ + "could not be opened and read" + raise RuntimeError(err_msg) + + else: + + # Create the input object for the Reshaper + spec = specification.create_specifier() - # Add input to the specifier - spec.input_file_list = input_file_list - spec.netcdf_format = options.netcdf_format - spec.output_file_prefix = options.output_prefix - spec.output_file_suffix = options.output_suffix - spec.time_variant_metadata = options.metadata + # Add input to the specifier + spec.input_file_list = input_file_list + spec.netcdf_format = options.netcdf_format + spec.output_file_prefix = options.output_prefix + spec.output_file_suffix = options.output_suffix + spec.time_variant_metadata = options.metadata # Create the PyReshaper object reshpr = reshaper.create_reshaper(spec, From 703ea6b4c5eceff509cec4ecbcbe824e034d3a65 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 9 Jul 2015 10:52:30 -0600 Subject: [PATCH 009/250] Using the recommended pickle formatting --- bin/slice2series | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/bin/slice2series b/bin/slice2series index b0270a3..d3176d3 100755 --- a/bin/slice2series +++ b/bin/slice2series @@ -90,9 +90,7 @@ def main(options, input_file_list): # Try importing the file try: - specfile = open(options.specfile, 'r') - spec = pickle.load(specfile) - specfile.close() + spec = pickle.load(specfile, open(options.specfile, 'rb')) except: err_msg = "Specifier File '" + str(options.specfile) + "' " + \ "could not be opened and read" From 934608f32bf48bec20a01905f4d945a25fdce589 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 9 Jul 2015 10:58:24 -0600 Subject: [PATCH 010/250] Updating the manual with the new options. --- docs/source/manual.rst | 107 +++++++++++++++++++++++++++++++++-------- 1 file changed, 88 insertions(+), 19 deletions(-) diff --git a/docs/source/manual.rst b/docs/source/manual.rst index 07d0a68..003e275 100644 --- a/docs/source/manual.rst +++ b/docs/source/manual.rst @@ -45,8 +45,22 @@ version. How do I set it up? =================== -Installation ------------- +Easy Installation +----------------- + +The easiest way to install the PyReshaper is from the Python Package Index, +PyPI. To do this, use the ``pip`` tool like follows. + +:: + + $ pip install [--user] PyReshaper + +If you do not have the required dependencies installed, then ``pip`` will +install them for you at this time. The ``--user`` option will be necessary +if you do not have system install privileges on the machine you are using. + +Installation from Source +------------------------ In this section, we describe how to install the PyReshaper package on a unix-like system. The procedure is similar for a Mac, but we have not @@ -65,7 +79,7 @@ Enter into the newly created directory and check out the stable tag. :: $ cd PyReshaper - $ git checkout v0.9.2 + $ git checkout [latest release] The contents of the repository will look like the following. @@ -79,7 +93,7 @@ To install in package, type the following command from this directory. :: - $ python setup.py install --user + $ python setup.py install [--user] If you are a system administrator, you can leave off the ``--user`` option, and the package will be installed in ``/usr/local``, by default. @@ -89,12 +103,11 @@ the ``--prefix`` option. Generating the API Documentation -------------------------------- -If you are a developer, you may find the Doxygen-generated API -documentation helpful in understanding the design and functionality of -the PyReshaper code. To generate this documentation, you must have -Sphinx available and installed. If you do, the API documentation can be -easily generated with the following command from the ``docs`` -directory. +If you are a developer, you may find the Sphinx API documentation helpful +in understanding the design and functionality of the PyReshaper code. To +generate this documentation, you must have Sphinx available and installed. +If you do, the API documentation can be easily generated with the following +command from the ``docs`` directory. :: @@ -120,11 +133,14 @@ to the manual in the HTML documentation. Before Using the PyReshaper --------------------------- -After the Pyreshaper package has been installed using the procedure -above, you must add the installation site-packages directory to your +If you installed the PyReshaper using ``pip``, then you should be ready to +go. However, if you using the ``--user`` option, the local install directories +using by ``pip`` may not be in your paths. + +First, you must add the installation site-packages directory to your ``PYTHONPATH``. If you installed with the ``--user`` option, this means -adding the ``$HOME/.local/lib/python2.X/site-packages`` directory to -your ``PYTHONPATH``. If you specified a different ``--prefix`` option, +adding the ``$HOME/.local/lib/python2.X/site-packages`` (on Linux) directory +to your ``PYTHONPATH``. If you specified a different ``--prefix`` option, then you must point to that prefix directory. For bash users, this is done with the following command. @@ -134,7 +150,7 @@ done with the following command. where the ``$PREFIX`` is the root installation directory used when installing the PyReshaper package (``$HOME/.local/`` if using the -``--user`` option), and the value of ``X`` will correspond to the +``--user`` option on Linux), and the value of ``X`` will correspond to the version of Python used to install the PyReshaper package. If you want to use the command-line interface to the PyReshaper, you @@ -383,6 +399,21 @@ By setting the ``verbosity`` parameter in the ``create_reshaper()`` function to a value of 2 or above will result in the greatest amount of output. +By default, the PyReshaper will not overwrite existing output files, if they +exist. In normal operation, this means the PyReshaper will error (and stop +execution) if output files are already present. This behavior can be +controlled with 2 other parameters: ``skip_existing`` and ``overwrite``. +Both parameters can be ``True`` or ``False``, and they both default to +``False``. When the ``overwrite`` parameter is set to ``True``, the +PyReshaper will delete existing files before running the reshaper operation. +When the ``skip_existing`` parameter is set to ``True``, the PyReshaper will +skip generating time-series files for the variables with existing files +present. Both decisions are done *before* the time-slice to time-series +convertion takes place, and in the case of the ``skip_existing`` parameter, +this means the remaining variables for which existing output files were not +found will be parallelized over during parallel operation. If both parameters +are used, then the ``overwrite`` parameter takes precedence. + Arguments to the ``convert()`` Function ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ @@ -395,7 +426,7 @@ time consumed in the ``convert()`` function. (A value of ``0`` indicates no limit, or all output files will be generated.) Using the PyReshaper from the Unix Command-Line -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +----------------------------------------------- While the most flexible way of using the PyReshaper is from within Python, as described above, it is also possible to run the PyReshaper @@ -406,7 +437,8 @@ Python script ``slice2series``, which provides a command-line interface directory.) Below is an example of how to use the PyReshaper CLI, ``slice2series``, -for a serial run. +for a serial run, with all options and parameters specified on the +command line. :: @@ -444,14 +476,51 @@ In the above example, this will launch the ``slice2series`` script into the MPI environment already created by either a request for an interactive session or from an LSF submission script. +It is also possible to run the ``slice2series` script with an existing +*specification* (or ``Specifier`` class instance). In this case, the existing +``Specifier`` instance must be saved to a *serialized* file (``pickle``), +such as with the following Python code. + +.. code:: py + + import pickle + + # Assume "spec" is an existing Specifier instance + pickle.dump(spec, open("specfile.p", "wb") ) + +Similarly, a serialized (*pickled*) ``Specifier`` instance can be read from +such a file with the following Python code. + +.. code:: py + + import pickle + + spec = pickle.load( open("specfile.p", "rb") ) + +This is what the ``slice2series`` code actually does under the hood. To +use such a serialized ``Specifier`` instance from the command-line interface, +use the ``--specfile`` option, as shown below. + +:: + + $ slice2series --serial --specfile=specfile.p + +Similarly, the parallel operation is simply preceded with the ``mpirun`` +command. + Additional Arguments to the ``slice2series`` Script ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -While the basic options shown in the previous two (2) examples above are +While the basic options shown in the previous examples above are sufficient for most purposes, two additional options are available. The ``--verbosity`` option can be used to set the verbosity level, just like the ``verbosity`` argument to the ``create_reshaper()`` function -described in the previous sections. Additionally, the ``--limit`` +described in the previous sections. The ``--limit`` command-line option can be used to set the ``output_limit`` argument of the Reshaper ``convert()`` function, also described in the previous sections. + +Additionally, the ``--skip_existing`` command-line option, if present, will +set the ``skip_existing`` parameter of the ``create_reshaper()`` function +to ``True``. Similarly, the ``--overwrite`` command-line option, if present, +will set the ``overwrite`` parameter to ``True``. From e34ceeab16096edaf246d793c535b3b802d17dee Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 9 Jul 2015 12:34:04 -0600 Subject: [PATCH 011/250] Adding runtools module for yellowstone job submission --- tests/yellowstone/utilities/runtools.py | 29 +++++++++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 tests/yellowstone/utilities/runtools.py diff --git a/tests/yellowstone/utilities/runtools.py b/tests/yellowstone/utilities/runtools.py new file mode 100644 index 0000000..6e1eaee --- /dev/null +++ b/tests/yellowstone/utilities/runtools.py @@ -0,0 +1,29 @@ +#============================================================================== +# +# TestTools +# +# This is a collection of functions that are useful for running the PyReshaper +# tests on the Yellowstone compute system. +# +#============================================================================== + +# Builtin Modules +import glob + +# Third-Party Modules +import numpy as np +import Nio + +# Package Modules +from pyreshaper import specification + + +#============================================================================== +# Script/Job Runner for Yellowstone +#============================================================================== +class Runner(object): + """ + A simple class for running jobs, writing submission scripts, etc + """ + + def __init__(self): \ No newline at end of file From 8e6999625f03ff668811a662645680f73d49b771 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 9 Jul 2015 12:56:54 -0600 Subject: [PATCH 012/250] Adding load/save to JSON file options for statistics --- tests/yellowstone/utilities/testtools.py | 182 +++++++++++++++++------ 1 file changed, 134 insertions(+), 48 deletions(-) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index 9f6703a..d1e14c6 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -9,6 +9,7 @@ # Builtin Modules import glob +import json # Third-Party Modules import numpy as np @@ -280,7 +281,70 @@ def analyze(self): # Close the file infile.close() - # Set the analyzed flag to Tru + # Compute self-analysis parameters + num_steps = self._statistics[test_name]['length'] + var_stats = self._statistics[test_name]['variables'] + num_vars = len(var_stats) + meta_mask = [var_stats[v]['meta'] for v in var_stats] + tvar_mask = [var_stats[v]['tvariant'] for v in var_stats] + + timd_mask = [meta_mask[i] and not tvar_mask[i] + for i in range(num_vars)] + tvmd_mask = [meta_mask[i] and tvar_mask[i] + for i in range(num_vars)] + tser_mask = [not meta_mask[i] and tvar_mask[i] + for i in range(num_vars)] + lost_mask = [not meta_mask[i] and not tvar_mask[i] + for i in range(num_vars)] + + # Compute numbers/counts + self._statistics[test_name]['counts'] = {} + self._statistics[test_name]['counts'][ + 'tseries'] = sum(tser_mask) + self._statistics[test_name]['counts'][ + 'tvariant'] = sum(tvmd_mask) + self._statistics[test_name]['counts'][ + 'tinvariant'] = sum(timd_mask) + self._statistics[test_name]['counts'][ + 'other'] = sum(lost_mask) + + # Compute shapes + self._statistics[test_name]['xshapes'] = {} + self._statistics[test_name]['xshapes'][ + 'tseries'] = set([d['xshape'] for d, m in + zip(var_stats.values(), tser_mask) if m]) + self._statistics[test_name]['xshapes'][ + 'tvariant'] = set([d['xshape'] for d, m in + zip(var_stats.values(), tvmd_mask) if m]) + self._statistics[test_name]['xshapes'][ + 'tinvariant'] = set([d['xshape'] for d, m in + zip(var_stats.values(), timd_mask) if m]) + + # Compute bytesizes + self._statistics[test_name]['totalsizes'] = {} + self._statistics[test_name]['totalsizes'][ + 'tseries'] = sum([d['xsize'] for d, m in + zip(var_stats.values(), tser_mask) if m]) * num_steps + self._statistics[test_name]['totalsizes'][ + 'tseries'] = sum([d['xsize'] for d, m in + zip(var_stats.values(), tvmd_mask) if m]) * num_steps + self._statistics[test_name]['totalsizes'][ + 'tseries'] = sum([d['xsize'] for d, m in + zip(var_stats.values(), timd_mask) if m]) + + # Compute maxima + self._statistics[test_name]['maxsizes'] = {} + self._statistics[test_name]['maxsizes'][ + 'tseries'] = max([d['xsize'] for d, m in + zip(var_stats.values(), tser_mask) if m]) * num_steps + self._statistics[test_name]['maxsizes'][ + 'tseries'] = max([d['xsize'] for d, m in + zip(var_stats.values(), tvmd_mask) if m]) * num_steps + self._statistics[test_name]['maxsizes'][ + 'tseries'] = max([d['xsize'] for d, m in + zip(var_stats.values(), timd_mask) if m]) + + # Set the analyzed flag to True self._analyzed = True def print_statistics(self): @@ -301,63 +365,85 @@ def print_statistics(self): var_stats = test_stats['variables'] num_steps = test_stats['length'] - num_vars = len(var_stats) - meta_mask = [var_stats[v]['meta'] for v in var_stats] - tvar_mask = [var_stats[v]['tvariant'] for v in var_stats] - - timd_mask = [meta_mask[i] and not tvar_mask[i] - for i in range(num_vars)] - tvmd_mask = [meta_mask[i] and tvar_mask[i] - for i in range(num_vars)] - tser_mask = [not meta_mask[i] and tvar_mask[i] - for i in range(num_vars)] - lost_mask = [not meta_mask[i] and not tvar_mask[i] - for i in range(num_vars)] + print " Number of Time Steps:", num_steps + print - num_tser = sum(tser_mask) + num_tser = test_stats['counts']['tseries'] print " Number of Time-Series Variables: ", num_tser - num_tvmd = sum(tvmd_mask) + num_tvmd = test_stats['counts']['tvariant'] print " Number of Time-Variant Metadata Variables: ", num_tvmd - num_timd = sum(timd_mask) + num_timd = test_stats['counts']['tinvariant'] print " Number of Time-Invariant Metadata Variables:", num_timd - num_lost = sum(lost_mask) + num_lost = test_stats['counts']['other'] if num_lost > 0: print " WARNING:", num_lost, " unclassified variables" print - print " Number of Time Steps:", num_steps + print " Time-Series Variable Transverse Shapes:" + print " ", " ".join(test_stats['xshapes']['tseries']) + print " Time-Variant Metadata Transverse Shapes:" + print " ", " ".join(test_stats['xshapes']['tvariant']) + print " Time-Invariant Metadata Transverse Shapes:" + print " ", " ".join(test_stats['xshapes']['tinvariant']) + print - tvmd_shapes = set() - timd_shapes = set() - tser_shapes = set() - for name, stats in var_stats.items(): - if stats['meta']: - if stats['tvariant']: - tvmd_shapes.add(stats['xshape']) - else: - timd_shapes.add(stats['xshape']) - else: - tser_shapes.add(stats['xshape']) - - print " Time-Series Variable Shapes:" - print " ", " ".join(tser_shapes) - print " Time-Variant Metadata Shapes:" - print " ", " ".join(tvmd_shapes) - print " Time-Invariant Metadata Shapes:" - print " ", " ".join(timd_shapes) + tser_totsize = test_stats['totalsizes']['tseries'] + tvmd_totsize = test_stats['totalsizes']['tvariant'] + timd_totsize = test_stats['totalsizes']['tinvariant'] + + print " Time-Series Variable Total Size: ", __nbyte_str(tser_totsize) + print " Time-Variant Metadata Total Size: ", __nbyte_str(tvmd_totsize) + print " Time-Invariant Metadata Total Size:", __nbyte_str(timd_totsize) print - tser_xsize = sum([d['xsize'] - for d, m in zip(var_stats.values(), tser_mask)]) - tvmd_xsize = sum([d['xsize'] - for d, m in zip(var_stats.values(), tvmd_mask)]) - timd_xsize = sum([d['xsize'] - for d, m in zip(var_stats.values(), timd_mask)]) + tser_maxsize = test_stats['maxsizes']['tseries'] + tvmd_maxsize = test_stats['maxsizes']['tvariant'] + timd_maxsize = test_stats['maxsizes']['tinvariant'] + + print " Time-Series Variable Max Size: ", __nbyte_str(tser_maxsize) + print " Time-Variant Metadata Max Size: ", __nbyte_str(tvmd_maxsize) + print " Time-Invariant Metadata Max Size:", __nbyte_str(timd_maxsize) + print + + def save_statistics(self, filename="teststats.json"): + """ + Save the statistics information to a JSON data file + + Parameters: + filename (str): The name of the JSON data file to write + """ + + # Check type + if type(filename) is not str: + err_msg = "File name must be a string" + raise TypeError(err_msg) + + # Check if statistics are available + if self._analyzed: + json.dump(self._statistics, open(filename, 'w')) - tser_bytesize = tser_xsize * num_steps - tvmd_bytesize = tvmd_xsize * num_steps - timd_bytesize = timd_xsize + def load_statistics(self, filename="teststats.json"): + """ + Load the statistics information from a JSON data file + + Parameters: + filename (str): The name of the JSON data file to read + """ - print " Time-Series Variable Total Size: ", __nbyte_str(tser_bytesize) - print " Time-Variant Metadata Total Size: ", __nbyte_str(tser_bytesize) - print " Time-Invariant Metadata Total Size:", __nbyte_str(tser_bytesize) + # Check type + if type(filename) is not str: + err_msg = "File name must be a string" + raise TypeError(err_msg) + + # Check if statistics are available + try: + statfile = open(filename, 'r') + self._statistics = dict(json.load(statfile)) + statfile.close() + except: + err_msg = "Failed to open and read statistics file '" + \ + str(filename) + "'" + raise RuntimeError(err_msg) + + # Set the analyzed flag + self._analyzed = True From 3b4ca907128f6fb8dacbdc8bf53316d7025724b3 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 9 Jul 2015 14:25:55 -0600 Subject: [PATCH 013/250] Adding script write function and launch function --- tests/yellowstone/utilities/runtools.py | 187 ++++++++++++++++++++++-- 1 file changed, 176 insertions(+), 11 deletions(-) diff --git a/tests/yellowstone/utilities/runtools.py b/tests/yellowstone/utilities/runtools.py index 6e1eaee..be39f5e 100644 --- a/tests/yellowstone/utilities/runtools.py +++ b/tests/yellowstone/utilities/runtools.py @@ -8,22 +8,187 @@ #============================================================================== # Builtin Modules -import glob - -# Third-Party Modules -import numpy as np -import Nio - -# Package Modules -from pyreshaper import specification +import os +import stat +from subprocess import Popen, PIPE, STDOUT #============================================================================== # Script/Job Runner for Yellowstone #============================================================================== -class Runner(object): +class Job(object): """ A simple class for running jobs, writing submission scripts, etc """ - - def __init__(self): \ No newline at end of file + + def __init__(self, filename="runscript.sh", nodes=0, tiling=16, + minutes=120, queue="small", pcode="STDD0002", runcmds=None): + """ + Constructor + + Parameters: + filename (str): Name of the run script + nodes (int): Number of nodes to request + tiling (int): Number of processors per node to request + minutes (int): Number of walltime minutes to request + queue (str): Name of queue to submit the job + runcmds (list): The list of commands to run + """ + self.set(filename=filename, nodes=nodes, tiling=tiling, + minutes=minutes, queue=queue, pcode=pcode, runcmds=runcmds) + + def set(self, filename=None, nodes=None, tiling=None, minutes=None, + queue=None, pcode=None, runcmds=None): + """ + Set the job specific parameters + + Parameters: + filename (str): Name of the run script + nodes (int): Number of nodes to request + tiling (int): Number of processors per node to request + minutes (int): Number of walltime minutes to request + queue (str): Name of queue to submit the job + runcmds (list): The list of commands to run + """ + if filename: + self._filename = str(filename) + self._rootname, runext = self._filename.rsplit('.', 1) + self._logext = 'log' if runext != 'log' else 'out' + self._rundir = os.path.dirname(os.path.realpath(self._filename)) + self._written = False + if nodes: + self._nodes = int(nodes) + self._written = False + if tiling: + self._tiling = int(tiling) + self._written = False + if minutes: + self._minutes = int(minutes) + self._written = False + if queue: + self._queue = str(queue) + self._written = False + if pcode: + self._pcode = str(pcode) + self._written = False + if runcmds: + self._written = False + self._runcmds = [] + if isinstance(runcmds, str): + self._runcmds.append(runcmds) + elif isinstance(runcmds, list): + strcmds = [str(cmd) for cmd in runcmds] + self._runcmds.extend(strcmds) + + def write(self): + """ + Write the run script associated with this job + + Parameters: + filename (str): Name of the run script file to write + """ + # Check if written already + if self._written: + return + + # Check that run commands have been set + if not self._runcmds: + err_msg = "Cannot write run script without run commands" + raise ValueError(err_msg) + + # Start creating the run scripts for each test + run_script_list = ['#!/bin/bash', ''] + + # If necessary, add the parallel preamble + if (self._nodes > 0): + + # Number of processors total + num_procs = self._nodes * self._tiling + + # Generate walltime in string form + wtime_hours = self._minutes / 60 + if (wtime_hours > 99): + wtime_hours = 99 + print 'Requested number of hours too large. Limiting to', \ + wtime_hours, '.' + wtime_minutes = self._minutes % 60 + wtime_str = '%02d:%02d' % (wtime_hours, wtime_minutes) + + # String list representing LSF preamble + run_script_list.extend([ + '#BSUB -n ' + str(num_procs), + '#BSUB -R "span[ptile=' + str(self._tiling) + ']"', + '#BSUB -q ' + self._queue, + '#BSUB -a poe', + '#BSUB -x', + '#BSUB -o ' + self._rootname + '.%J.' + self._logext, + '#BSUB -J ' + self._rootname, + '#BSUB -P ' + self._code, + '#BSUB -W ' + wtime_str, + '', + 'export MP_TIMEOUT=14400', + 'export MP_PULSE=1800', + 'export MP_DEBUG_NOTIMEOUT=yes', + '']) + + # Now create the rest of the run script + run_script_list.extend(['# Necessary modules to load', + 'module load python', + 'module load all-python-libs', + '']) + + run_script_list.extend(self._runcmds) + run_script_list.append('') + + # Write the script to file + run_script_file = open(self._filename, 'w') + run_script_file.write(os.linesep.join(run_script_list)) + run_script_file.close() + + def launch(self): + """ + Launch the job (or submit into the queue) + """ + + # Write run script, if not done yet + if not self._written: + self.write() + + # Now launch the test + cwd = os.getcwd() + os.chdir(self._rundir) + if (self._nodes == 0): + + # Make the script executable + os.chmod(self._filename, + stat.S_IRWXU | stat.S_IRGRP | stat.S_IROTH) + + # Launch the serial job as a subprocess + job = Popen([run_script], stdout=PIPE, stderr=STDOUT, + env=os.environ.copy()) + pid = str(job.pid) + + # Wait for job to finish and grab job output + job_output = job.communicate()[0] + + # Write output to log file + log_file = open(self._rootname + '.' + self._logext, 'w') + log_file.write(job_output) + log_file.close() + + else: + + # Open up the run script for input to LSF's bsub + run_script_file = open(self._filename, 'r') + + # Launch the parallel job with LSF bsub + job = Popen(['bsub'], stdout=PIPE, stderr=STDOUT, + stdin=run_script_file, env=os.environ.copy()) + + # Grab the bsub output + job_output = job.communicate()[0] + + # Close the script file and print submission info + run_script_file.close() + + os.chdir(cwd) From 0e093a0ed50f646c7c1adc0be361611cac4cc44e Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 9 Jul 2015 14:31:43 -0600 Subject: [PATCH 014/250] Auto importing the PyReshaper package --- tests/yellowstone/utilities/__init__.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/tests/yellowstone/utilities/__init__.py b/tests/yellowstone/utilities/__init__.py index e69de29..ef7d612 100644 --- a/tests/yellowstone/utilities/__init__.py +++ b/tests/yellowstone/utilities/__init__.py @@ -0,0 +1,2 @@ +import sys +sys.path.append("../../../source") \ No newline at end of file From c51c6aa11ee6a6797e2c086b2ca57d29b6e7172b Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 9 Jul 2015 14:36:07 -0600 Subject: [PATCH 015/250] Fixing imports --- tests/yellowstone/utilities/testtools.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index d1e14c6..3f843fd 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -8,11 +8,11 @@ #============================================================================== # Builtin Modules +import os import glob import json # Third-Party Modules -import numpy as np import Nio # Package Modules From f13f59e63520f684d31859313198809aaf1b8fab Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 9 Jul 2015 14:36:55 -0600 Subject: [PATCH 016/250] Fixing imports --- tests/yellowstone/utilities/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/utilities/__init__.py b/tests/yellowstone/utilities/__init__.py index ef7d612..79a87f9 100644 --- a/tests/yellowstone/utilities/__init__.py +++ b/tests/yellowstone/utilities/__init__.py @@ -1,2 +1,2 @@ import sys -sys.path.append("../../../source") \ No newline at end of file +sys.path.append("../../source") \ No newline at end of file From c081c46d35703f57c3fd54ff968d69bc697d8774 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 9 Jul 2015 14:38:36 -0600 Subject: [PATCH 017/250] Bugfix. Typo in abspath name --- tests/yellowstone/utilities/testtools.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index 3f843fd..e9c9648 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -72,7 +72,7 @@ def __init__(self, file_name=None): # otherwise look for default abs_path = '' if file_name: - abs_path = os.path.abs_path(file_name) + abs_path = os.path.abspath(file_name) else: this_dir = os.path.dirname(__file__) abs_path = os.path.join(this_dir, 'testinfo.json') From 242ea7b5641c8f71c6320988802c4d068353be61 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 9 Jul 2015 14:43:29 -0600 Subject: [PATCH 018/250] Type mismatch fixed when using test name keys --- tests/yellowstone/utilities/testtools.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index e9c9648..62fcade 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -208,7 +208,7 @@ def analyze(self): for test_name in self._database: # Create a specifier for this test - spec = self.create_specifier(test_name, ncfmt='netcdf') + spec = self.create_specifier(str(test_name), ncfmt='netcdf') # Validate the test information spec.validate() From c5cfdd1b5cf292c17a62d1963fbfdc3ac5ebaf00 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 9 Jul 2015 14:50:51 -0600 Subject: [PATCH 019/250] Storing unmodified output prefix in specifiers --- tests/yellowstone/utilities/testtools.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index 62fcade..4796193 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -138,9 +138,7 @@ def create_specifier(self, test_name, ncfmt='netcdf4c', **kwargs): input_glob_str = str(input_glob) full_input_glob = str(os.path.join(input_dir, input_glob)) infiles.extend(glob.glob(full_input_glob)) - prefix = str( - os.path.join(output_dir, - str(self._database[test_name]['output_prefix']))) + prefix = str(self._database[test_name]['output_prefix']) suffix = str(self._database[test_name]['output_suffix']) metadata = map(str, self._database[test_name]['metadata']) From 487a64c02eed0e5263b83a1b282ff2aec7f3674c Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 9 Jul 2015 14:52:34 -0600 Subject: [PATCH 020/250] Typo in variable name --- tests/yellowstone/utilities/testtools.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index 4796193..10ed350 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -241,7 +241,7 @@ def analyze(self): tvariant = False xshape = var_obj.shape if tdim in var_obj.dimensions: - xshape = list(shape) + xshape = list(xshape) tindex = var_obj.dimensions.index(tdim) xshape.pop(tindex) xshape = tuple(xshape) From 0a1430bc196b1d3fd6ea260690cebd23a28a64f8 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 9 Jul 2015 14:54:26 -0600 Subject: [PATCH 021/250] Function name changes to change scope --- tests/yellowstone/utilities/testtools.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index 10ed350..3578709 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -22,7 +22,7 @@ #============================================================================== # Private Bytesize from Typecode Calculator #============================================================================== -def __bytesize(tc): +def _bytesize(tc): DTYPE_MAP = {'d': np.float64, 'f': np.float32, 'l': np.long, 'i': np.int32, 'h': np.int16, 'b': np.int8, 'S1': np.character} return np.dtype(DTYPE_MAP.get(tc, np.float)).itemsize @@ -31,14 +31,14 @@ def __bytesize(tc): #============================================================================== # Private Size from Shape Calculator #============================================================================== -def __shape2size(shp): +def _shape2size(shp): return 1 if len(shp) < 1 else reduce(lambda x, y: x * y, shp) #============================================================================== # Private Bytesize to Unit-string Converter #============================================================================== -def __nbyte_str(n, exp=0): +def _nbyte_str(n, exp=0): BYTE_UNITS = ['Bytes', 'KB', 'MB', 'GB', 'PB'] if (n > 1024.): return __nbyte_str(n / 1024., exp=exp + 1) From 1c699911368b26c209833eb9abc19a555c48d9ba Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 9 Jul 2015 14:56:03 -0600 Subject: [PATCH 022/250] Fixed all other function names --- tests/yellowstone/utilities/testtools.py | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index 3578709..eb29759 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -41,7 +41,7 @@ def _shape2size(shp): def _nbyte_str(n, exp=0): BYTE_UNITS = ['Bytes', 'KB', 'MB', 'GB', 'PB'] if (n > 1024.): - return __nbyte_str(n / 1024., exp=exp + 1) + return _nbyte_str(n / 1024., exp=exp + 1) else: if exp < len(BYTE_UNITS): units = BYTE_UNITS[exp] @@ -251,8 +251,8 @@ def analyze(self): self._statistics[test_name]['variables'][ var_name]['xshape'] = xshape - xlen = __shape2size(xshape) - xsize = xlen * __bytesize(var_obj.typecode()) + xlen = _shape2size(xshape) + xsize = xlen * _bytesize(var_obj.typecode()) self._statistics[test_name]['variables'][ var_name]['xsize'] = xsize @@ -389,18 +389,18 @@ def print_statistics(self): tvmd_totsize = test_stats['totalsizes']['tvariant'] timd_totsize = test_stats['totalsizes']['tinvariant'] - print " Time-Series Variable Total Size: ", __nbyte_str(tser_totsize) - print " Time-Variant Metadata Total Size: ", __nbyte_str(tvmd_totsize) - print " Time-Invariant Metadata Total Size:", __nbyte_str(timd_totsize) + print " Time-Series Variable Total Size: ", _nbyte_str(tser_totsize) + print " Time-Variant Metadata Total Size: ", _nbyte_str(tvmd_totsize) + print " Time-Invariant Metadata Total Size:", _nbyte_str(timd_totsize) print tser_maxsize = test_stats['maxsizes']['tseries'] tvmd_maxsize = test_stats['maxsizes']['tvariant'] timd_maxsize = test_stats['maxsizes']['tinvariant'] - print " Time-Series Variable Max Size: ", __nbyte_str(tser_maxsize) - print " Time-Variant Metadata Max Size: ", __nbyte_str(tvmd_maxsize) - print " Time-Invariant Metadata Max Size:", __nbyte_str(timd_maxsize) + print " Time-Series Variable Max Size: ", _nbyte_str(tser_maxsize) + print " Time-Variant Metadata Max Size: ", _nbyte_str(tvmd_maxsize) + print " Time-Invariant Metadata Max Size:", _nbyte_str(timd_maxsize) print def save_statistics(self, filename="teststats.json"): From 06f514f9500b6cea99d2bf2304136928e1843bd8 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 9 Jul 2015 14:56:54 -0600 Subject: [PATCH 023/250] Cannot remove numpy import --- tests/yellowstone/utilities/testtools.py | 1 + 1 file changed, 1 insertion(+) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index eb29759..e3fdaf5 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -13,6 +13,7 @@ import json # Third-Party Modules +import numpy as np import Nio # Package Modules From f95ff4d3dd9574cbd414f6bc880f089e47e04ed9 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 9 Jul 2015 14:59:03 -0600 Subject: [PATCH 024/250] Misnamed dictionary keys when storing statistics info --- tests/yellowstone/utilities/testtools.py | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index e3fdaf5..f8012f8 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -325,11 +325,11 @@ def analyze(self): 'tseries'] = sum([d['xsize'] for d, m in zip(var_stats.values(), tser_mask) if m]) * num_steps self._statistics[test_name]['totalsizes'][ - 'tseries'] = sum([d['xsize'] for d, m in - zip(var_stats.values(), tvmd_mask) if m]) * num_steps + 'tvariant'] = sum([d['xsize'] for d, m in + zip(var_stats.values(), tvmd_mask) if m]) * num_steps self._statistics[test_name]['totalsizes'][ - 'tseries'] = sum([d['xsize'] for d, m in - zip(var_stats.values(), timd_mask) if m]) + 'tinvariant'] = sum([d['xsize'] for d, m in + zip(var_stats.values(), timd_mask) if m]) # Compute maxima self._statistics[test_name]['maxsizes'] = {} @@ -337,11 +337,11 @@ def analyze(self): 'tseries'] = max([d['xsize'] for d, m in zip(var_stats.values(), tser_mask) if m]) * num_steps self._statistics[test_name]['maxsizes'][ - 'tseries'] = max([d['xsize'] for d, m in - zip(var_stats.values(), tvmd_mask) if m]) * num_steps + 'tvariant'] = max([d['xsize'] for d, m in + zip(var_stats.values(), tvmd_mask) if m]) * num_steps self._statistics[test_name]['maxsizes'][ - 'tseries'] = max([d['xsize'] for d, m in - zip(var_stats.values(), timd_mask) if m]) + 'tinvariant'] = max([d['xsize'] for d, m in + zip(var_stats.values(), timd_mask) if m]) # Set the analyzed flag to True self._analyzed = True From 595d3dbf33852688c34ebffc7e76a853b61b7df2 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 9 Jul 2015 15:06:34 -0600 Subject: [PATCH 025/250] Need to check for len==0 since max fails with 0 length list --- tests/yellowstone/utilities/testtools.py | 31 +++++++++++++++--------- 1 file changed, 20 insertions(+), 11 deletions(-) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index f8012f8..08c2555 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -284,8 +284,8 @@ def analyze(self): num_steps = self._statistics[test_name]['length'] var_stats = self._statistics[test_name]['variables'] num_vars = len(var_stats) - meta_mask = [var_stats[v]['meta'] for v in var_stats] - tvar_mask = [var_stats[v]['tvariant'] for v in var_stats] + meta_mask = [var_stats[v]['meta'] for v in var_stats.keys()] + tvar_mask = [var_stats[v]['tvariant'] for v in var_stats.keys()] timd_mask = [meta_mask[i] and not tvar_mask[i] for i in range(num_vars)] @@ -333,15 +333,24 @@ def analyze(self): # Compute maxima self._statistics[test_name]['maxsizes'] = {} - self._statistics[test_name]['maxsizes'][ - 'tseries'] = max([d['xsize'] for d, m in - zip(var_stats.values(), tser_mask) if m]) * num_steps - self._statistics[test_name]['maxsizes'][ - 'tvariant'] = max([d['xsize'] for d, m in - zip(var_stats.values(), tvmd_mask) if m]) * num_steps - self._statistics[test_name]['maxsizes'][ - 'tinvariant'] = max([d['xsize'] for d, m in - zip(var_stats.values(), timd_mask) if m]) + if len(tser_mask) > 0: + maxsize = max([d['xsize'] for d, m in + zip(var_stats.values(), tser_mask) if m]) * num_steps + else: + maxsize = 0 + self._statistics[test_name]['maxsizes']['tseries'] = maxsize + if len(tser_mask) > 0: + maxsize = max([d['xsize'] for d, m in + zip(var_stats.values(), tvmd_mask) if m]) * num_steps + else: + maxsize = 0 + self._statistics[test_name]['maxsizes']['tvariant'] = maxsize + if len(tser_mask) > 0: + maxsize = max([d['xsize'] for d, m in + zip(var_stats.values(), timd_mask) if m]) + else: + maxsize = 0 + self._statistics[test_name]['maxsizes']['tinvariant'] = maxsize # Set the analyzed flag to True self._analyzed = True From 0a37045394d202f9528ecfeb9e2a1304b9629aae Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 9 Jul 2015 15:07:45 -0600 Subject: [PATCH 026/250] Check the wrong lengths. --- tests/yellowstone/utilities/testtools.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index 08c2555..588867f 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -339,13 +339,13 @@ def analyze(self): else: maxsize = 0 self._statistics[test_name]['maxsizes']['tseries'] = maxsize - if len(tser_mask) > 0: + if len(tvmd_mask) > 0: maxsize = max([d['xsize'] for d, m in zip(var_stats.values(), tvmd_mask) if m]) * num_steps else: maxsize = 0 self._statistics[test_name]['maxsizes']['tvariant'] = maxsize - if len(tser_mask) > 0: + if len(timd_mask) > 0: maxsize = max([d['xsize'] for d, m in zip(var_stats.values(), timd_mask) if m]) else: From ca701f402eb2ca59d0ad712b86e953e58f99bd9e Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 9 Jul 2015 15:11:00 -0600 Subject: [PATCH 027/250] Checking number of variables instead of length of mask --- tests/yellowstone/utilities/testtools.py | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index 588867f..4a47982 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -297,15 +297,15 @@ def analyze(self): for i in range(num_vars)] # Compute numbers/counts + num_tser = sum(tser_mask) + num_tvmd = sum(tvmd_mask) + num_timd = sum(timd_mask) + num_lost = sum(lost_mask) self._statistics[test_name]['counts'] = {} - self._statistics[test_name]['counts'][ - 'tseries'] = sum(tser_mask) - self._statistics[test_name]['counts'][ - 'tvariant'] = sum(tvmd_mask) - self._statistics[test_name]['counts'][ - 'tinvariant'] = sum(timd_mask) - self._statistics[test_name]['counts'][ - 'other'] = sum(lost_mask) + self._statistics[test_name]['counts']['tseries'] = num_tser + self._statistics[test_name]['counts']['tvariant'] = num_tvmd + self._statistics[test_name]['counts']['tinvariant'] = num_timd + self._statistics[test_name]['counts']['other'] = snum_lost # Compute shapes self._statistics[test_name]['xshapes'] = {} @@ -333,19 +333,19 @@ def analyze(self): # Compute maxima self._statistics[test_name]['maxsizes'] = {} - if len(tser_mask) > 0: + if num_tser > 0: maxsize = max([d['xsize'] for d, m in zip(var_stats.values(), tser_mask) if m]) * num_steps else: maxsize = 0 self._statistics[test_name]['maxsizes']['tseries'] = maxsize - if len(tvmd_mask) > 0: + if num_tvmd > 0: maxsize = max([d['xsize'] for d, m in zip(var_stats.values(), tvmd_mask) if m]) * num_steps else: maxsize = 0 self._statistics[test_name]['maxsizes']['tvariant'] = maxsize - if len(timd_mask) > 0: + if num_timd > 0: maxsize = max([d['xsize'] for d, m in zip(var_stats.values(), timd_mask) if m]) else: From 835389da87d014d2c241d52eee366b4213e927a3 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 9 Jul 2015 15:13:21 -0600 Subject: [PATCH 028/250] Typo fixed. --- tests/yellowstone/utilities/testtools.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index 4a47982..bedf777 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -305,7 +305,7 @@ def analyze(self): self._statistics[test_name]['counts']['tseries'] = num_tser self._statistics[test_name]['counts']['tvariant'] = num_tvmd self._statistics[test_name]['counts']['tinvariant'] = num_timd - self._statistics[test_name]['counts']['other'] = snum_lost + self._statistics[test_name]['counts']['other'] = num_lost # Compute shapes self._statistics[test_name]['xshapes'] = {} From 2989b6281f78b147915bb87169c91c84ca99df9b Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 9 Jul 2015 16:47:21 -0600 Subject: [PATCH 029/250] Attempt without the use of mask lists. --- tests/yellowstone/utilities/testtools.py | 93 ++++++++++-------------- 1 file changed, 37 insertions(+), 56 deletions(-) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index bedf777..4a4ceee 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -205,6 +205,7 @@ def analyze(self): # Generate statistics for each test for test_name in self._database: + print "Analyzing test:", str(test_name) # Create a specifier for this test spec = self.create_specifier(str(test_name), ncfmt='netcdf') @@ -243,8 +244,7 @@ def analyze(self): xshape = var_obj.shape if tdim in var_obj.dimensions: xshape = list(xshape) - tindex = var_obj.dimensions.index(tdim) - xshape.pop(tindex) + xshape.pop(var_obj.dimensions.index(tdim)) xshape = tuple(xshape) tvariant = True self._statistics[test_name]['variables'][ @@ -252,8 +252,7 @@ def analyze(self): self._statistics[test_name]['variables'][ var_name]['xshape'] = xshape - xlen = _shape2size(xshape) - xsize = xlen * _bytesize(var_obj.typecode()) + xsize = _shape2size(xshape) * _bytesize(var_obj.typecode()) self._statistics[test_name]['variables'][ var_name]['xsize'] = xsize @@ -261,8 +260,8 @@ def analyze(self): self._statistics[test_name][ 'variables'][var_name]['meta'] = True else: - self._statistics[test_name]['variables'][ - var_name]['meta'] = False + self._statistics[test_name][ + 'variables'][var_name]['meta'] = False # Close the first file infile.close() @@ -274,8 +273,8 @@ def analyze(self): infile = Nio.open_file(file_name, 'r') # And number of time steps to the test data - self._statistics[test_name][ - 'length'] += infile.dimensions[tdim] + self._statistics[test_name]['length'] += \ + infile.dimensions[tdim] # Close the file infile.close() @@ -284,23 +283,20 @@ def analyze(self): num_steps = self._statistics[test_name]['length'] var_stats = self._statistics[test_name]['variables'] num_vars = len(var_stats) - meta_mask = [var_stats[v]['meta'] for v in var_stats.keys()] - tvar_mask = [var_stats[v]['tvariant'] for v in var_stats.keys()] - - timd_mask = [meta_mask[i] and not tvar_mask[i] - for i in range(num_vars)] - tvmd_mask = [meta_mask[i] and tvar_mask[i] - for i in range(num_vars)] - tser_mask = [not meta_mask[i] and tvar_mask[i] - for i in range(num_vars)] - lost_mask = [not meta_mask[i] and not tvar_mask[i] - for i in range(num_vars)] + tser_vars = [str(v) for (v, s) in var_stats.items() + if not s['meta'] and s['tvariant']] + tvmd_vars = [str(v) for (v, s) in var_stats.items() + if s['meta'] and s['tvariant']] + timd_vars = [str(v) for (v, s) in var_stats.items() + if s['meta'] and not s['tvariant']] + lost_vars = [str(v) for (v, s) in var_stats.items() + if not s['meta'] and not s['tvariant']] # Compute numbers/counts - num_tser = sum(tser_mask) - num_tvmd = sum(tvmd_mask) - num_timd = sum(timd_mask) - num_lost = sum(lost_mask) + num_tser = sum(tser_vars) + num_tvmd = sum(tvmd_vars) + num_timd = sum(timd_vars) + num_lost = sum(lost_vars) self._statistics[test_name]['counts'] = {} self._statistics[test_name]['counts']['tseries'] = num_tser self._statistics[test_name]['counts']['tvariant'] = num_tvmd @@ -309,47 +305,32 @@ def analyze(self): # Compute shapes self._statistics[test_name]['xshapes'] = {} - self._statistics[test_name]['xshapes'][ - 'tseries'] = set([d['xshape'] for d, m in - zip(var_stats.values(), tser_mask) if m]) - self._statistics[test_name]['xshapes'][ - 'tvariant'] = set([d['xshape'] for d, m in - zip(var_stats.values(), tvmd_mask) if m]) - self._statistics[test_name]['xshapes'][ - 'tinvariant'] = set([d['xshape'] for d, m in - zip(var_stats.values(), timd_mask) if m]) + self._statistics[test_name]['xshapes']['tseries'] = list( + set([var_stats[v]['xshape'] for v in tser_vars])) + self._statistics[test_name]['xshapes']['tvariant'] = list( + set([var_stats[v]['xshape'] for v in tvmd_vars])) + self._statistics[test_name]['xshapes']['tinvariant'] = list( + set([var_stats[v]['xshape'] for v in timd_vars])) # Compute bytesizes self._statistics[test_name]['totalsizes'] = {} - self._statistics[test_name]['totalsizes'][ - 'tseries'] = sum([d['xsize'] for d, m in - zip(var_stats.values(), tser_mask) if m]) * num_steps - self._statistics[test_name]['totalsizes'][ - 'tvariant'] = sum([d['xsize'] for d, m in - zip(var_stats.values(), tvmd_mask) if m]) * num_steps - self._statistics[test_name]['totalsizes'][ - 'tinvariant'] = sum([d['xsize'] for d, m in - zip(var_stats.values(), timd_mask) if m]) + self._statistics[test_name]['totalsizes']['tseries'] = \ + sum([var_stats[v]['xsize'] for v in tser_vars]) + self._statistics[test_name]['totalsizes']['tvariant'] = \ + sum([var_stats[v]['xsize'] for v in tvmd_vars]) + self._statistics[test_name]['totalsizes']['tinvariant'] = \ + sum([var_stats[v]['xsize'] for v in timd_vars]) # Compute maxima self._statistics[test_name]['maxsizes'] = {} - if num_tser > 0: - maxsize = max([d['xsize'] for d, m in - zip(var_stats.values(), tser_mask) if m]) * num_steps - else: - maxsize = 0 + maxsize = 0 if num_tser == 0 else \ + max([var_stats[v]['xsize'] for v in tser_vars]) * num_steps self._statistics[test_name]['maxsizes']['tseries'] = maxsize - if num_tvmd > 0: - maxsize = max([d['xsize'] for d, m in - zip(var_stats.values(), tvmd_mask) if m]) * num_steps - else: - maxsize = 0 + maxsize = 0 if num_tvmd == 0 else \ + max([var_stats[v]['xsize'] for v in tvmd_vars]) * num_steps self._statistics[test_name]['maxsizes']['tvariant'] = maxsize - if num_timd > 0: - maxsize = max([d['xsize'] for d, m in - zip(var_stats.values(), timd_mask) if m]) - else: - maxsize = 0 + maxsize = 0 if num_timd == 0 else \ + max([var_stats[v]['xsize'] for v in timd_vars]) self._statistics[test_name]['maxsizes']['tinvariant'] = maxsize # Set the analyzed flag to True From 385bea147af72e424deb6e14a8a064f202de4dc7 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 9 Jul 2015 16:50:41 -0600 Subject: [PATCH 030/250] Typo. Need len not sum. --- tests/yellowstone/utilities/testtools.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index 4a4ceee..5705b6c 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -293,10 +293,10 @@ def analyze(self): if not s['meta'] and not s['tvariant']] # Compute numbers/counts - num_tser = sum(tser_vars) - num_tvmd = sum(tvmd_vars) - num_timd = sum(timd_vars) - num_lost = sum(lost_vars) + num_tser = len(tser_vars) + num_tvmd = len(tvmd_vars) + num_timd = len(timd_vars) + num_lost = len(lost_vars) self._statistics[test_name]['counts'] = {} self._statistics[test_name]['counts']['tseries'] = num_tser self._statistics[test_name]['counts']['tvariant'] = num_tvmd From 0b1b3809dc23393593c21c68783a3f0f62fd3282 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 9 Jul 2015 16:57:02 -0600 Subject: [PATCH 031/250] Need to convert lists to strings before printing --- tests/yellowstone/utilities/testtools.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index 5705b6c..50ef4d2 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -369,11 +369,11 @@ def print_statistics(self): print print " Time-Series Variable Transverse Shapes:" - print " ", " ".join(test_stats['xshapes']['tseries']) + print " ", " ".join(str(test_stats['xshapes']['tseries'])) print " Time-Variant Metadata Transverse Shapes:" - print " ", " ".join(test_stats['xshapes']['tvariant']) + print " ", " ".join(str(test_stats['xshapes']['tvariant'])) print " Time-Invariant Metadata Transverse Shapes:" - print " ", " ".join(test_stats['xshapes']['tinvariant']) + print " ", " ".join(str(test_stats['xshapes']['tinvariant'])) print tser_totsize = test_stats['totalsizes']['tseries'] From 9c285d3f24c564d2a0f127cc775e027e8cdff3c3 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 10 Jul 2015 08:35:10 -0600 Subject: [PATCH 032/250] Changing print format of shape tuples --- tests/yellowstone/utilities/testtools.py | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index 50ef4d2..d03074e 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -369,11 +369,14 @@ def print_statistics(self): print print " Time-Series Variable Transverse Shapes:" - print " ", " ".join(str(test_stats['xshapes']['tseries'])) + print " ", " ".join([str(s) for s in + test_stats['xshapes']['tseries']]) print " Time-Variant Metadata Transverse Shapes:" - print " ", " ".join(str(test_stats['xshapes']['tvariant'])) + print " ", " ".join([str(s) for s in + test_stats['xshapes']['tvariant']]) print " Time-Invariant Metadata Transverse Shapes:" - print " ", " ".join(str(test_stats['xshapes']['tinvariant'])) + print " ", " ".join([str(s) for s in + test_stats['xshapes']['tinvariant']]) print tser_totsize = test_stats['totalsizes']['tseries'] From 556f5e00e9b79f53febbefda0f2c019e8c89274e Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 10 Jul 2015 09:23:01 -0600 Subject: [PATCH 033/250] Adding some options to print/analyze only specified tests --- tests/yellowstone/utilities/testtools.py | 179 ++++++++++++++++------- 1 file changed, 128 insertions(+), 51 deletions(-) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index d03074e..10f586b 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -89,10 +89,28 @@ def __init__(self, file_name=None): + str(abs_path) raise ValueError(err_msg) - # Reset the analysis state to False - self._analyzed = False + # Initialize the statistics database + self._statistics = {} + + def get_database(self): + """ + Return the testing database as a dictionary + + Returns: + dict: The testing database + """ + return self._database + + def get_statistics(self): + """ + Return the test analysis statistics as a dictionary + + Returns: + dict: The statistics database + """ + return self._statistics - def list(self): + def print_list(self): """ List the tests in the test database. """ @@ -102,7 +120,8 @@ def list(self): print ' ' + str(test_name) return - def create_specifier(self, test_name, ncfmt='netcdf4c', **kwargs): + def create_specifier(self, test_name, ncfmt='netcdf4c', + outdir='', **kwargs): """ Create a Specifier object for the given named test. @@ -111,6 +130,10 @@ def create_specifier(self, test_name, ncfmt='netcdf4c', **kwargs): for which to construct the Specifier. ncfmt (str): The NetCDF format string to be passed to the Specifier. + outdir (str): An optional path string to be prepended to the + "output_prefix" argument of the Specifier. To be used to + direct output to a different location. Leave empty if using + absolute paths in the test's "output_prefix". kwargs (dict): A dictionary of additional options to be sent to the Specifier. @@ -126,6 +149,9 @@ def create_specifier(self, test_name, ncfmt='netcdf4c', **kwargs): if type(ncfmt) is not str: err_msg = "NetCDF format must be a string" raise TypeError(err_msg) + if type(outdir) is not str: + err_msg = "Output directory must be a string" + raise TypeError(err_msg) # Check for the given test name if test_name not in self._database: @@ -139,7 +165,8 @@ def create_specifier(self, test_name, ncfmt='netcdf4c', **kwargs): input_glob_str = str(input_glob) full_input_glob = str(os.path.join(input_dir, input_glob)) infiles.extend(glob.glob(full_input_glob)) - prefix = str(self._database[test_name]['output_prefix']) + prefix = str(os.path.join( + outdir, self._database[test_name]['output_prefix'])) suffix = str(self._database[test_name]['output_suffix']) metadata = map(str, self._database[test_name]['metadata']) @@ -154,58 +181,83 @@ def create_specifier(self, test_name, ncfmt='netcdf4c', **kwargs): prefix=prefix, suffix=suffix, metadata=metadata, **kwargs) - def create_specifiers(self, test_list=[], ncfmt='netcdf4c', **kwargs): + def create_specifiers(self, tests=[], ncfmt='netcdf4c', + outdir='', **kwargs): """ Create a dictionary of named Specifier objects for a list of tests. Parameters: - test_list (list): A list of string names of tests in the database + tests (list): A list of string names of tests in the database for which to construct Specifiers. ncfmt (str): The NetCDF format string to be passed to the Specifier. + outdir (str): An optional path string to be prepended to the + "output_prefix" argument of the Specifier. To be used to + direct output to a different location. Leave empty if using + absolute paths in the test's "output_prefix". kwargs (dict): A dictionary of additional options to be sent to the Specifier. Returns: - Specifier: A Specifier instance with the information to run the - named test. + list: A list of Specifier instances with the information to run the + named tests. """ # Check types - if type(test_list) is not list: - err_msg = "Test list must be a list of string test names" + if not isinstance(tests, (list, tuple)): + err_msg = "Test list must be a list or tuple of string test names" raise TypeError(err_msg) - test_types = [type(test_name) is str for test_name in test_list] + test_types = [type(test_name) is str for test_name in tests] if not all(test_types): err_msg = "Test list must be a list of string test names" raise TypeError(err_msg) # If test list is empty, assume all tests - if len(test_list) == 0: + if len(tests) == 0: test_list = self._database.keys() # Construct the list of specifiers - spec_list = [self.create_specifier(test_name, ncfmt, **kwargs) - for test_name in test_list] + specs = [self.create_specifier(test_name, ncfmt, **kwargs) + for test_name in tests] # Return a dictionary of named specifiers - return dict(zip(test_list, spec_list)) + return dict(zip(tests, specs)) - def analyze(self): + def analyze(self, tests=[], force=False): """ Analyze the test database to determine test statistics + + Parameters: + tests (list): A list of string names of tests in the database + to analyze. If empty, assume all tests. + force (bool): Whether to force reanalysis of tests that have + already been analyzed """ - # If analysis has already been done, skip - if self._analyzed: - return + # Check type + if not isinstance(tests, (list, tuple)): + err_msg = "Test name list must be of list or tuple type" + raise TypeError(err_msg) - # Initialize test statistics database - self._statistics = {} + # Error if tests not in database + bad_names = [t for t in tests if t not in self._database] + if len(bad_names) > 0: + err_msg = "Tests not found in database: " + ", ".join(bad_names) + raise ValueError(err_msg) + + # Assume all tests to be analyzed if empty input + if len(tests) == 0: + tests = self._database.keys() + + # If analysis has already been done, remove those tests + if not force: + tests = [t for t in tests if t not in self._statistics] + for test_name in [t for t in tests if t in self._statistics]: + print "Not Analyzing Test:", str(test_name) # Generate statistics for each test - for test_name in self._database: - print "Analyzing test:", str(test_name) + for test_name in tests: + print "Analyzing Test:", str(test_name) # Create a specifier for this test spec = self.create_specifier(str(test_name), ncfmt='netcdf') @@ -333,17 +385,29 @@ def analyze(self): max([var_stats[v]['xsize'] for v in timd_vars]) self._statistics[test_name]['maxsizes']['tinvariant'] = maxsize - # Set the analyzed flag to True - self._analyzed = True - - def print_statistics(self): + def print_statistics(self, tests=[]): """ Print the statistics information determined from self analysis + + Parameters: + tests (list): A list of string names of tests in the database + to print. If empty, assume all tests. """ - # Perform self analysis, if needed - if not self._analyzed: - self.analyze() + # Check type + if not isinstance(tests, (list, tuple)): + err_msg = "Test name list must be of list or tuple type" + raise TypeError(err_msg) + + # Error if tests not in database + bad_names = [t for t in tests if t not in self._statistics] + if len(bad_names) > 0: + err_msg = "Tests not found in statistics: " + ", ".join(bad_names) + raise ValueError(err_msg) + + # Assume all tests to be analyzed if empty input + if len(tests) == 0: + tests = self._statistics.keys() # Print the statistics information for test_name in self._statistics: @@ -397,45 +461,58 @@ def print_statistics(self): print " Time-Invariant Metadata Max Size:", _nbyte_str(timd_maxsize) print - def save_statistics(self, filename="teststats.json"): + def save_statistics(self, fileobj="teststats.json"): """ Save the statistics information to a JSON data file Parameters: - filename (str): The name of the JSON data file to write + fileobj (str, file): The name of the JSON data file to write, or an + open file instance with write permissions """ - # Check type - if type(filename) is not str: - err_msg = "File name must be a string" + # Check types + if isinstance(fileobj, str): + fp = open(fileobj, 'w') + elif isinstance(fileobj, file): + fp = fileobj + else: + err_msg = "File object must be a string or file instance" raise TypeError(err_msg) - # Check if statistics are available - if self._analyzed: - json.dump(self._statistics, open(filename, 'w')) + # Dump JSON data to file + try: + json.dump(self._statistics, fp) + except: + err_msg = "Failed to write statistics file" + raise RuntimeError(err_msg) + + # Close the file + fp.close() - def load_statistics(self, filename="teststats.json"): + def load_statistics(self, fileobj="teststats.json"): """ Load the statistics information from a JSON data file Parameters: - filename (str): The name of the JSON data file to read + fileobj (str): The name of the JSON data file to read or an + open file instance with read permissions """ - # Check type - if type(filename) is not str: - err_msg = "File name must be a string" + # Check types + if isinstance(fileobj, str): + fp = open(fileobj, 'r') + elif isinstance(fileobj, file): + fp = fileobj + else: + err_msg = "File object must be a string or file instance" raise TypeError(err_msg) - # Check if statistics are available + # Try reading the statistics try: - statfile = open(filename, 'r') self._statistics = dict(json.load(statfile)) - statfile.close() except: - err_msg = "Failed to open and read statistics file '" + \ - str(filename) + "'" + err_msg = "Failed to read statistics file" raise RuntimeError(err_msg) - # Set the analyzed flag - self._analyzed = True + # Close the file + fp.close() From 90779c96194f6bfe4a9e64fb66361ecf2bad147e Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 10 Jul 2015 09:34:54 -0600 Subject: [PATCH 034/250] Operation order was bad. Wasn't printing info message as a result. --- tests/yellowstone/utilities/testtools.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index 10f586b..a7b9325 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -251,9 +251,9 @@ def analyze(self, tests=[], force=False): # If analysis has already been done, remove those tests if not force: - tests = [t for t in tests if t not in self._statistics] for test_name in [t for t in tests if t in self._statistics]: print "Not Analyzing Test:", str(test_name) + tests = [t for t in tests if t not in self._statistics] # Generate statistics for each test for test_name in tests: From 801b3e1ea70f08d93104672e06657c56a95bdb96 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 10 Jul 2015 09:53:28 -0600 Subject: [PATCH 035/250] Not computing total sizes correct for time-variant variables --- tests/yellowstone/utilities/testtools.py | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index a7b9325..fb02df5 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -344,6 +344,13 @@ def analyze(self, tests=[], force=False): lost_vars = [str(v) for (v, s) in var_stats.items() if not s['meta'] and not s['tvariant']] + # Record the variables names + self._statistics[test_name]['names'] = {} + self._statistics[test_name]['names']['tseries'] = tser_vars + self._statistics[test_name]['names']['tvariant'] = tvmd_vars + self._statistics[test_name]['names']['tinvariant'] = timd_vars + self._statistics[test_name]['names']['other'] = lost_vars + # Compute numbers/counts num_tser = len(tser_vars) num_tvmd = len(tvmd_vars) @@ -367,9 +374,9 @@ def analyze(self, tests=[], force=False): # Compute bytesizes self._statistics[test_name]['totalsizes'] = {} self._statistics[test_name]['totalsizes']['tseries'] = \ - sum([var_stats[v]['xsize'] for v in tser_vars]) + sum([var_stats[v]['xsize'] for v in tser_vars]) * num_steps self._statistics[test_name]['totalsizes']['tvariant'] = \ - sum([var_stats[v]['xsize'] for v in tvmd_vars]) + sum([var_stats[v]['xsize'] for v in tvmd_vars]) * num_steps self._statistics[test_name]['totalsizes']['tinvariant'] = \ sum([var_stats[v]['xsize'] for v in timd_vars]) From ced3170808e86e0e92875e1371bcaa462f2b12ae Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 10 Jul 2015 09:58:16 -0600 Subject: [PATCH 036/250] Printing more statistics information --- tests/yellowstone/utilities/testtools.py | 28 +++++++++++++++++++----- 1 file changed, 22 insertions(+), 6 deletions(-) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index fb02df5..9555663 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -428,6 +428,7 @@ def print_statistics(self, tests=[]): print " Number of Time Steps:", num_steps print + # Print counts num_tser = test_stats['counts']['tseries'] print " Number of Time-Series Variables: ", num_tser num_tvmd = test_stats['counts']['tvariant'] @@ -439,6 +440,21 @@ def print_statistics(self, tests=[]): print " WARNING:", num_lost, " unclassified variables" print + # Print names + print " Time-Series Variables:" + print " ", ", ".join([str(v) for v in + test_stats['names']['tseries']]) + print " Time-Variant Metadata Variables:" + print " ", ", ".join([str(v) for v in + test_stats['names']['tvariant']]) + print " Time-Invariant Metadata Variables:" + print " ", ", ".join([str(v) for v in + test_stats['names']['tinvariant']]) + print " Unclassified Variables (neither meta not time-variant):" + print " ", ", ".join([str(v) for v in + test_stats['names']['other']]) + + # Print Transverse Shapes print " Time-Series Variable Transverse Shapes:" print " ", " ".join([str(s) for s in test_stats['xshapes']['tseries']]) @@ -450,21 +466,21 @@ def print_statistics(self, tests=[]): test_stats['xshapes']['tinvariant']]) print + # Print total bytesizes tser_totsize = test_stats['totalsizes']['tseries'] - tvmd_totsize = test_stats['totalsizes']['tvariant'] - timd_totsize = test_stats['totalsizes']['tinvariant'] - print " Time-Series Variable Total Size: ", _nbyte_str(tser_totsize) + tvmd_totsize = test_stats['totalsizes']['tvariant'] print " Time-Variant Metadata Total Size: ", _nbyte_str(tvmd_totsize) + timd_totsize = test_stats['totalsizes']['tinvariant'] print " Time-Invariant Metadata Total Size:", _nbyte_str(timd_totsize) print + # Print maximum bytesizes tser_maxsize = test_stats['maxsizes']['tseries'] - tvmd_maxsize = test_stats['maxsizes']['tvariant'] - timd_maxsize = test_stats['maxsizes']['tinvariant'] - print " Time-Series Variable Max Size: ", _nbyte_str(tser_maxsize) + tvmd_maxsize = test_stats['maxsizes']['tvariant'] print " Time-Variant Metadata Max Size: ", _nbyte_str(tvmd_maxsize) + timd_maxsize = test_stats['maxsizes']['tinvariant'] print " Time-Invariant Metadata Max Size:", _nbyte_str(timd_maxsize) print From 79391ed54e8212ba5e55ef6120cc73763e6c14ed Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 10 Jul 2015 10:19:27 -0600 Subject: [PATCH 037/250] Wrapping long lines of printed output --- tests/yellowstone/utilities/testtools.py | 23 ++++++++++++++--------- 1 file changed, 14 insertions(+), 9 deletions(-) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index 9555663..5727032 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -11,6 +11,7 @@ import os import glob import json +import textwrap # Third-Party Modules import numpy as np @@ -441,18 +442,22 @@ def print_statistics(self, tests=[]): print # Print names - print " Time-Series Variables:" - print " ", ", ".join([str(v) for v in - test_stats['names']['tseries']]) + print " Time-Series Variables:", + vlist = ", ".join([str(v) for v in + test_stats['names']['tseries']]) + print " " + "\n ".join(textwrap.wrap(vlist)) print " Time-Variant Metadata Variables:" - print " ", ", ".join([str(v) for v in - test_stats['names']['tvariant']]) + vlist = ", ".join([str(v) for v in + test_stats['names']['tvariant']]) + print " " + "\n ".join(textwrap.wrap(vlist)) print " Time-Invariant Metadata Variables:" - print " ", ", ".join([str(v) for v in - test_stats['names']['tinvariant']]) + vlist = ", ".join([str(v) for v in + test_stats['names']['tinvariant']]) + print " " + "\n ".join(textwrap.wrap(vlist)) print " Unclassified Variables (neither meta not time-variant):" - print " ", ", ".join([str(v) for v in - test_stats['names']['other']]) + vlist = ", ".join([str(v) for v in + test_stats['names']['other']]) + print " " + "\n ".join(textwrap.wrap(vlist)) # Print Transverse Shapes print " Time-Series Variable Transverse Shapes:" From a2e6a447f3e64083f61cfa1e764a84df129efa49 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 10 Jul 2015 10:20:22 -0600 Subject: [PATCH 038/250] Fixing formatting of printed output. --- tests/yellowstone/utilities/testtools.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index 5727032..42b63cd 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -442,7 +442,7 @@ def print_statistics(self, tests=[]): print # Print names - print " Time-Series Variables:", + print " Time-Series Variables:" vlist = ", ".join([str(v) for v in test_stats['names']['tseries']]) print " " + "\n ".join(textwrap.wrap(vlist)) From 6fa277df840d6e71eeb454ecd28096b272a6423c Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 10 Jul 2015 10:21:34 -0600 Subject: [PATCH 039/250] More format fixing --- tests/yellowstone/utilities/testtools.py | 1 + 1 file changed, 1 insertion(+) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index 42b63cd..aa1277c 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -458,6 +458,7 @@ def print_statistics(self, tests=[]): vlist = ", ".join([str(v) for v in test_stats['names']['other']]) print " " + "\n ".join(textwrap.wrap(vlist)) + print # Print Transverse Shapes print " Time-Series Variable Transverse Shapes:" From 9ab31c47574e72558f941776cb6b407980f1717e Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 10 Jul 2015 10:24:48 -0600 Subject: [PATCH 040/250] Adding all time-invariant variable names to metadata list --- tests/yellowstone/utilities/testtools.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index aa1277c..0e482ab 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -300,6 +300,8 @@ def analyze(self, tests=[], force=False): xshape.pop(var_obj.dimensions.index(tdim)) xshape = tuple(xshape) tvariant = True + if not tvariant: + metadata_names.add(var_name) self._statistics[test_name]['variables'][ var_name]['tvariant'] = tvariant self._statistics[test_name]['variables'][ From 5eeb8a0f6c370c27ee996fb2991d81c8b72af7d7 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 10 Jul 2015 10:26:07 -0600 Subject: [PATCH 041/250] Cleaning up output --- tests/yellowstone/utilities/testtools.py | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index 0e482ab..4952bc8 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -456,11 +456,12 @@ def print_statistics(self, tests=[]): vlist = ", ".join([str(v) for v in test_stats['names']['tinvariant']]) print " " + "\n ".join(textwrap.wrap(vlist)) - print " Unclassified Variables (neither meta not time-variant):" - vlist = ", ".join([str(v) for v in - test_stats['names']['other']]) - print " " + "\n ".join(textwrap.wrap(vlist)) - print + if num_lost > 0: + print " Unclassified Variables (neither meta nor time-variant):" + vlist = ", ".join([str(v) for v in + test_stats['names']['other']]) + print " " + "\n ".join(textwrap.wrap(vlist)) + print # Print Transverse Shapes print " Time-Series Variable Transverse Shapes:" From a6735c9cb577c28a8b831d8f26885805bf680a42 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 10 Jul 2015 10:26:28 -0600 Subject: [PATCH 042/250] Bugfix. Cleaning output more. --- tests/yellowstone/utilities/testtools.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index 4952bc8..c558287 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -461,7 +461,7 @@ def print_statistics(self, tests=[]): vlist = ", ".join([str(v) for v in test_stats['names']['other']]) print " " + "\n ".join(textwrap.wrap(vlist)) - print + print # Print Transverse Shapes print " Time-Series Variable Transverse Shapes:" From 349dfe9399c8cb137b1745f662d2b2b5d05b8a94 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 10 Jul 2015 10:46:36 -0600 Subject: [PATCH 043/250] Minor formatting change to output --- tests/yellowstone/utilities/testtools.py | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index c558287..3b163ac 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -465,14 +465,14 @@ def print_statistics(self, tests=[]): # Print Transverse Shapes print " Time-Series Variable Transverse Shapes:" - print " ", " ".join([str(s) for s in - test_stats['xshapes']['tseries']]) + print " " + " ".join([str(s) for s in + test_stats['xshapes']['tseries']]) print " Time-Variant Metadata Transverse Shapes:" - print " ", " ".join([str(s) for s in - test_stats['xshapes']['tvariant']]) + print " " + " ".join([str(s) for s in + test_stats['xshapes']['tvariant']]) print " Time-Invariant Metadata Transverse Shapes:" - print " ", " ".join([str(s) for s in - test_stats['xshapes']['tinvariant']]) + print " " + " ".join([str(s) for s in + test_stats['xshapes']['tinvariant']]) print # Print total bytesizes From 55e995744e03f916be424c346cb2daf2fd116ad9 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 10 Jul 2015 10:50:29 -0600 Subject: [PATCH 044/250] Bugfix. Cannot read from unintialized variable. --- tests/yellowstone/utilities/testtools.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index 3b163ac..2a8fdcb 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -541,7 +541,7 @@ def load_statistics(self, fileobj="teststats.json"): # Try reading the statistics try: - self._statistics = dict(json.load(statfile)) + self._statistics = dict(json.load(fp)) except: err_msg = "Failed to read statistics file" raise RuntimeError(err_msg) From cc090d949e61e125adf5074f018fc5865a381da7 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 10 Jul 2015 11:00:15 -0600 Subject: [PATCH 045/250] Adding test statistics database file --- tests/yellowstone/teststats.json | 1 + 1 file changed, 1 insertion(+) create mode 100644 tests/yellowstone/teststats.json diff --git a/tests/yellowstone/teststats.json b/tests/yellowstone/teststats.json new file mode 100644 index 0000000..771110e --- /dev/null +++ b/tests/yellowstone/teststats.json @@ -0,0 +1 @@ +{"camse-1deg": {"maxsizes": {"tseries": 699868800, "tinvariant": 388816, "tvariant": 1920}, "variables": {"CCN3": {"xshape": [30, 48602], "meta": false, "xsize": 5832240, "tvariant": true}, "ch4vmr": {"xshape": [], "meta": true, "xsize": 8, "tvariant": true}, "TS": {"xshape": [48602], "meta": false, "xsize": 194408, "tvariant": true}, "FSNTOAC": {"xshape": [48602], "meta": false, "xsize": 194408, "tvariant": true}, "BURDENSO4": {"xshape": [48602], "meta": false, "xsize": 194408, "tvariant": true}, "dst_a1_SRF": {"xshape": [48602], "meta": false, "xsize": 194408, "tvariant": true}, "TGCLDCWP": {"xshape": [48602], "meta": false, "xsize": 194408, "tvariant": true}, "time_bnds": {"xshape": [2], "meta": true, "xsize": 16, "tvariant": true}, "nbdate": {"xshape": [], "meta": true, "xsize": 4, "tvariant": false}, "date_written": {"xshape": [8], 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"length": 3285, "names": {"other": [], "tseries": ["SST2", "XMXL_2", "HMXL_2", "SST"], "tinvariant": ["latent_heat_fusion", "DXT", "REGION_MASK", "hflux_factor", "HT", "z_w_top", "ANGLET", "KMU", "KMT", "radius", "ANGLE", "cp_sw", "mass_to_Sv", "rho_fw", "z_t", "ULONG", "z_w", "DYT", "DYU", "fwflux_factor", "HUW", "salt_to_ppt", "HUS", "TLONG", "sea_ice_salinity", "salt_to_mmday", "rho_sw", "nsurface_t", "rho_air", "z_t_150m", "nsurface_u", "sflux_factor", "stefan_boltzmann", "dz", "cp_air", "momentum_factor", "ULAT", "HU", "omega", "sound", "HTE", "TLAT", "latent_heat_vapor", "heat_to_PW", "vonkar", "HTN", "DXU", "salinity_factor", "ocn_ref_salinity", "grav", "T0_Kelvin", "ppt_to_salt", "dzw", "z_w_bot", "salt_to_Svppt", "TAREA", "UAREA", "days_in_norm_year"], "tvariant": ["time_bound", "time"]}, "xshapes": {"tseries": [[384, 320]], "tinvariant": [[384, 320], [15], [], [60]], "tvariant": [[2], []]}, "counts": {"other": 0, "tseries": 4, "tinvariant": 58, "tvariant": 2}, "totalsizes": {"tseries": 6458572800, "tinvariant": 19171020, "tvariant": 78840}}} \ No newline at end of file From b116869e4ecf7ebd80277849969c50b5d77d6172 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 10 Jul 2015 11:01:27 -0600 Subject: [PATCH 046/250] Passing output directory prefix to create_specifier function --- tests/yellowstone/utilities/testtools.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index 2a8fdcb..165109c 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -218,7 +218,7 @@ def create_specifiers(self, tests=[], ncfmt='netcdf4c', test_list = self._database.keys() # Construct the list of specifiers - specs = [self.create_specifier(test_name, ncfmt, **kwargs) + specs = [self.create_specifier(test_name, ncfmt, outdir, **kwargs) for test_name in tests] # Return a dictionary of named specifiers From 9e97d93e0acd18d15f62577ab6a9bd1b39694254 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 13 Jul 2015 08:30:44 -0600 Subject: [PATCH 047/250] Starting to more test scripts over to new utility package --- tests/yellowstone/runtestsi.py | 27 +++++------------------- tests/yellowstone/utilities/testtools.py | 14 ++++++------ 2 files changed, 12 insertions(+), 29 deletions(-) diff --git a/tests/yellowstone/runtestsi.py b/tests/yellowstone/runtestsi.py index b9812b9..427e356 100755 --- a/tests/yellowstone/runtestsi.py +++ b/tests/yellowstone/runtestsi.py @@ -24,6 +24,8 @@ from subprocess import Popen, PIPE, STDOUT import json +from utilities import testtools + #============================================================================== # Command-Line Interface Definition @@ -100,31 +102,12 @@ def parse_cli(): #============================================================================== def get_testing_database(options): - # See if there is a user-defined testinfo file, otherwise look for default - testing_database_filename = '' - if (options.testing_database == None): - runtest_dir = os.path.dirname(__file__) - testing_database_filename = os.path.join(runtest_dir, 'testinfo.json') - else: - testing_database_filename = os.path.abspath(options.testing_database) - - # Try opening and reading the testinfo file - testing_database = {} - try: - testing_database_file = open(testing_database_filename, 'r') - testing_database = dict(json.load(testing_database_file)) - testing_database_file.close() - except: - err_msg = 'Problem reading and parsing test info file: ' \ - + str(testing_database_filename) - raise ValueError(err_msg) + # Create the testing database + testing_database = testtools.TestDB(options.testing_database) # List tests only, if option is set if (options.list_tests): - print 'Tests found in the Test Info file are:' - print - for test_name in testing_database: - print ' ' + str(test_name) + testing_database.print_list() sys.exit(0) return testing_database diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index 165109c..c0fe639 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -58,12 +58,12 @@ def _nbyte_str(n, exp=0): #============================================================================== class TestDB(object): - def __init__(self, file_name=None): + def __init__(self, filename=None): """ Constructor Parameters: - file_name (str): The name of the test database file. Defaults + filename (str): The name of the test database file. Defaults to 'testinfo.json'. Raises: @@ -73,8 +73,8 @@ def __init__(self, file_name=None): # See if there is a user-defined testinfo file, # otherwise look for default abs_path = '' - if file_name: - abs_path = os.path.abspath(file_name) + if filename: + abs_path = os.path.abspath(filename) else: this_dir = os.path.dirname(__file__) abs_path = os.path.join(this_dir, 'testinfo.json') @@ -82,7 +82,7 @@ def __init__(self, file_name=None): # Try opening and reading the testinfo file self._database = {} try: - dbfile = open(file_name, 'r') + dbfile = open(filename, 'r') self._database = dict(json.load(dbfile)) dbfile.close() except: @@ -322,10 +322,10 @@ def analyze(self, tests=[], force=False): infile.close() # Loop over all input files and compute time-variant variable sizes - for file_name in spec.input_file_list[1:]: + for filename in spec.input_file_list[1:]: # Open the file - infile = Nio.open_file(file_name, 'r') + infile = Nio.open_file(filename, 'r') # And number of time steps to the test data self._statistics[test_name]['length'] += \ From 86972d512725af65bc2fe06176e39df16ab17c75 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 13 Jul 2015 15:15:34 -0600 Subject: [PATCH 048/250] Adding new test-running script --- .pydevproject | 2 + tests/yellowstone/runtests.py | 101 ++++++++++++++++++++++++++++++++++ 2 files changed, 103 insertions(+) create mode 100644 tests/yellowstone/runtests.py diff --git a/.pydevproject b/.pydevproject index 9174370..359f70b 100644 --- a/.pydevproject +++ b/.pydevproject @@ -4,5 +4,7 @@ Homebrew Python 2.7 /${PROJECT_DIR_NAME}/source +/${PROJECT_DIR_NAME}/tests/yellowstone/utilities +/${PROJECT_DIR_NAME}/tests/yellowstone diff --git a/tests/yellowstone/runtests.py b/tests/yellowstone/runtests.py new file mode 100644 index 0000000..fc1926b --- /dev/null +++ b/tests/yellowstone/runtests.py @@ -0,0 +1,101 @@ +#!/usr/bin/env python +#============================================================================== +# +# runtests.py +# +# Command-line script to run the Yellowstone test suite (i.e., the "bakeoff"). +# This script can run any number of ways. +# +#============================================================================== + +# Builtin Modules +import optparse + +# Package Modules +from utilities import testtools as tt +from utilities import runtools as rt + + +#============================================================================== +# Command-Line Interface Definition +#============================================================================== +def parse_cli(): + usage = 'usage: %prog [run_opts] test_name1 test_name2 ...\n\n' \ + + ' This program is designed to run yellowstone-specific\n' \ + + ' tests of the PyReshaper. Each named test (or all tests if\n' \ + + ' the -a or --all option is used) will be given a run\n' \ + + ' directory in the "rundirs" directory with the same\n' \ + + ' name as the test itself. The run script will be placed\n' \ + + ' in this run directory, as will be placed the run output/\n' \ + + ' error file. All output data files will be placed in the\n' \ + + ' output subdirectory.' + parser = optparse.OptionParser(usage=usage) + parser.add_option('-a', '--all', default=False, + action='store_true', dest='all', + help='True or False, indicating whether to run all tests ' + '[Default: False]') + parser.add_option('-c', '--code', default='STDD0002', + help='The name of the project code for charging in ' + 'parallel runs (ignored if running in serial) ' + '[Default: STDD0002]') + parser.add_option('-d', '--database', default=None, + help='Location of the testinfo.json file ' + '[Default: None]') + parser.add_option('-f', '--format', default='netcdf4c', dest='ncformat', + help='The NetCDF file format to use for the output data ' + 'produced by the test. [Default: netcdf4c]') + parser.add_option('-l', '--list', default=False, + action='store_true', dest='list_tests', + help='True or False, indicating whether to list all tests, ' + 'instead of running tests. [Default: False]') + parser.add_option('-m', '--multiple', default=False, + action='store_true', dest='multiple', + help='True or False, indicating whether to run the tests ' + 'in a single MultiSpecReshaper instance, which runs ' + 'each parallel test in sequence in the same job, ' + 'instead of running each parallel test individually ' + 'with its own job. [Default: False]') + parser.add_option('-O', '--overwrite', default=False, + action='store_true', dest='overwrite', + help='True or False, indicating whether to force deleting ' + 'any existing test or run directories, if found ' + '[Default: False]') + parser.add_option('-q', '--queue', default='economy', + help='The name of the queue to request in parallel runs ' + '(ignored if running in serial) ' + '[Default: economy]') + parser.add_option('-n', '--nodes', default=0, type='int', + help='The integer number of nodes to request in parallel' + ' runs (0 means run in serial) [Default: 0]') + parser.add_option('-S', '--skip_existing', default=False, + action='store_true', dest='skip_existing', + help='Whether to skip time-series generation for ' + 'variables with existing output files. ' + '[Default: False]') + parser.add_option('-t', '--tiling', default=16, type='int', + help='The integer number of processes per node to request ' + 'in parallel runs (ignored if running in serial) ' + '[Default: 16]') + parser.add_option('-w', '--wtime', default=240, type='int', + help='The number of minutes to request for the wall clock ' + 'in parallel runs (ignored if running in serial) ' + '[Default: 240]') + + # Return the parsed CLI options + return parser.parse_args() + + +#============================================================================== +# Main Function +#============================================================================== +def runtests(options={}, tests=[]): + print options + print tests + + +#============================================================================== +# Main Command-line Operation +#============================================================================== +if __name__ == '__main__': + options, arguments = parse_cli() + runtests(dict(options), tests=list(arguments)) From 2eb7cef9bb0317c352d56138e7d9e896a900f5f8 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 14 Sep 2015 10:49:31 -0600 Subject: [PATCH 049/250] Remove warnings from PEP8 standards --- source/pyreshaper/reshaper.py | 62 +++++++++++++++--------------- source/pyreshaper/specification.py | 2 +- 2 files changed, 32 insertions(+), 32 deletions(-) diff --git a/source/pyreshaper/reshaper.py b/source/pyreshaper/reshaper.py index a89f1f4..150a6d3 100644 --- a/source/pyreshaper/reshaper.py +++ b/source/pyreshaper/reshaper.py @@ -36,7 +36,7 @@ def create_reshaper(specifier, serial=False, verbosity=1, Factory function for Reshaper class instantiations. Parameters: - specifier (Specifier): An instantiation of a Specifier class that + specifier (Specifier): An instantiation of a Specifier class that defines the type of operation to be performed. (That is, a Slice2SeriesSpecifier will invoke the creation of a matching Slice2SeriesReshaper object.) @@ -121,7 +121,7 @@ def _pprint_dictionary(title, dictionary, order=None): dictionary (dict): A dictionary of numeric values Keyword Arguments: - order (list): The print order for the keys in the dictionary (only + order (list): The print order for the keys in the dictionary (only items that are in both the order list and the dictionary will be printed) @@ -135,13 +135,13 @@ def _pprint_dictionary(title, dictionary, order=None): if (not isinstance(dictionary, dict)): err_msg = 'Input dictionary needs to be a dictionary type' raise TypeError(err_msg) - if (order != None and not isinstance(order, list)): + if (order is not None and not isinstance(order, list)): err_msg = 'Order list needs to be a list type' raise TypeError(err_msg) # Determine the print order, if present print_order = dictionary.keys() - if (order != None): + if (order is not None): print_order = [] for item in order: if (item in dictionary): @@ -203,7 +203,7 @@ class Slice2SeriesReshaper(Reshaper): """ The time-slice to time-series Reshaper class - This is the class that defines how the time-slice to time-series + This is the class that defines how the time-slice to time-series reshaping operation is to be performed. """ @@ -214,7 +214,7 @@ def __init__(self, specifier, serial=False, verbosity=1, Constructor Parameters: - specifier (Specifier): An instance of the Specifier class, + specifier (Specifier): An instance of the Specifier class, defining the input specification for this reshaper operation. Keyword Arguments: @@ -223,7 +223,7 @@ def __init__(self, specifier, serial=False, verbosity=1, (False). The default is to assume parallel operation (but serial will be chosen if the mpi4py cannot be found when trying to initialize decomposition. - verbosity(int): Level of printed output (stdout). A value of 0 + verbosity(int): Level of printed output (stdout). A value of 0 means no output, and a higher value means more output. The default value is 1. skip_existing (bool): Flag specifying whether to skip the generation @@ -233,7 +233,7 @@ def __init__(self, specifier, serial=False, verbosity=1, output files if they already exist. Default is False. once (bool): True or False, indicating whether the Reshaper should write all metadata to a 'once' file (separately). - simplecomm (SimpleComm): A SimpleComm object to handle the parallel + simplecomm (SimpleComm): A SimpleComm object to handle the parallel communication, if necessary """ @@ -359,9 +359,9 @@ def __init__(self, specifier, serial=False, verbosity=1, def _validate_input_files(self, specifier): """ - Perform validation of input data files themselves. + Perform validation of input data files themselves. - We check the file contents here, assuming that the files are already + We check the file contents here, assuming that the files are already open. Parameters: @@ -379,7 +379,7 @@ def _validate_input_files(self, specifier): if ifile.unlimited(dim): self._unlimited_dim = dim continue # There can only be 1! - if self._unlimited_dim == None: + if self._unlimited_dim is None: err_msg = 'Unlimited dimension not identified.' raise LookupError(err_msg) @@ -421,8 +421,8 @@ def _sort_input_files_by_time(self, specifier): Internal method for sorting the input files by time This assumes that 'time' is the unlimited dimension, and it checks - to make sure that all of the times spanning across each file do not - overlap with each other (i.e., that the times across all files are + to make sure that all of the times spanning across each file do not + overlap with each other (i.e., that the times across all files are monotonicly increasing). Currently, this method assumes that all of the input files @@ -488,11 +488,11 @@ def _sort_variables(self, specifier): """ Internal method for sorting the variables in each time-slice file - This method determines if each variable is to be treated as - time-invariant metadata, time-variant metadata (user defined), or - time-series variables. All metadata is written to every time-series - file, and any time-series variable is written to its own file. - The time-variant metadata variables are determined by user input, + This method determines if each variable is to be treated as + time-invariant metadata, time-variant metadata (user defined), or + time-series variables. All metadata is written to every time-series + file, and any time-series variable is written to its own file. + The time-variant metadata variables are determined by user input, and are contained in the Specifier data member: Specifier.time_variant_metadata. @@ -542,7 +542,7 @@ def _sort_variables(self, specifier): def _validate_output_files(self, specifier, skip_existing=False, overwrite=False): """ - Perform validation of output data files themselves. + Perform validation of output data files themselves. We compute the output file name from the prefix and suffix, and then we check whether the output files exist. By default, if the output @@ -608,7 +608,7 @@ def convert(self, output_limit=0): In this case, convert a list of time-slice files to time-series files. Keyword Arguments: - output_limit (int): Limit on the number of output (time-series) + output_limit (int): Limit on the number of output (time-series) files to write during the convert() operation. If set to 0, no limit is placed. This limits the number of output files produced by each processor in a @@ -887,8 +887,8 @@ class MultiSpecReshaper(Reshaper): """ Multiple Slice-to-Series Reshaper class - This class is designed to deal with lists of multiple - Slice2SeriesSpecifiers at a time. Instead of being instantiated + This class is designed to deal with lists of multiple + Slice2SeriesSpecifiers at a time. Instead of being instantiated (or initialized) with a single Slice2SeriesSpecifier, it takes a dictionary of Slice2SeriesSpecifier objects. """ @@ -909,7 +909,7 @@ def __init__(self, specifiers, serial=False, verbosity=1, (False). The default is to assume parallel operation (but serial will be chosen if the mpi4py cannot be found when trying to initialize decomposition. - verbosity(int): Level of printed output (stdout). A value of 0 + verbosity(int): Level of printed output (stdout). A value of 0 means no output, and a higher value means more output. The default value is 1. skip_existing (bool): Flag specifying whether to skip the generation @@ -919,7 +919,7 @@ def __init__(self, specifiers, serial=False, verbosity=1, output files if they already exist. Default is False. once (bool): True or False, indicating whether the Reshaper should write all metadata to a 'once' file (separately). - simplecomm (SimpleComm): A SimpleComm object to handle the parallel + simplecomm (SimpleComm): A SimpleComm object to handle the parallel communication, if necessary """ @@ -985,12 +985,12 @@ def convert(self, output_limit=0): """ Method to perform each Reshaper's designated operation. - Loops through and creates each Reshaper, calls each Reshaper's - convert() method, and pulls the timing data out for each convert + Loops through and creates each Reshaper, calls each Reshaper's + convert() method, and pulls the timing data out for each convert operation. Keyword Arguments: - output_limit (int): Limit on the number of output (time-series) + output_limit (int): Limit on the number of output (time-series) files to write during the convert() operation. If set to 0, no limit is placed. This limits the number of output files produced by each processor in a @@ -1004,8 +1004,8 @@ def convert(self, output_limit=0): # Loop over all specifiers for spec_name in self._specifiers: if self._simplecomm.is_manager(): - self._vprint('--- Converting Specifier: ' - + str(spec_name), verbosity=0) + self._vprint('--- Converting Specifier: ' + + str(spec_name), verbosity=0) rshpr = create_reshaper(self._specifiers[spec_name], serial=self._serial, @@ -1025,8 +1025,8 @@ def convert(self, output_limit=0): this_count, op='sum') if self._simplecomm.is_manager(): - self._vprint('--- Finished converting Specifier: ' - + str(spec_name) + os.linesep, verbosity=0) + self._vprint('--- Finished converting Specifier: ' + + str(spec_name) + os.linesep, verbosity=0) self._simplecomm.sync() def print_diagnostics(self): diff --git a/source/pyreshaper/specification.py b/source/pyreshaper/specification.py index 5bb719f..efa43c2 100644 --- a/source/pyreshaper/specification.py +++ b/source/pyreshaper/specification.py @@ -71,7 +71,7 @@ def __init__(self, metadata (list): List of variable names specifying the variables that should be included in every time-series output file - kwargs (dict): Optional arguments describing the + kwargs (dict): Optional arguments describing the Reshaper run """ From 85046235a5007d1ff8f0ea94a9bf05bf423ea5a0 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 14 Sep 2015 12:33:29 -0600 Subject: [PATCH 050/250] Make the runtests script executable --- tests/yellowstone/runtests.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) mode change 100644 => 100755 tests/yellowstone/runtests.py diff --git a/tests/yellowstone/runtests.py b/tests/yellowstone/runtests.py old mode 100644 new mode 100755 index fc1926b..5aea127 --- a/tests/yellowstone/runtests.py +++ b/tests/yellowstone/runtests.py @@ -55,7 +55,7 @@ def parse_cli(): 'each parallel test in sequence in the same job, ' 'instead of running each parallel test individually ' 'with its own job. [Default: False]') - parser.add_option('-O', '--overwrite', default=False, + parser.add_option('-o', '--overwrite', default=False, action='store_true', dest='overwrite', help='True or False, indicating whether to force deleting ' 'any existing test or run directories, if found ' From 7f961c8f27a27da4d4ee96aeb8d70610f436b3f2 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 14 Sep 2015 12:43:46 -0600 Subject: [PATCH 051/250] Switching to argparse (from optparse) --- tests/yellowstone/runtests.py | 121 +++++++++++++++++----------------- 1 file changed, 60 insertions(+), 61 deletions(-) diff --git a/tests/yellowstone/runtests.py b/tests/yellowstone/runtests.py index 5aea127..d13785a 100755 --- a/tests/yellowstone/runtests.py +++ b/tests/yellowstone/runtests.py @@ -9,7 +9,7 @@ #============================================================================== # Builtin Modules -import optparse +import argparse # Package Modules from utilities import testtools as tt @@ -20,66 +20,65 @@ # Command-Line Interface Definition #============================================================================== def parse_cli(): - usage = 'usage: %prog [run_opts] test_name1 test_name2 ...\n\n' \ - + ' This program is designed to run yellowstone-specific\n' \ - + ' tests of the PyReshaper. Each named test (or all tests if\n' \ - + ' the -a or --all option is used) will be given a run\n' \ - + ' directory in the "rundirs" directory with the same\n' \ - + ' name as the test itself. The run script will be placed\n' \ - + ' in this run directory, as will be placed the run output/\n' \ - + ' error file. All output data files will be placed in the\n' \ - + ' output subdirectory.' - parser = optparse.OptionParser(usage=usage) - parser.add_option('-a', '--all', default=False, - action='store_true', dest='all', - help='True or False, indicating whether to run all tests ' - '[Default: False]') - parser.add_option('-c', '--code', default='STDD0002', - help='The name of the project code for charging in ' - 'parallel runs (ignored if running in serial) ' - '[Default: STDD0002]') - parser.add_option('-d', '--database', default=None, - help='Location of the testinfo.json file ' - '[Default: None]') - parser.add_option('-f', '--format', default='netcdf4c', dest='ncformat', - help='The NetCDF file format to use for the output data ' - 'produced by the test. [Default: netcdf4c]') - parser.add_option('-l', '--list', default=False, - action='store_true', dest='list_tests', - help='True or False, indicating whether to list all tests, ' - 'instead of running tests. [Default: False]') - parser.add_option('-m', '--multiple', default=False, - action='store_true', dest='multiple', - help='True or False, indicating whether to run the tests ' - 'in a single MultiSpecReshaper instance, which runs ' - 'each parallel test in sequence in the same job, ' - 'instead of running each parallel test individually ' - 'with its own job. [Default: False]') - parser.add_option('-o', '--overwrite', default=False, - action='store_true', dest='overwrite', - help='True or False, indicating whether to force deleting ' - 'any existing test or run directories, if found ' - '[Default: False]') - parser.add_option('-q', '--queue', default='economy', - help='The name of the queue to request in parallel runs ' - '(ignored if running in serial) ' - '[Default: economy]') - parser.add_option('-n', '--nodes', default=0, type='int', - help='The integer number of nodes to request in parallel' - ' runs (0 means run in serial) [Default: 0]') - parser.add_option('-S', '--skip_existing', default=False, - action='store_true', dest='skip_existing', - help='Whether to skip time-series generation for ' - 'variables with existing output files. ' - '[Default: False]') - parser.add_option('-t', '--tiling', default=16, type='int', - help='The integer number of processes per node to request ' - 'in parallel runs (ignored if running in serial) ' - '[Default: 16]') - parser.add_option('-w', '--wtime', default=240, type='int', - help='The number of minutes to request for the wall clock ' - 'in parallel runs (ignored if running in serial) ' - '[Default: 240]') + desc = """This program is designed to run yellowstone-specific + tests of the PyReshaper. Each named test (or all tests if + the -a or --all option is used) will be given a run + directory in the "rundirs" directory with the same + name as the test itself. The run script will be placed + in this run directory, as will be placed the run output + error file. All output data files will be placed in the + output subdirectory.""" + parser = argparse.ArgumentParser(description=desc) + parser.add_argument('-a', '--all', default=False, + action='store_true', dest='all', + help='True or False, indicating whether to run all tests ' + '[Default: False]') + parser.add_argument('-c', '--code', default='STDD0002', + help='The name of the project code for charging in ' + 'parallel runs (ignored if running in serial) ' + '[Default: STDD0002]') + parser.add_argument('-d', '--database', default=None, + help='Location of the testinfo.json file ' + '[Default: None]') + parser.add_argument('-f', '--format', default='netcdf4c', dest='ncformat', + help='The NetCDF file format to use for the output data ' + 'produced by the test. [Default: netcdf4c]') + parser.add_argument('-l', '--list', default=False, + action='store_true', dest='list_tests', + help='True or False, indicating whether to list all tests, ' + 'instead of running tests. [Default: False]') + parser.add_argument('-m', '--multiple', default=False, + action='store_true', dest='multiple', + help='True or False, indicating whether to run the tests ' + 'in a single MultiSpecReshaper instance, which runs ' + 'each parallel test in sequence in the same job, ' + 'instead of running each parallel test individually ' + 'with its own job. [Default: False]') + parser.add_argument('-o', '--overwrite', default=False, + action='store_true', dest='overwrite', + help='True or False, indicating whether to force deleting ' + 'any existing test or run directories, if found ' + '[Default: False]') + parser.add_argument('-q', '--queue', default='economy', + help='The name of the queue to request in parallel runs ' + '(ignored if running in serial) ' + '[Default: economy]') + parser.add_argument('-n', '--nodes', default=0, type='int', + help='The integer number of nodes to request in parallel' + ' runs (0 means run in serial) [Default: 0]') + parser.add_argument('-S', '--skip_existing', default=False, + action='store_true', dest='skip_existing', + help='Whether to skip time-series generation for ' + 'variables with existing output files. ' + '[Default: False]') + parser.add_argument('-t', '--tiling', default=16, type='int', + help='The integer number of processes per node to request ' + 'in parallel runs (ignored if running in serial) ' + '[Default: 16]') + parser.add_argument('-w', '--wtime', default=240, type='int', + help='The number of minutes to request for the wall clock ' + 'in parallel runs (ignored if running in serial) ' + '[Default: 240]') # Return the parsed CLI options return parser.parse_args() From 5f8fb567f410ae7c953cbe1903574ffdb8916562 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 14 Sep 2015 12:45:10 -0600 Subject: [PATCH 052/250] Debugging statements --- tests/yellowstone/runtests.py | 2 ++ tests/yellowstone/utilities/testtools.py | 2 +- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/tests/yellowstone/runtests.py b/tests/yellowstone/runtests.py index d13785a..cc0aafd 100755 --- a/tests/yellowstone/runtests.py +++ b/tests/yellowstone/runtests.py @@ -97,4 +97,6 @@ def runtests(options={}, tests=[]): #============================================================================== if __name__ == '__main__': options, arguments = parse_cli() + print options + print arguments runtests(dict(options), tests=list(arguments)) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index c0fe639..6a55ec2 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -164,7 +164,7 @@ def create_specifier(self, test_name, ncfmt='netcdf4c', infiles = [] for input_glob in self._database[test_name]['input_globs']: input_glob_str = str(input_glob) - full_input_glob = str(os.path.join(input_dir, input_glob)) + full_input_glob = str(os.path.join(input_dir, input_glob_str)) infiles.extend(glob.glob(full_input_glob)) prefix = str(os.path.join( outdir, self._database[test_name]['output_prefix'])) From b2ff5203c5f5189c94939fe9adc8441cd4b637f7 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 14 Sep 2015 14:58:06 -0600 Subject: [PATCH 053/250] Adding coordinate data to statistics --- tests/yellowstone/utilities/testtools.py | 54 +++++++++++++----------- 1 file changed, 29 insertions(+), 25 deletions(-) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index 6a55ec2..183116c 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -60,7 +60,7 @@ class TestDB(object): def __init__(self, filename=None): """ - Constructor + Initializer Parameters: filename (str): The name of the test database file. Defaults @@ -76,13 +76,12 @@ def __init__(self, filename=None): if filename: abs_path = os.path.abspath(filename) else: - this_dir = os.path.dirname(__file__) - abs_path = os.path.join(this_dir, 'testinfo.json') + abs_path = os.path.join(os.getcwd(), 'testinfo.json') # Try opening and reading the testinfo file self._database = {} try: - dbfile = open(filename, 'r') + dbfile = open(abs_path, 'r') self._database = dict(json.load(dbfile)) dbfile.close() except: @@ -111,7 +110,7 @@ def get_statistics(self): """ return self._statistics - def print_list(self): + def print_tests(self): """ List the tests in the test database. """ @@ -216,13 +215,15 @@ def create_specifiers(self, tests=[], ncfmt='netcdf4c', # If test list is empty, assume all tests if len(tests) == 0: test_list = self._database.keys() + else: + test_list = tests # Construct the list of specifiers specs = [self.create_specifier(test_name, ncfmt, outdir, **kwargs) - for test_name in tests] + for test_name in test_list] # Return a dictionary of named specifiers - return dict(zip(tests, specs)) + return dict(zip(test_list, specs)) def analyze(self, tests=[], force=False): """ @@ -279,6 +280,9 @@ def analyze(self, tests=[], force=False): tdim = dim continue + # Coordinate variables and sizes + coordinates = infile.dimensions + # Get the data dimensions metadata_names = set(infile.dimensions.keys()) @@ -337,7 +341,6 @@ def analyze(self, tests=[], force=False): # Compute self-analysis parameters num_steps = self._statistics[test_name]['length'] var_stats = self._statistics[test_name]['variables'] - num_vars = len(var_stats) tser_vars = [str(v) for (v, s) in var_stats.items() if not s['meta'] and s['tvariant']] tvmd_vars = [str(v) for (v, s) in var_stats.items() @@ -347,6 +350,9 @@ def analyze(self, tests=[], force=False): lost_vars = [str(v) for (v, s) in var_stats.items() if not s['meta'] and not s['tvariant']] + # Store the coordinate sizes + self._statistics[test_name]['coords'] = coordinates + # Record the variables names self._statistics[test_name]['names'] = {} self._statistics[test_name]['names']['tseries'] = tser_vars @@ -425,7 +431,6 @@ def print_statistics(self, tests=[]): print test_stats = self._statistics[test_name] - var_stats = test_stats['variables'] num_steps = test_stats['length'] print " Number of Time Steps:", num_steps @@ -443,6 +448,11 @@ def print_statistics(self, tests=[]): print " WARNING:", num_lost, " unclassified variables" print + # Print the coordinate data + print " Coordinate Sizes:" + for coord, csize in test_stats['coords'].items(): + print " " + coord + ": " + csize + # Print names print " Time-Series Variables:" vlist = ", ".join([str(v) for v in @@ -493,22 +503,19 @@ def print_statistics(self, tests=[]): print " Time-Invariant Metadata Max Size:", _nbyte_str(timd_maxsize) print - def save_statistics(self, fileobj="teststats.json"): + def save_statistics(self, filename="teststats.json"): """ Save the statistics information to a JSON data file Parameters: - fileobj (str, file): The name of the JSON data file to write, or an - open file instance with write permissions + filename (str): The name of the JSON data file to write """ # Check types - if isinstance(fileobj, str): - fp = open(fileobj, 'w') - elif isinstance(fileobj, file): - fp = fileobj + if isinstance(filename, str): + fp = open(filename, 'w') else: - err_msg = "File object must be a string or file instance" + err_msg = "Statistics filename must be a string" raise TypeError(err_msg) # Dump JSON data to file @@ -521,22 +528,19 @@ def save_statistics(self, fileobj="teststats.json"): # Close the file fp.close() - def load_statistics(self, fileobj="teststats.json"): + def load_statistics(self, filename="teststats.json"): """ Load the statistics information from a JSON data file Parameters: - fileobj (str): The name of the JSON data file to read or an - open file instance with read permissions + filename (str): The name of the JSON data file to read """ # Check types - if isinstance(fileobj, str): - fp = open(fileobj, 'r') - elif isinstance(fileobj, file): - fp = fileobj + if isinstance(filename, str): + fp = open(filename, 'r') else: - err_msg = "File object must be a string or file instance" + err_msg = "Statistics filename must be a string" raise TypeError(err_msg) # Try reading the statistics From 848e92171f03c150bd6ee2243d78210cb83ac587 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 14 Sep 2015 14:58:30 -0600 Subject: [PATCH 054/250] Setting up to generate new statistics information --- tests/yellowstone/runtests.py | 46 ++++++++++++++++++----------------- 1 file changed, 24 insertions(+), 22 deletions(-) diff --git a/tests/yellowstone/runtests.py b/tests/yellowstone/runtests.py index cc0aafd..7d675f9 100755 --- a/tests/yellowstone/runtests.py +++ b/tests/yellowstone/runtests.py @@ -33,37 +33,37 @@ def parse_cli(): action='store_true', dest='all', help='True or False, indicating whether to run all tests ' '[Default: False]') - parser.add_argument('-c', '--code', default='STDD0002', + parser.add_argument('-c', '--code', default='STDD0002', type=str, help='The name of the project code for charging in ' 'parallel runs (ignored if running in serial) ' '[Default: STDD0002]') - parser.add_argument('-d', '--database', default=None, - help='Location of the testinfo.json file ' + parser.add_argument('-d', '--database', default=None, type=str, + help='Location of the testinfo.json database file ' '[Default: None]') - parser.add_argument('-f', '--format', default='netcdf4c', dest='ncformat', + parser.add_argument('-f', '--format', default='netcdf4c', + type=str, dest='ncformat', help='The NetCDF file format to use for the output data ' 'produced by the test. [Default: netcdf4c]') parser.add_argument('-l', '--list', default=False, action='store_true', dest='list_tests', help='True or False, indicating whether to list all tests, ' 'instead of running tests. [Default: False]') - parser.add_argument('-m', '--multiple', default=False, - action='store_true', dest='multiple', - help='True or False, indicating whether to run the tests ' - 'in a single MultiSpecReshaper instance, which runs ' - 'each parallel test in sequence in the same job, ' - 'instead of running each parallel test individually ' - 'with its own job. [Default: False]') parser.add_argument('-o', '--overwrite', default=False, action='store_true', dest='overwrite', help='True or False, indicating whether to force deleting ' 'any existing test or run directories, if found ' '[Default: False]') - parser.add_argument('-q', '--queue', default='economy', + parser.add_argument('-m', '--multiple', default=False, + action='store_true', dest='multispec', + help='True or False, indications whether the tests ' + 'should be run from a single Reshaper submission ' + '(i.e., multiple Specifiers in one run) ' + '[Default: False]') + parser.add_argument('-q', '--queue', default='economy', type=str, help='The name of the queue to request in parallel runs ' '(ignored if running in serial) ' '[Default: economy]') - parser.add_argument('-n', '--nodes', default=0, type='int', + parser.add_argument('-n', '--nodes', default=0, type=int, help='The integer number of nodes to request in parallel' ' runs (0 means run in serial) [Default: 0]') parser.add_argument('-S', '--skip_existing', default=False, @@ -71,14 +71,15 @@ def parse_cli(): help='Whether to skip time-series generation for ' 'variables with existing output files. ' '[Default: False]') - parser.add_argument('-t', '--tiling', default=16, type='int', + parser.add_argument('-t', '--tiling', default=16, type=int, help='The integer number of processes per node to request ' 'in parallel runs (ignored if running in serial) ' '[Default: 16]') - parser.add_argument('-w', '--wtime', default=240, type='int', + parser.add_argument('-w', '--wtime', default=240, type=int, help='The number of minutes to request for the wall clock ' 'in parallel runs (ignored if running in serial) ' '[Default: 240]') + parser.add_argument('tests', type=str, nargs='*') # Return the parsed CLI options return parser.parse_args() @@ -87,16 +88,17 @@ def parse_cli(): #============================================================================== # Main Function #============================================================================== -def runtests(options={}, tests=[]): - print options - print tests +def runtests(arguments): + testdb = tt.TestDB(filename=arguments.database) + testdb.print_tests() + print + testdb.analyze(force=True) + testdb.print_statistics() + testdb.save_statistics() #============================================================================== # Main Command-line Operation #============================================================================== if __name__ == '__main__': - options, arguments = parse_cli() - print options - print arguments - runtests(dict(options), tests=list(arguments)) + runtests(parse_cli()) From 61dd9ab82630bc52933ed50ade6c3c841a265e92 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 14 Sep 2015 15:14:48 -0600 Subject: [PATCH 055/250] Convert int to str before concatenation --- tests/yellowstone/utilities/testtools.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index 183116c..3384849 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -451,7 +451,7 @@ def print_statistics(self, tests=[]): # Print the coordinate data print " Coordinate Sizes:" for coord, csize in test_stats['coords'].items(): - print " " + coord + ": " + csize + print " " + coord + ": " + str(csize) # Print names print " Time-Series Variables:" From 05381cfe4d17f4ccdccc8e2cb7f003df558f0aec Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 14 Sep 2015 15:31:39 -0600 Subject: [PATCH 056/250] Storing transverse (to time) coordinates and sizes --- tests/yellowstone/utilities/testtools.py | 22 +++++++++++++++------- 1 file changed, 15 insertions(+), 7 deletions(-) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index 3384849..04ac920 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -280,9 +280,6 @@ def analyze(self, tests=[], force=False): tdim = dim continue - # Coordinate variables and sizes - coordinates = infile.dimensions - # Get the data dimensions metadata_names = set(infile.dimensions.keys()) @@ -322,6 +319,13 @@ def analyze(self, tests=[], force=False): self._statistics[test_name][ 'variables'][var_name]['meta'] = False + if var_name in infile.dimensions and var_name != tdim: + self._statistics[test_name][ + 'variables'][var_name]['xcoord'] = True + else: + self._statistics[test_name][ + 'variables'][var_name]['xcoord'] = False + # Close the first file infile.close() @@ -349,9 +353,12 @@ def analyze(self, tests=[], force=False): if s['meta'] and not s['tvariant']] lost_vars = [str(v) for (v, s) in var_stats.items() if not s['meta'] and not s['tvariant']] + xcoords = [str(v) for (v, s) in var_stats.items() + if s['xcoord']] - # Store the coordinate sizes - self._statistics[test_name]['coords'] = coordinates + # Store the transverse (to time) coordinate sizes + self._statistics[test_name]['xcoords'] = dict( + [(v, var_stats[v]['xshape']) for v in xcoords]) # Record the variables names self._statistics[test_name]['names'] = {} @@ -450,8 +457,9 @@ def print_statistics(self, tests=[]): # Print the coordinate data print " Coordinate Sizes:" - for coord, csize in test_stats['coords'].items(): - print " " + coord + ": " + str(csize) + for xcoord, cxsize in test_stats['xcoords'].items(): + print " " + xcoord + ": " + str(cxsize) + print # Print names print " Time-Series Variables:" From 98524ab0744662003db637210c001fe8e9fd30f8 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 14 Sep 2015 15:32:24 -0600 Subject: [PATCH 057/250] Labeling transverse coordinates in statistics output --- tests/yellowstone/utilities/testtools.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index 04ac920..44f948c 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -456,7 +456,7 @@ def print_statistics(self, tests=[]): print # Print the coordinate data - print " Coordinate Sizes:" + print " Transverse Coordinate Shapes:" for xcoord, cxsize in test_stats['xcoords'].items(): print " " + xcoord + ": " + str(cxsize) print From 6c3b745fa5b69eac2176f9ccbf46a88efe51ffae Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 14 Sep 2015 15:52:29 -0600 Subject: [PATCH 058/250] Only store actual file dimensions and sizes (other than time) --- tests/yellowstone/utilities/testtools.py | 16 +++++----------- 1 file changed, 5 insertions(+), 11 deletions(-) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index 44f948c..23b1d9f 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -280,6 +280,10 @@ def analyze(self, tests=[], force=False): tdim = dim continue + # Add the transverse (i.e., non-time) dimensions and sizes + xcoords = dict([(v, s) for (v, s) in infile.dimensions.items() + if v != tdim]) + # Get the data dimensions metadata_names = set(infile.dimensions.keys()) @@ -319,13 +323,6 @@ def analyze(self, tests=[], force=False): self._statistics[test_name][ 'variables'][var_name]['meta'] = False - if var_name in infile.dimensions and var_name != tdim: - self._statistics[test_name][ - 'variables'][var_name]['xcoord'] = True - else: - self._statistics[test_name][ - 'variables'][var_name]['xcoord'] = False - # Close the first file infile.close() @@ -353,12 +350,9 @@ def analyze(self, tests=[], force=False): if s['meta'] and not s['tvariant']] lost_vars = [str(v) for (v, s) in var_stats.items() if not s['meta'] and not s['tvariant']] - xcoords = [str(v) for (v, s) in var_stats.items() - if s['xcoord']] # Store the transverse (to time) coordinate sizes - self._statistics[test_name]['xcoords'] = dict( - [(v, var_stats[v]['xshape']) for v in xcoords]) + self._statistics[test_name]['xcoords'] = xcoords # Record the variables names self._statistics[test_name]['names'] = {} From fa538d77a01138efda747e410922f9d4ba06bbf0 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 14 Sep 2015 15:59:12 -0600 Subject: [PATCH 059/250] New test statistics with transverse coordinate information. --- tests/yellowstone/teststats.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/teststats.json b/tests/yellowstone/teststats.json index 771110e..fb14bf8 100644 --- a/tests/yellowstone/teststats.json +++ b/tests/yellowstone/teststats.json @@ -1 +1 @@ -{"camse-1deg": {"maxsizes": {"tseries": 699868800, "tinvariant": 388816, "tvariant": 1920}, "variables": {"CCN3": {"xshape": [30, 48602], "meta": false, "xsize": 5832240, "tvariant": true}, "ch4vmr": {"xshape": [], "meta": true, "xsize": 8, "tvariant": true}, "TS": {"xshape": [48602], "meta": false, "xsize": 194408, "tvariant": true}, "FSNTOAC": {"xshape": [48602], "meta": false, "xsize": 194408, "tvariant": true}, "BURDENSO4": {"xshape": [48602], "meta": false, "xsize": 194408, "tvariant": true}, "dst_a1_SRF": {"xshape": [48602], "meta": false, "xsize": 194408, "tvariant": true}, "TGCLDCWP": {"xshape": [48602], "meta": false, "xsize": 194408, "tvariant": true}, "time_bnds": {"xshape": [2], "meta": true, "xsize": 16, "tvariant": true}, "nbdate": {"xshape": [], "meta": true, "xsize": 4, "tvariant": false}, "date_written": {"xshape": [8], "meta": true, "xsize": 0, "tvariant": true}, "IWC": {"xshape": [30, 48602], "meta": false, "xsize": 5832240, "tvariant": true}, "nsteph": {"xshape": [], "meta": true, "xsize": 4, "tvariant": true}, "soa_a2_SRF": {"xshape": [48602], "meta": false, "xsize": 194408, "tvariant": true}, "QREFHT": {"xshape": [48602], "meta": false, "xsize": 194408, "tvariant": true}, "FSNS": {"xshape": [48602], "meta": false, "xsize": 194408, "tvariant": true}, "ntrm": {"xshape": [], "meta": true, "xsize": 4, "tvariant": false}, "ntrn": {"xshape": [], "meta": true, "xsize": 4, "tvariant": false}, "nsbase": {"xshape": [], "meta": true, "xsize": 4, "tvariant": false}, "EMISCLD": {"xshape": [30, 48602], "meta": false, "xsize": 5832240, "tvariant": true}, "FSNT": {"xshape": [48602], "meta": false, "xsize": 194408, "tvariant": true}, "co2vmr": {"xshape": [], "meta": true, "xsize": 8, "tvariant": true}, "CLDLIQ": {"xshape": [30, 48602], "meta": false, "xsize": 5832240, "tvariant": true}, "DCQ": {"xshape": [30, 48602], "meta": false, "xsize": 5832240, "tvariant": true}, "PRECSC": {"xshape": [48602], "meta": false, "xsize": 194408, "tvariant": true}, "dst_a3SF": {"xshape": [48602], "meta": false, "xsize": 194408, "tvariant": true}, "ndbase": {"xshape": [], "meta": true, "xsize": 4, "tvariant": false}, "PRECSL": {"xshape": [48602], "meta": false, "xsize": 194408, "tvariant": true}, "num_a1_SRF": {"xshape": [48602], "meta": false, "xsize": 194408, "tvariant": true}, "dst_a3_SRF": {"xshape": [48602], "meta": false, "xsize": 194408, "tvariant": true}, "datesec": {"xshape": [], "meta": true, "xsize": 4, "tvariant": true}, "T": {"xshape": [30, 48602], "meta": false, "xsize": 5832240, "tvariant": true}, "TAUY": {"xshape": [48602], "meta": false, "xsize": 194408, "tvariant": true}, "dst_a1SF": {"xshape": [48602], "meta": false, "xsize": 194408, "tvariant": true}, "H2SO4_SRF": {"xshape": [48602], "meta": false, "xsize": 194408, "tvariant": true}, "ncl_a3_SRF": {"xshape": [48602], "meta": false, "xsize": 194408, "tvariant": true}, "BURDENSOA": {"xshape": [48602], "meta": false, "xsize": 194408, "tvariant": true}, "CLDMED": {"xshape": [48602], "meta": false, "xsize": 194408, "tvariant": true}, "FSDS": {"xshape": [48602], "meta": false, "xsize": 194408, "tvariant": true}, "FSNTOA": {"xshape": [48602], "meta": false, "xsize": 194408, "tvariant": true}, "BURDENDUST": {"xshape": [48602], "meta": false, "xsize": 194408, "tvariant": true}, "BURDENPOM": {"xshape": [48602], "meta": false, "xsize": 194408, "tvariant": true}, "pom_a1_SRF": {"xshape": [48602], "meta": false, "xsize": 194408, "tvariant": true}, "f11vmr": {"xshape": [], "meta": true, "xsize": 8, "tvariant": true}, "so4_a2_SRF": {"xshape": [48602], "meta": false, "xsize": 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"momentum_factor", "ULAT", "HU", "omega", "sound", "HTE", "TLAT", "latent_heat_vapor", "heat_to_PW", "vonkar", "HTN", "DXU", "salinity_factor", "ocn_ref_salinity", "grav", "T0_Kelvin", "ppt_to_salt", "dzw", "z_w_bot", "salt_to_Svppt", "TAREA", "UAREA", "days_in_norm_year"], "tvariant": ["time_bound", "time"]}, "xshapes": {"tseries": [[384, 320]], "tinvariant": [[384, 320], [15], [], [60]], "tvariant": [[2], []]}, "counts": {"other": 0, "tseries": 4, "tinvariant": 58, "tvariant": 2}, "totalsizes": {"tseries": 6458572800, "tinvariant": 19171020, "tvariant": 78840}}} \ No newline at end of file From 745aa953d35c3691c2abd5f3c20326a0418a6937 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 14 Sep 2015 16:12:48 -0600 Subject: [PATCH 060/250] Reformatting statistics file --- tests/yellowstone/teststats.json | 16696 ++++++++++++++++++++++++++++- 1 file changed, 16695 insertions(+), 1 deletion(-) diff --git a/tests/yellowstone/teststats.json b/tests/yellowstone/teststats.json index fb14bf8..1e1dea4 100644 --- a/tests/yellowstone/teststats.json +++ b/tests/yellowstone/teststats.json @@ -1 +1,16695 @@ -{"camse-1deg": {"maxsizes": {"tseries": 699868800, "tinvariant": 388816, "tvariant": 1920}, "variables": {"CCN3": {"xshape": [30, 48602], "meta": false, "xsize": 5832240, "tvariant": true}, "ch4vmr": {"xshape": [], "meta": true, "xsize": 8, "tvariant": true}, "TS": {"xshape": [48602], "meta": false, "xsize": 194408, "tvariant": true}, "FSNTOAC": {"xshape": [48602], "meta": false, "xsize": 194408, "tvariant": true}, "BURDENSO4": {"xshape": [48602], "meta": false, "xsize": 194408, "tvariant": true}, "dst_a1_SRF": {"xshape": [48602], "meta": false, "xsize": 194408, "tvariant": true}, "TGCLDCWP": {"xshape": [48602], "meta": false, "xsize": 194408, "tvariant": true}, "time_bnds": {"xshape": [2], "meta": true, "xsize": 16, "tvariant": true}, "nbdate": {"xshape": [], "meta": true, "xsize": 4, "tvariant": false}, "date_written": {"xshape": [8], "meta": true, "xsize": 0, 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"tvariant":[ + "time_bound", + "time" + ] + }, + "xshapes":{ + "tseries":[ + [ + 384, + 320 + ] + ], + "tinvariant":[ + [ + 384, + 320 + ], + [ + 15 + ], + [ + + ], + [ + 60 + ] + ], + "tvariant":[ + [ + 2 + ], + [ + + ] + ] + }, + "counts":{ + "other":0, + "tseries":4, + "tinvariant":58, + "tvariant":2 + }, + "totalsizes":{ + "tseries":6458572800, + "tinvariant":19171020, + "tvariant":78840 + } + } +} \ No newline at end of file From 99720e873fb6733036d2d94d557e0b2d59a12ff2 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Tue, 15 Sep 2015 10:36:56 -0600 Subject: [PATCH 061/250] Cleaning up print_statistics output --- tests/yellowstone/runtests.py | 4 +--- tests/yellowstone/utilities/testtools.py | 26 +++++++++++++++++++----- 2 files changed, 22 insertions(+), 8 deletions(-) diff --git a/tests/yellowstone/runtests.py b/tests/yellowstone/runtests.py index 7d675f9..8253aa6 100755 --- a/tests/yellowstone/runtests.py +++ b/tests/yellowstone/runtests.py @@ -89,12 +89,10 @@ def parse_cli(): # Main Function #============================================================================== def runtests(arguments): - testdb = tt.TestDB(filename=arguments.database) + testdb = tt.TestDB(dbname=arguments.database) testdb.print_tests() print - testdb.analyze(force=True) testdb.print_statistics() - testdb.save_statistics() #============================================================================== diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index 23b1d9f..37a01f1 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -58,13 +58,15 @@ def _nbyte_str(n, exp=0): #============================================================================== class TestDB(object): - def __init__(self, filename=None): + def __init__(self, dbname=None, stname=None): """ Initializer Parameters: - filename (str): The name of the test database file. Defaults + dbname (str): The name of the test database file. Defaults to 'testinfo.json'. + stname (str): The name of the test statistics file. Defaults + to 'teststats.json'. Raises: ValueError: If the test database file cannot be opened and/or @@ -73,8 +75,8 @@ def __init__(self, filename=None): # See if there is a user-defined testinfo file, # otherwise look for default abs_path = '' - if filename: - abs_path = os.path.abspath(filename) + if dbname: + abs_path = os.path.abspath(dbname) else: abs_path = os.path.join(os.getcwd(), 'testinfo.json') @@ -90,7 +92,19 @@ def __init__(self, filename=None): raise ValueError(err_msg) # Initialize the statistics database + if stname: + abs_path = os.path.abspath(stname) + else: + abs_path = os.path.join(os.getcwd(), 'teststats.json') + + # Try opening and reading the testinfo file self._statistics = {} + try: + stfile = open(abs_path, 'r') + self._statistics = dict(json.load(stfile)) + stfile.close() + except: + print "Warning: Statistics file (" + stname + ") not found." def get_database(self): """ @@ -451,8 +465,10 @@ def print_statistics(self, tests=[]): # Print the coordinate data print " Transverse Coordinate Shapes:" + maxlenxcoord = max([len(xc) for xc in test_stats['xcoords']]) for xcoord, cxsize in test_stats['xcoords'].items(): - print " " + xcoord + ": " + str(cxsize) + spcr = ' ' * (maxlenxcoord - len(xcoord)) + print " " + xcoord + ": " + spcr + str(cxsize) print # Print names From 9b40810c7173969c36d925afccd6fec16bd1b2fa Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Wed, 16 Sep 2015 14:32:27 -0600 Subject: [PATCH 062/250] First pass at test runner --- tests/yellowstone/runtests.py | 212 ++++++++---- tests/yellowstone/utilities/runtools.py | 391 +++++++++++++++-------- tests/yellowstone/utilities/testtools.py | 91 ++---- 3 files changed, 417 insertions(+), 277 deletions(-) diff --git a/tests/yellowstone/runtests.py b/tests/yellowstone/runtests.py index 8253aa6..952a6c4 100755 --- a/tests/yellowstone/runtests.py +++ b/tests/yellowstone/runtests.py @@ -9,94 +9,164 @@ #============================================================================== # Builtin Modules +import os +import sys +import cPickle as pickle import argparse # Package Modules from utilities import testtools as tt from utilities import runtools as rt - #============================================================================== # Command-Line Interface Definition #============================================================================== -def parse_cli(): - desc = """This program is designed to run yellowstone-specific - tests of the PyReshaper. Each named test (or all tests if - the -a or --all option is used) will be given a run - directory in the "rundirs" directory with the same - name as the test itself. The run script will be placed - in this run directory, as will be placed the run output - error file. All output data files will be placed in the - output subdirectory.""" - parser = argparse.ArgumentParser(description=desc) - parser.add_argument('-a', '--all', default=False, - action='store_true', dest='all', - help='True or False, indicating whether to run all tests ' - '[Default: False]') - parser.add_argument('-c', '--code', default='STDD0002', type=str, - help='The name of the project code for charging in ' - 'parallel runs (ignored if running in serial) ' - '[Default: STDD0002]') - parser.add_argument('-d', '--database', default=None, type=str, - help='Location of the testinfo.json database file ' - '[Default: None]') - parser.add_argument('-f', '--format', default='netcdf4c', - type=str, dest='ncformat', - help='The NetCDF file format to use for the output data ' - 'produced by the test. [Default: netcdf4c]') - parser.add_argument('-l', '--list', default=False, - action='store_true', dest='list_tests', - help='True or False, indicating whether to list all tests, ' - 'instead of running tests. [Default: False]') - parser.add_argument('-o', '--overwrite', default=False, - action='store_true', dest='overwrite', - help='True or False, indicating whether to force deleting ' - 'any existing test or run directories, if found ' - '[Default: False]') - parser.add_argument('-m', '--multiple', default=False, - action='store_true', dest='multispec', - help='True or False, indications whether the tests ' - 'should be run from a single Reshaper submission ' - '(i.e., multiple Specifiers in one run) ' - '[Default: False]') - parser.add_argument('-q', '--queue', default='economy', type=str, - help='The name of the queue to request in parallel runs ' - '(ignored if running in serial) ' - '[Default: economy]') - parser.add_argument('-n', '--nodes', default=0, type=int, - help='The integer number of nodes to request in parallel' - ' runs (0 means run in serial) [Default: 0]') - parser.add_argument('-S', '--skip_existing', default=False, - action='store_true', dest='skip_existing', - help='Whether to skip time-series generation for ' - 'variables with existing output files. ' - '[Default: False]') - parser.add_argument('-t', '--tiling', default=16, type=int, - help='The integer number of processes per node to request ' - 'in parallel runs (ignored if running in serial) ' - '[Default: 16]') - parser.add_argument('-w', '--wtime', default=240, type=int, - help='The number of minutes to request for the wall clock ' - 'in parallel runs (ignored if running in serial) ' - '[Default: 240]') - parser.add_argument('tests', type=str, nargs='*') - - # Return the parsed CLI options - return parser.parse_args() +_DESC_ = """This program is designed to run yellowstone-specific + tests of the PyReshaper. Each named test (or all tests if + the -a or --all option is used) will be given a run + directory in the "rundirs" directory with the same + name as the test itself. The run script will be placed + in this run directory, as will be placed the run output + error file. All output data files will be placed in the + output subdirectory.""" + +_PARSER_ = argparse.ArgumentParser(description=_DESC_) +_PARSER_.add_argument('-a', '--all', default=False, + action='store_true', dest='all_tests', + help='True or False, indicating whether to run all ' + 'tests [Default: False]') +_PARSER_.add_argument('-c', '--code', default='STDD0002', type=str, + help='The name of the project code for charging in ' + 'parallel runs (ignored if running in serial) ' + '[Default: STDD0002]') +_PARSER_.add_argument('-i', '--infofile', default=None, type=str, + help='Location of the testinfo.json database file ' + '[Default: None]') +_PARSER_.add_argument('-f', '--format', default='netcdf4c', + type=str, dest='ncformat', + help='The NetCDF file format to use for the output ' + 'data produced by the test. [Default: netcdf4c]') +_PARSER_.add_argument('-l', '--list', default=False, + action='store_true', dest='list_tests', + help='True or False, indicating whether to list all ' + 'tests, instead of running tests. [Default: False]') +_PARSER_.add_argument('-m', '--multiple', default=False, + action='store_true', dest='multispec', + help='True or False, indications whether the tests ' + 'should be run from a single Reshaper submission ' + '(i.e., multiple Specifiers in one run) ' + '[Default: False]') +_PARSER_.add_argument('-n', '--nodes', default=0, type=int, + help='The integer number of nodes to request in parallel' + ' runs (0 means run in serial) [Default: 0]') +_PARSER_.add_argument('-o', '--overwrite', default=False, + action='store_true', dest='overwrite', + help='True or False, indicating whether to force ' + 'deleting any existing test or run directories, ' + 'if found [Default: False]') +_PARSER_.add_argument('-q', '--queue', default='economy', type=str, + help='The name of the queue to request in parallel runs ' + '(ignored if running in serial) ' + '[Default: economy]') +_PARSER_.add_argument('-s', '--skip_existing', default=False, + action='store_true', + help='Whether to skip time-series generation for ' + 'variables with existing output files. ' + '[Default: False]') +_PARSER_.add_argument('--statsfile', default=None, type=str, + help='Location of the teststats.json database file ' + '[Default: None]') +_PARSER_.add_argument('-t', '--tiling', default=16, type=int, + help='The integer number of processes per node to ' + 'request in parallel runs (ignored if running ' + 'in serial) [Default: 16]') +_PARSER_.add_argument('-w', '--wtime', default=240, type=int, + help='The number of minutes to request for the wall ' + 'clock in parallel runs (ignored if running in ' + 'serial) [Default: 240]') +_PARSER_.add_argument('-z', '--analyze', default=False, + action='store_true', + help='Whether to analyze (generate statistics for) the ' + 'test input, rather than run the tests. ' + '[Default: False]') +_PARSER_.add_argument('test', type=str, nargs='*', + help='Name of test to run or analyze.') #============================================================================== # Main Function #============================================================================== -def runtests(arguments): - testdb = tt.TestDB(dbname=arguments.database) - testdb.print_tests() - print - testdb.print_statistics() +def runtests(args): + """ + Run a set of tests + + Parameters: + args (argparse.Namespace): A namespace of command-line parsed arguments + describing the tests to run and how to run them + """ + + # Check for tests to run + if len(args.test) == 0 and not args.all_tests and not args.list_tests: + _PARSER_.print_help() + sys.exit(1) + + # Create/read the testing info and stats files + testdb = tt.TestDB(dbname=args.infofile, stname=args.statsfile) + + # List tests if only listing + if args.list_tests: + testdb.print_tests() + sys.exit(1) + + # Generate the list of tests to run/analyze + if args.all_tests: + test_list = testdb.get_database().keys() + else: + test_list = [t for t in args.test if t in testdb.get_database()] + + # Analyze test input, if requested (overwrite forces re-analysis) + if args.analyze: + testdb.analyze(tests=test_list, force=args.overwrite) + testdb.save_statistics(stname=args.statsfile) + sys.exit(0) + + # Run the requested tests + else: + for test_name in test_list: + if args.nodes > 0: + runtype = 'par' + str(args.nodes) + 'x' + str(args.tiling) + else: + runtype = 'ser' + testdir = os.path.abspath(os.path.join('rundirs', test_name, runtype)) + outputdir = os.path.join(testdir, 'output') + + # Create the specifier and write to file (specfile) + testspec = testdb.create_specifier(test_name=test_name, + ncfmt=args.ncformat, + outdir=outputdir) + testspecfile = test_name + '.p' + pickle.dump(testspec, open(testspecfile, 'wb')) + + # Generate the command and arguments + if args.nodes > 0: + runcmdargs = ['poe'] + else: + runcmdargs = [] + runcmdargs.extend(['slice2series', '--specfile', testspecfile]) + runcmd = ' '.join(runcmdargs) + + # Create and start the job + job = rt.Job(runcmds=[runcmd], nodes=args.nodes, name=test_name, + tiling=args.tiling, minutes=args.wtime, + queue=args.queue, project=args.code) + job.start() + if args.nodes == 0: + job.wait() #============================================================================== # Main Command-line Operation #============================================================================== if __name__ == '__main__': - runtests(parse_cli()) + args = _PARSER_.parse_args() + runtests(args) diff --git a/tests/yellowstone/utilities/runtools.py b/tests/yellowstone/utilities/runtools.py index be39f5e..eea3403 100644 --- a/tests/yellowstone/utilities/runtools.py +++ b/tests/yellowstone/utilities/runtools.py @@ -1,6 +1,6 @@ #============================================================================== # -# TestTools +# RunTools # # This is a collection of functions that are useful for running the PyReshaper # tests on the Yellowstone compute system. @@ -9,186 +9,299 @@ # Builtin Modules import os +import re +import abc import stat +import socket from subprocess import Popen, PIPE, STDOUT #============================================================================== -# Script/Job Runner for Yellowstone +# Job Class - Public Interface #============================================================================== class Job(object): + + def __init__(self, nodes=0, **kwargs): + """ + Factor function for job objects + + Parameters: + nodes (int): Number of nodes to run on (<=0 implies serial) + kwargs (dict): Additional arguments + """ + + self._nodes = int(nodes) + self._hostname = socket.gethostname() + if self._nodes <= 0: + self._job = _Job(**kwargs) + elif _YellowstoneJob.HOSTNAME_PATTERN.match(self._hostname): + self._job = _YellowstoneJob(nodes=self._nodes, **kwargs) + else: + err_msg = "Parallel job on " + self._hostname + " unsupported" + raise RuntimeError(err_msg) + + def start(self): + """ + Launch/start the job + """ + self._job.start() + + def wait(self): + """ + Wait for the job to complete + """ + self._job.wait() + + +#============================================================================== +# Job Base Abstract Class +#============================================================================== +class _Job(object): """ - A simple class for running jobs, writing submission scripts, etc + A class for defining a serial job type """ - def __init__(self, filename="runscript.sh", nodes=0, tiling=16, - minutes=120, queue="small", pcode="STDD0002", runcmds=None): + __metaclass__ = abc.ABCMeta + + def __init__(self, runcmds=[], name="job"): """ - Constructor + Initializer Parameters: - filename (str): Name of the run script - nodes (int): Number of nodes to request - tiling (int): Number of processors per node to request - minutes (int): Number of walltime minutes to request - queue (str): Name of queue to submit the job - runcmds (list): The list of commands to run + runcmds (list, tuple): The list of commands to run + name (str): Name of the run script """ - self.set(filename=filename, nodes=nodes, tiling=tiling, - minutes=minutes, queue=queue, pcode=pcode, runcmds=runcmds) - def set(self, filename=None, nodes=None, tiling=None, minutes=None, - queue=None, pcode=None, runcmds=None): + # Initialize internal data + self._jobname = str(name) + self._rundir = os.getcwd() + self._runscript = self._jobname + '.sh' + self._process = None + + self._runcmds = [] + if isinstance(runcmds, str): + self._runcmds.append(runcmds) + elif isinstance(runcmds, (list, tuple)): + strcmds = [str(cmd) for cmd in runcmds] + self._runcmds.extend(strcmds) + + @abc.abstractmethod + def start(self): + """ + Start the job (or submit into the queue) """ - Set the job specific parameters + pass - Parameters: - filename (str): Name of the run script - nodes (int): Number of nodes to request - tiling (int): Number of processors per node to request - minutes (int): Number of walltime minutes to request - queue (str): Name of queue to submit the job - runcmds (list): The list of commands to run - """ - if filename: - self._filename = str(filename) - self._rootname, runext = self._filename.rsplit('.', 1) - self._logext = 'log' if runext != 'log' else 'out' - self._rundir = os.path.dirname(os.path.realpath(self._filename)) - self._written = False - if nodes: - self._nodes = int(nodes) - self._written = False - if tiling: - self._tiling = int(tiling) - self._written = False - if minutes: - self._minutes = int(minutes) - self._written = False - if queue: - self._queue = str(queue) - self._written = False - if pcode: - self._pcode = str(pcode) - self._written = False - if runcmds: - self._written = False - self._runcmds = [] - if isinstance(runcmds, str): - self._runcmds.append(runcmds) - elif isinstance(runcmds, list): - strcmds = [str(cmd) for cmd in runcmds] - self._runcmds.extend(strcmds) - - def write(self): - """ - Write the run script associated with this job + @abc.abstractmethod + def wait(self): + """ + Wait for the job to complete + """ + pass - Parameters: - filename (str): Name of the run script file to write + +#============================================================================== +# Job Class for serial operation +#============================================================================== +class _SerialJob(_Job): + """ + A class for defining a serial job type + """ + + def __init__(self, runcmds=[], name="serialjob"): """ - # Check if written already - if self._written: - return + Initializer - # Check that run commands have been set - if not self._runcmds: - err_msg = "Cannot write run script without run commands" - raise ValueError(err_msg) + Parameters: + runcmds (list, tuple): The list of commands to run + name (str): Name of the run script + """ + # Call the base class initialization + super(_SerialJob, self).__init__(runcmds=runcmds, name=name) # Start creating the run scripts for each test - run_script_list = ['#!/bin/bash', ''] - - # If necessary, add the parallel preamble - if (self._nodes > 0): - - # Number of processors total - num_procs = self._nodes * self._tiling - - # Generate walltime in string form - wtime_hours = self._minutes / 60 - if (wtime_hours > 99): - wtime_hours = 99 - print 'Requested number of hours too large. Limiting to', \ - wtime_hours, '.' - wtime_minutes = self._minutes % 60 - wtime_str = '%02d:%02d' % (wtime_hours, wtime_minutes) - - # String list representing LSF preamble - run_script_list.extend([ - '#BSUB -n ' + str(num_procs), - '#BSUB -R "span[ptile=' + str(self._tiling) + ']"', - '#BSUB -q ' + self._queue, - '#BSUB -a poe', - '#BSUB -x', - '#BSUB -o ' + self._rootname + '.%J.' + self._logext, - '#BSUB -J ' + self._rootname, - '#BSUB -P ' + self._code, - '#BSUB -W ' + wtime_str, - '', - 'export MP_TIMEOUT=14400', - 'export MP_PULSE=1800', - 'export MP_DEBUG_NOTIMEOUT=yes', - '']) - - # Now create the rest of the run script - run_script_list.extend(['# Necessary modules to load', - 'module load python', - 'module load all-python-libs', - '']) - - run_script_list.extend(self._runcmds) - run_script_list.append('') + runscript_list = ['#!/bin/bash', + '', + '# Necessary modules to load', + 'module load python', + 'module load all-python-libs', + ''] + runscript_list.extend(self._runcmds) + runscript_list.append('') # Write the script to file - run_script_file = open(self._filename, 'w') - run_script_file.write(os.linesep.join(run_script_list)) - run_script_file.close() + runscript_file = open(self._runscript, 'w') + runscript_file.write(os.linesep.join(runscript_list)) + runscript_file.close() + + os.chmod(self._runscript, stat.S_IRWXU | stat.S_IRGRP | stat.S_IROTH) - def launch(self): + def start(self): """ - Launch the job (or submit into the queue) + Start the job (or submit into the queue) """ - # Write run script, if not done yet - if not self._written: - self.write() - - # Now launch the test + # Now launch the job cwd = os.getcwd() os.chdir(self._rundir) - if (self._nodes == 0): - # Make the script executable - os.chmod(self._filename, - stat.S_IRWXU | stat.S_IRGRP | stat.S_IROTH) + # if the process is already running, kill it + if self._process is not None: + self._process.kill() - # Launch the serial job as a subprocess - job = Popen([run_script], stdout=PIPE, stderr=STDOUT, - env=os.environ.copy()) - pid = str(job.pid) + # Launch the serial job as a subprocess + self._process = Popen([self._runscript], + stdout=PIPE, stderr=STDOUT, + env=os.environ.copy(), bufsize=1) + + os.chdir(cwd) + + def wait(self): + """ + Wait for the job to complete + """ + + if self._process is not None: + cwd = os.getcwd() + os.chdir(self._rundir) # Wait for job to finish and grab job output - job_output = job.communicate()[0] + job_output = '' + for line in iter(self._process.stdout.readline, b''): + print line, + job_output += line + self._process.stdout.close() + self._process.wait() + self._process = None # Write output to log file - log_file = open(self._rootname + '.' + self._logext, 'w') + log_file = open(self._jobname + '.log', 'w') log_file.write(job_output) log_file.close() - else: + os.chdir(cwd) + + +#============================================================================== +# Script/Job Runner for the Yellowstone LSF environment +#============================================================================== +class _YellowstoneJob(_Job): + """ + A simple class for running jobs on Yellowstone + """ + + HOSTNAME_PATTERN = re.compile('^(yslogin|caldera|geyser|pronghorn)') + + def __init__(self, runcmds=[], name="ysjob", nodes=1, tiling=16, + minutes=120, queue="small", project="STDD0002"): + """ + Constructor + + Parameters: + runcmds (list, tuple): The list of commands to run + name (str): Name of the run script + nodes (int): Number of nodes to request + tiling (int): Number of processors per node to request + minutes (int): Number of walltime minutes to request + queue (str): Name of queue to submit the job + project (str): Name of project with which to associate the job + """ + + # Call the base class initialization + super(_SerialJob, self).__init__(runcmds=runcmds, name=name) - # Open up the run script for input to LSF's bsub - run_script_file = open(self._filename, 'r') + # Initialize internal data + self._nodes = int(nodes) + self._tiling = int(tiling) + self._minutes = int(minutes) + self._queue = str(queue) + self._project = str(project) - # Launch the parallel job with LSF bsub - job = Popen(['bsub'], stdout=PIPE, stderr=STDOUT, - stdin=run_script_file, env=os.environ.copy()) + # Number of processors total + num_procs = self._nodes * self._tiling - # Grab the bsub output - job_output = job.communicate()[0] + # Generate walltime in string form + wtime_hours = self._minutes / 60 + if (wtime_hours > 99): + wtime_hours = 99 + print 'Requested number of hours too large. Limiting to', \ + wtime_hours, '.' + wtime_minutes = self._minutes % 60 + wtime_str = '%02d:%02d' % (wtime_hours, wtime_minutes) + + # String list representing LSF preamble + runscript_list = ['#!/bin/bash', + '#BSUB -n ' + str(num_procs), + '#BSUB -R "span[ptile=' + str(self._tiling) + ']"', + '#BSUB -q ' + self._queue, + '#BSUB -a poe', + '#BSUB -x', + '#BSUB -o ' + self._jobname + '.%J.log', + '#BSUB -J ' + self._jobname, + '#BSUB -P ' + self._code, + '#BSUB -W ' + wtime_str, + '', + 'export MP_TIMEOUT=14400', + 'export MP_PULSE=1800', + 'export MP_DEBUG_NOTIMEOUT=yes', + '', + '# Necessary modules to load', + 'module load python', + 'module load all-python-libs', + ''] + runscript_list.extend(self._runcmds) + runscript_list.append('') + + # Write the script to file + runscript_file = open(self._runscript, 'w') + runscript_file.write(os.linesep.join(runscript_list)) + runscript_file.close() + + def start(self): + """ + Start the job (or submit into the queue) + """ + + # Now launch the job + cwd = os.getcwd() + os.chdir(self._rundir) + + # If the process is still running, kill it first + if self._process is not None: + job = Popen(['bkill', self._process], + stdout=PIPE, stderr=STDOUT) + job.wait() + + # Open up the run script for input to LSF's bsub + runscript_file = open(self._runscript, 'r') + + # Launch the parallel job with LSF bsub + job = Popen(['bsub'], stdout=PIPE, stderr=STDOUT, + stdin=runscript_file, env=os.environ.copy()) + + # Get the process ID from bsub output + self._process = job.communicate()[0] + + # Close the script file and print submission info + runscript_file.close() + + os.chdir(cwd) + + def wait(self): + """ + Wait for the job to complete + """ + + cwd = os.getcwd() + os.chdir(self._rundir) + if self._process is not None: - # Close the script file and print submission info - run_script_file.close() + # Wait until the process completes + while self._process is not None: + job = Popen(['bjobs', self._process], + stdout=PIPE, stderr=PIPE) + job_output = job.communicate()[0] + if len(job_output) == 0: + self._process = None os.chdir(cwd) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index 37a01f1..2c765ea 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -128,6 +128,7 @@ def print_tests(self): """ List the tests in the test database. """ + print print 'Tests found in the Test Database are:' print for test_name in self._database: @@ -195,76 +196,32 @@ def create_specifier(self, test_name, ncfmt='netcdf4c', prefix=prefix, suffix=suffix, metadata=metadata, **kwargs) - def create_specifiers(self, tests=[], ncfmt='netcdf4c', - outdir='', **kwargs): - """ - Create a dictionary of named Specifier objects for a list of tests. - - Parameters: - tests (list): A list of string names of tests in the database - for which to construct Specifiers. - ncfmt (str): The NetCDF format string to be passed to the - Specifier. - outdir (str): An optional path string to be prepended to the - "output_prefix" argument of the Specifier. To be used to - direct output to a different location. Leave empty if using - absolute paths in the test's "output_prefix". - kwargs (dict): A dictionary of additional options to be - sent to the Specifier. - - Returns: - list: A list of Specifier instances with the information to run the - named tests. - """ - - # Check types - if not isinstance(tests, (list, tuple)): - err_msg = "Test list must be a list or tuple of string test names" - raise TypeError(err_msg) - test_types = [type(test_name) is str for test_name in tests] - if not all(test_types): - err_msg = "Test list must be a list of string test names" - raise TypeError(err_msg) - - # If test list is empty, assume all tests - if len(tests) == 0: - test_list = self._database.keys() - else: - test_list = tests - - # Construct the list of specifiers - specs = [self.create_specifier(test_name, ncfmt, outdir, **kwargs) - for test_name in test_list] - - # Return a dictionary of named specifiers - return dict(zip(test_list, specs)) - - def analyze(self, tests=[], force=False): + def analyze(self, tests=None, force=False): """ Analyze the test database to determine test statistics Parameters: tests (list): A list of string names of tests in the database - to analyze. If empty, assume all tests. + to analyze. If None, assume all tests. force (bool): Whether to force reanalysis of tests that have already been analyzed """ # Check type - if not isinstance(tests, (list, tuple)): + if tests is not None and not isinstance(tests, (list, tuple)): err_msg = "Test name list must be of list or tuple type" raise TypeError(err_msg) + # Assume all tests to be analyzed if None input + elif tests is None: + tests = self._database.keys() + # Error if tests not in database bad_names = [t for t in tests if t not in self._database] if len(bad_names) > 0: err_msg = "Tests not found in database: " + ", ".join(bad_names) raise ValueError(err_msg) - # Assume all tests to be analyzed if empty input - if len(tests) == 0: - tests = self._database.keys() - # If analysis has already been done, remove those tests if not force: for test_name in [t for t in tests if t in self._statistics]: @@ -416,32 +373,32 @@ def analyze(self, tests=[], force=False): max([var_stats[v]['xsize'] for v in timd_vars]) self._statistics[test_name]['maxsizes']['tinvariant'] = maxsize - def print_statistics(self, tests=[]): + def print_statistics(self, tests=None): """ Print the statistics information determined from self analysis Parameters: tests (list): A list of string names of tests in the database - to print. If empty, assume all tests. + to print. If None, assume all tests. """ # Check type - if not isinstance(tests, (list, tuple)): + if tests is not None and not isinstance(tests, (list, tuple)): err_msg = "Test name list must be of list or tuple type" raise TypeError(err_msg) + # Assume all tests to be analyzed if None input + elif tests is None: + tests = self._statistics.keys() + # Error if tests not in database bad_names = [t for t in tests if t not in self._statistics] if len(bad_names) > 0: err_msg = "Tests not found in statistics: " + ", ".join(bad_names) raise ValueError(err_msg) - # Assume all tests to be analyzed if empty input - if len(tests) == 0: - tests = self._statistics.keys() - # Print the statistics information - for test_name in self._statistics: + for test_name in tests: print "Statistics for Test:", test_name print @@ -521,17 +478,17 @@ def print_statistics(self, tests=[]): print " Time-Invariant Metadata Max Size:", _nbyte_str(timd_maxsize) print - def save_statistics(self, filename="teststats.json"): + def save_statistics(self, stname="teststats.json"): """ Save the statistics information to a JSON data file Parameters: - filename (str): The name of the JSON data file to write + stname (str): The name of the JSON statistics file to write """ # Check types - if isinstance(filename, str): - fp = open(filename, 'w') + if isinstance(stname, str): + fp = open(stname, 'w') else: err_msg = "Statistics filename must be a string" raise TypeError(err_msg) @@ -546,17 +503,17 @@ def save_statistics(self, filename="teststats.json"): # Close the file fp.close() - def load_statistics(self, filename="teststats.json"): + def load_statistics(self, stname="teststats.json"): """ Load the statistics information from a JSON data file Parameters: - filename (str): The name of the JSON data file to read + stname (str): The name of the JSON data file to read """ # Check types - if isinstance(filename, str): - fp = open(filename, 'r') + if isinstance(stname, str): + fp = open(stname, 'r') else: err_msg = "Statistics filename must be a string" raise TypeError(err_msg) From 84ab77b432640904365c7d6f40e62f72067bf580 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Wed, 16 Sep 2015 14:35:29 -0600 Subject: [PATCH 063/250] Moving this source to front of Python path --- tests/yellowstone/init.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/yellowstone/init.sh b/tests/yellowstone/init.sh index cf009c5..110cad1 100755 --- a/tests/yellowstone/init.sh +++ b/tests/yellowstone/init.sh @@ -10,6 +10,6 @@ function abspath { BIN_DIR=`abspath ../../bin` export PATH=$PATH:$BIN_DIR -# Add the PyReshaper module path to the python path +# Add this (local) PyReshaper module path to the python path MOD_DIR=`abspath ../../source` -export PYTHONPATH=$PYTHONPATH:$MOD_DIR +export PYTHONPATH=$MOD_DIR:$PYTHONPATH From 8da80ea9ae9fa4d66f50a3acce4d9c92fad5b583 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Wed, 16 Sep 2015 15:00:12 -0600 Subject: [PATCH 064/250] Can't implement abstract base class directly --- tests/yellowstone/utilities/runtools.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/utilities/runtools.py b/tests/yellowstone/utilities/runtools.py index eea3403..57aece1 100644 --- a/tests/yellowstone/utilities/runtools.py +++ b/tests/yellowstone/utilities/runtools.py @@ -33,7 +33,7 @@ def __init__(self, nodes=0, **kwargs): self._nodes = int(nodes) self._hostname = socket.gethostname() if self._nodes <= 0: - self._job = _Job(**kwargs) + self._job = _SerialJob(**kwargs) elif _YellowstoneJob.HOSTNAME_PATTERN.match(self._hostname): self._job = _YellowstoneJob(nodes=self._nodes, **kwargs) else: From 9ae5ac809e426cfbd7e409a66af00a63d806c72d Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Wed, 16 Sep 2015 15:01:29 -0600 Subject: [PATCH 065/250] Adding dictionary to catch extra arguments --- tests/yellowstone/utilities/runtools.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/yellowstone/utilities/runtools.py b/tests/yellowstone/utilities/runtools.py index 57aece1..578bb46 100644 --- a/tests/yellowstone/utilities/runtools.py +++ b/tests/yellowstone/utilities/runtools.py @@ -108,7 +108,7 @@ class _SerialJob(_Job): A class for defining a serial job type """ - def __init__(self, runcmds=[], name="serialjob"): + def __init__(self, runcmds=[], name="serialjob", **kwargs): """ Initializer @@ -193,7 +193,7 @@ class _YellowstoneJob(_Job): HOSTNAME_PATTERN = re.compile('^(yslogin|caldera|geyser|pronghorn)') def __init__(self, runcmds=[], name="ysjob", nodes=1, tiling=16, - minutes=120, queue="small", project="STDD0002"): + minutes=120, queue="small", project="STDD0002", **kwargs): """ Constructor From 9600a94924e088b7fada095a9cd4c6a8adc64e3c Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Wed, 16 Sep 2015 15:04:11 -0600 Subject: [PATCH 066/250] Changing to full path in runscript variable --- tests/yellowstone/utilities/runtools.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/utilities/runtools.py b/tests/yellowstone/utilities/runtools.py index 578bb46..b2c117b 100644 --- a/tests/yellowstone/utilities/runtools.py +++ b/tests/yellowstone/utilities/runtools.py @@ -75,7 +75,7 @@ def __init__(self, runcmds=[], name="job"): # Initialize internal data self._jobname = str(name) self._rundir = os.getcwd() - self._runscript = self._jobname + '.sh' + self._runscript = os.path.join([self._rundir, self._jobname + '.sh']) self._process = None self._runcmds = [] From 981ac58b2b2e902bb6b2893445f57ab1970112fb Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Wed, 16 Sep 2015 15:08:47 -0600 Subject: [PATCH 067/250] Debug statement --- tests/yellowstone/utilities/runtools.py | 1 + 1 file changed, 1 insertion(+) diff --git a/tests/yellowstone/utilities/runtools.py b/tests/yellowstone/utilities/runtools.py index b2c117b..f16933b 100644 --- a/tests/yellowstone/utilities/runtools.py +++ b/tests/yellowstone/utilities/runtools.py @@ -130,6 +130,7 @@ def __init__(self, runcmds=[], name="serialjob", **kwargs): runscript_list.append('') # Write the script to file + print self._runscript runscript_file = open(self._runscript, 'w') runscript_file.write(os.linesep.join(runscript_list)) runscript_file.close() From c11dc2c4429c9150c2a6d211fd88e15ae0e476b5 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Wed, 16 Sep 2015 15:09:49 -0600 Subject: [PATCH 068/250] Removing debug output. Fixing os.path.join call. --- tests/yellowstone/utilities/runtools.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/tests/yellowstone/utilities/runtools.py b/tests/yellowstone/utilities/runtools.py index f16933b..ef0c2af 100644 --- a/tests/yellowstone/utilities/runtools.py +++ b/tests/yellowstone/utilities/runtools.py @@ -75,7 +75,7 @@ def __init__(self, runcmds=[], name="job"): # Initialize internal data self._jobname = str(name) self._rundir = os.getcwd() - self._runscript = os.path.join([self._rundir, self._jobname + '.sh']) + self._runscript = os.path.join(self._rundir, self._jobname + '.sh') self._process = None self._runcmds = [] @@ -130,7 +130,6 @@ def __init__(self, runcmds=[], name="serialjob", **kwargs): runscript_list.append('') # Write the script to file - print self._runscript runscript_file = open(self._runscript, 'w') runscript_file.write(os.linesep.join(runscript_list)) runscript_file.close() From eaf3cedb2842d539f6a795cfb2f5b7691749fc28 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Wed, 16 Sep 2015 15:13:14 -0600 Subject: [PATCH 069/250] Make and move into test directory --- tests/yellowstone/runtests.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/tests/yellowstone/runtests.py b/tests/yellowstone/runtests.py index 952a6c4..4d85381 100755 --- a/tests/yellowstone/runtests.py +++ b/tests/yellowstone/runtests.py @@ -140,6 +140,10 @@ def runtests(args): testdir = os.path.abspath(os.path.join('rundirs', test_name, runtype)) outputdir = os.path.join(testdir, 'output') + # make test directory and move into it + os.mkdir(testdir) + os.chdir(testdir) + # Create the specifier and write to file (specfile) testspec = testdb.create_specifier(test_name=test_name, ncfmt=args.ncformat, From 561009526840cfbc4a5add471aa165a0b7fec643 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Wed, 16 Sep 2015 15:21:25 -0600 Subject: [PATCH 070/250] Make test and output directories, as needed --- tests/yellowstone/runtests.py | 15 ++++++++++++--- 1 file changed, 12 insertions(+), 3 deletions(-) diff --git a/tests/yellowstone/runtests.py b/tests/yellowstone/runtests.py index 4d85381..29044ab 100755 --- a/tests/yellowstone/runtests.py +++ b/tests/yellowstone/runtests.py @@ -133,17 +133,26 @@ def runtests(args): # Run the requested tests else: for test_name in test_list: + + # Set the test directory if args.nodes > 0: runtype = 'par' + str(args.nodes) + 'x' + str(args.tiling) else: runtype = 'ser' testdir = os.path.abspath(os.path.join('rundirs', test_name, runtype)) - outputdir = os.path.join(testdir, 'output') - # make test directory and move into it - os.mkdir(testdir) + # If the test directory doesn't exist, make it and move into it + if not os.path.exists(testdir): + os.makedirs(testdir) os.chdir(testdir) + # Set the output directory + outputdir = os.path.join(testdir, 'output') + + # If the output directory doesn't exists, create it + if not os.path.exists(outputdir): + os.mkdir(outputdir) + # Create the specifier and write to file (specfile) testspec = testdb.create_specifier(test_name=test_name, ncfmt=args.ncformat, From 9a01884c3306ccf5e1c1fdc39daceb8a36c3d6c8 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Wed, 16 Sep 2015 15:26:37 -0600 Subject: [PATCH 071/250] Bugfix for reading from a specfile. --- bin/slice2series | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/slice2series b/bin/slice2series index d3176d3..079256c 100755 --- a/bin/slice2series +++ b/bin/slice2series @@ -90,7 +90,7 @@ def main(options, input_file_list): # Try importing the file try: - spec = pickle.load(specfile, open(options.specfile, 'rb')) + spec = pickle.load(open(options.specfile, 'rb')) except: err_msg = "Specifier File '" + str(options.specfile) + "' " + \ "could not be opened and read" From 31d4024099396d459dcea98a36e67ffaf3d8ef88 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Wed, 16 Sep 2015 15:29:13 -0600 Subject: [PATCH 072/250] Fix to enable serial operation. --- tests/yellowstone/runtests.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/yellowstone/runtests.py b/tests/yellowstone/runtests.py index 29044ab..5a2c0db 100755 --- a/tests/yellowstone/runtests.py +++ b/tests/yellowstone/runtests.py @@ -162,10 +162,10 @@ def runtests(args): # Generate the command and arguments if args.nodes > 0: - runcmdargs = ['poe'] + runcmdargs = ['poe', 'slice2series'] else: - runcmdargs = [] - runcmdargs.extend(['slice2series', '--specfile', testspecfile]) + runcmdargs = ['slice2series', '--serial'] + runcmdargs.extend(['--specfile', testspecfile]) runcmd = ' '.join(runcmdargs) # Create and start the job From a2b9deebb1d7b7fbc4a7c859c0c633d78550c553 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Wed, 16 Sep 2015 16:16:08 -0600 Subject: [PATCH 073/250] Allow for overwriting existing tests --- tests/yellowstone/runtests.py | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/tests/yellowstone/runtests.py b/tests/yellowstone/runtests.py index 5a2c0db..3473a6d 100755 --- a/tests/yellowstone/runtests.py +++ b/tests/yellowstone/runtests.py @@ -11,8 +11,9 @@ # Builtin Modules import os import sys -import cPickle as pickle +import shutil import argparse +import cPickle as pickle # Package Modules from utilities import testtools as tt @@ -134,6 +135,8 @@ def runtests(args): else: for test_name in test_list: + print "Running test:", test_name + # Set the test directory if args.nodes > 0: runtype = 'par' + str(args.nodes) + 'x' + str(args.tiling) @@ -142,6 +145,12 @@ def runtests(args): testdir = os.path.abspath(os.path.join('rundirs', test_name, runtype)) # If the test directory doesn't exist, make it and move into it + if os.path.exists(testdir): + if args.overwrite: + shutil.rmtree(testdir) + else: + print " Skipping existing" + continue if not os.path.exists(testdir): os.makedirs(testdir) os.chdir(testdir) @@ -157,7 +166,7 @@ def runtests(args): testspec = testdb.create_specifier(test_name=test_name, ncfmt=args.ncformat, outdir=outputdir) - testspecfile = test_name + '.p' + testspecfile = test_name + '.spec' pickle.dump(testspec, open(testspecfile, 'wb')) # Generate the command and arguments From 8b039a81ca5f3557f66a0b120bf74998b06f5a99 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Wed, 16 Sep 2015 16:27:17 -0600 Subject: [PATCH 074/250] Attempt to print stdout in serial mode in real time --- tests/yellowstone/utilities/runtools.py | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/tests/yellowstone/utilities/runtools.py b/tests/yellowstone/utilities/runtools.py index ef0c2af..765e5fe 100644 --- a/tests/yellowstone/utilities/runtools.py +++ b/tests/yellowstone/utilities/runtools.py @@ -167,11 +167,10 @@ def wait(self): # Wait for job to finish and grab job output job_output = '' - for line in iter(self._process.stdout.readline, b''): + while self._process.poll() is None: + line = self._process.stdout.readline() print line, - job_output += line - self._process.stdout.close() - self._process.wait() + print self._process.stdout.read() self._process = None # Write output to log file From 7eb57f73bffb73778f3ffee50ff7e286499690a6 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Wed, 16 Sep 2015 16:27:47 -0600 Subject: [PATCH 075/250] Forgot to append lines to job ouput --- tests/yellowstone/utilities/runtools.py | 1 + 1 file changed, 1 insertion(+) diff --git a/tests/yellowstone/utilities/runtools.py b/tests/yellowstone/utilities/runtools.py index 765e5fe..5e65765 100644 --- a/tests/yellowstone/utilities/runtools.py +++ b/tests/yellowstone/utilities/runtools.py @@ -169,6 +169,7 @@ def wait(self): job_output = '' while self._process.poll() is None: line = self._process.stdout.readline() + job_output += line print line, print self._process.stdout.read() self._process = None From e4555b4c635b5f091842c14b260b0ba2e73a475a Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Wed, 16 Sep 2015 16:31:50 -0600 Subject: [PATCH 076/250] Removing bufsize --- tests/yellowstone/utilities/runtools.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/utilities/runtools.py b/tests/yellowstone/utilities/runtools.py index 5e65765..8cc7e13 100644 --- a/tests/yellowstone/utilities/runtools.py +++ b/tests/yellowstone/utilities/runtools.py @@ -152,7 +152,7 @@ def start(self): # Launch the serial job as a subprocess self._process = Popen([self._runscript], stdout=PIPE, stderr=STDOUT, - env=os.environ.copy(), bufsize=1) + env=os.environ.copy()) os.chdir(cwd) From e37c7ddd65da57ac98fdef4b6b096341faff7881 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Wed, 16 Sep 2015 16:33:22 -0600 Subject: [PATCH 077/250] Increasing verbosity --- tests/yellowstone/runtests.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/yellowstone/runtests.py b/tests/yellowstone/runtests.py index 3473a6d..5459195 100755 --- a/tests/yellowstone/runtests.py +++ b/tests/yellowstone/runtests.py @@ -171,9 +171,9 @@ def runtests(args): # Generate the command and arguments if args.nodes > 0: - runcmdargs = ['poe', 'slice2series'] + runcmdargs = ['poe', 'slice2series', '-v3'] else: - runcmdargs = ['slice2series', '--serial'] + runcmdargs = ['slice2series', '--serial', '-v3'] runcmdargs.extend(['--specfile', testspecfile]) runcmd = ' '.join(runcmdargs) From d58d2dc478192d2a3b06c4a8639cf41ac421ba0c Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Wed, 16 Sep 2015 16:34:46 -0600 Subject: [PATCH 078/250] putting bufsize back --- tests/yellowstone/utilities/runtools.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/utilities/runtools.py b/tests/yellowstone/utilities/runtools.py index 8cc7e13..5e65765 100644 --- a/tests/yellowstone/utilities/runtools.py +++ b/tests/yellowstone/utilities/runtools.py @@ -152,7 +152,7 @@ def start(self): # Launch the serial job as a subprocess self._process = Popen([self._runscript], stdout=PIPE, stderr=STDOUT, - env=os.environ.copy()) + env=os.environ.copy(), bufsize=1) os.chdir(cwd) From 5367a9d116dd7e305d62c657d51098bffc4cbe79 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Wed, 16 Sep 2015 16:35:53 -0600 Subject: [PATCH 079/250] Output remaining stdout buffer --- tests/yellowstone/utilities/runtools.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/tests/yellowstone/utilities/runtools.py b/tests/yellowstone/utilities/runtools.py index 5e65765..27971a0 100644 --- a/tests/yellowstone/utilities/runtools.py +++ b/tests/yellowstone/utilities/runtools.py @@ -171,7 +171,9 @@ def wait(self): line = self._process.stdout.readline() job_output += line print line, - print self._process.stdout.read() + remainder = self._process.stdout.read() + job_output += remainder + print remainder self._process = None # Write output to log file From 52312f6125bb41f7606db6cf463f797b1881034a Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Wed, 16 Sep 2015 16:39:40 -0600 Subject: [PATCH 080/250] Debug initializer of YS jobs --- tests/yellowstone/utilities/runtools.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/utilities/runtools.py b/tests/yellowstone/utilities/runtools.py index 27971a0..881e693 100644 --- a/tests/yellowstone/utilities/runtools.py +++ b/tests/yellowstone/utilities/runtools.py @@ -210,7 +210,7 @@ def __init__(self, runcmds=[], name="ysjob", nodes=1, tiling=16, """ # Call the base class initialization - super(_SerialJob, self).__init__(runcmds=runcmds, name=name) + super(_YellowstoneJob, self).__init__(runcmds=runcmds, name=name) # Initialize internal data self._nodes = int(nodes) From d8acf28574b80c4e88ed13c52e9f2030d5ceeb4d Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Wed, 16 Sep 2015 16:40:32 -0600 Subject: [PATCH 081/250] Renamed _code to _project --- tests/yellowstone/utilities/runtools.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/utilities/runtools.py b/tests/yellowstone/utilities/runtools.py index 881e693..638d3fc 100644 --- a/tests/yellowstone/utilities/runtools.py +++ b/tests/yellowstone/utilities/runtools.py @@ -240,7 +240,7 @@ def __init__(self, runcmds=[], name="ysjob", nodes=1, tiling=16, '#BSUB -x', '#BSUB -o ' + self._jobname + '.%J.log', '#BSUB -J ' + self._jobname, - '#BSUB -P ' + self._code, + '#BSUB -P ' + self._project, '#BSUB -W ' + wtime_str, '', 'export MP_TIMEOUT=14400', From d8dd68f19c6c95017dea862157ae9768d2507767 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Wed, 16 Sep 2015 16:41:34 -0600 Subject: [PATCH 082/250] Display LSF job id --- tests/yellowstone/utilities/runtools.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/tests/yellowstone/utilities/runtools.py b/tests/yellowstone/utilities/runtools.py index 638d3fc..3dad3bd 100644 --- a/tests/yellowstone/utilities/runtools.py +++ b/tests/yellowstone/utilities/runtools.py @@ -284,6 +284,9 @@ def start(self): # Get the process ID from bsub output self._process = job.communicate()[0] + # Display the job name + print self._process + # Close the script file and print submission info runscript_file.close() From 3352e4353643f5982b00bb46f82e5f98ae3a12aa Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Wed, 16 Sep 2015 16:55:06 -0600 Subject: [PATCH 083/250] Attempting different real-time output --- tests/yellowstone/utilities/runtools.py | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/tests/yellowstone/utilities/runtools.py b/tests/yellowstone/utilities/runtools.py index 3dad3bd..07317ba 100644 --- a/tests/yellowstone/utilities/runtools.py +++ b/tests/yellowstone/utilities/runtools.py @@ -167,13 +167,12 @@ def wait(self): # Wait for job to finish and grab job output job_output = '' - while self._process.poll() is None: + while True: line = self._process.stdout.readline() + if not line: + break job_output += line print line, - remainder = self._process.stdout.read() - job_output += remainder - print remainder self._process = None # Write output to log file From 49e22dcdb58f0b8ce08ec32f83d43ad2f2b97b69 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 10:35:18 -0600 Subject: [PATCH 084/250] Try reading log file in real time, rather than capture STDOUT --- tests/yellowstone/utilities/runtools.py | 42 +++++++++++++++---------- 1 file changed, 26 insertions(+), 16 deletions(-) diff --git a/tests/yellowstone/utilities/runtools.py b/tests/yellowstone/utilities/runtools.py index 07317ba..1b3693b 100644 --- a/tests/yellowstone/utilities/runtools.py +++ b/tests/yellowstone/utilities/runtools.py @@ -116,9 +116,13 @@ def __init__(self, runcmds=[], name="serialjob", **kwargs): runcmds (list, tuple): The list of commands to run name (str): Name of the run script """ + # Call the base class initialization super(_SerialJob, self).__init__(runcmds=runcmds, name=name) + # Define the name of the log file + self._logfile = os.path.join(self._rundir, self._jobname + '.log') + # Start creating the run scripts for each test runscript_list = ['#!/bin/bash', '', @@ -134,6 +138,7 @@ def __init__(self, runcmds=[], name="serialjob", **kwargs): runscript_file.write(os.linesep.join(runscript_list)) runscript_file.close() + # Make the script executable os.chmod(self._runscript, stat.S_IRWXU | stat.S_IRGRP | stat.S_IROTH) def start(self): @@ -141,7 +146,7 @@ def start(self): Start the job (or submit into the queue) """ - # Now launch the job + # Go to the run directory cwd = os.getcwd() os.chdir(self._rundir) @@ -151,9 +156,10 @@ def start(self): # Launch the serial job as a subprocess self._process = Popen([self._runscript], - stdout=PIPE, stderr=STDOUT, - env=os.environ.copy(), bufsize=1) + stdout=open(self._logfile, 'w'), + stderr=STDOUT, env=os.environ.copy(), bufsize=1) + # Go back to where you started os.chdir(cwd) def wait(self): @@ -162,24 +168,28 @@ def wait(self): """ if self._process is not None: + + # Go to the run directory cwd = os.getcwd() os.chdir(self._rundir) - # Wait for job to finish and grab job output - job_output = '' - while True: - line = self._process.stdout.readline() - if not line: - break - job_output += line - print line, - self._process = None + # Open the logfile for reading + logfile = open(self._logfile, 'r') - # Write output to log file - log_file = open(self._jobname + '.log', 'w') - log_file.write(job_output) - log_file.close() + # Get the existing contents of the log file and output to screen + print logfile.read(), + + # Wait for job to finish and continue to print output to screen + while self._process.poll(): + print logfile.readline(), + + # Now that the process is done, close the logfile + logfile.close() + + # Null the process pointer + self._process = None + # Go back to where you started os.chdir(cwd) From bfdf3fab3e4e71927342c9db807cdd573753828d Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 10:44:01 -0600 Subject: [PATCH 085/250] Keeping log file open for process duration --- tests/yellowstone/runtests.py | 2 +- tests/yellowstone/utilities/runtools.py | 15 ++++++++++----- 2 files changed, 11 insertions(+), 6 deletions(-) diff --git a/tests/yellowstone/runtests.py b/tests/yellowstone/runtests.py index 5459195..f24354c 100755 --- a/tests/yellowstone/runtests.py +++ b/tests/yellowstone/runtests.py @@ -182,7 +182,7 @@ def runtests(args): tiling=args.tiling, minutes=args.wtime, queue=args.queue, project=args.code) job.start() - if args.nodes == 0: + if args.nodes <= 0: job.wait() diff --git a/tests/yellowstone/utilities/runtools.py b/tests/yellowstone/utilities/runtools.py index 1b3693b..4b824fb 100644 --- a/tests/yellowstone/utilities/runtools.py +++ b/tests/yellowstone/utilities/runtools.py @@ -120,8 +120,9 @@ def __init__(self, runcmds=[], name="serialjob", **kwargs): # Call the base class initialization super(_SerialJob, self).__init__(runcmds=runcmds, name=name) - # Define the name of the log file - self._logfile = os.path.join(self._rundir, self._jobname + '.log') + # Define the name of the log file, and set the file object to None + self._logfilenm = os.path.join(self._rundir, self._jobname + '.log') + self._logfile = None # Start creating the run scripts for each test runscript_list = ['#!/bin/bash', @@ -153,11 +154,15 @@ def start(self): # if the process is already running, kill it if self._process is not None: self._process.kill() + self._logfile.close() + + # Open the log file + self._logfile = open(self._logfilenm, 'w') # Launch the serial job as a subprocess self._process = Popen([self._runscript], - stdout=open(self._logfile, 'w'), - stderr=STDOUT, env=os.environ.copy(), bufsize=1) + stdout=self._logfile, stderr=STDOUT, + env=os.environ.copy(), bufsize=1) # Go back to where you started os.chdir(cwd) @@ -174,7 +179,7 @@ def wait(self): os.chdir(self._rundir) # Open the logfile for reading - logfile = open(self._logfile, 'r') + logfile = open(self._logfilenm, 'r') # Get the existing contents of the log file and output to screen print logfile.read(), From 9df2a2e973a0206b573aac7adde732c518f61dfe Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 10:53:13 -0600 Subject: [PATCH 086/250] Attempting new log display --- tests/yellowstone/utilities/runtools.py | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/tests/yellowstone/utilities/runtools.py b/tests/yellowstone/utilities/runtools.py index 4b824fb..31cd25a 100644 --- a/tests/yellowstone/utilities/runtools.py +++ b/tests/yellowstone/utilities/runtools.py @@ -12,6 +12,7 @@ import re import abc import stat +import time import socket from subprocess import Popen, PIPE, STDOUT @@ -186,7 +187,13 @@ def wait(self): # Wait for job to finish and continue to print output to screen while self._process.poll(): - print logfile.readline(), + where = file.tell() + line = file.readline() + if not line: + time.sleep(1) + file.seek(where) + else: + print line, # Now that the process is done, close the logfile logfile.close() From 0ac1b9161653183edbb4757a95b78a5435a8f7b2 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 10:57:47 -0600 Subject: [PATCH 087/250] Debugging output --- tests/yellowstone/runtests.py | 1 + tests/yellowstone/utilities/runtools.py | 7 +++++++ 2 files changed, 8 insertions(+) diff --git a/tests/yellowstone/runtests.py b/tests/yellowstone/runtests.py index f24354c..dcc5ee3 100755 --- a/tests/yellowstone/runtests.py +++ b/tests/yellowstone/runtests.py @@ -183,6 +183,7 @@ def runtests(args): queue=args.queue, project=args.code) job.start() if args.nodes <= 0: + print "*** Waiting for serial job to complete..." job.wait() diff --git a/tests/yellowstone/utilities/runtools.py b/tests/yellowstone/utilities/runtools.py index 31cd25a..7b871c9 100644 --- a/tests/yellowstone/utilities/runtools.py +++ b/tests/yellowstone/utilities/runtools.py @@ -175,6 +175,8 @@ def wait(self): if self._process is not None: + print "*** Serial process is not None..." + # Go to the run directory cwd = os.getcwd() os.chdir(self._rundir) @@ -182,11 +184,15 @@ def wait(self): # Open the logfile for reading logfile = open(self._logfilenm, 'r') + print "*** Log file opened for reading..." + # Get the existing contents of the log file and output to screen print logfile.read(), # Wait for job to finish and continue to print output to screen + print "*** Checking if serial process is still running..." while self._process.poll(): + print "*** Serial process still running..." where = file.tell() line = file.readline() if not line: @@ -196,6 +202,7 @@ def wait(self): print line, # Now that the process is done, close the logfile + print "*** Log file closed" logfile.close() # Null the process pointer From 6bf6605ba975999659afd57fab3260b5be5e59d5 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 11:00:11 -0600 Subject: [PATCH 088/250] Subprocess poll needs to check for NOT None! --- tests/yellowstone/utilities/runtools.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/utilities/runtools.py b/tests/yellowstone/utilities/runtools.py index 7b871c9..2ca8003 100644 --- a/tests/yellowstone/utilities/runtools.py +++ b/tests/yellowstone/utilities/runtools.py @@ -191,7 +191,7 @@ def wait(self): # Wait for job to finish and continue to print output to screen print "*** Checking if serial process is still running..." - while self._process.poll(): + while self._process.poll() is None: print "*** Serial process still running..." where = file.tell() line = file.readline() From e035388d5e9bbe6b59bdcf8e804fada82309c9a8 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 11:01:21 -0600 Subject: [PATCH 089/250] Typo. Didn't rename 'file' to 'logfile'. --- tests/yellowstone/utilities/runtools.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/yellowstone/utilities/runtools.py b/tests/yellowstone/utilities/runtools.py index 2ca8003..4cf693f 100644 --- a/tests/yellowstone/utilities/runtools.py +++ b/tests/yellowstone/utilities/runtools.py @@ -193,11 +193,11 @@ def wait(self): print "*** Checking if serial process is still running..." while self._process.poll() is None: print "*** Serial process still running..." - where = file.tell() - line = file.readline() + where = logfile.tell() + line = logfile.readline() if not line: time.sleep(1) - file.seek(where) + logfile.seek(where) else: print line, From c7a961abad5dc2cb09e1ca8f1d154f8235bca636 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 11:03:19 -0600 Subject: [PATCH 090/250] Removing debug statements --- tests/yellowstone/runtests.py | 1 - tests/yellowstone/utilities/runtools.py | 7 ------- 2 files changed, 8 deletions(-) diff --git a/tests/yellowstone/runtests.py b/tests/yellowstone/runtests.py index dcc5ee3..f24354c 100755 --- a/tests/yellowstone/runtests.py +++ b/tests/yellowstone/runtests.py @@ -183,7 +183,6 @@ def runtests(args): queue=args.queue, project=args.code) job.start() if args.nodes <= 0: - print "*** Waiting for serial job to complete..." job.wait() diff --git a/tests/yellowstone/utilities/runtools.py b/tests/yellowstone/utilities/runtools.py index 4cf693f..95f64e9 100644 --- a/tests/yellowstone/utilities/runtools.py +++ b/tests/yellowstone/utilities/runtools.py @@ -175,8 +175,6 @@ def wait(self): if self._process is not None: - print "*** Serial process is not None..." - # Go to the run directory cwd = os.getcwd() os.chdir(self._rundir) @@ -184,15 +182,11 @@ def wait(self): # Open the logfile for reading logfile = open(self._logfilenm, 'r') - print "*** Log file opened for reading..." - # Get the existing contents of the log file and output to screen print logfile.read(), # Wait for job to finish and continue to print output to screen - print "*** Checking if serial process is still running..." while self._process.poll() is None: - print "*** Serial process still running..." where = logfile.tell() line = logfile.readline() if not line: @@ -202,7 +196,6 @@ def wait(self): print line, # Now that the process is done, close the logfile - print "*** Log file closed" logfile.close() # Null the process pointer From db9a7bf94f50844b64dd6a1df6dab23c7808d764 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 11:04:58 -0600 Subject: [PATCH 091/250] Faster subprocess polling (no need for sleep) --- tests/yellowstone/utilities/runtools.py | 9 +-------- 1 file changed, 1 insertion(+), 8 deletions(-) diff --git a/tests/yellowstone/utilities/runtools.py b/tests/yellowstone/utilities/runtools.py index 95f64e9..d71f9ff 100644 --- a/tests/yellowstone/utilities/runtools.py +++ b/tests/yellowstone/utilities/runtools.py @@ -12,7 +12,6 @@ import re import abc import stat -import time import socket from subprocess import Popen, PIPE, STDOUT @@ -187,13 +186,7 @@ def wait(self): # Wait for job to finish and continue to print output to screen while self._process.poll() is None: - where = logfile.tell() - line = logfile.readline() - if not line: - time.sleep(1) - logfile.seek(where) - else: - print line, + print logfile.readline(), # Now that the process is done, close the logfile logfile.close() From 10bca3618450d05355161d689a50a2d52e71a009 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 11:08:31 -0600 Subject: [PATCH 092/250] Print entire log file to screen using only readline --- tests/yellowstone/utilities/runtools.py | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/tests/yellowstone/utilities/runtools.py b/tests/yellowstone/utilities/runtools.py index d71f9ff..addbeb7 100644 --- a/tests/yellowstone/utilities/runtools.py +++ b/tests/yellowstone/utilities/runtools.py @@ -181,12 +181,11 @@ def wait(self): # Open the logfile for reading logfile = open(self._logfilenm, 'r') - # Get the existing contents of the log file and output to screen - print logfile.read(), - # Wait for job to finish and continue to print output to screen while self._process.poll() is None: - print logfile.readline(), + line = logfile.readline() + if line: + print line, # Now that the process is done, close the logfile logfile.close() From dbe62367fa43a596b72194b82bb76b6d4b071cee Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 11:09:41 -0600 Subject: [PATCH 093/250] Not buffering subprocess output --- tests/yellowstone/utilities/runtools.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/utilities/runtools.py b/tests/yellowstone/utilities/runtools.py index addbeb7..a4ec612 100644 --- a/tests/yellowstone/utilities/runtools.py +++ b/tests/yellowstone/utilities/runtools.py @@ -162,7 +162,7 @@ def start(self): # Launch the serial job as a subprocess self._process = Popen([self._runscript], stdout=self._logfile, stderr=STDOUT, - env=os.environ.copy(), bufsize=1) + env=os.environ.copy(), bufsize=0) # Go back to where you started os.chdir(cwd) From 19c20cd46a9447d414d1442976cf78af13f90f41 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 11:42:30 -0600 Subject: [PATCH 094/250] Don't attempt to pipe output to screen in real time --- tests/yellowstone/utilities/runtools.py | 54 ++++++++----------------- 1 file changed, 16 insertions(+), 38 deletions(-) diff --git a/tests/yellowstone/utilities/runtools.py b/tests/yellowstone/utilities/runtools.py index a4ec612..fbf2160 100644 --- a/tests/yellowstone/utilities/runtools.py +++ b/tests/yellowstone/utilities/runtools.py @@ -164,6 +164,9 @@ def start(self): stdout=self._logfile, stderr=STDOUT, env=os.environ.copy(), bufsize=0) + # Display PID on screen and let run in background + print " Process launched in background with PID", self._process.pid + # Go back to where you started os.chdir(cwd) @@ -173,29 +176,9 @@ def wait(self): """ if self._process is not None: - - # Go to the run directory - cwd = os.getcwd() - os.chdir(self._rundir) - - # Open the logfile for reading - logfile = open(self._logfilenm, 'r') - - # Wait for job to finish and continue to print output to screen - while self._process.poll() is None: - line = logfile.readline() - if line: - print line, - - # Now that the process is done, close the logfile - logfile.close() - - # Null the process pointer + self._process.wait() self._process = None - # Go back to where you started - os.chdir(cwd) - #============================================================================== # Script/Job Runner for the Yellowstone LSF environment @@ -277,7 +260,7 @@ def start(self): Start the job (or submit into the queue) """ - # Now launch the job + # Go to the run directory cwd = os.getcwd() os.chdir(self._rundir) @@ -291,18 +274,19 @@ def start(self): runscript_file = open(self._runscript, 'r') # Launch the parallel job with LSF bsub - job = Popen(['bsub'], stdout=PIPE, stderr=STDOUT, + job = Popen(['bsub'], stdout=PIPE, stderr=PIPE, stdin=runscript_file, env=os.environ.copy()) # Get the process ID from bsub output - self._process = job.communicate()[0] + self._process, output = job.communicate() # Display the job name - print self._process + print " ", output # Close the script file and print submission info runscript_file.close() + # Go back to where we started os.chdir(cwd) def wait(self): @@ -310,16 +294,10 @@ def wait(self): Wait for the job to complete """ - cwd = os.getcwd() - os.chdir(self._rundir) - if self._process is not None: - - # Wait until the process completes - while self._process is not None: - job = Popen(['bjobs', self._process], - stdout=PIPE, stderr=PIPE) - job_output = job.communicate()[0] - if len(job_output) == 0: - self._process = None - - os.chdir(cwd) + # Wait until the process completes + while self._process is not None: + job = Popen(['bjobs', self._process], + stdout=PIPE, stderr=PIPE) + job_output = job.communicate()[0] + if len(job_output) == 0: + self._process = None From 740514e731bebc8e8eb312210d6e52562267e461 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 12:05:21 -0600 Subject: [PATCH 095/250] Fixing display output. --- tests/yellowstone/utilities/runtools.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/tests/yellowstone/utilities/runtools.py b/tests/yellowstone/utilities/runtools.py index fbf2160..3a39e30 100644 --- a/tests/yellowstone/utilities/runtools.py +++ b/tests/yellowstone/utilities/runtools.py @@ -274,15 +274,18 @@ def start(self): runscript_file = open(self._runscript, 'r') # Launch the parallel job with LSF bsub - job = Popen(['bsub'], stdout=PIPE, stderr=PIPE, + job = Popen(['bsub'], stdout=PIPE, stderr=STDOUT, stdin=runscript_file, env=os.environ.copy()) # Get the process ID from bsub output - self._process, output = job.communicate() + output = job.communicate()[0] # Display the job name print " ", output + # Get the job ID (first integer in output) + self._process = re.findall('\d+', output)[0] + # Close the script file and print submission info runscript_file.close() From 24459bb9770f91b8925feec7126a36ea8636d537 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 12:08:58 -0600 Subject: [PATCH 096/250] Casting test_name to str --- tests/yellowstone/runtests.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/runtests.py b/tests/yellowstone/runtests.py index f24354c..28aef75 100755 --- a/tests/yellowstone/runtests.py +++ b/tests/yellowstone/runtests.py @@ -163,7 +163,7 @@ def runtests(args): os.mkdir(outputdir) # Create the specifier and write to file (specfile) - testspec = testdb.create_specifier(test_name=test_name, + testspec = testdb.create_specifier(test_name=str(test_name), ncfmt=args.ncformat, outdir=outputdir) testspecfile = test_name + '.spec' From 012fc99c6b2a76641a8f82f279f568822d6c9b8a Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 12:11:19 -0600 Subject: [PATCH 097/250] More string casting --- tests/yellowstone/runtests.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/yellowstone/runtests.py b/tests/yellowstone/runtests.py index 28aef75..92c836a 100755 --- a/tests/yellowstone/runtests.py +++ b/tests/yellowstone/runtests.py @@ -142,7 +142,7 @@ def runtests(args): runtype = 'par' + str(args.nodes) + 'x' + str(args.tiling) else: runtype = 'ser' - testdir = os.path.abspath(os.path.join('rundirs', test_name, runtype)) + testdir = os.path.abspath(os.path.join('rundirs', str(test_name), runtype)) # If the test directory doesn't exist, make it and move into it if os.path.exists(testdir): @@ -166,7 +166,7 @@ def runtests(args): testspec = testdb.create_specifier(test_name=str(test_name), ncfmt=args.ncformat, outdir=outputdir) - testspecfile = test_name + '.spec' + testspecfile = str(test_name) + '.spec' pickle.dump(testspec, open(testspecfile, 'wb')) # Generate the command and arguments @@ -178,7 +178,7 @@ def runtests(args): runcmd = ' '.join(runcmdargs) # Create and start the job - job = rt.Job(runcmds=[runcmd], nodes=args.nodes, name=test_name, + job = rt.Job(runcmds=[runcmd], nodes=args.nodes, name=str(test_name), tiling=args.tiling, minutes=args.wtime, queue=args.queue, project=args.code) job.start() From c38aa5d5c7251df75d1779b47f8b3fe4c0c16855 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 12:14:56 -0600 Subject: [PATCH 098/250] Stripping whitespace from output --- tests/yellowstone/utilities/runtools.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/utilities/runtools.py b/tests/yellowstone/utilities/runtools.py index 3a39e30..8a13563 100644 --- a/tests/yellowstone/utilities/runtools.py +++ b/tests/yellowstone/utilities/runtools.py @@ -278,7 +278,7 @@ def start(self): stdin=runscript_file, env=os.environ.copy()) # Get the process ID from bsub output - output = job.communicate()[0] + output = str(job.communicate()[0]).strip() # Display the job name print " ", output From b43a3a23e69993da5f5220856c30d889c4f1c8c5 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 12:42:07 -0600 Subject: [PATCH 099/250] Using str.format in all strings/output --- tests/yellowstone/runtests.py | 4 +- tests/yellowstone/utilities/runtools.py | 23 +++++----- tests/yellowstone/utilities/testtools.py | 54 ++++++++++++------------ 3 files changed, 40 insertions(+), 41 deletions(-) diff --git a/tests/yellowstone/runtests.py b/tests/yellowstone/runtests.py index 92c836a..07fe26a 100755 --- a/tests/yellowstone/runtests.py +++ b/tests/yellowstone/runtests.py @@ -135,11 +135,11 @@ def runtests(args): else: for test_name in test_list: - print "Running test:", test_name + print 'Running test: {0!s}'.format(test_name) # Set the test directory if args.nodes > 0: - runtype = 'par' + str(args.nodes) + 'x' + str(args.tiling) + runtype = 'par{0!s}x{1!s}'.format(args.nodes, args.tiling) else: runtype = 'ser' testdir = os.path.abspath(os.path.join('rundirs', str(test_name), runtype)) diff --git a/tests/yellowstone/utilities/runtools.py b/tests/yellowstone/utilities/runtools.py index 8a13563..163c382 100644 --- a/tests/yellowstone/utilities/runtools.py +++ b/tests/yellowstone/utilities/runtools.py @@ -165,7 +165,7 @@ def start(self): env=os.environ.copy(), bufsize=0) # Display PID on screen and let run in background - print " Process launched in background with PID", self._process.pid + print " Process launched in background with PID {0!s}".format(self._process.pid) # Go back to where you started os.chdir(cwd) @@ -222,22 +222,21 @@ def __init__(self, runcmds=[], name="ysjob", nodes=1, tiling=16, wtime_hours = self._minutes / 60 if (wtime_hours > 99): wtime_hours = 99 - print 'Requested number of hours too large. Limiting to', \ - wtime_hours, '.' + print 'Requested number of hours too large. Limiting to {0!s}.'.format(wtime_hours) wtime_minutes = self._minutes % 60 - wtime_str = '%02d:%02d' % (wtime_hours, wtime_minutes) + wtime_str = '{:0>2}:{:0>2}'.format(wtime_hours, wtime_minutes) # String list representing LSF preamble runscript_list = ['#!/bin/bash', - '#BSUB -n ' + str(num_procs), - '#BSUB -R "span[ptile=' + str(self._tiling) + ']"', - '#BSUB -q ' + self._queue, + '#BSUB -n {0!s}'.format(num_procs), + '#BSUB -R "span[ptile={0!s}]"'.format(self._tiling), + '#BSUB -q {0!s}'.format(self._queue), '#BSUB -a poe', '#BSUB -x', - '#BSUB -o ' + self._jobname + '.%J.log', - '#BSUB -J ' + self._jobname, - '#BSUB -P ' + self._project, - '#BSUB -W ' + wtime_str, + '#BSUB -o {0!s}.%J.log'.format(self._jobname), + '#BSUB -J {0!s}'.format(self._jobname), + '#BSUB -P {0!s}'.format(self._project), + '#BSUB -W {0!s}'.format(wtime_str), '', 'export MP_TIMEOUT=14400', 'export MP_PULSE=1800', @@ -281,7 +280,7 @@ def start(self): output = str(job.communicate()[0]).strip() # Display the job name - print " ", output + print ' {0!s}'.format(output) # Get the job ID (first integer in output) self._process = re.findall('\d+', output)[0] diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index 2c765ea..e35f7a8 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -104,7 +104,7 @@ def __init__(self, dbname=None, stname=None): self._statistics = dict(json.load(stfile)) stfile.close() except: - print "Warning: Statistics file (" + stname + ") not found." + print "Warning: Statistics file ({0!s}) not found.".format(stname) def get_database(self): """ @@ -132,7 +132,7 @@ def print_tests(self): print 'Tests found in the Test Database are:' print for test_name in self._database: - print ' ' + str(test_name) + print ' {0!s}'.format(test_name) return def create_specifier(self, test_name, ncfmt='netcdf4c', @@ -225,12 +225,12 @@ def analyze(self, tests=None, force=False): # If analysis has already been done, remove those tests if not force: for test_name in [t for t in tests if t in self._statistics]: - print "Not Analyzing Test:", str(test_name) + print "Not Analyzing Test: {0!s}".format(test_name) tests = [t for t in tests if t not in self._statistics] # Generate statistics for each test for test_name in tests: - print "Analyzing Test:", str(test_name) + print "Analyzing Test: {0!s}".format(test_name) # Create a specifier for this test spec = self.create_specifier(str(test_name), ncfmt='netcdf') @@ -399,25 +399,25 @@ def print_statistics(self, tests=None): # Print the statistics information for test_name in tests: - print "Statistics for Test:", test_name + print "Statistics for Test: {0!s}".format(test_name) print test_stats = self._statistics[test_name] num_steps = test_stats['length'] - print " Number of Time Steps:", num_steps + print " Number of Time Steps: {0!s}".format(num_steps) print # Print counts num_tser = test_stats['counts']['tseries'] - print " Number of Time-Series Variables: ", num_tser + print " Number of Time-Series Variables: {0!s}".format(num_tser) num_tvmd = test_stats['counts']['tvariant'] - print " Number of Time-Variant Metadata Variables: ", num_tvmd + print " Number of Time-Variant Metadata Variables: {0!s}".format(num_tvmd) num_timd = test_stats['counts']['tinvariant'] - print " Number of Time-Invariant Metadata Variables:", num_timd + print " Number of Time-Invariant Metadata Variables: {0!s}".format(num_timd) num_lost = test_stats['counts']['other'] if num_lost > 0: - print " WARNING:", num_lost, " unclassified variables" + print " WARNING: {0!s} unclassified variables".format(num_lost) print # Print the coordinate data @@ -425,57 +425,57 @@ def print_statistics(self, tests=None): maxlenxcoord = max([len(xc) for xc in test_stats['xcoords']]) for xcoord, cxsize in test_stats['xcoords'].items(): spcr = ' ' * (maxlenxcoord - len(xcoord)) - print " " + xcoord + ": " + spcr + str(cxsize) + print " {0!s}:{1!s}{2!s}".format(xcoord, spcr, cxsize) print # Print names print " Time-Series Variables:" vlist = ", ".join([str(v) for v in test_stats['names']['tseries']]) - print " " + "\n ".join(textwrap.wrap(vlist)) + print " ", "\n ".join(textwrap.wrap(vlist)) print " Time-Variant Metadata Variables:" vlist = ", ".join([str(v) for v in test_stats['names']['tvariant']]) - print " " + "\n ".join(textwrap.wrap(vlist)) + print " ", "\n ".join(textwrap.wrap(vlist)) print " Time-Invariant Metadata Variables:" vlist = ", ".join([str(v) for v in test_stats['names']['tinvariant']]) - print " " + "\n ".join(textwrap.wrap(vlist)) + print " ", "\n ".join(textwrap.wrap(vlist)) if num_lost > 0: print " Unclassified Variables (neither meta nor time-variant):" vlist = ", ".join([str(v) for v in test_stats['names']['other']]) - print " " + "\n ".join(textwrap.wrap(vlist)) + print " ", "\n ".join(textwrap.wrap(vlist)) print # Print Transverse Shapes print " Time-Series Variable Transverse Shapes:" - print " " + " ".join([str(s) for s in - test_stats['xshapes']['tseries']]) + print " ", " ".join([str(s) for s in + test_stats['xshapes']['tseries']]) print " Time-Variant Metadata Transverse Shapes:" - print " " + " ".join([str(s) for s in - test_stats['xshapes']['tvariant']]) + print " ", " ".join([str(s) for s in + test_stats['xshapes']['tvariant']]) print " Time-Invariant Metadata Transverse Shapes:" - print " " + " ".join([str(s) for s in - test_stats['xshapes']['tinvariant']]) + print " ", " ".join([str(s) for s in + test_stats['xshapes']['tinvariant']]) print # Print total bytesizes tser_totsize = test_stats['totalsizes']['tseries'] - print " Time-Series Variable Total Size: ", _nbyte_str(tser_totsize) + print " Time-Series Variable Total Size: {}".format(_nbyte_str(tser_totsize)) tvmd_totsize = test_stats['totalsizes']['tvariant'] - print " Time-Variant Metadata Total Size: ", _nbyte_str(tvmd_totsize) + print " Time-Variant Metadata Total Size: {}".format(_nbyte_str(tvmd_totsize)) timd_totsize = test_stats['totalsizes']['tinvariant'] - print " Time-Invariant Metadata Total Size:", _nbyte_str(timd_totsize) + print " Time-Invariant Metadata Total Size: {}".format(_nbyte_str(timd_totsize)) print # Print maximum bytesizes tser_maxsize = test_stats['maxsizes']['tseries'] - print " Time-Series Variable Max Size: ", _nbyte_str(tser_maxsize) + print " Time-Series Variable Max Size: {}".format(_nbyte_str(tser_maxsize)) tvmd_maxsize = test_stats['maxsizes']['tvariant'] - print " Time-Variant Metadata Max Size: ", _nbyte_str(tvmd_maxsize) + print " Time-Variant Metadata Max Size: {}".format(_nbyte_str(tvmd_maxsize)) timd_maxsize = test_stats['maxsizes']['tinvariant'] - print " Time-Invariant Metadata Max Size:", _nbyte_str(timd_maxsize) + print " Time-Invariant Metadata Max Size: {}".format(_nbyte_str(timd_maxsize)) print def save_statistics(self, stname="teststats.json"): From 227fabbd60da591acc12a6869744c6d0347e47ec Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 12:54:01 -0600 Subject: [PATCH 100/250] Move back to the current working directory after each test launch --- tests/yellowstone/runtests.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/tests/yellowstone/runtests.py b/tests/yellowstone/runtests.py index 07fe26a..8ca4c4d 100755 --- a/tests/yellowstone/runtests.py +++ b/tests/yellowstone/runtests.py @@ -145,6 +145,7 @@ def runtests(args): testdir = os.path.abspath(os.path.join('rundirs', str(test_name), runtype)) # If the test directory doesn't exist, make it and move into it + cwd = os.getcwd() if os.path.exists(testdir): if args.overwrite: shutil.rmtree(testdir) @@ -185,6 +186,8 @@ def runtests(args): if args.nodes <= 0: job.wait() + os.chdir(cwd) + #============================================================================== # Main Command-line Operation From 080e38ee38b1e2509919e7907ef7e1d2b395ab71 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 12:54:29 -0600 Subject: [PATCH 101/250] Only grab the CWD once --- tests/yellowstone/runtests.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/runtests.py b/tests/yellowstone/runtests.py index 8ca4c4d..d9534aa 100755 --- a/tests/yellowstone/runtests.py +++ b/tests/yellowstone/runtests.py @@ -133,6 +133,7 @@ def runtests(args): # Run the requested tests else: + cwd = os.getcwd() for test_name in test_list: print 'Running test: {0!s}'.format(test_name) @@ -145,7 +146,6 @@ def runtests(args): testdir = os.path.abspath(os.path.join('rundirs', str(test_name), runtype)) # If the test directory doesn't exist, make it and move into it - cwd = os.getcwd() if os.path.exists(testdir): if args.overwrite: shutil.rmtree(testdir) From be1439d482b76d9df8b49b73cc3de11af99697bc Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 13:00:25 -0600 Subject: [PATCH 102/250] Don't bother waiting for serial jobs to finish --- tests/yellowstone/runtests.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/tests/yellowstone/runtests.py b/tests/yellowstone/runtests.py index d9534aa..22850bb 100755 --- a/tests/yellowstone/runtests.py +++ b/tests/yellowstone/runtests.py @@ -183,8 +183,6 @@ def runtests(args): tiling=args.tiling, minutes=args.wtime, queue=args.queue, project=args.code) job.start() - if args.nodes <= 0: - job.wait() os.chdir(cwd) From 5be703f5995e889d5ed96ff5bc1e033ec2a47937 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 13:15:08 -0600 Subject: [PATCH 103/250] Formatting only --- tests/yellowstone/runtests.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/tests/yellowstone/runtests.py b/tests/yellowstone/runtests.py index 22850bb..b3726f8 100755 --- a/tests/yellowstone/runtests.py +++ b/tests/yellowstone/runtests.py @@ -179,9 +179,10 @@ def runtests(args): runcmd = ' '.join(runcmdargs) # Create and start the job - job = rt.Job(runcmds=[runcmd], nodes=args.nodes, name=str(test_name), - tiling=args.tiling, minutes=args.wtime, - queue=args.queue, project=args.code) + job = rt.Job(runcmds=[runcmd], nodes=args.nodes, + name=str(test_name), tiling=args.tiling, + minutes=args.wtime, queue=args.queue, + project=args.code) job.start() os.chdir(cwd) From 6dd8140d85938cc95c6ad6b89228929405eb788b Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 13:27:26 -0600 Subject: [PATCH 104/250] Using cPickle instead of default pickle --- bin/slice2series | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/slice2series b/bin/slice2series index 079256c..dd62ae2 100755 --- a/bin/slice2series +++ b/bin/slice2series @@ -13,7 +13,7 @@ See the LICENSE.txt file for details # Builtin Modules import optparse -import pickle +import cPickle as pickle # Package Modules from pyreshaper import specification From 2fdb54b0cf6be1364a8594c189663398888c7c5a Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 14:13:01 -0600 Subject: [PATCH 105/250] Not using slice2series. Allowing for multispec reshaper use. --- tests/yellowstone/runtests.py | 132 ++++++++++++++++++++++++++++++++-- 1 file changed, 125 insertions(+), 7 deletions(-) diff --git a/tests/yellowstone/runtests.py b/tests/yellowstone/runtests.py index b3726f8..d9096d2 100755 --- a/tests/yellowstone/runtests.py +++ b/tests/yellowstone/runtests.py @@ -11,6 +11,7 @@ # Builtin Modules import os import sys +import stat import shutil import argparse import cPickle as pickle @@ -94,6 +95,56 @@ help='Name of test to run or analyze.') +#============================================================================== +# Write an executable Python script to run the Reshaper +#============================================================================== +def write_pyscript(args, testnames, scriptname='runscript.py'): + """ + Write an executable Python script to run the PyReshaper with a set of specs + + Parameters: + args (argparse.Namespace): arguments to pass to the Reshaper + testnames (str, list): Name of a single test, or list of tests + scriptname (str): Name of the Python script to write + """ + + # Start defining the Python script + runscript_list = ['#!/usr/bin/env python', + '', + '# Created automatically by runtests.py', + '', + 'from pyreshaper import specification', + 'from pyreshaper import reshaper', + ''] + + # Check for single or multiple specifiers + if isinstance(testnames, (str, unicode)): + runscript_list.append( + 'specs = pickle.load(open("{0!s}.spec", "rb"))'.format(testnames)) + elif isinstance(testnames, (list, tuple)): + runscript_list.append('specs = []') + for testname in testnames: + runscript_list.append( + 'specs.append(pickle.load(open("{0!s}.spec", "rb")))'.format(testname)) + + # Define the rest of the python script + runscript_list.extend([ + 'rshpr = reshaper.create_reshaper(specs, serial={0!s}, ' + 'verbosity=3, skip_existing={1!s}, overwrite={2!s})'.format( + args.nodes <= 0, args.skip_existing, args.overwrite), + 'rshpr.convert()', + 'rshpr.print_diagnostics()', + '']) + + # Write the script to file + runscript_file = open(scriptname, 'w') + runscript_file.write(os.linesep.join(runscript_list)) + runscript_file.close() + + # Make the script executable + os.chmod(scriptname, stat.S_IRWXU | stat.S_IRGRP | stat.S_IROTH) + + #============================================================================== # Main Function #============================================================================== @@ -131,8 +182,9 @@ def runtests(args): testdb.save_statistics(stname=args.statsfile) sys.exit(0) - # Run the requested tests - else: + # Run the requested tests individually + elif not args.multiple: + cwd = os.getcwd() for test_name in test_list: @@ -150,7 +202,7 @@ def runtests(args): if args.overwrite: shutil.rmtree(testdir) else: - print " Skipping existing" + print " Already exists. Skipping." continue if not os.path.exists(testdir): os.makedirs(testdir) @@ -167,15 +219,18 @@ def runtests(args): testspec = testdb.create_specifier(test_name=str(test_name), ncfmt=args.ncformat, outdir=outputdir) - testspecfile = str(test_name) + '.spec' + testspecfile = '{0!s}.spec'.format(test_name) pickle.dump(testspec, open(testspecfile, 'wb')) + # Write the Python executable to be run + pyscript_name = '{0!s}.py'.format(test_name) + write_pyscript(args, testnames=test_name, scriptname=pyscript_name) + # Generate the command and arguments if args.nodes > 0: - runcmdargs = ['poe', 'slice2series', '-v3'] + runcmdargs = ['poe', pyscript_name] else: - runcmdargs = ['slice2series', '--serial', '-v3'] - runcmdargs.extend(['--specfile', testspecfile]) + runcmdargs = [pyscript_name] runcmd = ' '.join(runcmdargs) # Create and start the job @@ -187,6 +242,69 @@ def runtests(args): os.chdir(cwd) + # Run the tests in a MultiSpecReshaper + else: + + print 'Running tests in single submission:' + for test_name in test_list: + print ' {0!s}'.format(test_name) + + # Set the test directory + if args.nodes > 0: + runtype = 'par{0!s}x{1!s}'.format(args.nodes, args.tiling) + else: + runtype = 'ser' + testdir = os.path.abspath(os.path.join('rundirs', 'multitest', runtype)) + + # If the test directory doesn't exist, make it and move into it + cwd = os.getcwd() + if os.path.exists(testdir): + if args.overwrite: + shutil.rmtree(testdir) + else: + print " Already exists. Skipping." + continue + if not os.path.exists(testdir): + os.makedirs(testdir) + os.chdir(testdir) + + # Create a separate output directory and specifier for each test + for test_name in test_list: + + # Set the output directory + outputdir = os.path.join(testdir, 'output', str(test_name)) + + # If the output directory doesn't exists, create it + if not os.path.exists(outputdir): + os.mkdir(outputdir) + + # Create the specifier and write to file (specfile) + testspec = testdb.create_specifier(test_name=str(test_name), + ncfmt=args.ncformat, + outdir=outputdir) + testspecfile = str(test_name) + '.spec' + pickle.dump(testspec, open(testspecfile, 'wb')) + + # Write the Python executable to be run + pyscript_name = 'multitest.py'.format(test_name) + write_pyscript(args, testnames=test_list, scriptname=pyscript_name) + + # Generate the command and arguments + if args.nodes > 0: + runcmdargs = ['poe', pyscript_name] + else: + runcmdargs = [pyscript_name] + runcmd = ' '.join(runcmdargs) + + # Create and start the job + job = rt.Job(runcmds=[runcmd], nodes=args.nodes, + name=str(test_name), tiling=args.tiling, + minutes=args.wtime, queue=args.queue, + project=args.code) + job.start() + + os.chdir(cwd) + #============================================================================== # Main Command-line Operation From c9a1f4323c579a35e00cc305a7222243c6de935d Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 14:15:55 -0600 Subject: [PATCH 106/250] Return instead of continue (not in loop) --- tests/yellowstone/runtests.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/runtests.py b/tests/yellowstone/runtests.py index d9096d2..1d21dba 100755 --- a/tests/yellowstone/runtests.py +++ b/tests/yellowstone/runtests.py @@ -263,7 +263,7 @@ def runtests(args): shutil.rmtree(testdir) else: print " Already exists. Skipping." - continue + return if not os.path.exists(testdir): os.makedirs(testdir) os.chdir(testdir) From 06643bad83200413a9682d3d54afa66116ea98c6 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 14:16:59 -0600 Subject: [PATCH 107/250] Using correct argument name --- tests/yellowstone/runtests.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/runtests.py b/tests/yellowstone/runtests.py index 1d21dba..fb43414 100755 --- a/tests/yellowstone/runtests.py +++ b/tests/yellowstone/runtests.py @@ -183,7 +183,7 @@ def runtests(args): sys.exit(0) # Run the requested tests individually - elif not args.multiple: + elif not args.multispec: cwd = os.getcwd() for test_name in test_list: From b0b85688431dbc51f2a598632b2d6d72241eff40 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 14:20:15 -0600 Subject: [PATCH 108/250] Using format to define run command --- tests/yellowstone/runtests.py | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/tests/yellowstone/runtests.py b/tests/yellowstone/runtests.py index fb43414..c079fab 100755 --- a/tests/yellowstone/runtests.py +++ b/tests/yellowstone/runtests.py @@ -228,10 +228,9 @@ def runtests(args): # Generate the command and arguments if args.nodes > 0: - runcmdargs = ['poe', pyscript_name] + runcmd = 'poe ./{0!s}'.format(pyscript_name) else: - runcmdargs = [pyscript_name] - runcmd = ' '.join(runcmdargs) + runcmd = './{0!s}'.format(pyscript_name) # Create and start the job job = rt.Job(runcmds=[runcmd], nodes=args.nodes, @@ -291,10 +290,9 @@ def runtests(args): # Generate the command and arguments if args.nodes > 0: - runcmdargs = ['poe', pyscript_name] + runcmd = 'poe ./{0!s}'.format(pyscript_name) else: - runcmdargs = [pyscript_name] - runcmd = ' '.join(runcmdargs) + runcmd = './{0!s}'.format(pyscript_name) # Create and start the job job = rt.Job(runcmds=[runcmd], nodes=args.nodes, From ae9543c9413b7f55a2ba11ff0de83ee6084c411e Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 14:21:51 -0600 Subject: [PATCH 109/250] Need to import pickle into python run script --- tests/yellowstone/runtests.py | 1 + 1 file changed, 1 insertion(+) diff --git a/tests/yellowstone/runtests.py b/tests/yellowstone/runtests.py index c079fab..a61a66f 100755 --- a/tests/yellowstone/runtests.py +++ b/tests/yellowstone/runtests.py @@ -113,6 +113,7 @@ def write_pyscript(args, testnames, scriptname='runscript.py'): '', '# Created automatically by runtests.py', '', + 'import cPickle as pickle', 'from pyreshaper import specification', 'from pyreshaper import reshaper', ''] From b69246f766ba05f5e36efb4a083f56cb652f4001 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 14:25:12 -0600 Subject: [PATCH 110/250] Nicer formatting of python script file --- tests/yellowstone/runtests.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/tests/yellowstone/runtests.py b/tests/yellowstone/runtests.py index a61a66f..f938f4e 100755 --- a/tests/yellowstone/runtests.py +++ b/tests/yellowstone/runtests.py @@ -110,8 +110,9 @@ def write_pyscript(args, testnames, scriptname='runscript.py'): # Start defining the Python script runscript_list = ['#!/usr/bin/env python', - '', + '#', '# Created automatically by runtests.py', + '#', '', 'import cPickle as pickle', 'from pyreshaper import specification', From a0a5c23d906fc907a758bb25937070afc2ab6197 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 14:27:15 -0600 Subject: [PATCH 111/250] Need to make nested directory --- tests/yellowstone/runtests.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/runtests.py b/tests/yellowstone/runtests.py index f938f4e..b8755a9 100755 --- a/tests/yellowstone/runtests.py +++ b/tests/yellowstone/runtests.py @@ -277,7 +277,7 @@ def runtests(args): # If the output directory doesn't exists, create it if not os.path.exists(outputdir): - os.mkdir(outputdir) + os.makedirs(outputdir) # Create the specifier and write to file (specfile) testspec = testdb.create_specifier(test_name=str(test_name), From 0783faa3f9c831327913872c50c9ed5de668b452 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 14:27:56 -0600 Subject: [PATCH 112/250] Output formatting. --- tests/yellowstone/runtests.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/runtests.py b/tests/yellowstone/runtests.py index b8755a9..345bbe5 100755 --- a/tests/yellowstone/runtests.py +++ b/tests/yellowstone/runtests.py @@ -263,7 +263,7 @@ def runtests(args): if args.overwrite: shutil.rmtree(testdir) else: - print " Already exists. Skipping." + print "Already exists. Skipping." return if not os.path.exists(testdir): os.makedirs(testdir) From f80e4d26d9179e040ce42a4bc1afda5287169ad8 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 14:31:46 -0600 Subject: [PATCH 113/250] Naming multitest job --- tests/yellowstone/runtests.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/runtests.py b/tests/yellowstone/runtests.py index 345bbe5..0e15f98 100755 --- a/tests/yellowstone/runtests.py +++ b/tests/yellowstone/runtests.py @@ -298,7 +298,7 @@ def runtests(args): # Create and start the job job = rt.Job(runcmds=[runcmd], nodes=args.nodes, - name=str(test_name), tiling=args.tiling, + name='multitest', tiling=args.tiling, minutes=args.wtime, queue=args.queue, project=args.code) job.start() From a9f14e30eefafad6c03e34afb1e5c9359cbe23e6 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 14:38:53 -0600 Subject: [PATCH 114/250] Debugging output for multispec reshaper --- source/pyreshaper/reshaper.py | 1 + 1 file changed, 1 insertion(+) diff --git a/source/pyreshaper/reshaper.py b/source/pyreshaper/reshaper.py index 150a6d3..4f9031b 100644 --- a/source/pyreshaper/reshaper.py +++ b/source/pyreshaper/reshaper.py @@ -256,6 +256,7 @@ def __init__(self, specifier, serial=False, verbosity=1, if simplecomm is not None: if simplecomm is not isinstance(simplecomm, SimpleComm): err_msg = "Simple communicator object is not a SimpleComm" + print "simplecomm = {0!s}".format(type(simplecomm)) raise TypeError(err_msg) # Whether to write a once file From 4ae16b0b051874ec6bb8f3020826d2afc5a2e4a1 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 15:01:49 -0600 Subject: [PATCH 115/250] Removing debugging output --- source/pyreshaper/reshaper.py | 1 - 1 file changed, 1 deletion(-) diff --git a/source/pyreshaper/reshaper.py b/source/pyreshaper/reshaper.py index 4f9031b..150a6d3 100644 --- a/source/pyreshaper/reshaper.py +++ b/source/pyreshaper/reshaper.py @@ -256,7 +256,6 @@ def __init__(self, specifier, serial=False, verbosity=1, if simplecomm is not None: if simplecomm is not isinstance(simplecomm, SimpleComm): err_msg = "Simple communicator object is not a SimpleComm" - print "simplecomm = {0!s}".format(type(simplecomm)) raise TypeError(err_msg) # Whether to write a once file From 8e49b2ec4ad253e32ed6a39b09d92c19b592a79c Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 15:02:07 -0600 Subject: [PATCH 116/250] Adding debugging output --- tests/yellowstone/utilities/runtools.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/tests/yellowstone/utilities/runtools.py b/tests/yellowstone/utilities/runtools.py index 163c382..7201857 100644 --- a/tests/yellowstone/utilities/runtools.py +++ b/tests/yellowstone/utilities/runtools.py @@ -130,7 +130,8 @@ def __init__(self, runcmds=[], name="serialjob", **kwargs): '# Necessary modules to load', 'module load python', 'module load all-python-libs', - ''] + '', + 'echo $PYTHONPATH'] runscript_list.extend(self._runcmds) runscript_list.append('') @@ -245,7 +246,8 @@ def __init__(self, runcmds=[], name="ysjob", nodes=1, tiling=16, '# Necessary modules to load', 'module load python', 'module load all-python-libs', - ''] + '', + 'echo $PYTHONPATH'] runscript_list.extend(self._runcmds) runscript_list.append('') From 15571ca7d8fb24fa0323a1f1ce9990de907f7332 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 15:19:14 -0600 Subject: [PATCH 117/250] Better type checking --- source/pyreshaper/reshaper.py | 33 +++++++++++++-------------------- 1 file changed, 13 insertions(+), 20 deletions(-) diff --git a/source/pyreshaper/reshaper.py b/source/pyreshaper/reshaper.py index 150a6d3..684d710 100644 --- a/source/pyreshaper/reshaper.py +++ b/source/pyreshaper/reshaper.py @@ -67,7 +67,7 @@ def create_reshaper(specifier, serial=False, verbosity=1, Reshaper: An instance of the Reshaper object requested """ # Determine the type of Reshaper object to instantiate - if type(specifier) is Specifier: + if isinstance(specifier, Specifier): return Slice2SeriesReshaper(specifier, serial=serial, verbosity=verbosity, @@ -75,7 +75,7 @@ def create_reshaper(specifier, serial=False, verbosity=1, overwrite=overwrite, once=once, simplecomm=simplecomm) - elif isinstance(specifier, list): + elif isinstance(specifier, (list, tuple)): spec_dict = dict([(str(i), s) for (i, s) in enumerate(specifier)]) return create_reshaper(spec_dict, serial=serial, @@ -85,23 +85,16 @@ def create_reshaper(specifier, serial=False, verbosity=1, once=once, simplecomm=simplecomm) elif isinstance(specifier, dict): - spec_types = set([type(s) for s in specifier.values()]) - if len(spec_types) > 1: - err_msg = 'Multiple specifiers must all have the same type' - raise TypeError(err_msg) - spec_type = spec_types.pop() - if spec_type is Specifier: - return MultiSpecReshaper(specifier, - serial=serial, - verbosity=verbosity, - skip_existing=skip_existing, - overwrite=overwrite, - once=once, - simplecomm=simplecomm) - else: - err_msg = 'Multiple specifiers of type ' + str(spec_type) \ - + ' are not valid.' + if not all([isinstance(s, Specifier) for s in specifier.values()]): + err_msg = 'Multiple specifiers must all be of Specifier type' raise TypeError(err_msg) + return MultiSpecReshaper(specifier, + serial=serial, + verbosity=verbosity, + skip_existing=skip_existing, + overwrite=overwrite, + once=once, + simplecomm=simplecomm) else: err_msg = 'Specifier of type ' + str(type(specifier)) + ' is not a ' \ + 'valid Specifier object.' @@ -254,7 +247,7 @@ def __init__(self, specifier, serial=False, verbosity=1, err_msg = "Once-file indicator must be True or False." raise TypeError(err_msg) if simplecomm is not None: - if simplecomm is not isinstance(simplecomm, SimpleComm): + if not isinstance(simplecomm, SimpleComm): err_msg = "Simple communicator object is not a SimpleComm" raise TypeError(err_msg) @@ -940,7 +933,7 @@ def __init__(self, specifiers, serial=False, verbosity=1, err_msg = "Once-file indicator must be True or False." raise TypeError(err_msg) if simplecomm is not None: - if simplecomm is not isinstance(simplecomm, SimpleComm): + if not isinstance(simplecomm, SimpleComm): err_msg = "Simple communicator object is not a SimpleComm" raise TypeError(err_msg) From 171c3a6cbbb855964456bae652889ef4598a1db8 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 15:20:27 -0600 Subject: [PATCH 118/250] Removing debugging output --- tests/yellowstone/utilities/runtools.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/tests/yellowstone/utilities/runtools.py b/tests/yellowstone/utilities/runtools.py index 7201857..163c382 100644 --- a/tests/yellowstone/utilities/runtools.py +++ b/tests/yellowstone/utilities/runtools.py @@ -130,8 +130,7 @@ def __init__(self, runcmds=[], name="serialjob", **kwargs): '# Necessary modules to load', 'module load python', 'module load all-python-libs', - '', - 'echo $PYTHONPATH'] + ''] runscript_list.extend(self._runcmds) runscript_list.append('') @@ -246,8 +245,7 @@ def __init__(self, runcmds=[], name="ysjob", nodes=1, tiling=16, '# Necessary modules to load', 'module load python', 'module load all-python-libs', - '', - 'echo $PYTHONPATH'] + ''] runscript_list.extend(self._runcmds) runscript_list.append('') From 209d2b21eccbff16c48ab7530032eead252901c9 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 15:23:43 -0600 Subject: [PATCH 119/250] Using dictionary for multitest specifier --- tests/yellowstone/runtests.py | 34 +++++++++++++++++----------------- 1 file changed, 17 insertions(+), 17 deletions(-) diff --git a/tests/yellowstone/runtests.py b/tests/yellowstone/runtests.py index 0e15f98..9dc727e 100755 --- a/tests/yellowstone/runtests.py +++ b/tests/yellowstone/runtests.py @@ -109,28 +109,28 @@ def write_pyscript(args, testnames, scriptname='runscript.py'): """ # Start defining the Python script - runscript_list = ['#!/usr/bin/env python', - '#', - '# Created automatically by runtests.py', - '#', - '', - 'import cPickle as pickle', - 'from pyreshaper import specification', - 'from pyreshaper import reshaper', - ''] + pyscript_list = ['#!/usr/bin/env python', + '#', + '# Created automatically by runtests.py', + '#', + '', + 'import cPickle as pickle', + 'from pyreshaper import specification', + 'from pyreshaper import reshaper', + ''] # Check for single or multiple specifiers if isinstance(testnames, (str, unicode)): - runscript_list.append( + pyscript_list.append( 'specs = pickle.load(open("{0!s}.spec", "rb"))'.format(testnames)) elif isinstance(testnames, (list, tuple)): - runscript_list.append('specs = []') + pyscript_list.append('specs = {}') for testname in testnames: - runscript_list.append( - 'specs.append(pickle.load(open("{0!s}.spec", "rb")))'.format(testname)) + pyscript_list.append( + 'specs["{0!s}"] = pickle.load(open("{0!s}.spec", "rb"))'.format(testname)) # Define the rest of the python script - runscript_list.extend([ + pyscript_list.extend([ 'rshpr = reshaper.create_reshaper(specs, serial={0!s}, ' 'verbosity=3, skip_existing={1!s}, overwrite={2!s})'.format( args.nodes <= 0, args.skip_existing, args.overwrite), @@ -139,9 +139,9 @@ def write_pyscript(args, testnames, scriptname='runscript.py'): '']) # Write the script to file - runscript_file = open(scriptname, 'w') - runscript_file.write(os.linesep.join(runscript_list)) - runscript_file.close() + pyscript_file = open(scriptname, 'w') + pyscript_file.write(os.linesep.join(pyscript_list)) + pyscript_file.close() # Make the script executable os.chmod(scriptname, stat.S_IRWXU | stat.S_IRGRP | stat.S_IROTH) From ac871780592e0f0ba2d5b7cf47286d317c94cc0e Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 15:26:49 -0600 Subject: [PATCH 120/250] Changing formatting --- tests/yellowstone/utilities/runtools.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/yellowstone/utilities/runtools.py b/tests/yellowstone/utilities/runtools.py index 163c382..4070367 100644 --- a/tests/yellowstone/utilities/runtools.py +++ b/tests/yellowstone/utilities/runtools.py @@ -165,7 +165,7 @@ def start(self): env=os.environ.copy(), bufsize=0) # Display PID on screen and let run in background - print " Process launched in background with PID {0!s}".format(self._process.pid) + print "Process launched in background with PID {0!s}".format(self._process.pid) # Go back to where you started os.chdir(cwd) @@ -280,7 +280,7 @@ def start(self): output = str(job.communicate()[0]).strip() # Display the job name - print ' {0!s}'.format(output) + print str(output) # Get the job ID (first integer in output) self._process = re.findall('\d+', output)[0] From 34a3b431744523637d75fee1cbbd0e4ee17f1828 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 15:34:39 -0600 Subject: [PATCH 121/250] Spacing output. --- tests/yellowstone/utilities/runtools.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/tests/yellowstone/utilities/runtools.py b/tests/yellowstone/utilities/runtools.py index 4070367..8256523 100644 --- a/tests/yellowstone/utilities/runtools.py +++ b/tests/yellowstone/utilities/runtools.py @@ -166,6 +166,7 @@ def start(self): # Display PID on screen and let run in background print "Process launched in background with PID {0!s}".format(self._process.pid) + print # Go back to where you started os.chdir(cwd) @@ -281,6 +282,7 @@ def start(self): # Display the job name print str(output) + print # Get the job ID (first integer in output) self._process = re.findall('\d+', output)[0] From 7017ead7fb0cca68fea3509bee88a3218ba800d2 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 15:58:17 -0600 Subject: [PATCH 122/250] Reorganize script --- tests/yellowstone/runtests.py | 234 +++++++++++++++++++--------------- 1 file changed, 131 insertions(+), 103 deletions(-) diff --git a/tests/yellowstone/runtests.py b/tests/yellowstone/runtests.py index 9dc727e..3196272 100755 --- a/tests/yellowstone/runtests.py +++ b/tests/yellowstone/runtests.py @@ -148,147 +148,150 @@ def write_pyscript(args, testnames, scriptname='runscript.py'): #============================================================================== -# Main Function +# Analyze the tests #============================================================================== -def runtests(args): +def analyzetests(args, tests): """ - Run a set of tests + Analyze a set of tests Parameters: args (argparse.Namespace): A namespace of command-line parsed arguments describing the tests to run and how to run them + tests (list, tuple): List or tuple of test names to analyze """ - # Check for tests to run - if len(args.test) == 0 and not args.all_tests and not args.list_tests: - _PARSER_.print_help() - sys.exit(1) + # Analyze test input, if requested (overwrite forces re-analysis) + testdb.analyze(tests=tests, force=args.overwrite) + testdb.save_statistics(stname=args.statsfile) - # Create/read the testing info and stats files - testdb = tt.TestDB(dbname=args.infofile, stname=args.statsfile) - # List tests if only listing - if args.list_tests: - testdb.print_tests() - sys.exit(1) +#============================================================================== +# Run a single multitest (using a MultiSpecReshaper) +#============================================================================== +def runmultitest(args, tests): + """ + Run a set of tests - # Generate the list of tests to run/analyze - if args.all_tests: - test_list = testdb.get_database().keys() - else: - test_list = [t for t in args.test if t in testdb.get_database()] + Parameters: + args (argparse.Namespace): A namespace of command-line parsed arguments + describing the tests to run and how to run them + tests (list, tuple): List or tuple of test names to run + """ - # Analyze test input, if requested (overwrite forces re-analysis) - if args.analyze: - testdb.analyze(tests=test_list, force=args.overwrite) - testdb.save_statistics(stname=args.statsfile) - sys.exit(0) + print 'Running tests in single submission:' + for test_name in tests: + print ' {0!s}'.format(test_name) + print - # Run the requested tests individually - elif not args.multispec: + # Set the test directory + if args.nodes > 0: + runtype = 'par{0!s}x{1!s}'.format(args.nodes, args.tiling) + else: + runtype = 'ser' + testdir = os.path.abspath(os.path.join('rundirs', 'multitest', runtype)) + + # If the test directory doesn't exist, make it and move into it + cwd = os.getcwd() + if os.path.exists(testdir): + if args.overwrite: + shutil.rmtree(testdir) + else: + print "Already exists. Skipping." + return + if not os.path.exists(testdir): + os.makedirs(testdir) + os.chdir(testdir) + + # Create a separate output directory and specifier for each test + for test_name in tests: + + # Set the output directory + outputdir = os.path.join(testdir, 'output', str(test_name)) + + # If the output directory doesn't exists, create it + if not os.path.exists(outputdir): + os.makedirs(outputdir) + + # Create the specifier and write to file (specfile) + testspec = testdb.create_specifier(test_name=str(test_name), + ncfmt=args.ncformat, + outdir=outputdir) + testspecfile = str(test_name) + '.spec' + pickle.dump(testspec, open(testspecfile, 'wb')) + + # Write the Python executable to be run + pyscript_name = 'multitest.py' + write_pyscript(args, testnames=tests, scriptname=pyscript_name) + + # Generate the command and arguments + if args.nodes > 0: + runcmd = 'poe ./{0!s}'.format(pyscript_name) + else: + runcmd = './{0!s}'.format(pyscript_name) - cwd = os.getcwd() - for test_name in test_list: + # Create and start the job + job = rt.Job(runcmds=[runcmd], nodes=args.nodes, + name='multitest', tiling=args.tiling, + minutes=args.wtime, queue=args.queue, + project=args.code) + job.start() - print 'Running test: {0!s}'.format(test_name) + os.chdir(cwd) - # Set the test directory - if args.nodes > 0: - runtype = 'par{0!s}x{1!s}'.format(args.nodes, args.tiling) - else: - runtype = 'ser' - testdir = os.path.abspath(os.path.join('rundirs', str(test_name), runtype)) - - # If the test directory doesn't exist, make it and move into it - if os.path.exists(testdir): - if args.overwrite: - shutil.rmtree(testdir) - else: - print " Already exists. Skipping." - continue - if not os.path.exists(testdir): - os.makedirs(testdir) - os.chdir(testdir) - - # Set the output directory - outputdir = os.path.join(testdir, 'output') - - # If the output directory doesn't exists, create it - if not os.path.exists(outputdir): - os.mkdir(outputdir) - - # Create the specifier and write to file (specfile) - testspec = testdb.create_specifier(test_name=str(test_name), - ncfmt=args.ncformat, - outdir=outputdir) - testspecfile = '{0!s}.spec'.format(test_name) - pickle.dump(testspec, open(testspecfile, 'wb')) - - # Write the Python executable to be run - pyscript_name = '{0!s}.py'.format(test_name) - write_pyscript(args, testnames=test_name, scriptname=pyscript_name) - - # Generate the command and arguments - if args.nodes > 0: - runcmd = 'poe ./{0!s}'.format(pyscript_name) - else: - runcmd = './{0!s}'.format(pyscript_name) - # Create and start the job - job = rt.Job(runcmds=[runcmd], nodes=args.nodes, - name=str(test_name), tiling=args.tiling, - minutes=args.wtime, queue=args.queue, - project=args.code) - job.start() +#============================================================================== +# Run tests +#============================================================================== +def runtests(args, tests): + """ + Run a set of tests - os.chdir(cwd) + Parameters: + args (argparse.Namespace): A namespace of command-line parsed arguments + describing the tests to run and how to run them + tests (list, tuple): List or tuple of test names to run + """ - # Run the tests in a MultiSpecReshaper - else: + cwd = os.getcwd() + for test_name in test_list: - print 'Running tests in single submission:' - for test_name in test_list: - print ' {0!s}'.format(test_name) + print 'Running test: {0!s}'.format(test_name) # Set the test directory if args.nodes > 0: runtype = 'par{0!s}x{1!s}'.format(args.nodes, args.tiling) else: runtype = 'ser' - testdir = os.path.abspath(os.path.join('rundirs', 'multitest', runtype)) + testdir = os.path.abspath(os.path.join('rundirs', str(test_name), runtype)) # If the test directory doesn't exist, make it and move into it - cwd = os.getcwd() if os.path.exists(testdir): if args.overwrite: shutil.rmtree(testdir) else: - print "Already exists. Skipping." - return + print " Already exists. Skipping." + continue if not os.path.exists(testdir): os.makedirs(testdir) os.chdir(testdir) - # Create a separate output directory and specifier for each test - for test_name in test_list: - - # Set the output directory - outputdir = os.path.join(testdir, 'output', str(test_name)) + # Set the output directory + outputdir = os.path.join(testdir, 'output') - # If the output directory doesn't exists, create it - if not os.path.exists(outputdir): - os.makedirs(outputdir) + # If the output directory doesn't exists, create it + if not os.path.exists(outputdir): + os.mkdir(outputdir) - # Create the specifier and write to file (specfile) - testspec = testdb.create_specifier(test_name=str(test_name), - ncfmt=args.ncformat, - outdir=outputdir) - testspecfile = str(test_name) + '.spec' - pickle.dump(testspec, open(testspecfile, 'wb')) + # Create the specifier and write to file (specfile) + testspec = testdb.create_specifier(test_name=str(test_name), + ncfmt=args.ncformat, + outdir=outputdir) + testspecfile = '{0!s}.spec'.format(test_name) + pickle.dump(testspec, open(testspecfile, 'wb')) # Write the Python executable to be run - pyscript_name = 'multitest.py'.format(test_name) - write_pyscript(args, testnames=test_list, scriptname=pyscript_name) + pyscript_name = '{0!s}.py'.format(test_name) + write_pyscript(args, testnames=test_name, scriptname=pyscript_name) # Generate the command and arguments if args.nodes > 0: @@ -298,7 +301,7 @@ def runtests(args): # Create and start the job job = rt.Job(runcmds=[runcmd], nodes=args.nodes, - name='multitest', tiling=args.tiling, + name=str(test_name), tiling=args.tiling, minutes=args.wtime, queue=args.queue, project=args.code) job.start() @@ -311,4 +314,29 @@ def runtests(args): #============================================================================== if __name__ == '__main__': args = _PARSER_.parse_args() - runtests(args) + + # Check for tests to analyze + if len(args.test) == 0 and not args.all_tests and not args.list_tests: + _PARSER_.print_help() + sys.exit(1) + + # Create/read the testing info and stats files + testdb = tt.TestDB(dbname=args.infofile, stname=args.statsfile) + + # List tests if only listing + if args.list_tests: + testdb.print_tests() + sys.exit(1) + + # Generate the list of tests to run/analyze + if args.all_tests: + test_list = testdb.get_database().keys() + else: + test_list = [t for t in args.test if t in testdb.get_database()] + + if args.analyze: + analyzetests(args, test_list) + elif args.multispec: + runmultitest(args, test_list) + else: + runtests(args, test_list) From cf10cbee235c5ec705be2ba1ebc3cf08a596bf42 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 16:09:48 -0600 Subject: [PATCH 123/250] Removing now unnecessary runtest scripts --- tests/yellowstone/runtestsi.py | 346 --------------------------------- tests/yellowstone/runtestsm.py | 128 ------------ 2 files changed, 474 deletions(-) delete mode 100755 tests/yellowstone/runtestsi.py delete mode 100755 tests/yellowstone/runtestsm.py diff --git a/tests/yellowstone/runtestsi.py b/tests/yellowstone/runtestsi.py deleted file mode 100755 index 427e356..0000000 --- a/tests/yellowstone/runtestsi.py +++ /dev/null @@ -1,346 +0,0 @@ -#!/usr/bin/env python -#============================================================================== -# -# scripttest.py -# -# This script is written to make running the "Bake-Off" time-slice to -# time-series tests on Yellowstone easy and efficient. This allows code -# re-use for the various tests. -# -# This script requires the testinfo.json file be present in the same directory -# as the runtest script itself. -# -# This script runs a single test at a time. It does not use the multi-spec -# reshaper. It runs the single-stream script: slice2series -# -#============================================================================== -import optparse -import os -import sys -import stat -import shutil -import glob - -from subprocess import Popen, PIPE, STDOUT -import json - -from utilities import testtools - - -#============================================================================== -# Command-Line Interface Definition -#============================================================================== -def parse_cli(): - usage = 'usage: %prog [run_opts] test_name1 test_name2 ...\n\n' \ - + ' This program is designed to run yellowstone-specific\n' \ - + ' tests of the PyReshaper. Each named test (or all tests if\n' \ - + ' the -a or --all option is used) will be given a run\n' \ - + ' directory in the current working directory with the same\n' \ - + ' name as the test itself. The run script will be placed\n' \ - + ' in this run directory, as will be placed the run output/\n' \ - + ' error file. All output data files will be placed in the\n' \ - + ' output subdirectory.' - parser = optparse.OptionParser(usage=usage) - parser.add_option('-a', '--all', default=False, - action='store_true', dest='all', - help='True or False, indicating whether to run all tests ' - '[Default: False]') - parser.add_option('-c', '--code', default='STDD0002', - help='The name of the project code for charging in ' - 'parallel runs (ignored if running in serial) ' - '[Default: STDD0002]') - parser.add_option('-O', '--overwrite', default=False, - action='store_true', dest='overwrite', - help='True or False, indicating whether to force deleting ' - 'any existing test or run directories, if found ' - '[Default: False]') - parser.add_option('-f', '--format', default='netcdf4c', dest='ncformat', - help='The NetCDF file format to use for the output data ' - 'produced by the test. [Default: netcdf4c]') - parser.add_option('-i', '--testing_database', default=None, - help='Location of the testinfo.json file ' - '[Default: None]') - parser.add_option('-l', '--list', default=False, - action='store_true', dest='list_tests', - help='True or False, indicating whether to list all tests, ' - 'instead of running tests. [Default: False]') - parser.add_option('-o', '--only', default=0, type='int', - help='Runs each test limited to the indicated number of ' - 'output files per processor. A value of 0 means ' - 'no limit (i.e., all output files) [Default: 0]') - parser.add_option('--once', default=False, - action='store_true', dest='once_file', - help='True or False, indicating whether to write metadata ' - 'to a once file. [Default: False]') - parser.add_option('--skip_existing', default=False, - action='store_true', dest='skip_existing', - help='Whether to skip time-series generation for ' - 'variables with existing output files. ' - '[Default: False]') - parser.add_option('-q', '--queue', default='economy', - help='The name of the queue to request in parallel runs ' - '(ignored if running in serial) ' - '[Default: economy]') - parser.add_option('-n', '--nodes', default=0, type='int', - help='The integer number of nodes to request in parallel' - ' runs (0 means run in serial) [Default: 0]') - parser.add_option('-t', '--tiling', default=16, type='int', - help='The integer number of processes per node to request ' - 'in parallel runs (ignored if running in serial) ' - '[Default: 16]') - parser.add_option('-w', '--wtime', default=240, type='int', - help='The number of minutes to request for the wall clock ' - 'in parallel runs (ignored if running in serial) ' - '[Default: 240]') - - # Return the parsed CLI options - return parser.parse_args() - - -#============================================================================== -# Find and generate the testing database -#============================================================================== -def get_testing_database(options): - - # Create the testing database - testing_database = testtools.TestDB(options.testing_database) - - # List tests only, if option is set - if (options.list_tests): - testing_database.print_list() - sys.exit(0) - - return testing_database - - -#============================================================================== -# Generate the list of tests to run -#============================================================================== -def get_tests_to_run(options, arguments, testing_database): - - # Determine which tests to run - tests_to_run = arguments - if (options.all): - tests_to_run = testing_database.keys() - else: - for test_name in tests_to_run: - if (test_name not in testing_database): - print str(test_name) + ' not in testinfo file. Ignoring.' - print 'Tests to be run:', - for test_name in tests_to_run: - print str(test_name), - print ' ' - print - - return tests_to_run - - -#============================================================================== -# Initialize the test for running -#============================================================================== -def get_test_dirname(options, test_name): - - # Create the test directory - test_dir = os.path.abspath(os.path.join('results', test_name)) - if (options.nodes > 0): - test_dir = os.path.join( - test_dir, 'par' + str(options.nodes) + 'x' + str(options.tiling)) - else: - test_dir = os.path.join(test_dir, 'ser') - test_dir = os.path.join(test_dir, options.ncformat) - - return test_dir - - -#============================================================================== -# Create the output directory -#============================================================================== -def create_dir(name, path): - # Create the output subdirectory - if os.path.isdir(path): - print ' ' + name.capitalize() + ' directory (' \ - + output_dir + ') already exists.' - else: - os.makedirs(path) - print ' ' + name.capitalize() + ' directory (' \ - + output_dir + ') created.' - - -#============================================================================== -# Generate the test run command -#============================================================================== -def create_run_command(options, test_name, output_dir, test_database): - - # Generate the command line run_args - run_cmd = [] - if (options.nodes > 0): - run_cmd.append('mpirun.lsf') - run_cmd.append('slice2series') - if (options.nodes == 0): - run_cmd.append('--serial') - if (options.once_file): - run_cmd.append('--once') - if (options.skip_existing): - run_cmd.append('--skip_existing') - if (options.overwrite): - run_cmd.append('--overwrite') - run_cmd.extend(['-v', '3']) - if (options.only > 0): - run_cmd.extend(['-l', str(options.only)]) - - format_str = options.ncformat - run_cmd.extend(['-f', format_str]) - - prefix_str = os.path.join( - output_dir, str(test_database[test_name]['output_prefix'])) - run_cmd.extend(['-p', prefix_str]) - - suffix_str = str(test_database[test_name]['output_suffix']) - run_cmd.extend(['-s', suffix_str]) - - for var_name in test_database[test_name]['metadata']: - run_cmd.extend(['-m', str(var_name)]) - - input_files_list = [] - for input_glob in test_database[test_name]['input_globs']: - full_input_glob = os.path.join( - str(test_database[test_name]['input_dir']), input_glob) - #input_files_list.extend(glob.glob(full_input_glob)) - input_files_list.append(full_input_glob) - run_cmd.extend(input_files_list) - - return ' '.join(run_cmd) - - -#============================================================================== -# create_run_script - write bash run script as string -#============================================================================== -def create_run_script(options, test_name, test_dir, run_command): - - # Generate the run script name and path - run_script_filename = 'run-' + test_name + '.sh' - run_script_abspath = os.path.join(test_dir, run_script_filename) - - # Start creating the run scripts for each test - run_script_list = ['#!/bin/bash'] - - # If necessary, add the parallel preamble - if (options.nodes > 0): - - # Number of processors total - num_procs = options.nodes * options.tiling - - # Generate walltime in string form - wtime_hours = options.wtime / 60 - if (wtime_hours > 99): - wtime_hours = 99 - print 'Requested number of hours too large. Limiting to', wtime_hours, '.' - wtime_minutes = options.wtime % 60 - wtime_str = '%02d:%02d' % (wtime_hours, wtime_minutes) - - # String list representing LSF preamble - run_script_list.extend([ - '#BSUB -n ' + str(num_procs), - '#BSUB -R "span[ptile=' + str(options.tiling) + ']"', - '#BSUB -q ' + options.queue, - '#BSUB -a poe', - '#BSUB -x', - '#BSUB -o reshaper-' + test_name + '.%J.log', - '#BSUB -J reshaper-' + test_name, - '#BSUB -P ' + options.code, - '#BSUB -W ' + wtime_str, - '', - 'export MP_TIMEOUT=14400', - 'export MP_PULSE=1800', - 'export MP_DEBUG_NOTIMEOUT=yes', - '']) - - # Now create the rest of the run script - run_script_list.extend(['# NOTE: Your PATH and PYTHONPATH must be properly set', - '# before this script will run without error', - '', - '# Necessary modules to load', - 'module load python', - 'module load all-python-libs', - '']) - - run_script_list.append(run_command) - run_script_list.append('') - - run_script_file = open(run_script_abspath, 'w') - run_script_file.write(os.linesep.join(run_script_list)) - run_script_file.close() - print ' Run script written to', run_script_abspath - - return run_script_abspath - - -#============================================================================== -# run_test - Run/Launch a test -#============================================================================== -def run_test(test_name, test_dir, run_script): - # Now launch the test - cwd = os.getcwd() - os.chdir(test_dir) - print ' Launching test job:', - if (options.nodes == 0): - # Make the script executable - os.chmod(run_script, stat.S_IRWXU | stat.S_IRGRP | stat.S_IROTH) - - # Launch the serial job as a subprocess - job = Popen([run_script], stdout=PIPE, stderr=STDOUT, - env=os.environ.copy()) - print 'PID:', str(job.pid) - sys.stdout.flush() - - # Wait for job to finish and grab job output - job_output = job.communicate()[0] - - # Write output to log file - log_file = open('reshaper-' + test_name + '.log', 'w') - log_file.write(job_output) - log_file.close() - - else: - # Open up the run script for input to LSF's bsub - run_script_file = open(run_script, 'r') - - # Launch the parallel job with LSF bsub - job = Popen(['bsub'], stdout=PIPE, stderr=STDOUT, - stdin=run_script_file, env=os.environ.copy()) - - # Grab the bsub output - job_output = job.communicate()[0] - - # Close the script file and print submission info - run_script_file.close() - print job_output - print - sys.stdout.flush() - - os.chdir(cwd) - - -#============================================================================== -# Command-Line Operation -#============================================================================== -if __name__ == '__main__': - options, arguments = parse_cli() - testing_database = get_testing_database(options) - tests_to_run = get_tests_to_run(options, arguments, testing_database) - for test_name in tests_to_run: - print 'Currently preparing test:', test_name - - test_dir = get_test_dirname(options, test_name) - create_dir('test', test_dir) - - output_dir = os.path.join(test_dir, 'output') - create_dir('output', output_dir) - - run_command = create_run_command( - options, test_name, output_dir, testing_database) - - run_script = create_run_script( - options, test_name, test_dir, run_command) - - #run_test(test_name, test_dir, run_script) diff --git a/tests/yellowstone/runtestsm.py b/tests/yellowstone/runtestsm.py deleted file mode 100755 index b5b4c66..0000000 --- a/tests/yellowstone/runtestsm.py +++ /dev/null @@ -1,128 +0,0 @@ -#!/usr/bin/env python -#============================================================================== -# -# runtestsm.py -# -# This script is written to make running the "Bake-Off" time-slice to -# time-series tests on Yellowstone easy and efficient. This allows code -# re-use for the various tests. -# -# This script requires the testinfo.json file be present in the same directory -# as the runtest script itself. -# -# This script runs MULTIPLE tests at one time through a single instance of -# the multi-specifier reshaper class. -# -#============================================================================== -import optparse -import os -import sys -import shutil -import glob - -from subprocess import Popen, PIPE, STDOUT -import json - -from runtestsi import * - - -#============================================================================== -# Generate the test run command -#============================================================================== -def create_run_command(options, python_script_name): - - # Generate the command line run_args - run_cmd = [] - if (options.nodes > 0): - run_cmd.append('mpirun.lsf') - run_cmd.extend(['python', python_script_name]) - - return ' '.join(run_cmd) - - -#============================================================================== -# Generate the python script -#============================================================================== -def create_python_script(options, test_name, output_dir, testing_database): - - # Start the python script strings - python_script_str = [ - '#!/usr/bin/env python', - 'import glob', - '#', - '# PYTHONPATH must be set for this to work', - '#', - 'from pyreshaper import specification', - 'from pyreshaper import reshaper', - '', - 'spec_list = {}', - ''] - - # Define the Specifiers for each test - input_dir = str(testing_database[test_name]['input_dir']) - input_file_list = [] - for input_glob in testing_database[test_name]['input_globs']: - input_glob_str = str(input_glob) - full_input_glob = str(os.path.join(input_dir, input_glob)) - input_file_list.extend(glob.glob(full_input_glob)) - netcdf_format = str(testing_database[test_name]['netcdf_format']) - output_prefix = str( - os.path.join(output_dir, - str(testing_database[test_name]['output_prefix']))) - output_suffix = str(testing_database[test_name]['output_suffix']) - time_variant_metadata = map( - str, testing_database[test_name]['metadata']) - - python_script_str.extend([ - 'spec = specification.create_specifier()', - 'spec.input_file_list = ' + repr(input_file_list), - 'spec.netcdf_format = ' + repr(netcdf_format), - 'spec.output_file_prefix = ' + repr(output_prefix), - 'spec.output_file_suffix = ' + repr(output_suffix), - 'spec.time_variant_metadata = ' + repr(time_variant_metadata), - 'spec_list[' + repr(str(test_name)) + '] = spec', - '']) - - # Now create the multi-spec reshaper and run - ser = str(num_procs == 0) - reshaper_params = 'spec_list, serial=' + ser + ', verbosity=2' - python_script_str.extend([ - 'rshpr = reshaper.create_reshaper(' + reshaper_params + ')', - 'rshpr.convert(output_limit=' + str(output_limit) + ')', - 'rshpr.print_diagnostics()' - '']) - - # Open the python script file and write script - python_script_name = 'run-' + test_name + '.py' - python_script_file = open(python_script_name, 'w') - python_script_file.write(os.linesep.join(python_script_str)) - python_script_file.close() - - return python_script_name - - -#============================================================================== -# Command-Line Operation -#============================================================================== -if __name__ == '__main__': - options, arguments = parse_cli() - testing_database = get_testing_database(options) - tests_to_run = get_tests_to_run(options, arguments, testing_database) - for test_name in tests_to_run: - print 'Currently preparing test:', test_name - - test_dir = get_test_dirname(options, test_name) - create_dir('test', test_dir) - - output_dir = os.path.join(test_dir, 'output') - create_dir('output', output_dir) - - python_script = create_python_script( - options, test_name, output_dir, testing_database) - - run_command = create_run_command(options, python_script) - - run_script = create_run_script( - options, test_name, test_dir, run_command) - - #run_test(test_name, test_dir, run_script) From 275b5c9c6b902a0bbf299dd3499a6dc6f48c347e Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 16:17:53 -0600 Subject: [PATCH 124/250] New readme for testing directory --- tests/yellowstone/README | 31 ++++++++++++------------------- 1 file changed, 12 insertions(+), 19 deletions(-) diff --git a/tests/yellowstone/README b/tests/yellowstone/README index c8078e4..03fcdac 100644 --- a/tests/yellowstone/README +++ b/tests/yellowstone/README @@ -1,20 +1,20 @@ This directory contains the tests that should be run on NCAR's Yellowstone compute system. The general order of operations is described below: +0) Analyze Test Input: + + getstats.py: Generate statistics describing the test input files. This + writes the test statistics to the 'teststats.json' file. + 1) Run Tests - runtestsi.py: Run any number of selected tests as individual jobs - submitted to the queue. This uses a single Specifier - for each PyReshaper job, and each job runs in parallel - with all of the other jobs. - - runtestsm.py: Run any number of selected tests as a single job submitted - to the queue. This uses a list of Specifiers for a single - MultiSpecReshaper job. + runtests.py: Run any number of selected tests in serial or in parallel, + submitted to a queue. This can use a single Specifier, + or multiple Specifiers, for each PyReshaper job. 2) Check Test Results - checkresults.py: Compare output from each test that has been run with + checkresults.py: Compare output from each test that has been run against accepted results (found in /glade/u/tdd/asap/bakeoff) 3) Get Timing Data @@ -23,14 +23,7 @@ compute system. The general order of operations is described below: and extract the timing data from the output logs. Add this timing data to the 'timings.json' database. -4) Additional +4) Make Plots - Additional useful scripts can be found in the postproc/ directory, - including the following: - - getsizes.py: Reads the test input data and computes test information - such as variable sizes and numbers. The information is - printed to STDOUT. - - mkplots.py: Creates typical timing and throughput plots from information - found in the 'timings.json' database. + mkplots.py: Creates typical timing and throughput plots from information + found in the 'timings.json' database. From 301ac2af685fc1774ee3b3e85d7a0d1e91b57054 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 16:25:37 -0600 Subject: [PATCH 125/250] Not throwing warning when no stats file given --- tests/yellowstone/utilities/testtools.py | 28 +++++++++++------------- 1 file changed, 13 insertions(+), 15 deletions(-) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index e35f7a8..59cc161 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -87,24 +87,22 @@ def __init__(self, dbname=None, stname=None): self._database = dict(json.load(dbfile)) dbfile.close() except: - err_msg = 'Problem reading and parsing test info file: ' \ - + str(abs_path) + err_msg = 'Problem reading and parsing test info file: {0!s}'.format(abs_path) raise ValueError(err_msg) - # Initialize the statistics database - if stname: - abs_path = os.path.abspath(stname) - else: - abs_path = os.path.join(os.getcwd(), 'teststats.json') - - # Try opening and reading the testinfo file + # Initialize test statistics self._statistics = {} - try: - stfile = open(abs_path, 'r') - self._statistics = dict(json.load(stfile)) - stfile.close() - except: - print "Warning: Statistics file ({0!s}) not found.".format(stname) + + # If the stats filename is given, then try to read it + if stname is not None: + abs_path = os.path.abspath(stname) + try: + stfile = open(abs_path, 'r') + self._statistics = dict(json.load(stfile)) + stfile.close() + except: + err_msg = 'Problem reading and parsing test stats file: {0!s}'.format(abs_path) + raise ValueError(err_msg) def get_database(self): """ From 4b645bf3e40c975829283161878e774a42e576a0 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 16:31:10 -0600 Subject: [PATCH 126/250] Pulling test analysis out of runtests and into getstats --- tests/yellowstone/getstats.py | 89 +++++++++++++++++++++++++++++++++++ tests/yellowstone/runtests.py | 31 ++---------- 2 files changed, 92 insertions(+), 28 deletions(-) create mode 100755 tests/yellowstone/getstats.py diff --git a/tests/yellowstone/getstats.py b/tests/yellowstone/getstats.py new file mode 100755 index 0000000..99dd0b8 --- /dev/null +++ b/tests/yellowstone/getstats.py @@ -0,0 +1,89 @@ +#!/usr/bin/env python +#============================================================================== +# +# getstats.py +# +# Analyse test input and gather statistics. +# +#============================================================================== + +# Builtin Modules +import sys +import argparse + +# Package Modules +from utilities import testtools as tt + +#============================================================================== +# Command-Line Interface Definition +#============================================================================== +_DESC_ = """This program is designed to gather statistics for tests and + test input defined in the testing database file.""" + +_PARSER_ = argparse.ArgumentParser(description=_DESC_) +_PARSER_.add_argument('-a', '--all', default=False, + action='store_true', dest='all_tests', + help='True or False, indicating whether to run all ' + 'tests [Default: False]') +_PARSER_.add_argument('-i', '--infofile', default=None, type=str, + help='Location of the testinfo.json database file ' + '[Default: None]') +_PARSER_.add_argument('-l', '--list', default=False, + action='store_true', dest='list_tests', + help='True or False, indicating whether to list all ' + 'tests, instead of running tests. [Default: False]') +_PARSER_.add_argument('-o', '--overwrite', default=False, + action='store_true', dest='overwrite', + help='True or False, indicating whether to force ' + 'deleting any existing test or run directories, ' + 'if found [Default: False]') +_PARSER_.add_argument('-s', '--statsfile', default=None, type=str, + help='Location of the teststats.json database file ' + '[Default: None]') +_PARSER_.add_argument('test', type=str, nargs='*', + help='Name of test to analyze') + + +#============================================================================== +# Analyze the tests +#============================================================================== +def analyzetests(args, tests): + """ + Analyze a set of tests + + Parameters: + args (argparse.Namespace): A namespace of command-line parsed arguments + describing the tests to run and how to run them + tests (list, tuple): List or tuple of test names to analyze + """ + + # Analyze test input, if requested (overwrite forces re-analysis) + testdb.analyze(tests=tests, force=args.overwrite) + testdb.save_statistics(stname=args.statsfile) + +#============================================================================== +# Main Command-line Operation +#============================================================================== +if __name__ == '__main__': + args = _PARSER_.parse_args() + + # Check for tests to analyze + if len(args.test) == 0 and not args.all_tests and not args.list_tests: + _PARSER_.print_help() + sys.exit(1) + + # Create/read the testing info and stats files + testdb = tt.TestDB(dbname=args.infofile, stname=args.statsfile) + + # List tests if only listing + if args.list_tests: + testdb.print_tests() + sys.exit(1) + + # Generate the list of tests to run/analyze + if args.all_tests: + test_list = testdb.get_database().keys() + else: + test_list = [t for t in args.test if t in testdb.get_database()] + + analyzetests(args, test_list) diff --git a/tests/yellowstone/runtests.py b/tests/yellowstone/runtests.py index 3196272..d3f5b9e 100755 --- a/tests/yellowstone/runtests.py +++ b/tests/yellowstone/runtests.py @@ -86,13 +86,8 @@ help='The number of minutes to request for the wall ' 'clock in parallel runs (ignored if running in ' 'serial) [Default: 240]') -_PARSER_.add_argument('-z', '--analyze', default=False, - action='store_true', - help='Whether to analyze (generate statistics for) the ' - 'test input, rather than run the tests. ' - '[Default: False]') _PARSER_.add_argument('test', type=str, nargs='*', - help='Name of test to run or analyze.') + help='Name of test to run') #============================================================================== @@ -147,24 +142,6 @@ def write_pyscript(args, testnames, scriptname='runscript.py'): os.chmod(scriptname, stat.S_IRWXU | stat.S_IRGRP | stat.S_IROTH) -#============================================================================== -# Analyze the tests -#============================================================================== -def analyzetests(args, tests): - """ - Analyze a set of tests - - Parameters: - args (argparse.Namespace): A namespace of command-line parsed arguments - describing the tests to run and how to run them - tests (list, tuple): List or tuple of test names to analyze - """ - - # Analyze test input, if requested (overwrite forces re-analysis) - testdb.analyze(tests=tests, force=args.overwrite) - testdb.save_statistics(stname=args.statsfile) - - #============================================================================== # Run a single multitest (using a MultiSpecReshaper) #============================================================================== @@ -321,7 +298,7 @@ def runtests(args, tests): sys.exit(1) # Create/read the testing info and stats files - testdb = tt.TestDB(dbname=args.infofile, stname=args.statsfile) + testdb = tt.TestDB(dbname=args.infofile) # List tests if only listing if args.list_tests: @@ -334,9 +311,7 @@ def runtests(args, tests): else: test_list = [t for t in args.test if t in testdb.get_database()] - if args.analyze: - analyzetests(args, test_list) - elif args.multispec: + if args.multispec: runmultitest(args, test_list) else: runtests(args, test_list) From 41ea9cbdf9dbe054b67187b1183d1381e7e6a2d3 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 16:31:37 -0600 Subject: [PATCH 127/250] Removing getsizes. Replaced by getstats. --- tests/yellowstone/getsizes.out | 160 ------------------------ tests/yellowstone/getsizes.py | 222 --------------------------------- 2 files changed, 382 deletions(-) delete mode 100644 tests/yellowstone/getsizes.out delete mode 100755 tests/yellowstone/getsizes.py diff --git a/tests/yellowstone/getsizes.out b/tests/yellowstone/getsizes.out deleted file mode 100644 index 65d200b..0000000 --- a/tests/yellowstone/getsizes.out +++ /dev/null @@ -1,160 +0,0 @@ -camfv-1deg: - No. of TI Metadata Variables: 26 - No. of TV Metadata Variables: 15 - No. of Time-Series Variables (1D): 0 - No. of Time-Series Variables (2D): 0 - No. of Time-Series Variables (3D): 82 - No. of Time-Series Variables (?D): 40 - No. of Variables (TOTAL): 163 - Size of TI Metadata Variables: 13.758 KB - Size of TV Metadata Variables: 10.781 KB - Size of Time-Series Variables (1D): 0.000 Bytes - Size of Time-Series Variables (2D): 0.000 Bytes - Size of Time-Series Variables (3D): 2.027 GB - Size of Time-Series Variables (?D): 25.754 GB - TOTAL Size of Variables: 27.781 GB - -camse-0.25deg: - No. of TI Metadata Variables: 18 - No. of TV Metadata Variables: 15 - No. of Time-Series Variables (1D): 0 - No. of Time-Series Variables (2D): 101 - No. of Time-Series Variables (3D): 97 - No. of Time-Series Variables (?D): 0 - No. of Variables (TOTAL): 231 - Size of TI Metadata Variables: 17.799 MB - Size of TV Metadata Variables: 10.781 KB - Size of Time-Series Variables (1D): 0.000 Bytes - Size of Time-Series Variables (2D): 35.109 GB - Size of Time-Series Variables (3D): 1014.689 GB - Size of Time-Series Variables (?D): 0.000 Bytes - TOTAL Size of Variables: 1.025 TB - -camse-1deg: - No. of TI Metadata Variables: 18 - No. of TV Metadata Variables: 15 - No. of Time-Series Variables (1D): 0 - No. of Time-Series Variables (2D): 89 - No. of Time-Series Variables (3D): 43 - No. of Time-Series Variables (?D): 0 - No. of Variables (TOTAL): 165 - Size of TI Metadata Variables: 1.114 MB - Size of TV Metadata Variables: 10.781 KB - Size of Time-Series Variables (1D): 0.000 Bytes - Size of Time-Series Variables (2D): 1.934 GB - Size of Time-Series Variables (3D): 28.028 GB - Size of Time-Series Variables (?D): 0.000 Bytes - TOTAL Size of Variables: 29.962 GB - -cice-0.1deg: - No. of TI Metadata Variables: 20 - No. of TV Metadata Variables: 2 - No. of Time-Series Variables (1D): 0 - No. of Time-Series Variables (2D): 0 - No. of Time-Series Variables (3D): 112 - No. of Time-Series Variables (?D): 0 - No. of Variables (TOTAL): 134 - Size of TI Metadata Variables: 1.030 GB - Size of TV Metadata Variables: 1.406 KB - Size of Time-Series Variables (1D): 0.000 Bytes - Size of Time-Series Variables (2D): 0.000 Bytes - Size of Time-Series Variables (3D): 432.587 GB - Size of Time-Series Variables (?D): 0.000 Bytes - TOTAL Size of Variables: 433.617 GB - -cice-1deg: - No. of TI Metadata Variables: 20 - No. of TV Metadata Variables: 2 - No. of Time-Series Variables (1D): 0 - No. of Time-Series Variables (2D): 0 - No. of Time-Series Variables (3D): 117 - No. of Time-Series Variables (?D): 0 - No. of Variables (TOTAL): 139 - Size of TI Metadata Variables: 15.000 MB - Size of TV Metadata Variables: 1.406 KB - Size of Time-Series Variables (1D): 0.000 Bytes - Size of Time-Series Variables (2D): 0.000 Bytes - Size of Time-Series Variables (3D): 6.427 GB - Size of Time-Series Variables (?D): 0.000 Bytes - TOTAL Size of Variables: 6.442 GB - -clmse-0.25deg: - No. of TI Metadata Variables: 15 - No. of TV Metadata Variables: 9 - No. of Time-Series Variables (1D): 0 - No. of Time-Series Variables (2D): 144 - No. of Time-Series Variables (3D): 6 - No. of Time-Series Variables (?D): 0 - No. of Variables (TOTAL): 174 - Size of TI Metadata Variables: 287.733 MB - Size of TV Metadata Variables: 4.688 KB - Size of Time-Series Variables (1D): 0.000 Bytes - Size of Time-Series Variables (2D): 50.057 GB - Size of Time-Series Variables (3D): 29.547 GB - Size of Time-Series Variables (?D): 0.000 Bytes - TOTAL Size of Variables: 79.885 GB - -clmse-1deg: - No. of TI Metadata Variables: 15 - No. of TV Metadata Variables: 9 - No. of Time-Series Variables (1D): 0 - No. of Time-Series Variables (2D): 290 - No. of Time-Series Variables (3D): 7 - No. of Time-Series Variables (?D): 0 - No. of Variables (TOTAL): 321 - Size of TI Metadata Variables: 17.984 MB - Size of TV Metadata Variables: 4.688 KB - Size of Time-Series Variables (1D): 0.000 Bytes - Size of Time-Series Variables (2D): 6.301 GB - Size of Time-Series Variables (3D): 2.173 GB - Size of Time-Series Variables (?D): 0.000 Bytes - TOTAL Size of Variables: 8.491 GB - -pop-0.1deg: - No. of TI Metadata Variables: 58 - No. of TV Metadata Variables: 2 - No. of Time-Series Variables (1D): 0 - No. of Time-Series Variables (2D): 0 - No. of Time-Series Variables (3D): 22 - No. of Time-Series Variables (?D): 12 - No. of Variables (TOTAL): 94 - Size of TI Metadata Variables: 1.255 GB - Size of TV Metadata Variables: 2.812 KB - Size of Time-Series Variables (1D): 0.000 Bytes - Size of Time-Series Variables (2D): 0.000 Bytes - Size of Time-Series Variables (3D): 84.972 GB - Size of Time-Series Variables (?D): 2.806 TB - TOTAL Size of Variables: 2.890 TB - -pop-1deg: - No. of TI Metadata Variables: 63 - No. of TV Metadata Variables: 2 - No. of Time-Series Variables (1D): 0 - No. of Time-Series Variables (2D): 0 - No. of Time-Series Variables (3D): 55 - No. of Time-Series Variables (?D): 59 - No. of Variables (TOTAL): 179 - Size of TI Metadata Variables: 18.285 MB - Size of TV Metadata Variables: 2.812 KB - Size of Time-Series Variables (1D): 0.000 Bytes - Size of Time-Series Variables (2D): 0.000 Bytes - Size of Time-Series Variables (3D): 3.021 GB - Size of Time-Series Variables (?D): 184.638 GB - TOTAL Size of Variables: 187.678 GB - -pop-daily-1deg: - No. of TI Metadata Variables: 58 - No. of TV Metadata Variables: 2 - No. of Time-Series Variables (1D): 0 - No. of Time-Series Variables (2D): 0 - No. of Time-Series Variables (3D): 4 - No. of Time-Series Variables (?D): 0 - No. of Variables (TOTAL): 64 - Size of TI Metadata Variables: 18.283 MB - Size of TV Metadata Variables: 85.523 KB - Size of Time-Series Variables (1D): 0.000 Bytes - Size of Time-Series Variables (2D): 0.000 Bytes - Size of Time-Series Variables (3D): 6.682 GB - Size of Time-Series Variables (?D): 0.000 Bytes - TOTAL Size of Variables: 6.699 GB - diff --git a/tests/yellowstone/getsizes.py b/tests/yellowstone/getsizes.py deleted file mode 100755 index 28ec9b6..0000000 --- a/tests/yellowstone/getsizes.py +++ /dev/null @@ -1,222 +0,0 @@ -#!/usr/bin/env python -#============================================================================== -# -# This script is designed to look through all of the datasets and determine -# there total data sizes. In particular, it determines the -# total size, size of all time-series variables, and metadata sizes. -# -#============================================================================== - -import os -import Nio -import json -import glob -import optparse -import numpy as np -np.set_printoptions(precision=2) - -#============================================================================== -# Command-Line Interface Definition -#============================================================================== -usage = 'usage: %prog [options]' -parser = optparse.OptionParser(usage=usage) -parser.add_option('-i', '--testinfo', default=None, - help='Location of the testinfo.json file ' - '[Default: None]') - -# Parse the CLI options and assemble the Reshaper inputs -(options, arguments) = parser.parse_args() - -# Read the data file -data_file_name = '../testinfo.json' -if options.testinfo != None and os.path.isfile(options.testinfo): - data_file_name = options.testinfo -data_file = open(data_file_name) -jsondata = dict(json.load(data_file)) -data_file.close() - - -#============================================================================== -# Helper function to convert typecodes into dtype itemsizes - -def get_itemsize(tc): - dt = None - if (tc == 'd'): - dt = np.float64 - elif (tc == 'f'): - dt = np.float32 - elif (tc == 'l'): - dt = np.long - elif (tc == 'i'): - dt = np.int32 - elif (tc == 'h'): - dt = np.int16 - elif (tc == 'b'): - dt = np.int8 - elif (tc == 'S1'): - dt = np.character - else: - dt = np.float - return np.dtype(dt).itemsize - - -#============================================================================== -# Helper function to return the size of an array given its shape - -def get_size(shp): - if (len(shp) > 0): - return reduce(lambda x, y: x * y, shp) - else: - return 1 - - -#============================================================================== -# Helper function to represent an integer number of bytes as a string w/ units - -def nbyte_str(n, exp=0): - if (n > 1024.): - return nbyte_str(n / 1024., exp=exp + 1) - else: - units = '' - if (exp == 0): - units = 'Bytes' - elif (exp == 1): - units = 'KB' - elif (exp == 2): - units = 'MB' - elif (exp == 3): - units = 'GB' - elif (exp == 4): - units = 'TB' - elif (exp == 5): - units = 'PB' - else: - n *= 1024.**(exp - 5) - units = 'PB' - return '%.3f %s' % (n, units) - - -#============================================================================== -# Loop over all tests -#============================================================================== - -for test_name in jsondata: - print test_name + ':' - - # Generate the list of input files - input_dir = jsondata[test_name]['input_dir'] - input_files = [] - for glob_str in jsondata[test_name]['input_globs']: - full_glob_str = os.path.join(input_dir, glob_str) - glob_files = glob.glob(full_glob_str) - input_files.extend(glob_files) - - # Sort by name - input_files.sort() - - # Open the first file - infile0 = Nio.open_file(input_files[0], 'r') - - # Get the name of the unlimited dimension (e.g., time) - udim = None - for dim in infile0.dimensions: - if infile0.unlimited(dim): - udim = dim - continue - - # Get the data dimensions - metadata_names = set(infile0.dimensions.keys()) - - # Add the extra metadata variable names - metadata_names.update(set(jsondata[test_name]['metadata'])) - - # Determine sizes of variables - timeseries_vars_1D = {} - timeseries_vars_2D = {} - timeseries_vars_3D = {} - timeseries_vars_oD = {} - ti_metadata_vars = {} - tv_metadata_vars = {} - for var_name in infile0.variables.keys(): - var_obj = infile0.variables[var_name] - var_shape = var_obj.shape - var_size = get_size(var_shape) - var_bytesize = var_size * get_itemsize(var_obj.typecode()) - if (udim in var_obj.dimensions): - if var_name in metadata_names: - tv_metadata_vars[var_name] = var_bytesize - elif len(var_shape) == 1: - timeseries_vars_1D[var_name] = var_bytesize - elif len(var_shape) == 2: - timeseries_vars_2D[var_name] = var_bytesize - elif len(var_shape) == 3: - timeseries_vars_3D[var_name] = var_bytesize - else: - timeseries_vars_oD[var_name] = var_bytesize - else: - ti_metadata_vars[var_name] = var_bytesize - - ts1d_num = len(timeseries_vars_1D) - ts2d_num = len(timeseries_vars_2D) - ts3d_num = len(timeseries_vars_3D) - tsod_num = len(timeseries_vars_oD) - timd_num = len(ti_metadata_vars) - tvmd_num = len(tv_metadata_vars) - tot_num = ts1d_num + ts2d_num + ts3d_num + tsod_num + timd_num + tvmd_num - - # Close the file - infile0.close() - - # Some output (numbers) - print ' No. of TI Metadata Variables: ', timd_num - print ' No. of TV Metadata Variables: ', tvmd_num - print ' No. of Time-Series Variables (1D): ', ts1d_num - print ' No. of Time-Series Variables (2D): ', ts2d_num - print ' No. of Time-Series Variables (3D): ', ts3d_num - print ' No. of Time-Series Variables (?D): ', tsod_num - print ' No. of Variables (TOTAL): ', tot_num - - # Loop over all input files and compute time-variant variable sizes - for file_name in input_files[1:]: - # Open the first file - infile = Nio.open_file(file_name, 'r') - - # Compute variable sizes - for var_name in infile.variables.keys(): - var_obj = infile.variables[var_name] - if (udim in var_obj.dimensions): - var_shape = var_obj.shape - var_size = get_size(var_shape) - var_bytesize = var_size * get_itemsize(var_obj.typecode()) - if var_name in metadata_names: - tv_metadata_vars[var_name] += var_bytesize - elif len(var_shape) == 1: - timeseries_vars_1D[var_name] += var_bytesize - elif len(var_shape) == 2: - timeseries_vars_2D[var_name] += var_bytesize - elif len(var_shape) == 3: - timeseries_vars_3D[var_name] += var_bytesize - else: - timeseries_vars_oD[var_name] += var_bytesize - - # Close the file - infile.close() - - # Compute totals - ts1d_size = np.sum(timeseries_vars_1D.values()) - ts2d_size = np.sum(timeseries_vars_2D.values()) - ts3d_size = np.sum(timeseries_vars_3D.values()) - tsod_size = np.sum(timeseries_vars_oD.values()) - timd_size = np.sum(ti_metadata_vars.values()) - tvmd_size = np.sum(tv_metadata_vars.values()) - tot_isize = ts1d_size + ts2d_size + \ - ts3d_size + tsod_size + timd_size + tvmd_size - - print ' Size of TI Metadata Variables:', nbyte_str(timd_size) - print ' Size of TV Metadata Variables:', nbyte_str(tvmd_size) - print ' Size of Time-Series Variables (1D):', nbyte_str(ts1d_size) - print ' Size of Time-Series Variables (2D):', nbyte_str(ts2d_size) - print ' Size of Time-Series Variables (3D):', nbyte_str(ts3d_size) - print ' Size of Time-Series Variables (?D):', nbyte_str(tsod_size) - print ' TOTAL Size of Variables: ', nbyte_str(tot_isize) - print From d14ba9236d7dd24b269c90c40a0f5e3207f0002f Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 16:40:06 -0600 Subject: [PATCH 128/250] Some cleanup. --- tests/yellowstone/runtests.py | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/tests/yellowstone/runtests.py b/tests/yellowstone/runtests.py index d3f5b9e..25365d3 100755 --- a/tests/yellowstone/runtests.py +++ b/tests/yellowstone/runtests.py @@ -75,9 +75,6 @@ help='Whether to skip time-series generation for ' 'variables with existing output files. ' '[Default: False]') -_PARSER_.add_argument('--statsfile', default=None, type=str, - help='Location of the teststats.json database file ' - '[Default: None]') _PARSER_.add_argument('-t', '--tiling', default=16, type=int, help='The integer number of processes per node to ' 'request in parallel runs (ignored if running ' @@ -217,9 +214,9 @@ def runmultitest(args, tests): #============================================================================== -# Run tests +# Run tests individually #============================================================================== -def runtests(args, tests): +def runindivtests(args, tests): """ Run a set of tests @@ -314,4 +311,4 @@ def runtests(args, tests): if args.multispec: runmultitest(args, test_list) else: - runtests(args, test_list) + runindivtests(args, test_list) From 6c83aa4bab6ef8ad697ef97ced13d77e2b784009 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 16:41:07 -0600 Subject: [PATCH 129/250] Change default value of testinfo filename --- tests/yellowstone/runtests.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/yellowstone/runtests.py b/tests/yellowstone/runtests.py index 25365d3..f1a93b0 100755 --- a/tests/yellowstone/runtests.py +++ b/tests/yellowstone/runtests.py @@ -41,9 +41,9 @@ help='The name of the project code for charging in ' 'parallel runs (ignored if running in serial) ' '[Default: STDD0002]') -_PARSER_.add_argument('-i', '--infofile', default=None, type=str, +_PARSER_.add_argument('-i', '--infofile', default='testinfo.json', type=str, help='Location of the testinfo.json database file ' - '[Default: None]') + '[Default: testinfo.json]') _PARSER_.add_argument('-f', '--format', default='netcdf4c', type=str, dest='ncformat', help='The NetCDF file format to use for the output ' From b3c1fd5a77707fe6a2ea854414993e4b6e255e26 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 16:41:41 -0600 Subject: [PATCH 130/250] Update getstats script --- tests/yellowstone/getstats.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/yellowstone/getstats.py b/tests/yellowstone/getstats.py index 99dd0b8..61aba40 100755 --- a/tests/yellowstone/getstats.py +++ b/tests/yellowstone/getstats.py @@ -25,9 +25,9 @@ action='store_true', dest='all_tests', help='True or False, indicating whether to run all ' 'tests [Default: False]') -_PARSER_.add_argument('-i', '--infofile', default=None, type=str, +_PARSER_.add_argument('-i', '--infofile', default='testinfo.json', type=str, help='Location of the testinfo.json database file ' - '[Default: None]') + '[Default: testinfo.json]') _PARSER_.add_argument('-l', '--list', default=False, action='store_true', dest='list_tests', help='True or False, indicating whether to list all ' @@ -37,9 +37,9 @@ help='True or False, indicating whether to force ' 'deleting any existing test or run directories, ' 'if found [Default: False]') -_PARSER_.add_argument('-s', '--statsfile', default=None, type=str, +_PARSER_.add_argument('-s', '--statsfile', default='teststats.json', type=str, help='Location of the teststats.json database file ' - '[Default: None]') + '[Default: teststats.json]') _PARSER_.add_argument('test', type=str, nargs='*', help='Name of test to analyze') From 1e96186af7c786f4a2a48c7adbcd4146ad2f8160 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 16:45:38 -0600 Subject: [PATCH 131/250] Beginning update of checkresults script. --- tests/yellowstone/checkresults.py | 92 +++++++++++++++---------------- 1 file changed, 44 insertions(+), 48 deletions(-) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index 0a43e69..6fbc27f 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -10,59 +10,46 @@ import sys import glob import string -import optparse +import argparse import json - from subprocess import Popen, PIPE, STDOUT +# Package Modules +from utilities import testtools as tt +from utilities import runtools as rt #============================================================================== # Command-Line Interface Definition #============================================================================== -def parse_cli(): - usage = 'usage: %prog [options] test_dir1 test_dir2 ...' - parser = optparse.OptionParser(usage=usage) - parser.add_option('-a', '--all', default=False, - action='store_true', dest='all', - help='True or False, indicating whether to run all tests ' - '[Default: False]') - parser.add_option('-i', '--testing_database', default=None, +_DESC_ = 'Check the results of tests found in the rundirs directory.' +_PARSER_ = argparse.ArgumentParser(desc=_DESC_) +_PARSER_.add_argument('-c', '--code', default='STDD0002', type=str, + help='The name of the project code for charging in ' + 'parallel runs (ignored if running in serial) ' + '[Default: STDD0002]') +_PARSER_.add_argument('-i', '--infofile', default=None, help='Location of the testinfo.json file ' '[Default: None]') - parser.add_option('-l', '--list', default=False, +_PARSER_.add_argument('-l', '--list', default=False, action='store_true', dest='list_tests', - help='True or False, indicating whether to list all tests ' - 'that have been run with resulting output, instead of ' - 'actually comparing any tests. ' - '[Default: False]') - parser.add_option('-s', '--serial', default=False, - action='store_true', dest='serial', - help='True or False, indicating whether to check tests ' - 'in serial (True), rather than parallel (False). ' + help='True or False, indicating whether to list all ' + 'tests that have been run with resulting output, ' + 'instead of actually comparing any tests. ' '[Default: False]') - parser.add_option('-x', '--executable', default=None, - help='The path to the CPRNC executable. ' - '[Default: None]') - - # Parse the CLI options and arguments - (options, arguments) = parser.parse_args() - - # Set serial if listing only - if options.list_tests: - options.serial = True - options.all = True - - # Check for CPRNC executable - if not options.executable: - options.executable = "/glade/p/work/kpaul/installs/intel/12.1.5/" + \ - "cprnc/bin/cprnc" - if not os.path.isfile(options.executable): - err_msg = "Cannot find cprnc executable file: " + \ - str(options.executable) - raise RuntimeError(err_msg) - - # and return - return (options, arguments) +_PARSER_.add_argument('-n', '--nodes', default=0, type=int, + help='The integer number of nodes to request in parallel' + ' runs (0 means run in serial) [Default: 0]') +_PARSER_.add_argument('-q', '--queue', default='economy', type=str, + help='The name of the queue to request in parallel runs ' + '(ignored if running in serial) ' + '[Default: economy]') +_PARSER_.add_argument('-w', '--wtime', default=240, type=int, + help='The number of minutes to request for the wall ' + 'clock in parallel runs (ignored if running in ' + 'serial) [Default: 240]') +_PARSER_.add_argument('-x', '--executable', + default='/glade/p/work/kpaul/installs/intel/12.1.5/cprnc/bin/cprnc', + help='The path to the CPRNC executable.') #============================================================================== @@ -96,10 +83,10 @@ def gather(self, data): #============================================================================== # Get the testing database info #============================================================================== -def get_testing_database(options): +def get_infofile(options): # Get the testinfo.json data - testing_database_filename = '' + infofile_filename = '' if (options.testing_database == None): runtest_dir = os.path.dirname(__file__) testing_database_filename = os.path.join(runtest_dir, 'testinfo.json') @@ -133,7 +120,7 @@ def get_comparison_info(options, arguments, comm, testing_database): # Parse each test argument for test directories possible_test_dirs = [] - if (options.all): + if (options.all_tests): possible_test_dirs = glob.glob( os.path.join('results', '*', 'ser', '*')) possible_test_dirs.extend( @@ -396,7 +383,7 @@ def compare_results(comparison_info, comm, cprnc_exec): #============================================================================== # Main Program #============================================================================== -def main(options, arguments): +def checkresults(args): comm = BasicComm(serial=options.serial) testing_database = get_testing_database(options) comparison_info = get_comparison_info( @@ -408,5 +395,14 @@ def main(options, arguments): # Command-Line Operation #============================================================================== if __name__ == '__main__': - options, arguments = parse_cli() - main(options, arguments) + args = _PARSER_.parse_args() + + # Create/read the testing info and stats files + testdb = tt.TestDB(dbname=args.infofile) + + # List tests if only listing + if args.list_tests: + testdb.print_tests() + sys.exit(1) + + checkresults(args, testdirs) \ No newline at end of file From 40152e02d164b9973de209eb7f67cdc62b46e224 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 16:46:28 -0600 Subject: [PATCH 132/250] Updated test statistics file. --- tests/yellowstone/teststats.json | 16696 +---------------------------- 1 file changed, 1 insertion(+), 16695 deletions(-) diff --git a/tests/yellowstone/teststats.json b/tests/yellowstone/teststats.json index 1e1dea4..e929d04 100644 --- a/tests/yellowstone/teststats.json +++ b/tests/yellowstone/teststats.json @@ -1,16695 +1 @@ -{ - "camse-1deg":{ - "maxsizes":{ - "tseries":699868800, - "tinvariant":388816, - "tvariant":1920 - }, - "variables":{ - "CCN3":{ - "xshape":[ - 30, - 48602 - ], - "meta":false, - "xsize":5832240, - "tvariant":true - }, - "ch4vmr":{ - "xshape":[ - - ], - "meta":true, - "xsize":8, - "tvariant":true - 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cf3a16d409207bf701f471fab2487d37e5c34123 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 17 Sep 2015 16:48:48 -0600 Subject: [PATCH 133/250] Reformatting statistics file. --- tests/yellowstone/teststats.json | 16696 ++++++++++++++++++++++++++++- 1 file changed, 16695 insertions(+), 1 deletion(-) diff --git a/tests/yellowstone/teststats.json b/tests/yellowstone/teststats.json index e929d04..c790731 100644 --- a/tests/yellowstone/teststats.json +++ b/tests/yellowstone/teststats.json @@ -1 +1,16695 @@ -{"clmse-0.25deg": {"maxsizes": {"tseries": 5598734400, "tinvariant": 46656120, "tvariant": 1920}, "variables": {"URBAN_AC": {"xshape": [777602], "meta": false, "xsize": 3110408, "tvariant": true}, "QSOIL": {"xshape": [777602], "meta": false, "xsize": 3110408, "tvariant": true}, "WA": {"xshape": [777602], "meta": false, "xsize": 3110408, "tvariant": true}, "ZBOT": {"xshape": [777602], "meta": false, "xsize": 3110408, "tvariant": true}, "WT": {"xshape": [777602], "meta": false, "xsize": 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files to be consistent. --- tests/yellowstone/README | 4 ++-- tests/yellowstone/{getstats.py => mkstats.py} | 0 tests/yellowstone/{gettimings.py => mktimings.py} | 0 3 files changed, 2 insertions(+), 2 deletions(-) rename tests/yellowstone/{getstats.py => mkstats.py} (100%) rename tests/yellowstone/{gettimings.py => mktimings.py} (100%) diff --git a/tests/yellowstone/README b/tests/yellowstone/README index 03fcdac..1525dfa 100644 --- a/tests/yellowstone/README +++ b/tests/yellowstone/README @@ -3,7 +3,7 @@ compute system. The general order of operations is described below: 0) Analyze Test Input: - getstats.py: Generate statistics describing the test input files. This + mkstats.py: Generate statistics describing the test input files. This writes the test statistics to the 'teststats.json' file. 1) Run Tests @@ -19,7 +19,7 @@ compute system. The general order of operations is described below: 3) Get Timing Data - gettimings.py: Read the PyReshaper output for each test that has been run + mktimings.py: Read the PyReshaper output for each test that has been run and extract the timing data from the output logs. Add this timing data to the 'timings.json' database. diff --git a/tests/yellowstone/getstats.py b/tests/yellowstone/mkstats.py similarity index 100% rename from tests/yellowstone/getstats.py rename to tests/yellowstone/mkstats.py diff --git a/tests/yellowstone/gettimings.py b/tests/yellowstone/mktimings.py similarity index 100% rename from tests/yellowstone/gettimings.py rename to tests/yellowstone/mktimings.py From 2c4b19eed8dc14e30936d5d74913b68f18c3ceaf Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 18 Sep 2015 12:09:52 -0600 Subject: [PATCH 135/250] Script cleanup. --- tests/yellowstone/mkstats.py | 24 +++++------------------- 1 file changed, 5 insertions(+), 19 deletions(-) diff --git a/tests/yellowstone/mkstats.py b/tests/yellowstone/mkstats.py index 61aba40..49c3dba 100755 --- a/tests/yellowstone/mkstats.py +++ b/tests/yellowstone/mkstats.py @@ -43,24 +43,6 @@ _PARSER_.add_argument('test', type=str, nargs='*', help='Name of test to analyze') - -#============================================================================== -# Analyze the tests -#============================================================================== -def analyzetests(args, tests): - """ - Analyze a set of tests - - Parameters: - args (argparse.Namespace): A namespace of command-line parsed arguments - describing the tests to run and how to run them - tests (list, tuple): List or tuple of test names to analyze - """ - - # Analyze test input, if requested (overwrite forces re-analysis) - testdb.analyze(tests=tests, force=args.overwrite) - testdb.save_statistics(stname=args.statsfile) - #============================================================================== # Main Command-line Operation #============================================================================== @@ -86,4 +68,8 @@ def analyzetests(args, tests): else: test_list = [t for t in args.test if t in testdb.get_database()] - analyzetests(args, test_list) + # Analyze test input, if requested (overwrite forces re-analysis) + testdb.analyze(test_list, force=args.overwrite) + + # Save to the stats file + testdb.save_statistics(stname=args.statsfile) From 0161b25d5bc11750dcdab2ecf1453beabfb26ab4 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 18 Sep 2015 12:31:56 -0600 Subject: [PATCH 136/250] Interface cleanup --- tests/yellowstone/runtests.py | 100 +++++++++++++++++++++++----------- 1 file changed, 68 insertions(+), 32 deletions(-) diff --git a/tests/yellowstone/runtests.py b/tests/yellowstone/runtests.py index f1a93b0..2d44aa7 100755 --- a/tests/yellowstone/runtests.py +++ b/tests/yellowstone/runtests.py @@ -90,14 +90,20 @@ #============================================================================== # Write an executable Python script to run the Reshaper #============================================================================== -def write_pyscript(args, testnames, scriptname='runscript.py'): +def write_pyscript(testnames, scriptname='runscript.py', verbosity=3, + serial=False, skip_existing=False, overwrite=False): """ Write an executable Python script to run the PyReshaper with a set of specs Parameters: - args (argparse.Namespace): arguments to pass to the Reshaper testnames (str, list): Name of a single test, or list of tests scriptname (str): Name of the Python script to write + verbosity (int): Level of output verbosity + serial (bool): Whether to run in serial (True) or not (False) + skip_existing (bool): Whether to skip the generation of existing + time-series files (True) or not (False) + overwrite (bool): Whether to overwrite existing time-series files + (True) or not (False) """ # Start defining the Python script @@ -124,8 +130,8 @@ def write_pyscript(args, testnames, scriptname='runscript.py'): # Define the rest of the python script pyscript_list.extend([ 'rshpr = reshaper.create_reshaper(specs, serial={0!s}, ' - 'verbosity=3, skip_existing={1!s}, overwrite={2!s})'.format( - args.nodes <= 0, args.skip_existing, args.overwrite), + 'verbosity={1!s}, skip_existing={2!s}, overwrite={3!s})'.format( + serial, verbosity, skip_existing, overwrite), 'rshpr.convert()', 'rshpr.print_diagnostics()', '']) @@ -142,14 +148,24 @@ def write_pyscript(args, testnames, scriptname='runscript.py'): #============================================================================== # Run a single multitest (using a MultiSpecReshaper) #============================================================================== -def runmultitest(args, tests): +def runmultitest(tests, nodes=0, tiling=16, minutes=120, + queue='economy', project='STDD0002', + skip_existing=False, overwrite=False, ncformat='netcdf4c'): """ Run a set of tests Parameters: - args (argparse.Namespace): A namespace of command-line parsed arguments - describing the tests to run and how to run them tests (list, tuple): List or tuple of test names to run + nodes (int): Number of nodes to run the test(s) with + tiling (int): Number of processes per node to run the test(s) with + minutes (int): Number of minutes to run the test(s) for + queue (str): Name of the queue to submit the job(s) to + project (str): Name of the project to charge the job time to + skip_existing (bool): Whether to skip the generation of existing + time-series files (True) or not (False) + overwrite (bool): Whether to overwrite existing time-series files + (True) or not (False) + ncformat (str): NetCDF format for the output """ print 'Running tests in single submission:' @@ -158,8 +174,8 @@ def runmultitest(args, tests): print # Set the test directory - if args.nodes > 0: - runtype = 'par{0!s}x{1!s}'.format(args.nodes, args.tiling) + if nodes > 0: + runtype = 'par{0!s}x{1!s}'.format(nodes, tiling) else: runtype = 'ser' testdir = os.path.abspath(os.path.join('rundirs', 'multitest', runtype)) @@ -167,7 +183,7 @@ def runmultitest(args, tests): # If the test directory doesn't exist, make it and move into it cwd = os.getcwd() if os.path.exists(testdir): - if args.overwrite: + if overwrite: shutil.rmtree(testdir) else: print "Already exists. Skipping." @@ -188,26 +204,28 @@ def runmultitest(args, tests): # Create the specifier and write to file (specfile) testspec = testdb.create_specifier(test_name=str(test_name), - ncfmt=args.ncformat, + ncfmt=ncformat, outdir=outputdir) testspecfile = str(test_name) + '.spec' pickle.dump(testspec, open(testspecfile, 'wb')) # Write the Python executable to be run pyscript_name = 'multitest.py' - write_pyscript(args, testnames=tests, scriptname=pyscript_name) + write_pyscript(testnames=tests, scriptname=pyscript_name, + serial=(nodes <= 0), skip_existing=skip_existing, + overwrite=overwrite) # Generate the command and arguments - if args.nodes > 0: + if nodes > 0: runcmd = 'poe ./{0!s}'.format(pyscript_name) else: runcmd = './{0!s}'.format(pyscript_name) # Create and start the job - job = rt.Job(runcmds=[runcmd], nodes=args.nodes, - name='multitest', tiling=args.tiling, - minutes=args.wtime, queue=args.queue, - project=args.code) + job = rt.Job(runcmds=[runcmd], nodes=nodes, + name='multitest', tiling=tiling, + minutes=minutes, queue=queue, + project=project) job.start() os.chdir(cwd) @@ -216,14 +234,24 @@ def runmultitest(args, tests): #============================================================================== # Run tests individually #============================================================================== -def runindivtests(args, tests): +def runindivtests(tests, nodes=0, tiling=16, minutes=120, + queue='economy', project='STDD0002', + skip_existing=False, overwrite=False, ncformat='netcdf4c'): """ Run a set of tests Parameters: - args (argparse.Namespace): A namespace of command-line parsed arguments - describing the tests to run and how to run them tests (list, tuple): List or tuple of test names to run + nodes (int): Number of nodes to run the test(s) with + tiling (int): Number of processes per node to run the test(s) with + minutes (int): Number of minutes to run the test(s) for + queue (str): Name of the queue to submit the job(s) to + project (str): Name of the project to charge the job time to + skip_existing (bool): Whether to skip the generation of existing + time-series files (True) or not (False) + overwrite (bool): Whether to overwrite existing time-series files + (True) or not (False) + ncformat (str): NetCDF format for the output """ cwd = os.getcwd() @@ -232,15 +260,15 @@ def runindivtests(args, tests): print 'Running test: {0!s}'.format(test_name) # Set the test directory - if args.nodes > 0: - runtype = 'par{0!s}x{1!s}'.format(args.nodes, args.tiling) + if nodes > 0: + runtype = 'par{0!s}x{1!s}'.format(nodes, tiling) else: runtype = 'ser' testdir = os.path.abspath(os.path.join('rundirs', str(test_name), runtype)) # If the test directory doesn't exist, make it and move into it if os.path.exists(testdir): - if args.overwrite: + if overwrite: shutil.rmtree(testdir) else: print " Already exists. Skipping." @@ -258,26 +286,28 @@ def runindivtests(args, tests): # Create the specifier and write to file (specfile) testspec = testdb.create_specifier(test_name=str(test_name), - ncfmt=args.ncformat, + ncfmt=ncformat, outdir=outputdir) testspecfile = '{0!s}.spec'.format(test_name) pickle.dump(testspec, open(testspecfile, 'wb')) # Write the Python executable to be run pyscript_name = '{0!s}.py'.format(test_name) - write_pyscript(args, testnames=test_name, scriptname=pyscript_name) + write_pyscript(testnames=test_name, scriptname=pyscript_name, + serial=(nodes <= 0), skip_existing=skip_existing, + overwrite=overwrite) # Generate the command and arguments - if args.nodes > 0: + if nodes > 0: runcmd = 'poe ./{0!s}'.format(pyscript_name) else: runcmd = './{0!s}'.format(pyscript_name) # Create and start the job - job = rt.Job(runcmds=[runcmd], nodes=args.nodes, - name=str(test_name), tiling=args.tiling, - minutes=args.wtime, queue=args.queue, - project=args.code) + job = rt.Job(runcmds=[runcmd], nodes=nodes, + name=str(test_name), tiling=tiling, + minutes=minutes, queue=queue, + project=project) job.start() os.chdir(cwd) @@ -309,6 +339,12 @@ def runindivtests(args, tests): test_list = [t for t in args.test if t in testdb.get_database()] if args.multispec: - runmultitest(args, test_list) + runmultitest(test_list, nodes=args.nodes, tiling=args.tiling, + minutes=args.wtime, queue=args.queue, project=args.code, + skip_existing=args.skip_existing, overwrite=args.overwrite, + ncformat=args.ncformat) else: - runindivtests(args, test_list) + runindivtests(test_list, nodes=args.nodes, tiling=args.tiling, + minutes=args.wtime, queue=args.queue, project=args.code, + skip_existing=args.skip_existing, overwrite=args.overwrite, + ncformat=args.ncformat) From 2cac0ea8583fbe4c002a988c17edbce946f002e6 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 18 Sep 2015 12:42:44 -0600 Subject: [PATCH 137/250] Change results directory to 'results.d' --- tests/yellowstone/runtests.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/yellowstone/runtests.py b/tests/yellowstone/runtests.py index 2d44aa7..8812c17 100755 --- a/tests/yellowstone/runtests.py +++ b/tests/yellowstone/runtests.py @@ -178,7 +178,7 @@ def runmultitest(tests, nodes=0, tiling=16, minutes=120, runtype = 'par{0!s}x{1!s}'.format(nodes, tiling) else: runtype = 'ser' - testdir = os.path.abspath(os.path.join('rundirs', 'multitest', runtype)) + testdir = os.path.abspath(os.path.join('results.d', 'multitest', runtype)) # If the test directory doesn't exist, make it and move into it cwd = os.getcwd() @@ -264,7 +264,7 @@ def runindivtests(tests, nodes=0, tiling=16, minutes=120, runtype = 'par{0!s}x{1!s}'.format(nodes, tiling) else: runtype = 'ser' - testdir = os.path.abspath(os.path.join('rundirs', str(test_name), runtype)) + testdir = os.path.abspath(os.path.join('results.d', str(test_name), runtype)) # If the test directory doesn't exist, make it and move into it if os.path.exists(testdir): From 721a9db489eeb3a6c13e9406bf18ad27b969b9ca Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 18 Sep 2015 12:57:04 -0600 Subject: [PATCH 138/250] Debug statements for testing --- tests/yellowstone/checkresults.py | 56 ++++++------------------------- 1 file changed, 11 insertions(+), 45 deletions(-) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index 6fbc27f..e755b27 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -47,9 +47,11 @@ help='The number of minutes to request for the wall ' 'clock in parallel runs (ignored if running in ' 'serial) [Default: 240]') -_PARSER_.add_argument('-x', '--executable', +_PARSER_.add_argument('-x', '--executable', type=str, default='/glade/p/work/kpaul/installs/intel/12.1.5/cprnc/bin/cprnc', help='The path to the CPRNC executable.') +_PARSER_.add_argument('testdir', type=str, nargs='*', + help='Name of a test directory to check') #============================================================================== @@ -80,33 +82,6 @@ def gather(self, data): return self.MPI.COMM_WORLD.gather(data) -#============================================================================== -# Get the testing database info -#============================================================================== -def get_infofile(options): - - # Get the testinfo.json data - infofile_filename = '' - if (options.testing_database == None): - runtest_dir = os.path.dirname(__file__) - testing_database_filename = os.path.join(runtest_dir, 'testinfo.json') - else: - testing_database_filename = os.path.abspath(options.testing_database) - - # Try opening and reading the testinfo file - testing_database = {} - try: - testing_database_file = open(testing_database_filename, 'r') - testing_database = dict(json.load(testing_database_file)) - testing_database_file.close() - except: - err_msg = 'Problem reading and parsing test info file: ' \ - + str(testing_database_filename) - raise ValueError(err_msg) - - return testing_database - - #============================================================================== # Parse input and set up comparison information #============================================================================== @@ -379,18 +354,6 @@ def compare_results(comparison_info, comm, cprnc_exec): print comparison_info[full_test_name]['num_checks'], print 'total comparisons)' - -#============================================================================== -# Main Program -#============================================================================== -def checkresults(args): - comm = BasicComm(serial=options.serial) - testing_database = get_testing_database(options) - comparison_info = get_comparison_info( - options, arguments, comm, testing_database) - compare_results(comparison_info, comm, options.executable) - - #============================================================================== # Command-Line Operation #============================================================================== @@ -400,9 +363,12 @@ def checkresults(args): # Create/read the testing info and stats files testdb = tt.TestDB(dbname=args.infofile) - # List tests if only listing - if args.list_tests: - testdb.print_tests() - sys.exit(1) + # Get the list of the available test names for comparison + valid_names = testdb.get_database().keys() + print str(valid_names) + name_pattern = str(valid_names).replace(' ', '') + print str(name_pattern) - checkresults(args, testdirs) \ No newline at end of file + # Search for all possible test run directories + found_testdirs = glob.glob(os.path.join('results.d', '*', '[ser,par]*')) + print str(found_testdirs) From ce9e7ac0bda2932104d4492c7325ae250252c495 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 18 Sep 2015 12:58:25 -0600 Subject: [PATCH 139/250] Typo (desc -> description) --- tests/yellowstone/checkresults.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index e755b27..8225fe9 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -22,7 +22,7 @@ # Command-Line Interface Definition #============================================================================== _DESC_ = 'Check the results of tests found in the rundirs directory.' -_PARSER_ = argparse.ArgumentParser(desc=_DESC_) +_PARSER_ = argparse.ArgumentParser(description=_DESC_) _PARSER_.add_argument('-c', '--code', default='STDD0002', type=str, help='The name of the project code for charging in ' 'parallel runs (ignored if running in serial) ' From d2f572c9474c5869b9f220989a36919b6b4af3eb Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 18 Sep 2015 13:00:41 -0600 Subject: [PATCH 140/250] Fixing list of name types and name_pattern --- tests/yellowstone/checkresults.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index 8225fe9..37555c2 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -364,9 +364,9 @@ def compare_results(comparison_info, comm, cprnc_exec): testdb = tt.TestDB(dbname=args.infofile) # Get the list of the available test names for comparison - valid_names = testdb.get_database().keys() + valid_names = [str(t) for t in testdb.get_database().keys()] print str(valid_names) - name_pattern = str(valid_names).replace(' ', '') + name_pattern = str(valid_names).replace(' ', '').replace("'", '') print str(name_pattern) # Search for all possible test run directories From 0cf15c911deb887bf0851fb70553ab23fb723d79 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 18 Sep 2015 13:02:06 -0600 Subject: [PATCH 141/250] Adding 'multitest' to valid test names --- tests/yellowstone/checkresults.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index 37555c2..39e5b34 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -365,10 +365,11 @@ def compare_results(comparison_info, comm, cprnc_exec): # Get the list of the available test names for comparison valid_names = [str(t) for t in testdb.get_database().keys()] + valid_names.append('multitest') print str(valid_names) name_pattern = str(valid_names).replace(' ', '').replace("'", '') print str(name_pattern) # Search for all possible test run directories - found_testdirs = glob.glob(os.path.join('results.d', '*', '[ser,par]*')) + found_testdirs = glob.glob(os.path.join('results.d', name_pattern, '[ser,par]*')) print str(found_testdirs) From be3cf21c360292f16392ebc4fa51cdb41a827bcd Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 18 Sep 2015 13:51:26 -0600 Subject: [PATCH 142/250] Adding NetCDF format name to test directory structure --- tests/yellowstone/runtests.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/runtests.py b/tests/yellowstone/runtests.py index 8812c17..132efdb 100755 --- a/tests/yellowstone/runtests.py +++ b/tests/yellowstone/runtests.py @@ -178,7 +178,7 @@ def runmultitest(tests, nodes=0, tiling=16, minutes=120, runtype = 'par{0!s}x{1!s}'.format(nodes, tiling) else: runtype = 'ser' - testdir = os.path.abspath(os.path.join('results.d', 'multitest', runtype)) + testdir = os.path.abspath(os.path.join('results.d', 'multitest', runtype, ncformat)) # If the test directory doesn't exist, make it and move into it cwd = os.getcwd() From ec31c322eb10a1c37b63043b9c026f28db152ba4 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 18 Sep 2015 13:56:13 -0600 Subject: [PATCH 143/250] Adding NetCDF format to individual test directories, too --- tests/yellowstone/runtests.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/runtests.py b/tests/yellowstone/runtests.py index 132efdb..6911766 100755 --- a/tests/yellowstone/runtests.py +++ b/tests/yellowstone/runtests.py @@ -264,7 +264,7 @@ def runindivtests(tests, nodes=0, tiling=16, minutes=120, runtype = 'par{0!s}x{1!s}'.format(nodes, tiling) else: runtype = 'ser' - testdir = os.path.abspath(os.path.join('results.d', str(test_name), runtype)) + testdir = os.path.abspath(os.path.join('results.d', str(test_name), runtype, ncformat)) # If the test directory doesn't exist, make it and move into it if os.path.exists(testdir): From 62e4e982250e3815e9602e9ac01aa06dac0b6be4 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 18 Sep 2015 14:08:41 -0600 Subject: [PATCH 144/250] Testing. --- tests/yellowstone/checkresults.py | 55 ++++++++++++++++++++++++++----- 1 file changed, 46 insertions(+), 9 deletions(-) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index 39e5b34..b00bfdb 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -7,6 +7,7 @@ #====================================================================== import os +import re import sys import glob import string @@ -54,6 +55,20 @@ help='Name of a test directory to check') +#============================================================================== +# grep - Search through a file for a given pattern +#============================================================================== +def grep(pattern, filename, start=0, end=0): + if not os.path.exists(filename): + return None + with open(filename, 'r') as fobj: + results = [line.rstrip() for line in fobj if re.search(pattern, line)] + if len(results) == 0: + return None + else: + return results + + #============================================================================== # Local MPI options and handling #============================================================================== @@ -362,14 +377,36 @@ def compare_results(comparison_info, comm, cprnc_exec): # Create/read the testing info and stats files testdb = tt.TestDB(dbname=args.infofile) + testdb_dict = testdb.get_database() # Get the list of the available test names for comparison - valid_names = [str(t) for t in testdb.get_database().keys()] - valid_names.append('multitest') - print str(valid_names) - name_pattern = str(valid_names).replace(' ', '').replace("'", '') - print str(name_pattern) - - # Search for all possible test run directories - found_testdirs = glob.glob(os.path.join('results.d', name_pattern, '[ser,par]*')) - print str(found_testdirs) + valid_names = [str(t) for t in testdb_dict.keys()] + + # Find valid tests + found_tests = {} + for rdir in glob.glob(os.path.join('results.d', '*', '[ser,par]*', '*')): + tempdir, ncfmt = os.path.split(rdir) + tempdir, runtype = os.path.split(tempdir) + tempdir, test_name = os.path.split(tempdir) + if test_name in valid_names: + + print 'Found test results for name: {}'.format(test_name) + print 'Results directory: {}'.format(rdir) + + # Look for the corresponding log file and check for successful run + logfile = os.path.join(rdir, '{0!s}.log'.format(test_name)) + if not grep(r'Successfully completed.', logfile): + continue + print 'Test completed successfully.' + + # Look for the specfile + specfile = os.path.join(rdir, '{0!s}.spec'.format(test_name)) + if not os.path.exists(specfile): + continue + print 'Found specfile: {}'.format(specfile) + + # Look for the output directory + outdir = os.path.join(rdir, 'output') + if not os.path.exists(outdir): + continue + print 'Found output directory: {}'.format(outdir) From 6220e501536a75195c9b4441e8f6d1a88ea71cd5 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 18 Sep 2015 14:11:48 -0600 Subject: [PATCH 145/250] Debugging output --- tests/yellowstone/checkresults.py | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index b00bfdb..215fcd4 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -58,15 +58,17 @@ #============================================================================== # grep - Search through a file for a given pattern #============================================================================== -def grep(pattern, filename, start=0, end=0): +def grep(pattern, filename): if not os.path.exists(filename): return None - with open(filename, 'r') as fobj: - results = [line.rstrip() for line in fobj if re.search(pattern, line)] - if len(results) == 0: - return None - else: - return results + fobj = open(filename, 'r') + results = [line.rstrip() for line in fobj if re.search(pattern, line)] + print results + fobj.close() + if len(results) == 0: + return None + else: + return results #============================================================================== From 1df428824c6de532142499a2755d55fe2fefa3dd Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 18 Sep 2015 14:15:03 -0600 Subject: [PATCH 146/250] debugging output --- tests/yellowstone/checkresults.py | 1 + 1 file changed, 1 insertion(+) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index 215fcd4..66bac79 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -60,6 +60,7 @@ #============================================================================== def grep(pattern, filename): if not os.path.exists(filename): + print 'filename doesn\'t exist' return None fobj = open(filename, 'r') results = [line.rstrip() for line in fobj if re.search(pattern, line)] From 279713c0f9d25c5b85e27eb884d6b1b6a1a9d982 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 18 Sep 2015 14:15:45 -0600 Subject: [PATCH 147/250] More debugging output --- tests/yellowstone/checkresults.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index 66bac79..6fe049c 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -60,7 +60,7 @@ #============================================================================== def grep(pattern, filename): if not os.path.exists(filename): - print 'filename doesn\'t exist' + print 'filename {} doesn\'t exist'.filename return None fobj = open(filename, 'r') results = [line.rstrip() for line in fobj if re.search(pattern, line)] From 9f067fd1bf1e5fb30f21d3f277d06e126a4f85fa Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 18 Sep 2015 14:16:15 -0600 Subject: [PATCH 148/250] Fix syntax error --- tests/yellowstone/checkresults.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index 6fe049c..7b7c17b 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -60,7 +60,7 @@ #============================================================================== def grep(pattern, filename): if not os.path.exists(filename): - print 'filename {} doesn\'t exist'.filename + print 'filename {} doesn\'t exist'.format(filename) return None fobj = open(filename, 'r') results = [line.rstrip() for line in fobj if re.search(pattern, line)] From 97770b1d223cda3601f34cc514657f576f86a47c Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 18 Sep 2015 14:20:09 -0600 Subject: [PATCH 149/250] Debugging output. --- tests/yellowstone/checkresults.py | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index 7b7c17b..7206491 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -397,10 +397,11 @@ def compare_results(comparison_info, comm, cprnc_exec): print 'Results directory: {}'.format(rdir) # Look for the corresponding log file and check for successful run - logfile = os.path.join(rdir, '{0!s}.log'.format(test_name)) - if not grep(r'Successfully completed.', logfile): - continue - print 'Test completed successfully.' + logfiles = [] + for logfile in glob.glob(os.path.join(rdir, '{0!s}*.log'.format(test_name))): + if grep(r'Successfully completed.', logfile): + logfiles.append(logfile) + print 'Test {} completed successfully.'.format(logfile) # Look for the specfile specfile = os.path.join(rdir, '{0!s}.spec'.format(test_name)) From 955ddab4f0f8817a341d80d5f9219019e24d1c33 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 18 Sep 2015 14:22:26 -0600 Subject: [PATCH 150/250] Check for valid log files --- tests/yellowstone/checkresults.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index 7206491..3a54cea 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -396,12 +396,14 @@ def compare_results(comparison_info, comm, cprnc_exec): print 'Found test results for name: {}'.format(test_name) print 'Results directory: {}'.format(rdir) - # Look for the corresponding log file and check for successful run + # Look for the corresponding log files and check for successful run logfiles = [] for logfile in glob.glob(os.path.join(rdir, '{0!s}*.log'.format(test_name))): if grep(r'Successfully completed.', logfile): logfiles.append(logfile) - print 'Test {} completed successfully.'.format(logfile) + if len(logfiles) == 0: + continue + print 'Test(s) completed successfully.'.format(logfile) # Look for the specfile specfile = os.path.join(rdir, '{0!s}.spec'.format(test_name)) From 19dd97f56e8d212a587c28d1399bc4a049c9b186 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 18 Sep 2015 14:23:14 -0600 Subject: [PATCH 151/250] Remove some debugging output --- tests/yellowstone/checkresults.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index 3a54cea..d87af0d 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -60,11 +60,9 @@ #============================================================================== def grep(pattern, filename): if not os.path.exists(filename): - print 'filename {} doesn\'t exist'.format(filename) return None fobj = open(filename, 'r') results = [line.rstrip() for line in fobj if re.search(pattern, line)] - print results fobj.close() if len(results) == 0: return None From f52d41a5e65b1446c6150552d87abcd84732e067 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 18 Sep 2015 14:24:45 -0600 Subject: [PATCH 152/250] Separating test output --- tests/yellowstone/checkresults.py | 1 + 1 file changed, 1 insertion(+) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index d87af0d..9bfd95b 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -414,3 +414,4 @@ def compare_results(comparison_info, comm, cprnc_exec): if not os.path.exists(outdir): continue print 'Found output directory: {}'.format(outdir) + print From d7a9172eb8c3e29bceecd56e093cb145d5be5c11 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 18 Sep 2015 14:25:43 -0600 Subject: [PATCH 153/250] Moving separator to front out output, or invalid results not printed --- tests/yellowstone/checkresults.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index 9bfd95b..5722e29 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -390,6 +390,7 @@ def compare_results(comparison_info, comm, cprnc_exec): tempdir, runtype = os.path.split(tempdir) tempdir, test_name = os.path.split(tempdir) if test_name in valid_names: + print print 'Found test results for name: {}'.format(test_name) print 'Results directory: {}'.format(rdir) @@ -414,4 +415,3 @@ def compare_results(comparison_info, comm, cprnc_exec): if not os.path.exists(outdir): continue print 'Found output directory: {}'.format(outdir) - print From 82fec412a90070c16987a66da0a7a81f63d75d92 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 18 Sep 2015 14:30:51 -0600 Subject: [PATCH 154/250] Don't need specfile or logfiles --- tests/yellowstone/checkresults.py | 40 ++++--------------------------- 1 file changed, 5 insertions(+), 35 deletions(-) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index 5722e29..09d9238 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -55,21 +55,6 @@ help='Name of a test directory to check') -#============================================================================== -# grep - Search through a file for a given pattern -#============================================================================== -def grep(pattern, filename): - if not os.path.exists(filename): - return None - fobj = open(filename, 'r') - results = [line.rstrip() for line in fobj if re.search(pattern, line)] - fobj.close() - if len(results) == 0: - return None - else: - return results - - #============================================================================== # Local MPI options and handling #============================================================================== @@ -390,28 +375,13 @@ def compare_results(comparison_info, comm, cprnc_exec): tempdir, runtype = os.path.split(tempdir) tempdir, test_name = os.path.split(tempdir) if test_name in valid_names: - print - - print 'Found test results for name: {}'.format(test_name) - print 'Results directory: {}'.format(rdir) - - # Look for the corresponding log files and check for successful run - logfiles = [] - for logfile in glob.glob(os.path.join(rdir, '{0!s}*.log'.format(test_name))): - if grep(r'Successfully completed.', logfile): - logfiles.append(logfile) - if len(logfiles) == 0: - continue - print 'Test(s) completed successfully.'.format(logfile) - - # Look for the specfile - specfile = os.path.join(rdir, '{0!s}.spec'.format(test_name)) - if not os.path.exists(specfile): - continue - print 'Found specfile: {}'.format(specfile) # Look for the output directory outdir = os.path.join(rdir, 'output') if not os.path.exists(outdir): continue - print 'Found output directory: {}'.format(outdir) + + print 'Found test results for name: {}'.format(test_name) + print ' Results directory: {}'.format(rdir) + print ' Found output directory: {}'.format(outdir) + print From 10e9476fd697d1f8ba54c4604aa7afd0710bdf73 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 18 Sep 2015 14:41:35 -0600 Subject: [PATCH 155/250] Putting search results in dictionary --- tests/yellowstone/checkresults.py | 34 ++++++++++++++++++++++++------- 1 file changed, 27 insertions(+), 7 deletions(-) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index 09d9238..f301e0a 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -374,14 +374,34 @@ def compare_results(comparison_info, comm, cprnc_exec): tempdir, ncfmt = os.path.split(rdir) tempdir, runtype = os.path.split(tempdir) tempdir, test_name = os.path.split(tempdir) + + # Individually run test results if test_name in valid_names: - # Look for the output directory - outdir = os.path.join(rdir, 'output') - if not os.path.exists(outdir): + # Look for the new output directory + newdir = os.path.join(rdir, 'output') + if not os.path.exists(newdir): continue - print 'Found test results for name: {}'.format(test_name) - print ' Results directory: {}'.format(rdir) - print ' Found output directory: {}'.format(outdir) - print + # Get the output directory to compare against + olddir = testdb_dict[test_name]['results_dir'] + + # Put together comparison info + found_tests[test_name] = (newdir, olddir) + + # Multitest results + elif test_name == 'multitest': + + # Look for the new output directories + for newdir in glob.glob(os.path.join(rdir, 'output', '*')): + + tempdir, results_name = os.path.split(newdir) + if results_name in valid_names: + + # Get the output directory to compare against + olddir = testdb_dict[results_name]['results_dir'] + + # Put together comparison info + found_tests[test_name] = (newdir, olddir) + + print found_tests From 41c13032ea937535686ed383505d8194d948d82f Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 18 Sep 2015 14:43:19 -0600 Subject: [PATCH 156/250] Separating dictionary into individual and multispec tests --- tests/yellowstone/checkresults.py | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index f301e0a..b08c593 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -369,7 +369,8 @@ def compare_results(comparison_info, comm, cprnc_exec): valid_names = [str(t) for t in testdb_dict.keys()] # Find valid tests - found_tests = {} + individual_tests = {} + multispec_tests = {} for rdir in glob.glob(os.path.join('results.d', '*', '[ser,par]*', '*')): tempdir, ncfmt = os.path.split(rdir) tempdir, runtype = os.path.split(tempdir) @@ -387,7 +388,7 @@ def compare_results(comparison_info, comm, cprnc_exec): olddir = testdb_dict[test_name]['results_dir'] # Put together comparison info - found_tests[test_name] = (newdir, olddir) + individual_tests[test_name] = (newdir, olddir) # Multitest results elif test_name == 'multitest': @@ -402,6 +403,7 @@ def compare_results(comparison_info, comm, cprnc_exec): olddir = testdb_dict[results_name]['results_dir'] # Put together comparison info - found_tests[test_name] = (newdir, olddir) + multispec_tests[test_name] = (newdir, olddir) - print found_tests + print individual_tests + print multispec_tests From ca0919c577b5501a62f0197df2f8258c0fc50093 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 18 Sep 2015 14:45:20 -0600 Subject: [PATCH 157/250] No need for extra list, just use dictionary directly --- tests/yellowstone/checkresults.py | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index b08c593..6ec6494 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -365,9 +365,6 @@ def compare_results(comparison_info, comm, cprnc_exec): testdb = tt.TestDB(dbname=args.infofile) testdb_dict = testdb.get_database() - # Get the list of the available test names for comparison - valid_names = [str(t) for t in testdb_dict.keys()] - # Find valid tests individual_tests = {} multispec_tests = {} @@ -377,7 +374,7 @@ def compare_results(comparison_info, comm, cprnc_exec): tempdir, test_name = os.path.split(tempdir) # Individually run test results - if test_name in valid_names: + if test_name in testdb_dict: # Look for the new output directory newdir = os.path.join(rdir, 'output') @@ -397,7 +394,7 @@ def compare_results(comparison_info, comm, cprnc_exec): for newdir in glob.glob(os.path.join(rdir, 'output', '*')): tempdir, results_name = os.path.split(newdir) - if results_name in valid_names: + if results_name in testdb_dict: # Get the output directory to compare against olddir = testdb_dict[results_name]['results_dir'] From 2b1eb10712057080b79eee41fb46ebe946b11cd8 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 18 Sep 2015 14:51:02 -0600 Subject: [PATCH 158/250] List tests, if requested --- tests/yellowstone/checkresults.py | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index 6ec6494..18e46df 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -365,7 +365,7 @@ def compare_results(comparison_info, comm, cprnc_exec): testdb = tt.TestDB(dbname=args.infofile) testdb_dict = testdb.get_database() - # Find valid tests + # Find valid tests for comparison individual_tests = {} multispec_tests = {} for rdir in glob.glob(os.path.join('results.d', '*', '[ser,par]*', '*')): @@ -402,5 +402,12 @@ def compare_results(comparison_info, comm, cprnc_exec): # Put together comparison info multispec_tests[test_name] = (newdir, olddir) - print individual_tests - print multispec_tests + # Print tests that will be checked, if list requested + if args.list_tests: + print 'Individually run tests to be checked:' + for test_name in individual_tests: + print ' {0!s}'.format(test_name) + print 'Multitest results to be checked:' + for test_name in multispec_tests: + print ' {0!s}'.format(test_name) + sys.exit(1) From 77c1d2e5b66106bfab3c8715d45c6f6cf5fbc968 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 18 Sep 2015 14:53:35 -0600 Subject: [PATCH 159/250] Cleaner list_tests output --- tests/yellowstone/checkresults.py | 18 ++++++++++++------ 1 file changed, 12 insertions(+), 6 deletions(-) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index 18e46df..b32607d 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -404,10 +404,16 @@ def compare_results(comparison_info, comm, cprnc_exec): # Print tests that will be checked, if list requested if args.list_tests: - print 'Individually run tests to be checked:' - for test_name in individual_tests: - print ' {0!s}'.format(test_name) - print 'Multitest results to be checked:' - for test_name in multispec_tests: - print ' {0!s}'.format(test_name) + if len(individual_tests) > 0: + print 'Individually run tests to be checked:' + for test_name in individual_tests: + print ' {0!s}'.format(test_name) + else: + print 'No individually run tests to be checked.' + if len(multispec_tests) > 0: + print 'Multitest results to be checked:' + for test_name in multispec_tests: + print ' {0!s}'.format(test_name) + else: + print 'No multitest results to be checked.' sys.exit(1) From 01aab24f733554ca687ecfd779f905e7cd9accad Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 18 Sep 2015 15:26:21 -0600 Subject: [PATCH 160/250] Skipping unsuccessful/incomplete runs --- tests/yellowstone/checkresults.py | 28 +++++++++++++++++++++------- 1 file changed, 21 insertions(+), 7 deletions(-) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index b32607d..7c47fec 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -371,10 +371,24 @@ def compare_results(comparison_info, comm, cprnc_exec): for rdir in glob.glob(os.path.join('results.d', '*', '[ser,par]*', '*')): tempdir, ncfmt = os.path.split(rdir) tempdir, runtype = os.path.split(tempdir) - tempdir, test_name = os.path.split(tempdir) + tempdir, runname = os.path.split(tempdir) + + # Look for the newest log file + logfiles = glob.glob(os.path.join(rdir, '{0!s}*.log'.format(runname))) + if len(logfiles) == 0: + continue + lastlog = max(logfiles, key=os.path.getctime) + successful = False + for logline in open(lastlog, 'r'): + if re.search(r'Successfully completed.', logline): + successful = True + continue + if not successful: + continue # Individually run test results - if test_name in testdb_dict: + if runname in testdb_dict: + test_name = runname # Look for the new output directory newdir = os.path.join(rdir, 'output') @@ -388,16 +402,16 @@ def compare_results(comparison_info, comm, cprnc_exec): individual_tests[test_name] = (newdir, olddir) # Multitest results - elif test_name == 'multitest': + elif runname == 'multitest': # Look for the new output directories - for newdir in glob.glob(os.path.join(rdir, 'output', '*')): + for rdir2 in glob.glob(os.path.join(rdir, 'output', '*')): - tempdir, results_name = os.path.split(newdir) - if results_name in testdb_dict: + tempdir, test_name = os.path.split(rdir2) + if test_name in testdb_dict: # Get the output directory to compare against - olddir = testdb_dict[results_name]['results_dir'] + olddir = testdb_dict[test_name]['results_dir'] # Put together comparison info multispec_tests[test_name] = (newdir, olddir) From 2ef80aba5eebfbc265d73f67a7ebe17150197c32 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 18 Sep 2015 15:50:46 -0600 Subject: [PATCH 161/250] Generalizing test search --- tests/yellowstone/checkresults.py | 82 ++++++++++++++++--------------- 1 file changed, 42 insertions(+), 40 deletions(-) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index 7c47fec..19dc424 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -37,6 +37,10 @@ 'tests that have been run with resulting output, ' 'instead of actually comparing any tests. ' '[Default: False]') +_PARSER_.add_argument('-m', '--multiple', default=False, + action='store_true', dest='multispec', + help='True or False, indicating whether to look for ' + 'multispec results [Default: False]') _PARSER_.add_argument('-n', '--nodes', default=0, type=int, help='The integer number of nodes to request in parallel' ' runs (0 means run in serial) [Default: 0]') @@ -51,8 +55,8 @@ _PARSER_.add_argument('-x', '--executable', type=str, default='/glade/p/work/kpaul/installs/intel/12.1.5/cprnc/bin/cprnc', help='The path to the CPRNC executable.') -_PARSER_.add_argument('testdir', type=str, nargs='*', - help='Name of a test directory to check') +_PARSER_.add_argument('rundir', type=str, nargs='*', + help='Name of a test run directory to check') #============================================================================== @@ -362,13 +366,25 @@ def compare_results(comparison_info, comm, cprnc_exec): args = _PARSER_.parse_args() # Create/read the testing info and stats files - testdb = tt.TestDB(dbname=args.infofile) - testdb_dict = testdb.get_database() + testdb = tt.TestDB(dbname=args.infofile).get_database() + + # Get a list of valid rundir names to look for + if len(args.rundir) > 0: + rundirs = args.rundir + else: + rundirs = glob.glob(os.path.join('results.d', '*', '[ser,par]*', '*')) + + # Get the list of valid run names and the output directory pattern + if args.multispec: + valid_runnames = ['multitest'] + outdir_pattern = os.path.join('output', '*') + else: + valid_runnames = testdb.keys() + outdir_pattern = 'output' # Find valid tests for comparison - individual_tests = {} - multispec_tests = {} - for rdir in glob.glob(os.path.join('results.d', '*', '[ser,par]*', '*')): + tests_to_check = {} + for rdir in rundirs: tempdir, ncfmt = os.path.split(rdir) tempdir, runtype = os.path.split(tempdir) tempdir, runname = os.path.split(tempdir) @@ -386,48 +402,34 @@ def compare_results(comparison_info, comm, cprnc_exec): if not successful: continue - # Individually run test results - if runname in testdb_dict: - test_name = runname - - # Look for the new output directory - newdir = os.path.join(rdir, 'output') - if not os.path.exists(newdir): - continue - - # Get the output directory to compare against - olddir = testdb_dict[test_name]['results_dir'] - - # Put together comparison info - individual_tests[test_name] = (newdir, olddir) - - # Multitest results - elif runname == 'multitest': + # Check if the runname is a valid name + if runname in valid_runnames: # Look for the new output directories - for rdir2 in glob.glob(os.path.join(rdir, 'output', '*')): + for odir in glob.glob(os.path.join(rdir, outdir_pattern)): - tempdir, test_name = os.path.split(rdir2) - if test_name in testdb_dict: + # Get the test name (allowing for multitest results) + if runname in testdb: + test_name = runname + else: + tempdir, test_name = os.path.split(odir) - # Get the output directory to compare against - olddir = testdb_dict[test_name]['results_dir'] + # Get the output directory to compare against + olddir = testdb[test_name]['results_dir'] - # Put together comparison info - multispec_tests[test_name] = (newdir, olddir) + # Put together comparison info + tests_to_check[test_name] = (odir, olddir) # Print tests that will be checked, if list requested if args.list_tests: - if len(individual_tests) > 0: - print 'Individually run tests to be checked:' - for test_name in individual_tests: - print ' {0!s}'.format(test_name) + if args.multispec: + print 'Checking multitest results.' else: - print 'No individually run tests to be checked.' - if len(multispec_tests) > 0: - print 'Multitest results to be checked:' - for test_name in multispec_tests: + print 'Checking individual test results.' + if len(tests_to_check) > 0: + print 'Tests to be checked:' + for test_name in tests_to_check: print ' {0!s}'.format(test_name) else: - print 'No multitest results to be checked.' + print 'No tests to be checked.' sys.exit(1) From 5df0eb7ed21033fc7f954fadad41453170dbf7f7 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 18 Sep 2015 16:22:31 -0600 Subject: [PATCH 162/250] Assembling list of file pairs to check --- tests/yellowstone/checkresults.py | 24 +++++++++++++++++++++--- 1 file changed, 21 insertions(+), 3 deletions(-) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index 19dc424..1442b99 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -359,6 +359,7 @@ def compare_results(comparison_info, comm, cprnc_exec): print comparison_info[full_test_name]['num_checks'], print 'total comparisons)' + #============================================================================== # Command-Line Operation #============================================================================== @@ -406,19 +407,19 @@ def compare_results(comparison_info, comm, cprnc_exec): if runname in valid_runnames: # Look for the new output directories - for odir in glob.glob(os.path.join(rdir, outdir_pattern)): + for newdir in glob.iglob(os.path.join(rdir, outdir_pattern)): # Get the test name (allowing for multitest results) if runname in testdb: test_name = runname else: - tempdir, test_name = os.path.split(odir) + tempdir, test_name = os.path.split(newdir) # Get the output directory to compare against olddir = testdb[test_name]['results_dir'] # Put together comparison info - tests_to_check[test_name] = (odir, olddir) + tests_to_check[test_name] = (newdir, olddir) # Print tests that will be checked, if list requested if args.list_tests: @@ -433,3 +434,20 @@ def compare_results(comparison_info, comm, cprnc_exec): else: print 'No tests to be checked.' sys.exit(1) + + # Get a basic MPI comm + comm = BasicComm(serial=args.nodes <= 0) + + # Expand the test directories into (new, old) file pairs + files_to_check = {} + for test_name, (newdir, olddir) in tests_to_check.items(): + file_pairs = [] + for newfile in glob.iglob(os.path.join(newdir, '*.nc')): + filename = os.path.split(newfile)[1] + oldfile = os.path.join(olddir, filename) + if os.path.exists(oldfile): + file_pairs.append((newfile, oldfile)) + + files_to_check[test_name] = file_pairs[comm.rank::comm.size] + + print files_to_check From 8af1a1c177011c0791902a534add98726bd22fce Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 18 Sep 2015 16:23:33 -0600 Subject: [PATCH 163/250] Casting unicode dirnames to str --- tests/yellowstone/checkresults.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index 1442b99..14c4768 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -416,7 +416,7 @@ def compare_results(comparison_info, comm, cprnc_exec): tempdir, test_name = os.path.split(newdir) # Get the output directory to compare against - olddir = testdb[test_name]['results_dir'] + olddir = str(testdb[test_name]['results_dir']) # Put together comparison info tests_to_check[test_name] = (newdir, olddir) From 180407f678c955e7af61d8d94643837f314f79f3 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 18 Sep 2015 16:27:13 -0600 Subject: [PATCH 164/250] Check for valid rundirs and use full paths --- tests/yellowstone/checkresults.py | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index 14c4768..c13d125 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -386,12 +386,15 @@ def compare_results(comparison_info, comm, cprnc_exec): # Find valid tests for comparison tests_to_check = {} for rdir in rundirs: - tempdir, ncfmt = os.path.split(rdir) + if not os.path.exists(rdir): + continue + rundir = os.path.realpath(rdir) + tempdir, ncfmt = os.path.split(rundir) tempdir, runtype = os.path.split(tempdir) tempdir, runname = os.path.split(tempdir) # Look for the newest log file - logfiles = glob.glob(os.path.join(rdir, '{0!s}*.log'.format(runname))) + logfiles = glob.glob(os.path.join(rundir, '{0!s}*.log'.format(runname))) if len(logfiles) == 0: continue lastlog = max(logfiles, key=os.path.getctime) @@ -407,7 +410,7 @@ def compare_results(comparison_info, comm, cprnc_exec): if runname in valid_runnames: # Look for the new output directories - for newdir in glob.iglob(os.path.join(rdir, outdir_pattern)): + for newdir in glob.iglob(os.path.join(rundir, outdir_pattern)): # Get the test name (allowing for multitest results) if runname in testdb: From d61f6afc88322db8197749666fa184418476c9dd Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 18 Sep 2015 16:35:51 -0600 Subject: [PATCH 165/250] Printing output for all cases --- tests/yellowstone/checkresults.py | 43 ++++++++++++++++--------------- 1 file changed, 22 insertions(+), 21 deletions(-) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index c13d125..47a398f 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -424,33 +424,34 @@ def compare_results(comparison_info, comm, cprnc_exec): # Put together comparison info tests_to_check[test_name] = (newdir, olddir) - # Print tests that will be checked, if list requested - if args.list_tests: - if args.multispec: - print 'Checking multitest results.' - else: - print 'Checking individual test results.' - if len(tests_to_check) > 0: - print 'Tests to be checked:' - for test_name in tests_to_check: - print ' {0!s}'.format(test_name) - else: - print 'No tests to be checked.' - sys.exit(1) - - # Get a basic MPI comm - comm = BasicComm(serial=args.nodes <= 0) - # Expand the test directories into (new, old) file pairs files_to_check = {} for test_name, (newdir, olddir) in tests_to_check.items(): - file_pairs = [] + files_to_check[test_name] = [] for newfile in glob.iglob(os.path.join(newdir, '*.nc')): filename = os.path.split(newfile)[1] oldfile = os.path.join(olddir, filename) if os.path.exists(oldfile): - file_pairs.append((newfile, oldfile)) + files_to_check[test_name].append((newfile, oldfile)) + + # Get a basic MPI comm + comm = BasicComm(serial=args.nodes <= 0) + + # Print tests that will be checked + if comm.rank == 0: + if args.multispec: + print 'Checking multitest results.' + else: + print 'Checking individual test results.' + print - files_to_check[test_name] = file_pairs[comm.rank::comm.size] + for test_name in files_to_check: + print 'Test {0!s}:'.format(test_name), + num_files = len(files_to_check[test_name]) + if num_files > 0: + print ' Checking {0!s} files'.format() + else: + print ' Not checking.' - print files_to_check + if args.list_tests: + sys.exit(1) From 742c525a806bc5a14bfd551285f6fa78413624ec Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 18 Sep 2015 16:36:29 -0600 Subject: [PATCH 166/250] Bugfix: no input to format --- tests/yellowstone/checkresults.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index 47a398f..0fd73b4 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -449,7 +449,7 @@ def compare_results(comparison_info, comm, cprnc_exec): print 'Test {0!s}:'.format(test_name), num_files = len(files_to_check[test_name]) if num_files > 0: - print ' Checking {0!s} files'.format() + print ' Checking {0!s} files'.format(num_files) else: print ' Not checking.' From f652d41b8c0249a95f1c3819552f43a8b950af7c Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 21 Sep 2015 09:07:09 -0600 Subject: [PATCH 167/250] Making list of dicts for checking information --- tests/yellowstone/checkresults.py | 39 ++++++++++++++++++++----------- 1 file changed, 26 insertions(+), 13 deletions(-) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index 0fd73b4..686a429 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -394,7 +394,8 @@ def compare_results(comparison_info, comm, cprnc_exec): tempdir, runname = os.path.split(tempdir) # Look for the newest log file - logfiles = glob.glob(os.path.join(rundir, '{0!s}*.log'.format(runname))) + logfiles = glob.glob( + os.path.join(rundir, '{0!s}*.log'.format(runname))) if len(logfiles) == 0: continue lastlog = max(logfiles, key=os.path.getctime) @@ -425,14 +426,26 @@ def compare_results(comparison_info, comm, cprnc_exec): tests_to_check[test_name] = (newdir, olddir) # Expand the test directories into (new, old) file pairs - files_to_check = {} + items_to_check = [] for test_name, (newdir, olddir) in tests_to_check.items(): - files_to_check[test_name] = [] - for newfile in glob.iglob(os.path.join(newdir, '*.nc')): + newfiles = set(glob.glob(os.path.join(newdir, '*.nc'))) + oldfiles = set(glob.glob(os.path.join(olddir, '*.nc'))) + for newfile in newfiles: + item_dict = {'test': test_name} + item_dict['new'] = newfile filename = os.path.split(newfile)[1] oldfile = os.path.join(olddir, filename) - if os.path.exists(oldfile): - files_to_check[test_name].append((newfile, oldfile)) + if oldfile in oldfiles: + item_dict['old'] = oldfile + oldfiles.remove(oldfile) + else: + item_dict['old'] = None + items_to_check.append(item_dict) + for oldfile in oldfiles: + item_dict = {'test': test_name} + item_dict['new'] = None + item_dict['old'] = oldfile + items_to_check.append(item_dict) # Get a basic MPI comm comm = BasicComm(serial=args.nodes <= 0) @@ -445,13 +458,13 @@ def compare_results(comparison_info, comm, cprnc_exec): print 'Checking individual test results.' print - for test_name in files_to_check: - print 'Test {0!s}:'.format(test_name), - num_files = len(files_to_check[test_name]) - if num_files > 0: - print ' Checking {0!s} files'.format(num_files) - else: - print ' Not checking.' + for test_name in tests_to_check: + print 'Test {0!s}: '.format(test_name), + num_new = sum(bool(i['new']) for i in items_to_check) + num_old = sum(bool(i['old']) for i in items_to_check) + num_to_check = sum(bool(i['new'] and i['old']) + for i in items_to_check) + print 'Checking {0!s} files'.format(num_to_check, num_new, num_old) if args.list_tests: sys.exit(1) From 03d07ec6ec557de4f206bc9837c56c07a900f70f Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 21 Sep 2015 09:57:29 -0600 Subject: [PATCH 168/250] Printing statistics before running comparison --- tests/yellowstone/checkresults.py | 17 +++++++++++------ 1 file changed, 11 insertions(+), 6 deletions(-) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index 686a429..976f5f8 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -459,12 +459,17 @@ def compare_results(comparison_info, comm, cprnc_exec): print for test_name in tests_to_check: - print 'Test {0!s}: '.format(test_name), - num_new = sum(bool(i['new']) for i in items_to_check) - num_old = sum(bool(i['old']) for i in items_to_check) - num_to_check = sum(bool(i['new'] and i['old']) - for i in items_to_check) - print 'Checking {0!s} files'.format(num_to_check, num_new, num_old) + print 'Test {0!s}:'.format(test_name) + num_new = sum(1 for i in items_to_check + if i['new'] is not None) + num_old = sum(1 for i in items_to_check + if i['old'] is not None) + num_chk = sum(1 for i in items_to_check + if i['old'] is not None and i['new'] is not None) + print ' Checking {0!s} of {1!s}'.format(num_chk, num_new), + print ' new files generated.' + print ' Checking against {0!s} of {1!s}'.format(num_chk, num_old), + print ' old files found.' if args.list_tests: sys.exit(1) From 2625c080879688cbd99fa07c254119cd39afa85a Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 21 Sep 2015 09:57:58 -0600 Subject: [PATCH 169/250] Code comments --- tests/yellowstone/checkresults.py | 1 + 1 file changed, 1 insertion(+) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index 976f5f8..18ccd81 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -471,5 +471,6 @@ def compare_results(comparison_info, comm, cprnc_exec): print ' Checking against {0!s} of {1!s}'.format(num_chk, num_old), print ' old files found.' + # Quit now, if just listing tests to be checked if args.list_tests: sys.exit(1) From a1bc31e1fde07373666f3eec951d66dbf1238cdc Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 21 Sep 2015 11:03:27 -0600 Subject: [PATCH 170/250] Sum only for given test --- tests/yellowstone/checkresults.py | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index 18ccd81..f9ef3df 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -460,12 +460,12 @@ def compare_results(comparison_info, comm, cprnc_exec): for test_name in tests_to_check: print 'Test {0!s}:'.format(test_name) - num_new = sum(1 for i in items_to_check - if i['new'] is not None) - num_old = sum(1 for i in items_to_check - if i['old'] is not None) - num_chk = sum(1 for i in items_to_check - if i['old'] is not None and i['new'] is not None) + num_new = sum(1 for i in items_to_check if i['test'] == test_name and + i['new'] is not None) + num_old = sum(1 for i in items_to_check if i['test'] == test_name and + i['old'] is not None) + num_chk = sum(1 for i in items_to_check if i['test'] == test_name and + i['old'] is not None and i['new'] is not None) print ' Checking {0!s} of {1!s}'.format(num_chk, num_new), print ' new files generated.' print ' Checking against {0!s} of {1!s}'.format(num_chk, num_old), From 6ab603448952867c83ad762f5ded06571a5f4770 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 21 Sep 2015 11:04:18 -0600 Subject: [PATCH 171/250] Format changing (removing extra space) --- tests/yellowstone/checkresults.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index f9ef3df..69d7fd2 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -467,9 +467,9 @@ def compare_results(comparison_info, comm, cprnc_exec): num_chk = sum(1 for i in items_to_check if i['test'] == test_name and i['old'] is not None and i['new'] is not None) print ' Checking {0!s} of {1!s}'.format(num_chk, num_new), - print ' new files generated.' + print 'new files generated.' print ' Checking against {0!s} of {1!s}'.format(num_chk, num_old), - print ' old files found.' + print 'old files found.' # Quit now, if just listing tests to be checked if args.list_tests: From 1f49572895db0b00086110ea4b05a982434b6f7f Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 21 Sep 2015 11:06:07 -0600 Subject: [PATCH 172/250] Single line formatting --- tests/yellowstone/checkresults.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index 69d7fd2..db0ef76 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -467,8 +467,7 @@ def compare_results(comparison_info, comm, cprnc_exec): num_chk = sum(1 for i in items_to_check if i['test'] == test_name and i['old'] is not None and i['new'] is not None) print ' Checking {0!s} of {1!s}'.format(num_chk, num_new), - print 'new files generated.' - print ' Checking against {0!s} of {1!s}'.format(num_chk, num_old), + print 'new files generated against {0!s}'.format(num_old), print 'old files found.' # Quit now, if just listing tests to be checked From 25203255c02630696c16e436b7481de3511105fc Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 21 Sep 2015 13:18:35 -0600 Subject: [PATCH 173/250] Running checks and printing summaries --- tests/yellowstone/checkresults.py | 479 +++++++++++------------------- 1 file changed, 168 insertions(+), 311 deletions(-) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index db0ef76..030e724 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -12,12 +12,13 @@ import glob import string import argparse -import json -from subprocess import Popen, PIPE, STDOUT +from subprocess import Popen, PIPE, STDOUT, call + +# ASAP Toolbox Modules +from asaptools.simplecomm import create_comm # Package Modules from utilities import testtools as tt -from utilities import runtools as rt #============================================================================== # Command-Line Interface Definition @@ -60,304 +61,88 @@ #============================================================================== -# Local MPI options and handling -#============================================================================== -class BasicComm(object): - - def __init__(self, serial=False): - self.serial = serial - self.rank = 0 - self.size = 1 - if not self.serial: - from mpi4py import MPI - self.MPI = MPI - self.rank = MPI.COMM_WORLD.Get_rank() - self.size = MPI.COMM_WORLD.Get_size() - - def sync(self): - if self.serial: - return - else: - self.MPI.COMM_WORLD.Barrier() - - def gather(self, data): - if self.serial: - return data - else: - return self.MPI.COMM_WORLD.gather(data) - - -#============================================================================== -# Parse input and set up comparison information +# CPRNC Class - Compares two NetCDF files #============================================================================== -def get_comparison_info(options, arguments, comm, testing_database): - - # Current working directory - cwd = os.getcwd() - - # Comparison info - Organized by full_test_name - comparison_info = {} - - # Parse each test argument for test directories - possible_test_dirs = [] - if (options.all_tests): - possible_test_dirs = glob.glob( - os.path.join('results', '*', 'ser', '*')) - possible_test_dirs.extend( - glob.glob(os.path.join('results', '*', 'par*', '*'))) - else: - possible_test_dirs = arguments - - # Validate each possible test - for possible_test_dir in possible_test_dirs: - if (comm.rank == 0): - print 'Validating possible test dir:', possible_test_dir - - # Split out the NetCDF format, run type (serial, parallel), and - # test name from the directory name - root, ncformat = os.path.split(possible_test_dir) - root, run_type = os.path.split(root) - root, test_name = os.path.split(root) - if (comm.rank == 0): - print ' Test Name:', test_name - print ' Run Type:', run_type - print ' NetCDF Format:', ncformat - - # Check that the test name is in the database - # Define this as a "Good" test - good_test = (test_name in testing_database) - - # If still "good", check for results/output directory - if (good_test): - if (comm.rank == 0): - print ' Test found in test info' - new_results_dir = os.path.join( - cwd, 'results', test_name, run_type, ncformat, 'output') - good_test = good_test and os.path.isdir(new_results_dir) - if (comm.rank == 0): - print ' New results dir found:', new_results_dir - - # If still "good", check for >0 output/result file - if (good_test): - os.chdir(new_results_dir) - new_results_ls = glob.glob('*.nc') - os.chdir(cwd) - good_test = good_test and (len(new_results_ls) > 0) - if (comm.rank == 0): - print ' ' + str(len(new_results_ls)) + ' files found in directory' - - # If still "good", check for results dir for comparison - if (good_test): - old_results_dir = testing_database[test_name]['results_dir'] - good_test = good_test and os.path.isdir(old_results_dir) - if (comm.rank == 0): - print ' Old results dir found:', old_results_dir - - # If still "good", look for missing files and make sure there are - # some new files to compare against the old - if (good_test): - os.chdir(old_results_dir) - old_results_ls = glob.glob('*.nc') - os.chdir(cwd) - missing_tests = set(new_results_ls) - set(old_results_ls) - if (len(missing_tests) > 0): - if (comm.rank == 0): - print ' Did not find', len(missing_tests), - print 'new test files in old results dir:' - for missing_test in missing_tests: - new_results_ls.remove(missing_test) - if (comm.rank == 0): - print ' ', missing_test - if (comm.rank == 0): - print ' Missing tests have been removed from comparison list' - good_test = good_test and (len(new_results_ls) > 0) - else: - if (comm.rank == 0): - print ' All new test files found in old results dir' - - # If still "good", generate the name of the log file and the directory - # in which comparison (CPRNC) results will be placed - if (good_test): - full_test_name = os.path.join(test_name, run_type, ncformat) - if (comm.rank == 0): - print ' Full test name:', full_test_name - - log_dir = os.path.join(cwd, 'results', full_test_name) - log_filename = os.path.join(log_dir, 'check-' + test_name + '.log') - if (comm.rank == 0): - print ' Log file will be:', log_filename - - cprnc_out_dir = os.path.join(log_dir, 'compare') - if (comm.rank == 0): - print ' CPRNC output directory will be:', cprnc_out_dir - - comparison_info[full_test_name] = {} - comparison_info[full_test_name][ - 'results_filenames'] = new_results_ls - comparison_info[full_test_name][ - 'new_results_dir'] = new_results_dir - comparison_info[full_test_name][ - 'old_results_dir'] = old_results_dir - comparison_info[full_test_name]['cprnc_out_dir'] = cprnc_out_dir - comparison_info[full_test_name]['log_filename'] = log_filename - comparison_info[full_test_name]['log_output'] = [] - - if (comm.rank == 0): - print - - # Print out tests to be checked - if (comm.rank == 0): - if len(comparison_info.keys()) == 0: - print 'No valid tests found.' - sys.exit(0) - else: - print 'Valid tests for checking are:' - total_num_files = 0 - for full_test_name in comparison_info.keys(): - num_files = len( - comparison_info[full_test_name]['results_filenames']) - total_num_files += num_files - print ' ', full_test_name, ' (' + str(num_files) + ' files)' - print 'Total number of file comparisons:', total_num_files - print - - # Exit now, if only listing tests - if (options.list_tests): - sys.exit(0) - - # Add slots for counting failures and total results - for full_test_name in comparison_info.keys(): - comparison_info[full_test_name]['num_failures'] = 0 - comparison_info[full_test_name]['num_checks'] = len( - comparison_info[full_test_name]['results_filenames']) - - return comparison_info - - -#============================================================================== -# Run comparison tests -#============================================================================== -def compare_results(comparison_info, comm, cprnc_exec): - - # Base arguments to running cprnc - cprnc_args = [cprnc_exec, "-m", "", ""] - - # String indicating IDENTITY (valid comparison) - ident_str = "files seem to be IDENTICAL" - - # Before checking files, create CPRNC output directories for each test - for full_test_name in comparison_info.keys(): - cprnc_out_dir = comparison_info[full_test_name]['cprnc_out_dir'] - if (comm.rank == 0): - if (not os.path.isdir(cprnc_out_dir)): - os.makedirs(cprnc_out_dir) - - # Wait for for master rank to create the output directory - comm.sync() - - # Create a flat list of files to check - files_to_check = [] - for full_test_name in comparison_info.keys(): - for file_name in comparison_info[full_test_name]['results_filenames']: - check_dict = {'file_name': file_name, - 'full_test_name': full_test_name} - files_to_check.append(check_dict) - - # Start comparing output files - if (comm.rank == 0): - print 'Checking files:' - print - - # Loop over all files (designated for this processor) - for file_to_check in files_to_check[comm.rank::comm.size]: - - full_test_name = file_to_check['full_test_name'] - file_name = file_to_check['file_name'] - - new_results_dir = comparison_info[ - full_test_name]['new_results_dir'] - old_results_dir = comparison_info[ - full_test_name]['old_results_dir'] - cprnc_out_dir = comparison_info[ - full_test_name]['cprnc_out_dir'] - - # Create the old and new file paths - new_results_path = os.path.join(new_results_dir, file_name) - old_results_path = os.path.join(old_results_dir, file_name) - - # CPRNC output file - cprnc_out_filename = file_name + '.cprnc' - cprnc_out_path = os.path.join(cprnc_out_dir, cprnc_out_filename) - - # If the output file already exists, read it, otherwise write it - cprnc_out = '' - if (os.path.exists(cprnc_out_path)): - cprnc_out_file = open(cprnc_out_path, 'r') - cprnc_out = cprnc_out_file.read() - cprnc_out_file.close() - else: - # Set the arguments to CPRNC, run, and catch output - cprnc_args[2:] = [old_results_path, new_results_path] - cprnc_proc = Popen(cprnc_args, stdout=PIPE, stderr=STDOUT) - cprnc_out = cprnc_proc.communicate()[0] - - # Write the output file - cprnc_out_file = open(cprnc_out_path, 'w') +class CPRNC(object): + """ + Compares two NetCDF files against one another + """ + + def __init__(self, executable='cprnc'): + """ + Initializer + + Parameters: + executable (str): Path to the cprnc executable. If not defined, + it will be assumed that the cprnc executable is in the user's + path. + """ + + # Check that the executable works + if call("type " + executable, shell=True, stdout=PIPE, stderr=PIPE) != 0: + err_msg = "CPRNC executable '{0!s}' does not appear to work".format(executable) + raise ValueError(err_msg) + + # Save the executable location + self._executable = executable + + def compare(self, nc1, nc2, outfile=None, alltimes=True, verbose=False): + """ + Compare two NetCDF files + + Parameters: + nc1 (str): NetCDF file name/path + nc2 (str): NetCDF file name/path + outfile (str): Name of output file to log CPRNC output + alltimes (bool): Whether to compare all times, or not + verbose (bool): Whether to produce verbose output + + Returns: + bool: True if the two files are the same, False otherwise + """ + + # Check valid NetCDF files + if not os.path.isfile(nc1): + err_msg = "File '{0!s}' does not appear to exist".format(nc1) + raise ValueError(err_msg) + if not os.path.isfile(nc2): + err_msg = "File '{0!s}' does not appear to exist".format(nc2) + raise ValueError(err_msg) + + # If the output file is set, check that the + # directory to contain the output file exists + if outfile: + outdir = os.path.split(outfile)[0] + if not os.path.isdir(outdir): + err_msg = "Directory '{0!s}' ".format(outdir) + err_msg += "to contain CPRNC output file doesn't exist" + raise ValueError(err_msg) + + # Arguments for running cprnc + cprnc_args = [self._executable] + if alltimes: + cprnc_args.append('-m') + if verbose: + cprnc_args.append('-v') + cprnc_args.extend([nc1, nc2]) + + # String indicating IDENTITY (valid comparison) + ident_str = "files seem to be IDENTICAL" + + # Start the CPRNC process + cprnc_proc = Popen(cprnc_args, stdout=PIPE, stderr=STDOUT) + + # Wait for the process to finish and capture the output + cprnc_out = cprnc_proc.communicate()[0] + + # Write the output file + if outfile: + cprnc_out_file = open(outfile, 'w') cprnc_out_file.write(cprnc_out) cprnc_out_file.close() - # Add to the list of log file output - log_result = ' GOOD: ' - if (string.rfind(cprnc_out, ident_str) < 0): - comparison_info[full_test_name]['num_failures'] += 1 - log_result = '* BAD: ' - log_str = log_result + file_name + os.linesep - comparison_info[full_test_name]['log_output'].append(log_str) - - print ' ', log_result + file_name - - # Now wait for all files to be processed - comm.sync() - - # Assemble rank info to gather - rank_log_output = {} - rank_num_failures = {} - for full_test_name in comparison_info.keys(): - rank_log_output[full_test_name] = comparison_info[ - full_test_name]['log_output'] - rank_num_failures[full_test_name] = comparison_info[ - full_test_name]['num_failures'] - - # Gather all of the statitics and log files from all processors - all_log_output = comm.gather(rank_log_output) - all_num_failures = comm.gather(rank_num_failures) - - if comm.rank == 0: - - # Open and write all log files - print - print 'Writing log files.' - print - for full_test_name in comparison_info.keys(): - log_file = open( - comparison_info[full_test_name]['log_filename'], 'w') - for r_log_output in all_log_output: - log_strings = r_log_output[full_test_name] - for log_str in log_strings: - log_file.write(log_str) - log_file.close() - - # Print diagnostic info to stdout - print - print 'Number of File Comparison Failures:' - print - for full_test_name in comparison_info.keys(): - num_test_failures = sum([nf[full_test_name] - for nf in all_num_failures]) - print ' ', full_test_name + ':', num_test_failures, - print 'failures (of', - print comparison_info[full_test_name]['num_checks'], - print 'total comparisons)' + # Return whether the comparison is identical + return string.rfind(cprnc_out, ident_str) == 0 #============================================================================== @@ -386,7 +171,7 @@ def compare_results(comparison_info, comm, cprnc_exec): # Find valid tests for comparison tests_to_check = {} for rdir in rundirs: - if not os.path.exists(rdir): + if not os.path.isdir(rdir): continue rundir = os.path.realpath(rdir) tempdir, ncfmt = os.path.split(rundir) @@ -414,20 +199,31 @@ def compare_results(comparison_info, comm, cprnc_exec): for newdir in glob.iglob(os.path.join(rundir, outdir_pattern)): # Get the test name (allowing for multitest results) + # and generate the cprnc output directory if runname in testdb: test_name = runname + cprncdir = os.path.join(rundir, 'compare') else: tempdir, test_name = os.path.split(newdir) + cprncdir = os.path.join(rundir, 'compare', test_name) # Get the output directory to compare against olddir = str(testdb[test_name]['results_dir']) # Put together comparison info - tests_to_check[test_name] = (newdir, olddir) + tests_to_check[test_name] = {} + tests_to_check[test_name]['run'] = rundir + tests_to_check[test_name]['new'] = newdir + tests_to_check[test_name]['old'] = olddir + tests_to_check[test_name]['cpr'] = cprncdir - # Expand the test directories into (new, old) file pairs + # Expand the test directories into individual file-test dictionaries items_to_check = [] - for test_name, (newdir, olddir) in tests_to_check.items(): + unchecked_new_items = [] + unchecked_old_items = [] + for test_name, test_info in tests_to_check.items(): + newdir = test_info['new'] + olddir = test_info['old'] newfiles = set(glob.glob(os.path.join(newdir, '*.nc'))) oldfiles = set(glob.glob(os.path.join(olddir, '*.nc'))) for newfile in newfiles: @@ -438,20 +234,21 @@ def compare_results(comparison_info, comm, cprnc_exec): if oldfile in oldfiles: item_dict['old'] = oldfile oldfiles.remove(oldfile) + items_to_check.append(item_dict) else: item_dict['old'] = None - items_to_check.append(item_dict) + unchecked_new_items.append(item_dict) for oldfile in oldfiles: item_dict = {'test': test_name} item_dict['new'] = None item_dict['old'] = oldfile - items_to_check.append(item_dict) + unchecked_old_items.append(item_dict) # Get a basic MPI comm - comm = BasicComm(serial=args.nodes <= 0) + comm = create_comm(serial=args.nodes <= 0) # Print tests that will be checked - if comm.rank == 0: + if comm.is_manager(): if args.multispec: print 'Checking multitest results.' else: @@ -460,12 +257,11 @@ def compare_results(comparison_info, comm, cprnc_exec): for test_name in tests_to_check: print 'Test {0!s}:'.format(test_name) - num_new = sum(1 for i in items_to_check if i['test'] == test_name and - i['new'] is not None) - num_old = sum(1 for i in items_to_check if i['test'] == test_name and - i['old'] is not None) - num_chk = sum(1 for i in items_to_check if i['test'] == test_name and - i['old'] is not None and i['new'] is not None) + num_chk = sum(1 for i in items_to_check if i['test'] == test_name) + num_new = num_chk + sum(1 for i in unchecked_new_items + if i['test'] == test_name) + num_old = num_chk + sum(1 for i in unchecked_old_items + if i['test'] == test_name) print ' Checking {0!s} of {1!s}'.format(num_chk, num_new), print 'new files generated against {0!s}'.format(num_old), print 'old files found.' @@ -473,3 +269,64 @@ def compare_results(comparison_info, comm, cprnc_exec): # Quit now, if just listing tests to be checked if args.list_tests: sys.exit(1) + + # For each test to be compared, generate the cprnc output directories + if comm.is_manager(): + print + print "Results:" + for test_name, test_info in tests_to_check.items(): + if not os.path.isdir(test_info['cpr']): + os.makedirs(test_info['cpr']) + + # Wait for processes to sync + comm.sync() + + # Create the CPRNC object + cprnc = CPRNC(args.executable) + + # For each file on this partition, do the CPRNC Comparison + local_results = [] + local_items_to_check = comm.partition(items_to_check, involved=True) + for item_dict in local_items_to_check: + + # Name the cprnc output file + cprncdir = tests_to_check[item_dict['test']] + filename = os.path.split(item_dict['new'])[1] + outfile = os.path.join(cprncdir, filename + '.cprnc') + + # Compare the files with CPRNC + rslt = cprnc.compare(item_dict['new'], item_dict['old'], outfile=outfile) + + # Save the result in the result dictionary + rslt_dict = {} + rslt_dict['test'] = item_dict['test'] + rslt_dict['file'] = filename + rslt_dict['result'] = rslt + local_results.append(rslt_dict) + + # Print results to screen + str_rslt = ' GOOD:' if rslt else ' BAD:' + print str_rslt, filename, '({0!s})'.format(rslt_dict['test']) + + # Wait for processes to sync + comm.sync() + + # Send results from workers + if not comm.is_manager(): + comm.collect(local_results) + + # Collect results + if comm.is_manager(): + results = local_results + for i in range(comm.get_size() - 1): + results.extend(comm.collect()) + + for test_name, test_info in tests_to_check.items(): + summfile = os.path.join(test_info['run'], test_name + '.cprnc') + sfile = open(summfile, 'w') + for result in results: + if result['test'] == test_name: + str_rslt = ' GOOD:' if result['result'] else ' BAD:' + summ = str_rslt + ' ' + result['file'] + ' ({0!s})'.format(rslt_dict['test']) + sfile.write(summ + os.linesep) + sfile.close() From 7194d45cfcc1b20acfba39907445e2537f1e23dc Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 21 Sep 2015 13:21:26 -0600 Subject: [PATCH 174/250] Doesn't launch into queue --- tests/yellowstone/checkresults.py | 17 +++++------------ 1 file changed, 5 insertions(+), 12 deletions(-) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index 030e724..ec93b1d 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -42,17 +42,10 @@ action='store_true', dest='multispec', help='True or False, indicating whether to look for ' 'multispec results [Default: False]') -_PARSER_.add_argument('-n', '--nodes', default=0, type=int, - help='The integer number of nodes to request in parallel' - ' runs (0 means run in serial) [Default: 0]') -_PARSER_.add_argument('-q', '--queue', default='economy', type=str, - help='The name of the queue to request in parallel runs ' - '(ignored if running in serial) ' - '[Default: economy]') -_PARSER_.add_argument('-w', '--wtime', default=240, type=int, - help='The number of minutes to request for the wall ' - 'clock in parallel runs (ignored if running in ' - 'serial) [Default: 240]') +_PARSER_.add_argument('-s', '--serial', default=False, + action='store_true', dest='multispec', + help='True or False, indicating whether to run checks ' + 'serial or not [Default: False]') _PARSER_.add_argument('-x', '--executable', type=str, default='/glade/p/work/kpaul/installs/intel/12.1.5/cprnc/bin/cprnc', help='The path to the CPRNC executable.') @@ -245,7 +238,7 @@ def compare(self, nc1, nc2, outfile=None, alltimes=True, verbose=False): unchecked_old_items.append(item_dict) # Get a basic MPI comm - comm = create_comm(serial=args.nodes <= 0) + comm = create_comm(serial=args.serial) # Print tests that will be checked if comm.is_manager(): From 107d2b10cd8a7e1e480cbbd2ccb8145752fcdd43 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 21 Sep 2015 13:26:03 -0600 Subject: [PATCH 175/250] Typo in argument name --- tests/yellowstone/checkresults.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index ec93b1d..f36a366 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -43,7 +43,7 @@ help='True or False, indicating whether to look for ' 'multispec results [Default: False]') _PARSER_.add_argument('-s', '--serial', default=False, - action='store_true', dest='multispec', + action='store_true', dest='serial', help='True or False, indicating whether to run checks ' 'serial or not [Default: False]') _PARSER_.add_argument('-x', '--executable', type=str, From f2d4bbfee33195844c1759084dfe39a159797ef5 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 21 Sep 2015 13:30:40 -0600 Subject: [PATCH 176/250] Bugfix: need to get item from dictionary --- tests/yellowstone/checkresults.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index f36a366..ddbb576 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -283,7 +283,7 @@ def compare(self, nc1, nc2, outfile=None, alltimes=True, verbose=False): for item_dict in local_items_to_check: # Name the cprnc output file - cprncdir = tests_to_check[item_dict['test']] + cprncdir = tests_to_check[item_dict['test']]['cpr'] filename = os.path.split(item_dict['new'])[1] outfile = os.path.join(cprncdir, filename + '.cprnc') From f7d7ee90729f3e9d33f2c0bd2b67f12ec6079ec1 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 21 Sep 2015 13:35:57 -0600 Subject: [PATCH 177/250] Correcting the "identical" comparison check --- tests/yellowstone/checkresults.py | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index ddbb576..77bc9c7 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -119,9 +119,6 @@ def compare(self, nc1, nc2, outfile=None, alltimes=True, verbose=False): cprnc_args.append('-v') cprnc_args.extend([nc1, nc2]) - # String indicating IDENTITY (valid comparison) - ident_str = "files seem to be IDENTICAL" - # Start the CPRNC process cprnc_proc = Popen(cprnc_args, stdout=PIPE, stderr=STDOUT) @@ -135,7 +132,7 @@ def compare(self, nc1, nc2, outfile=None, alltimes=True, verbose=False): cprnc_out_file.close() # Return whether the comparison is identical - return string.rfind(cprnc_out, ident_str) == 0 + return cprnc_out.rfind("the two files seem to be IDENTICAL") >= 0 #============================================================================== From 7808a1a1f620a1eb63c03b396b5bb028ac851968 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 21 Sep 2015 13:37:58 -0600 Subject: [PATCH 178/250] Removing unnecessary import --- tests/yellowstone/checkresults.py | 1 - 1 file changed, 1 deletion(-) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index 77bc9c7..ae921df 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -10,7 +10,6 @@ import re import sys import glob -import string import argparse from subprocess import Popen, PIPE, STDOUT, call From 367caf776e10e03708ad243a0cd0e915507d28b1 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 21 Sep 2015 14:54:28 -0600 Subject: [PATCH 179/250] Sync and finished output message --- tests/yellowstone/checkresults.py | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index ae921df..e2c97f2 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -319,3 +319,10 @@ def compare(self, nc1, nc2, outfile=None, alltimes=True, verbose=False): summ = str_rslt + ' ' + result['file'] + ' ({0!s})'.format(rslt_dict['test']) sfile.write(summ + os.linesep) sfile.close() + + # Wait for processes to sync + comm.sync() + + # Finished + if comm.is_manager(): + print "Done." From e34cb6aa87d5e18ab8860610e57133e436c200d4 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 21 Sep 2015 14:54:46 -0600 Subject: [PATCH 180/250] Extra line in output --- tests/yellowstone/checkresults.py | 1 + 1 file changed, 1 insertion(+) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index e2c97f2..f5d182e 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -325,4 +325,5 @@ def compare(self, nc1, nc2, outfile=None, alltimes=True, verbose=False): # Finished if comm.is_manager(): + print print "Done." From ede5862fd7a3f40b1479e5acc5714dad92767121 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 21 Sep 2015 14:56:11 -0600 Subject: [PATCH 181/250] Adding LSF submission script for results checking. --- tests/yellowstone/checkresults.lsf | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 tests/yellowstone/checkresults.lsf diff --git a/tests/yellowstone/checkresults.lsf b/tests/yellowstone/checkresults.lsf new file mode 100644 index 0000000..ab59fc8 --- /dev/null +++ b/tests/yellowstone/checkresults.lsf @@ -0,0 +1,14 @@ +#!/bin/bash +# +# LSF batch script to run an MPI application +# +#BSUB -P STDD0002 # project code +#BSUB -W 02:00 # wall-clock time (hrs:mins) +#BSUB -n 64 # number of tasks in job +#BSUB -R "span[ptile=16]" # run 16 MPI tasks per node +#BSUB -J checkresults # job name +#BSUB -o checkresults.%J.out # output file name in which %J is replaced by the job ID +#BSUB -q small # queue + +#run the executable +mpirun.lsf ./checkresults.py From aece38e8927ab4e54418c6ff9bfcc533be579195 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 21 Sep 2015 15:15:53 -0600 Subject: [PATCH 182/250] Changing to use bigmem queue --- tests/yellowstone/checkresults.lsf | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/tests/yellowstone/checkresults.lsf b/tests/yellowstone/checkresults.lsf index ab59fc8..77f3e77 100644 --- a/tests/yellowstone/checkresults.lsf +++ b/tests/yellowstone/checkresults.lsf @@ -4,11 +4,12 @@ # #BSUB -P STDD0002 # project code #BSUB -W 02:00 # wall-clock time (hrs:mins) -#BSUB -n 64 # number of tasks in job -#BSUB -R "span[ptile=16]" # run 16 MPI tasks per node +#BSUB -n 80 # number of tasks in job +#BSUB -x # exclusive nodes +#BSUB -R "span[ptile=40]" # run 16 MPI tasks per node #BSUB -J checkresults # job name #BSUB -o checkresults.%J.out # output file name in which %J is replaced by the job ID -#BSUB -q small # queue +#BSUB -q bigmem # queue #run the executable mpirun.lsf ./checkresults.py From b826273f0f2693b13971f13b21de817e32da3249 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 21 Sep 2015 15:49:45 -0600 Subject: [PATCH 183/250] Updating the timing generation script --- tests/yellowstone/mktimings.py | 246 +++++++++++---------------------- 1 file changed, 77 insertions(+), 169 deletions(-) diff --git a/tests/yellowstone/mktimings.py b/tests/yellowstone/mktimings.py index 5a1d39d..eaf7a8d 100755 --- a/tests/yellowstone/mktimings.py +++ b/tests/yellowstone/mktimings.py @@ -11,51 +11,28 @@ import os import glob import datetime -import optparse +import argparse import json +# Package Modules +from utilities import testtools as tt #============================================================================== # Command-Line Interface Definition #============================================================================== -def parse_cli(): - usage = 'usage: %prog [options]' - parser = optparse.OptionParser(usage=usage) - parser.add_option('-i', '--testing_database', default=None, - help='Location of the testinfo.json file ' - '[Default: None]') - parser.add_option('-o', '--timings_database', default=None, - help='Location of the timings.json file ' - '[Default: None]') - # Parse the CLI options and return - return parser.parse_args()[0] +_DESC_ = """This program is designed to gather statistics for tests and + test input defined in the testing database file.""" - -#============================================================================== -# get_testing_database -#============================================================================== -def get_testing_database(options): - - # Get the testinfo.json data - testing_database_filename = '' - if (options.testing_database == None): - runtest_dir = os.path.dirname(__file__) - testing_database_filename = os.path.join(runtest_dir, 'testinfo.json') - else: - testing_database_filename = os.path.abspath(options.testing_database) - - # Try opening and reading the testinfo file - testing_database = {} - try: - testing_database_file = open(testing_database_filename, 'r') - testing_database = dict(json.load(testing_database_file)) - testing_database_file.close() - except: - err_msg = 'Problem reading and parsing test info file: ' \ - + str(testing_database_filename) - raise ValueError(err_msg) - - return testing_database +_PARSER_ = argparse.ArgumentParser(description=_DESC_) +_PARSER_.add_argument('-i', '--infofile', default='testinfo.json', type=str, + help='Location of the testinfo.json database file ' + '[Default: testinfo.json]') +_PARSER_.add_argument('-s', '--statsfile', default='teststats.json', type=str, + help='Location of the teststats.json database file ' + '[Default: teststats.json]') +_PARSER_.add_argument('-t', '--timefile', default='timings.json', type=str, + help='Location of the timings.json database file ' + '[Default: timings.json]') #============================================================================== @@ -71,68 +48,69 @@ def find_shortest_str(strng, left, right=os.linesep, loc=0): #============================================================================== -# Extract timing info and put in JSON file +# Command-line Operation #============================================================================== -def make_timings_file(options, testing_database): +if __name__ == '__main__': + args = _PARSER_.parse_args() - # Get the timings.json data - timings_database_filename = '' - if (options.timings_database == None): - runtest_dir = os.path.dirname(__file__) - timings_database_filename = os.path.join(runtest_dir, 'timings.json') - else: - timings_database_filename = os.path.abspath(options.timings_database) + # Create/read the testing info and stats files + testdb = tt.TestDB(dbname=args.infofile, stname=args.statsfile).get_database() + + # Get the timings.json data file + timefn = os.path.abspath(args.timefile) # Open JSON file - json_data = {} - if (os.path.isfile(timings_database_filename)): - json_file = open(timings_database_filename) - json_data = dict(json.load(json_file)) + timedb = {} + if (os.path.isfile(timefn)): + json_file = open(timefn) + timedb = dict(json.load(json_file)) json_file.close() # Current working directory cwd = os.getcwd() - # Parse each test argument for test directories - test_names = glob.glob(os.path.join('*', 'ser', '*')) - test_names.extend(glob.glob(os.path.join('*', 'par*', '*'))) - # Extract each possible test - for full_test_name in test_names: + for rundir in glob.iglob(os.path.join('results.d', '*', '[ser,par]*', '*')): print - print 'Extracting times from test dir:', full_test_name - root, run_type = os.path.split(full_test_name) + print 'Extracting times from test dir:', rundir + root, ncfmt = os.path.split(rundir) + root, run_type = os.path.split(root) root, test_name = os.path.split(root) - root, ncfmt = os.path.split(root) print ' Test Name:', test_name print ' Run Type:', run_type print ' NetCDF Format:', ncfmt - common_name = testing_database[test_name]['common_name'] + # Skip if not an individual test + if test_name not in testdb: + print ' Test name not found in database. Skipping.' + continue + + # Prepare the timing database information + common_name = testdb[test_name]['common_name'] print ' Common Name:', common_name method_name = 'pyreshaper4c' - if (ncfmt == 'netcdf'): + if ncfmt == 'netcdf': method_name = 'pyreshaper' - elif (ncfmt == 'netcdf4'): + elif ncfmt == 'netcdf4': method_name = 'pyreshaper4' - # Check for this test in the JSON data - if (common_name not in json_data): - json_data[common_name] = {'results': {}} + # Check for this test in the timing database + if common_name not in timedb: + timedb[common_name] = {'results': {}} # Check for method in results - if (method_name not in json_data[common_name]['results']): - json_data[common_name]['results'][method_name] = {} + if method_name not in timedb[common_name]['results']: + timedb[common_name]['results'][method_name] = {} - # Get the number of cores from the run type + # Get the number of cores and nodes from the run type num_cores = 1 - if (run_type[0:3] == 'par'): - num_cores = int(run_type[3:]) + num_nodes = 0 + if run_type[0:3] == 'par': + num_nodes, nppn = map(int, run_type[3:].split('x')) + num_cores = num_nodes * nppn # Look for log files - test_dir = os.path.join(cwd, test_name, run_type) - glob_name = ''.join(['reshaper-', test_name, '.*.log']) - glob_path = os.path.join(test_dir, glob_name) + glob_path = os.path.join(rundir, '{0!s}*.log'.format(test_name)) glob_names = glob.glob(glob_path) # Continue if nothing to do here @@ -144,8 +122,8 @@ def make_timings_file(options, testing_database): for log_name in glob_names: # Get the JOBID from the log filename - job_id = log_name.rsplit('.', 2)[1] - print ' Processing Job ID:', job_id + lognm = os.path.split(log_name)[1] + print ' Processing log:', lognm # Open the log file and read the contents log_file = open(log_name) @@ -183,120 +161,50 @@ def make_timings_file(options, testing_database): requested_str, nloc = find_shortest_str( log_str, 'Requested Data: ', loc=loc) - # Find the job hosts string - host_str, loc = find_shortest_str( - log_str, 'Job was executed on host(s) ', loc=loc) - if (loc == 0): - print ' Could not find host string. Skipping.' - continue - queue_str, sloc = find_shortest_str( - host_str, 'in queue <', right='>', loc=0) - if (sloc == 0): - print ' Could not find queue string. Skipping.' - continue - print ' Queue:', queue_str - user_str, sloc = find_shortest_str( - host_str, 'as user <', right='>', loc=sloc) - if (sloc == 0): - print ' Could not find user string. Skipping.' - continue - print ' User:', user_str - sys_str, sloc = find_shortest_str( - host_str, 'in cluster <', right='>', loc=sloc) - if (sloc == 0): - print ' Could not find system string. Skipping.' - continue - print ' System:', sys_str - - # Get the starting timestamp - start_str, loc = find_shortest_str( - log_str, 'Started at ', loc=loc) - if (loc == 0): - print ' Could not find start timestamp. Skipping.' - continue - start = datetime.datetime.strptime(start_str, '%c') - print ' Starting Timestamp:', start - - # Get the ending timestamp - end_str, loc = find_shortest_str( - log_str, 'Results reported at ', loc=loc) - if (loc == 0): - print ' Could not find end timestamp. Skipping.' - continue - end = datetime.datetime.strptime(end_str, '%c') - print ' Ending Timestamp:', end - - # Compute the job number from the end timestamp - job_num = end.strftime('%y%m%d-%H%M%S') + # Compute the job number from the log file timestamp + timestamp = os.path.getmtime(log_name) + dt = datetime.datetime.fromtimestamp(timestamp) + job_num = dt.strftime('%y%m%d-%H%M%S') # Compute the elapsed time - elapsed = (end - start).total_seconds() - print ' Elapsed time (REAL): ', elapsed, 'sec' + elapsed = float(tot_timing_str) # Display the internal timing info for comparison - print ' Elapsed time (INTERNAL):', float(tot_timing_str), 'sec' - - # Find the BSUB submission properties - nprocs_str, loc = find_shortest_str( - log_str, '#BSUB -n ', loc=loc) - if (loc == 0): - print ' Could not find num procs string. Skipping.' - continue - print ' BSUB Cores:', nprocs_str - tiling_str, loc = find_shortest_str( - log_str, '#BSUB -R "span[ptile=', right=']', loc=loc) - if (loc == 0): - print ' Could not find num procs string. Skipping.' - continue - print ' BSUB Tiling:', tiling_str - num_nodes = int(nprocs_str) / int(tiling_str) + print ' Elapsed time (INTERNAL):', elapsed, 'sec' # Write the JSON data - if (job_num not in json_data[common_name]['results'][method_name]): - json_data[common_name]['results'][method_name][job_num] = {} + if (job_num not in timedb[common_name]['results'][method_name]): + timedb[common_name]['results'][method_name][job_num] = {} - json_data[common_name]['results'][ - method_name][job_num]['sys'] = sys_str - json_data[common_name]['results'][ + timedb[common_name]['results'][ + method_name][job_num]['sys'] = "yellowstone" + timedb[common_name]['results'][ method_name][job_num]['cores'] = num_cores - json_data[common_name]['results'][ + timedb[common_name]['results'][ method_name][job_num]['nodes'] = num_nodes - json_data[common_name]['results'][ + timedb[common_name]['results'][ method_name][job_num]['real'] = elapsed - json_data[common_name]['results'][ + timedb[common_name]['results'][ method_name][job_num]['metadata'] = True - json_data[common_name]['results'][ + timedb[common_name]['results'][ method_name][job_num]['once'] = used_once_file - json_data[common_name]['results'][ + timedb[common_name]['results'][ method_name][job_num]['actual'] = float(actual_str) - json_data[common_name]['results'][ + timedb[common_name]['results'][ method_name][job_num]['request'] = float(requested_str) - json_data[common_name]['results'][ + timedb[common_name]['results'][ method_name][job_num]['openi'] = float(openi_str) - json_data[common_name]['results'][ + timedb[common_name]['results'][ method_name][job_num]['openo'] = float(openo_str) - json_data[common_name]['results'][ + timedb[common_name]['results'][ method_name][job_num]['metaTI'] = float(metaTI_str) - json_data[common_name]['results'][ + timedb[common_name]['results'][ method_name][job_num]['metaTV'] = float(metaTV_str) - json_data[common_name]['results'][ + timedb[common_name]['results'][ method_name][job_num]['TS'] = float(TS_str) # Write the JSON data file - json_file = open(timings_database_filename, 'w') - json_file.write(json.dumps(json_data, sort_keys=True, + json_file = open(timefn, 'w') + json_file.write(json.dumps(timedb, sort_keys=True, indent=4, separators=(',', ': '))) json_file.close() - - -#============================================================================== -# Main Program -#============================================================================== -def main(options): - testing_database = get_testing_database(options) - make_timings_file(options, testing_database) - - -if __name__ == '__main__': - options = parse_cli() - main(options) From 048ea5e0210cb2ae6a93f1ce4b68014e5c67be3e Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 21 Sep 2015 15:55:35 -0600 Subject: [PATCH 184/250] Not overwriting old data (just skipping). --- tests/yellowstone/mktimings.py | 57 ++++++++++++++++++---------------- 1 file changed, 30 insertions(+), 27 deletions(-) diff --git a/tests/yellowstone/mktimings.py b/tests/yellowstone/mktimings.py index eaf7a8d..d8bf0be 100755 --- a/tests/yellowstone/mktimings.py +++ b/tests/yellowstone/mktimings.py @@ -173,35 +173,38 @@ def find_shortest_str(strng, left, right=os.linesep, loc=0): print ' Elapsed time (INTERNAL):', elapsed, 'sec' # Write the JSON data - if (job_num not in timedb[common_name]['results'][method_name]): + if job_num in timedb[common_name]['results'][method_name]: + print ' Job already exists in database. Skipping.' + else: + print ' Adding new job to timings database.' timedb[common_name]['results'][method_name][job_num] = {} - timedb[common_name]['results'][ - method_name][job_num]['sys'] = "yellowstone" - timedb[common_name]['results'][ - method_name][job_num]['cores'] = num_cores - timedb[common_name]['results'][ - method_name][job_num]['nodes'] = num_nodes - timedb[common_name]['results'][ - method_name][job_num]['real'] = elapsed - timedb[common_name]['results'][ - method_name][job_num]['metadata'] = True - timedb[common_name]['results'][ - method_name][job_num]['once'] = used_once_file - timedb[common_name]['results'][ - method_name][job_num]['actual'] = float(actual_str) - timedb[common_name]['results'][ - method_name][job_num]['request'] = float(requested_str) - timedb[common_name]['results'][ - method_name][job_num]['openi'] = float(openi_str) - timedb[common_name]['results'][ - method_name][job_num]['openo'] = float(openo_str) - timedb[common_name]['results'][ - method_name][job_num]['metaTI'] = float(metaTI_str) - timedb[common_name]['results'][ - method_name][job_num]['metaTV'] = float(metaTV_str) - timedb[common_name]['results'][ - method_name][job_num]['TS'] = float(TS_str) + timedb[common_name]['results'][ + method_name][job_num]['sys'] = "yellowstone" + timedb[common_name]['results'][ + method_name][job_num]['cores'] = num_cores + timedb[common_name]['results'][ + method_name][job_num]['nodes'] = num_nodes + timedb[common_name]['results'][ + method_name][job_num]['real'] = elapsed + timedb[common_name]['results'][ + method_name][job_num]['metadata'] = True + timedb[common_name]['results'][ + method_name][job_num]['once'] = used_once_file + timedb[common_name]['results'][ + method_name][job_num]['actual'] = float(actual_str) + timedb[common_name]['results'][ + method_name][job_num]['request'] = float(requested_str) + timedb[common_name]['results'][ + method_name][job_num]['openi'] = float(openi_str) + timedb[common_name]['results'][ + method_name][job_num]['openo'] = float(openo_str) + timedb[common_name]['results'][ + method_name][job_num]['metaTI'] = float(metaTI_str) + timedb[common_name]['results'][ + method_name][job_num]['metaTV'] = float(metaTV_str) + timedb[common_name]['results'][ + method_name][job_num]['TS'] = float(TS_str) # Write the JSON data file json_file = open(timefn, 'w') From 60cbfaa1225d210d0db7dc143af134dd467d738a Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 21 Sep 2015 15:56:49 -0600 Subject: [PATCH 185/250] Adding new timings to database. --- tests/yellowstone/timings.json | 8594 ++++++++++++++++---------------- 1 file changed, 4372 insertions(+), 4222 deletions(-) diff --git a/tests/yellowstone/timings.json b/tests/yellowstone/timings.json index a9a9128..8905d0b 100644 --- a/tests/yellowstone/timings.json +++ b/tests/yellowstone/timings.json @@ -1,4234 +1,4384 @@ { - "CAMFV-1.0":{ - "baseline":"/glade/u/tdd/asap/bakeoff/tseries/camfv-1.0", - "endYear":"1859", - "input":"/glade/u/tdd/asap/bakeoff/hist/camfv-1.0", - "isize":28447.744, - "n2dVars":82, - "n3dVars":40, - "nVars":122, - "osize":28525.4, - "results":{ - "cdo":{ - "??????-??????":{ - "cores":1, - "correct":"pass", - "metadata":true, - "nodes":1, - "real":1940.0, - "sys":"caldera" + "CAMFV-1.0": { + "baseline": "/glade/u/tdd/asap/bakeoff/tseries/camfv-1.0", + "endYear": "1859", + "input": "/glade/u/tdd/asap/bakeoff/hist/camfv-1.0", + "isize": 28447.744, + "n2dVars": 82, + "n3dVars": 40, + "nVars": 122, + "osize": 28525.4, + "results": { + "cdo": { + "??????-??????": { + "cores": 1, + "correct": "pass", + "metadata": true, + "nodes": 1, + "real": 1940.0, + "sys": "caldera" + } + }, + "ncl": { + "140226-105745": { + "cores": 1, + "correct": "fail", + "kernel": 120.93, + "metadata": false, + "nodes": 1, + "real": 1767.76, + "sys": "geyser", + "user": 153.4 + } + }, + "nco": { + "??????-??????": { + "cores": 1, + "correct": "pass", + "metadata": true, + "nodes": 1, + "real": 1768.0, + "sys": "geyser" + } + }, + "ncr": { + "140226-173803": { + "cores": 4, + "correct": "fail", + "metadata": true, + "nodes": 1, + "real": 3353.0, + "sys": "caldera" + }, + "140303-175041": { + "cores": 4, + "correct": "pass", + "metadata": true, + "nodes": 1, + "real": 3251.0, + "sys": "caldera" + }, + "140312-182909": { + "TS": 732.7, + "cores": 16, + "correct": "pass", + "metaTI": 1.27, + "metaTV": 164.81, + "metadata": true, + "nodes": 4, + "real": 936.0, + "sys": "caldera" + } + }, + "pagoda": { + "??????-??????": { + "cores": 4, + "correct": "pass", + "metadata": true, + "nodes": 1, + "real": 1236.0, + "sys": "caldera" + } + }, + "pynio": { + "140305-193740": { + "cores": 1, + "correct": "fail", + "kernel": 32.6, + "metadata": false, + "nodes": 1, + "real": 1523.02, + "sys": "geyser", + "user": 112.72 + }, + "140307-113151": { + "TS": 1463.81, + "actual": 84000.0, + "cores": 1, + "correct": false, + "kernel": 31.82, + "metaTI": 6.29, + "metaTV": 50.86, + "metadata": false, + "nodes": 1, + "openi": 6.65, + "openo": 0.78, + "real": 1542.99, + "request": 28447.83, + "sys": "geyser", + "user": 114.6 + }, + "140307-120707": { + "TS": 1824.31, + "actual": 77760.0, + "cores": 1, + "correct": false, + "kernel": 46.61, + "metaTI": 7.74, + "metaTV": 82.0, + "metadata": true, + "nodes": 1, + "openi": 6.19, + "openo": 0.44, + "real": 1933.83, + "request": 28447.83, + "sys": "geyser", + "user": 141.55 + } + }, + "pynio4_0": { + "140317-232104": { + "TS": 1900.95, + "actual": 956160.0, + "cores": 1, + "correct": false, + "kernel": 64.18, + "metaTI": 2.7, + "metaTV": 161.9, + "metadata": true, + "nodes": 1, + "openi": 6.46, + "openo": 0.26, + "real": 2077.05, + "request": 28447.83, + "sys": "geyser", + "user": 498.48 + } + }, + "pynio4_1": { + "140318-114642": { + "TS": 2706.45, + "actual": 956160.0, + "cores": 1, + "correct": false, + "kernel": 62.85, + "metaTI": 3.59, + "metaTV": 291.47, + "metadata": true, + "nodes": 1, + "openi": 7.08, + "openo": 0.91, + "real": 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2.29843902588, + "metaTV": 142.575973034, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 165.554438829, + "openo": 0.451182126999, + "real": 484.280472994, + "request": 187507.280182, + "sys": "yellowstone" + } } - } - }, - "startYear":"0001" - } + }, + "startYear": "0001" + } } \ No newline at end of file From bf88aeea6b127d4288d5b8fe2c85b1c080cae303 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 21 Sep 2015 16:10:28 -0600 Subject: [PATCH 186/250] Cleanup plottools --- tests/yellowstone/utilities/plottools.py | 24 +++++------------------- 1 file changed, 5 insertions(+), 19 deletions(-) diff --git a/tests/yellowstone/utilities/plottools.py b/tests/yellowstone/utilities/plottools.py index 6c1f7b3..139ee9f 100755 --- a/tests/yellowstone/utilities/plottools.py +++ b/tests/yellowstone/utilities/plottools.py @@ -80,7 +80,6 @@ def read_json_data(file_name='../timings.json'): #============================================================================== # Return the list of datasets in the dictionary #============================================================================== - def list_datasets(input_dict): return input_dict.keys() @@ -88,7 +87,6 @@ def list_datasets(input_dict): #============================================================================== # Return the dictionary of methods found for each given dataset #============================================================================== - def list_methods(input_dict, datasets=None): if not datasets: datasets = list_datasets(input_dict) @@ -107,7 +105,6 @@ def list_methods(input_dict, datasets=None): #============================================================================== # Get the 'results' section (as a dictionary) for given dataset(s) #============================================================================== - def get_results(input_dict, datasets=None): if not datasets: datasets = list_datasets(input_dict) @@ -126,7 +123,6 @@ def get_results(input_dict, datasets=None): #============================================================================== # Get everything but the 'results' section (as a dictionary) for given dataset(s) #============================================================================== - def get_nonresults(input_dict, datasets=None): if not datasets: datasets = list_datasets(input_dict) @@ -148,7 +144,6 @@ def get_nonresults(input_dict, datasets=None): # Return the subset of the input dictionary that contains only the listed # datasets. #============================================================================== - def subselect_datasets(input_dict, datasets): if (type(datasets) is not list): raise TypeError('List of datasets must be of list type.') @@ -171,7 +166,6 @@ def subselect_datasets(input_dict, datasets): # When True, the exclusive option will include a dataset only if it contains # ALL of the listed methods. #============================================================================== - def subselect_methods(input_dict, methods, exclusive=False): if (type(methods) is not list): raise TypeError('List of methods must be of list type.') @@ -216,7 +210,6 @@ def subselect_methods(input_dict, methods, exclusive=False): # EITHER (False) before or after conditions must be met for the # job to be kept. #============================================================================== - def subselect_jobs_by_time(input_dict, before=__MAXTIME__, after=__MINTIME__, exclusive=True): subset_dict = {} for dataset in input_dict: @@ -268,7 +261,6 @@ def subselect_jobs_by_time(input_dict, before=__MAXTIME__, after=__MINTIME__, ex # If ANY of the dictionaries' criteria return a valid result, # then the job is considered valid. #============================================================================== - def subselect_jobs_by_data(input_dict, criteria_list): if type(criteria_list) is not list: raise TypeError('Data criteria list must be of type list.') @@ -288,7 +280,7 @@ def subselect_jobs_by_data(input_dict, criteria_list): for ic in range(len(criteria_list)): for ckey, cval in criteria_list[ic].items(): if ckey in job_data: - if cval != None: + if cval is not None: if type(cval) is list: if job_data[ckey] not in cval: good_jobs[ic] = False @@ -313,7 +305,6 @@ def subselect_jobs_by_data(input_dict, criteria_list): #============================================================================== # Create a union of 2 nested dictionaries #============================================================================== - def union(dict1, dict2): if type(dict1) is dict and type(dict2) is dict: udict = dict1.copy() @@ -330,14 +321,13 @@ def union(dict1, dict2): #============================================================================== # Create the intersection of 2 nested dictionaries #============================================================================== - def intersect(dict1, dict2): if type(dict1) is dict and type(dict2) is dict: udict = {} for key in dict2: if key in dict1: kintersection = intersect(dict1[key], dict2[key]) - if kintersection != None: + if kintersection is not None: udict[key] = kintersection return udict else: @@ -350,7 +340,6 @@ def intersect(dict1, dict2): #============================================================================== # Gather duration data from a data dictionary and return a plot dictionary #============================================================================== - def get_duration_pdata(data_dict): plot_dict = {} for dataset in data_dict: @@ -367,7 +356,6 @@ def get_duration_pdata(data_dict): #============================================================================== # Gather throughput data from a data dictionary and return a plot dictionary #============================================================================== - def get_throughput_pdata(data_dict): plot_dict = {} for dataset in data_dict: @@ -385,7 +373,6 @@ def get_throughput_pdata(data_dict): #============================================================================== # Compute the reduction of data for multiple jobs in a plot dicitonary #============================================================================== - def reduce_pdata(plot_dict, func=numpy.average): for dataset in plot_dict: for method in plot_dict[dataset]: @@ -397,7 +384,6 @@ def reduce_pdata(plot_dict, func=numpy.average): #============================================================================== # Make a bar plot from a REDUCED plot dictionary #============================================================================== - def make_bar_plot(pdata, filename, dataset_order, method_order, method_colors, dataset_labels, method_labels, @@ -477,12 +463,12 @@ def make_bar_plot(pdata, filename, if dataset in dataset_names: xlabels.append(dataset_labels[str(dataset)]) - if title != None: + if title is not None: plt.title(title, fontsize=titlefontsize, ha='center', va='bottom') - if ylabel != None: + if ylabel is not None: plt.ylabel(ylabel, fontsize=labelfontsize, ha='center', va='bottom') plt.yticks(fontsize=tickfontsize) - if xlabel != None: + if xlabel is not None: plt.xlabel(xlabel, fontsize=labelfontsize, ha='center', va='top') plt.xticks(xbase, xlabels, rotation=labelrotation, ha='right', fontsize=tickfontsize) From 210201a72114e56f32bc1e03c61de6201c929e7c Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 21 Sep 2015 16:13:37 -0600 Subject: [PATCH 187/250] Cleanup mkplots --- tests/yellowstone/mkplots.py | 139 +++++++++++++++++------------------ 1 file changed, 69 insertions(+), 70 deletions(-) diff --git a/tests/yellowstone/mkplots.py b/tests/yellowstone/mkplots.py index 7eb5b41..5a5d2d8 100755 --- a/tests/yellowstone/mkplots.py +++ b/tests/yellowstone/mkplots.py @@ -20,36 +20,31 @@ # #============================================================================== -import optparse +import argparse from utilities import plottools as pt #============================================================================== # Command-Line Interface Definition #============================================================================== -usage = 'usage: %prog [options] [dataset] [dataset] ...' -parser = optparse.OptionParser(usage=usage) -parser.add_option('-f', '--data_file', action='store', type='str', - dest='data_file', default='../timings.json', - help='Path to the timings.json file ' - '[Default: "../timings.json"]') -parser.add_option('-m', '--method', action='append', type='str', - dest='methods', default=[], - help='Include a methods to plot, by name. If no methods ' - 'are listed, then assume all methods in the data') -parser.add_option('-x', '--exclusive', action='store_true', - dest='exclusive', default=False, - help='Option indicating that datasets that do not include ' - 'all of the desired methods should not be plotted') - - -# Parse the CLI options and assemble the Reshaper inputs -(options, arguments) = parser.parse_args() - -# Read the data file -jsondata = pt.read_json_data(options.data_file) -if jsondata == None: - raise ValueError('Could not find timings JSON data file.') +_DESC_ = 'Create throughput and duration plots of timing data' +_PARSER_ = argparse.ArgumentParser(description=_DESC_) +_PARSER_.add_argument('-t', '--timefile', type=str, + default='timings.json', + help='Path to the timings.json file ' + '[Default: "timings.json"]') +_PARSER_.add_argument('-m', '--method', action='append', type=str, + dest='methods', default=[], + help='Include a method to plot, by name. If no methods ' + 'are listed, then include all methods found') +_PARSER_.add_argument('-x', '--exclusive', action='store_true', + dest='exclusive', default=False, + help='Option indicating that datasets that do not ' + 'include all of the desired methods should not ' + 'be plotted [Default: False]') +_PARSER_.add_argument('dataset', nargs='*', default=[], + help='Dataset to be plotted. If none are listed, ' + 'assume all datasets found will be plotted.') #============================================================================== # Some common data for plotting @@ -97,52 +92,56 @@ 'pyniompi', 'pyniompi4_0', 'pyniompi4_1', 'pyreshaper', 'pyreshaper4', 'pyreshaper4c'] -#============================================================================== -# Pull out only the data we need -#============================================================================== - -# Initialize the data to the entire file contents -data = jsondata - -# If datasets are listed, extract only them -if (len(arguments) > 0): - datasets_to_plot = [] - for arg in arguments: - if arg in dataset_order: - datasets_to_plot.append(arg) - data = pt.subselect_datasets(data, datasets=datasets_to_plot) - -# If methods are listed, extract only them -if (len(options.methods) > 0): - methods_to_plot = [] - for method in options.methods: - if method in method_order: - methods_to_plot.append(arg) - data = pt.subselect_methods(data, methods=methods_to_plot, - exclusive=options.exclusive) - -#============================================================================== -# THROUGHPUT PLOTS -#============================================================================== - -tdata = pt.get_throughput_pdata(data) -pt.make_bar_plot(tdata, 'throughput.pdf', - title='Throughput', ylabel='Throughput [MB/sec]', - dataset_order=dataset_order, - method_order=method_order, - method_colors=method_colors, - dataset_labels=dataset_labels, - method_labels=method_labels) #============================================================================== -# DURATION PLOTS +# Command-line Operation #============================================================================== - -ddata = pt.get_duration_pdata(data) -pt.make_bar_plot(ddata, 'duration.pdf', - title='Duration', ylabel='Duration [min]', - dataset_order=dataset_order, - method_order=method_order, - method_colors=method_colors, - dataset_labels=dataset_labels, - method_labels=method_labels) +if __name__ == '__main__': + args = _PARSER_.parse_args() + + # Read the data file + jsondata = pt.read_json_data(args.timefile) + if jsondata is None: + raise ValueError('Could not find timings JSON data file.') + + # Initialize the data to the entire file contents + data = jsondata + + # If datasets are listed, extract only them + datasets = args.dataset + if (len(datasets) > 0): + datasets_to_plot = [] + for dataset in datasets: + if dataset in dataset_order: + datasets_to_plot.append(dataset) + data = pt.subselect_datasets(data, datasets=datasets_to_plot) + + # If methods are listed, extract only them + methods = args.methods + if (len(methods) > 0): + methods_to_plot = [] + for method in methods: + if method in method_order: + methods_to_plot.append(method) + data = pt.subselect_methods(data, methods=methods_to_plot, + exclusive=args.exclusive) + + # THROUGHPUT PLOTS + tdata = pt.get_throughput_pdata(data) + pt.make_bar_plot(tdata, 'throughput.pdf', + title='Throughput', ylabel='Throughput [MB/sec]', + dataset_order=dataset_order, + method_order=method_order, + method_colors=method_colors, + dataset_labels=dataset_labels, + method_labels=method_labels) + + # DURATION PLOTS + ddata = pt.get_duration_pdata(data) + pt.make_bar_plot(ddata, 'duration.pdf', + title='Duration', ylabel='Duration [min]', + dataset_order=dataset_order, + method_order=method_order, + method_colors=method_colors, + dataset_labels=dataset_labels, + method_labels=method_labels) From 1ea280cfadf2658ade237dafc5dfa069acc7506a Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Tue, 22 Sep 2015 09:34:01 -0600 Subject: [PATCH 188/250] Splitting statistics part of TestDB out --- tests/yellowstone/checkresults.py | 11 +- tests/yellowstone/mkstats.py | 13 +- tests/yellowstone/mktimings.py | 3 +- tests/yellowstone/runtests.py | 14 +- tests/yellowstone/utilities/testtools.py | 167 +++++++++++++++++------ 5 files changed, 150 insertions(+), 58 deletions(-) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index f5d182e..39353de 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -72,7 +72,8 @@ def __init__(self, executable='cprnc'): # Check that the executable works if call("type " + executable, shell=True, stdout=PIPE, stderr=PIPE) != 0: - err_msg = "CPRNC executable '{0!s}' does not appear to work".format(executable) + err_msg = "CPRNC executable '{0!s}' does not appear to work".format( + executable) raise ValueError(err_msg) # Save the executable location @@ -141,7 +142,7 @@ def compare(self, nc1, nc2, outfile=None, alltimes=True, verbose=False): args = _PARSER_.parse_args() # Create/read the testing info and stats files - testdb = tt.TestDB(dbname=args.infofile).get_database() + testdb = tt.TestDB(name=args.infofile).getdb() # Get a list of valid rundir names to look for if len(args.rundir) > 0: @@ -284,7 +285,8 @@ def compare(self, nc1, nc2, outfile=None, alltimes=True, verbose=False): outfile = os.path.join(cprncdir, filename + '.cprnc') # Compare the files with CPRNC - rslt = cprnc.compare(item_dict['new'], item_dict['old'], outfile=outfile) + rslt = cprnc.compare( + item_dict['new'], item_dict['old'], outfile=outfile) # Save the result in the result dictionary rslt_dict = {} @@ -316,7 +318,8 @@ def compare(self, nc1, nc2, outfile=None, alltimes=True, verbose=False): for result in results: if result['test'] == test_name: str_rslt = ' GOOD:' if result['result'] else ' BAD:' - summ = str_rslt + ' ' + result['file'] + ' ({0!s})'.format(rslt_dict['test']) + summ = str_rslt + ' ' + \ + result['file'] + ' ({0!s})'.format(rslt_dict['test']) sfile.write(summ + os.linesep) sfile.close() diff --git a/tests/yellowstone/mkstats.py b/tests/yellowstone/mkstats.py index 49c3dba..e2d36ca 100755 --- a/tests/yellowstone/mkstats.py +++ b/tests/yellowstone/mkstats.py @@ -55,21 +55,22 @@ sys.exit(1) # Create/read the testing info and stats files - testdb = tt.TestDB(dbname=args.infofile, stname=args.statsfile) + testdb = tt.TestDB(name=args.infofile) + statdb = tt.StatsDB(testdb, name=args.statsfile) # List tests if only listing if args.list_tests: - testdb.print_tests() + testdb.display() sys.exit(1) # Generate the list of tests to run/analyze if args.all_tests: - test_list = testdb.get_database().keys() + test_list = testdb.getdb().keys() else: - test_list = [t for t in args.test if t in testdb.get_database()] + test_list = [t for t in args.test if t in testdb.getdb()] # Analyze test input, if requested (overwrite forces re-analysis) - testdb.analyze(test_list, force=args.overwrite) + statdb.analyze(test_list, force=args.overwrite) # Save to the stats file - testdb.save_statistics(stname=args.statsfile) + statdb.save_statistics(name=args.statsfile) diff --git a/tests/yellowstone/mktimings.py b/tests/yellowstone/mktimings.py index d8bf0be..6090fcb 100755 --- a/tests/yellowstone/mktimings.py +++ b/tests/yellowstone/mktimings.py @@ -54,7 +54,8 @@ def find_shortest_str(strng, left, right=os.linesep, loc=0): args = _PARSER_.parse_args() # Create/read the testing info and stats files - testdb = tt.TestDB(dbname=args.infofile, stname=args.statsfile).get_database() + testdb = tt.TestDB(name=args.infofile).getdb() + statdb = tt.StatsDB(testdb, name=args.statsfile).getdb() # Get the timings.json data file timefn = os.path.abspath(args.timefile) diff --git a/tests/yellowstone/runtests.py b/tests/yellowstone/runtests.py index 6911766..83296ef 100755 --- a/tests/yellowstone/runtests.py +++ b/tests/yellowstone/runtests.py @@ -178,7 +178,8 @@ def runmultitest(tests, nodes=0, tiling=16, minutes=120, runtype = 'par{0!s}x{1!s}'.format(nodes, tiling) else: runtype = 'ser' - testdir = os.path.abspath(os.path.join('results.d', 'multitest', runtype, ncformat)) + testdir = os.path.abspath( + os.path.join('results.d', 'multitest', runtype, ncformat)) # If the test directory doesn't exist, make it and move into it cwd = os.getcwd() @@ -264,7 +265,8 @@ def runindivtests(tests, nodes=0, tiling=16, minutes=120, runtype = 'par{0!s}x{1!s}'.format(nodes, tiling) else: runtype = 'ser' - testdir = os.path.abspath(os.path.join('results.d', str(test_name), runtype, ncformat)) + testdir = os.path.abspath( + os.path.join('results.d', str(test_name), runtype, ncformat)) # If the test directory doesn't exist, make it and move into it if os.path.exists(testdir): @@ -325,18 +327,18 @@ def runindivtests(tests, nodes=0, tiling=16, minutes=120, sys.exit(1) # Create/read the testing info and stats files - testdb = tt.TestDB(dbname=args.infofile) + testdb = tt.TestDB(name=args.infofile) # List tests if only listing if args.list_tests: - testdb.print_tests() + testdb.display() sys.exit(1) # Generate the list of tests to run/analyze if args.all_tests: - test_list = testdb.get_database().keys() + test_list = testdb.getdb().keys() else: - test_list = [t for t in args.test if t in testdb.get_database()] + test_list = [t for t in args.test if t in testdb.getdb()] if args.multispec: runmultitest(test_list, nodes=args.nodes, tiling=args.tiling, diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index 59cc161..2941d0f 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -58,15 +58,13 @@ def _nbyte_str(n, exp=0): #============================================================================== class TestDB(object): - def __init__(self, dbname=None, stname=None): + def __init__(self, name=None): """ Initializer Parameters: - dbname (str): The name of the test database file. Defaults + name (str): The name of the test database file. Defaults to 'testinfo.json'. - stname (str): The name of the test statistics file. Defaults - to 'teststats.json'. Raises: ValueError: If the test database file cannot be opened and/or @@ -75,8 +73,8 @@ def __init__(self, dbname=None, stname=None): # See if there is a user-defined testinfo file, # otherwise look for default abs_path = '' - if dbname: - abs_path = os.path.abspath(dbname) + if name: + abs_path = os.path.abspath(name) else: abs_path = os.path.join(os.getcwd(), 'testinfo.json') @@ -87,24 +85,11 @@ def __init__(self, dbname=None, stname=None): self._database = dict(json.load(dbfile)) dbfile.close() except: - err_msg = 'Problem reading and parsing test info file: {0!s}'.format(abs_path) + err_msg = 'Problem reading and parsing test info file: {0!s}'.format( + abs_path) raise ValueError(err_msg) - # Initialize test statistics - self._statistics = {} - - # If the stats filename is given, then try to read it - if stname is not None: - abs_path = os.path.abspath(stname) - try: - stfile = open(abs_path, 'r') - self._statistics = dict(json.load(stfile)) - stfile.close() - except: - err_msg = 'Problem reading and parsing test stats file: {0!s}'.format(abs_path) - raise ValueError(err_msg) - - def get_database(self): + def getdb(self): """ Return the testing database as a dictionary @@ -113,16 +98,7 @@ def get_database(self): """ return self._database - def get_statistics(self): - """ - Return the test analysis statistics as a dictionary - - Returns: - dict: The statistics database - """ - return self._statistics - - def print_tests(self): + def display(self): """ List the tests in the test database. """ @@ -194,6 +170,58 @@ def create_specifier(self, test_name, ncfmt='netcdf4c', prefix=prefix, suffix=suffix, metadata=metadata, **kwargs) + +#============================================================================== +# StatsDB - Statistics Database +#============================================================================== +class StatsDB(object): + + def __init__(self, tdb, name=None): + """ + Initializer + + Parameters: + tdb (TestDB): A testing database for which to associate statistics + name (str): The name of the test statistics file. Defaults + to 'teststats.json'. + + Raises: + ValueError: If the test database file cannot be opened and/or + read. + """ + + # Check type of testing db object + if not isinstance(tdb, TestDB): + err_msg = "Testing database must be of TestDB type" + raise TypeError(err_msg) + + # Initialize the testing database + self._database = tdb.getdb() + + # Initialize test statistics + self._statistics = {} + + # If the stats filename is given, then try to read it + if name is not None: + abs_path = os.path.abspath(name) + try: + stfile = open(abs_path, 'r') + self._statistics = dict(json.load(stfile)) + stfile.close() + except: + err_msg = 'Problem reading and parsing test stats file: {0!s}'.format( + abs_path) + raise ValueError(err_msg) + + def getdb(self): + """ + Return the test analysis statistics as a dictionary + + Returns: + dict: The statistics database + """ + return self._statistics + def analyze(self, tests=None, force=False): """ Analyze the test database to determine test statistics @@ -371,7 +399,7 @@ def analyze(self, tests=None, force=False): max([var_stats[v]['xsize'] for v in timd_vars]) self._statistics[test_name]['maxsizes']['tinvariant'] = maxsize - def print_statistics(self, tests=None): + def display(self, tests=None): """ Print the statistics information determined from self analysis @@ -476,17 +504,17 @@ def print_statistics(self, tests=None): print " Time-Invariant Metadata Max Size: {}".format(_nbyte_str(timd_maxsize)) print - def save_statistics(self, stname="teststats.json"): + def save(self, name="teststats.json"): """ Save the statistics information to a JSON data file Parameters: - stname (str): The name of the JSON statistics file to write + name (str): The name of the JSON statistics file to write """ # Check types - if isinstance(stname, str): - fp = open(stname, 'w') + if isinstance(name, str): + fp = open(name, 'w') else: err_msg = "Statistics filename must be a string" raise TypeError(err_msg) @@ -501,17 +529,17 @@ def save_statistics(self, stname="teststats.json"): # Close the file fp.close() - def load_statistics(self, stname="teststats.json"): + def load(self, name="teststats.json"): """ Load the statistics information from a JSON data file Parameters: - stname (str): The name of the JSON data file to read + name (str): The name of the JSON data file to read """ # Check types - if isinstance(stname, str): - fp = open(stname, 'r') + if isinstance(name, str): + fp = open(name, 'r') else: err_msg = "Statistics filename must be a string" raise TypeError(err_msg) @@ -525,3 +553,60 @@ def load_statistics(self, stname="teststats.json"): # Close the file fp.close() + + +#============================================================================== +# TimeDB - Database for Timing Data +#============================================================================== +class TimeDB(object): + + def __init__(self, name=None): + """ + Initializer + + Parameters: + name (str): The name of the timing database file. Defaults + to 'timing.json'. + + Raises: + ValueError: If the timing database file cannot be opened and/or + read. + """ + # See if there is a user-defined testinfo file, + # otherwise look for default + abs_path = '' + if name: + abs_path = os.path.abspath(name) + else: + abs_path = os.path.join(os.getcwd(), 'testinfo.json') + + # Try opening and reading the testinfo file + self._timings = {} + try: + dbfile = open(abs_path, 'r') + self._timings = dict(json.load(dbfile)) + dbfile.close() + except: + err_msg = 'Problem reading and parsing timings file: {0!s}'.format( + abs_path) + raise ValueError(err_msg) + + def getdb(self): + """ + Return the testing database as a dictionary + + Returns: + dict: The testing database + """ + return self._timings + + def display(self): + """ + List the tests in the test database. + """ + print + print 'Tests found in the Test Database are:' + print + for test_name in self._timings: + print ' {0!s}'.format(test_name) + return From 304bec21e52e3ce0e4f2812d0f3ce8da638717cb Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Tue, 22 Sep 2015 12:32:18 -0600 Subject: [PATCH 189/250] Updating timing and statistics database use --- tests/yellowstone/mkstats.py | 4 +- tests/yellowstone/mktimings.py | 75 ++----- tests/yellowstone/utilities/testtools.py | 272 +++++++++++++++++------ 3 files changed, 228 insertions(+), 123 deletions(-) diff --git a/tests/yellowstone/mkstats.py b/tests/yellowstone/mkstats.py index e2d36ca..968f3e9 100755 --- a/tests/yellowstone/mkstats.py +++ b/tests/yellowstone/mkstats.py @@ -56,7 +56,7 @@ # Create/read the testing info and stats files testdb = tt.TestDB(name=args.infofile) - statdb = tt.StatsDB(testdb, name=args.statsfile) + statdb = tt.StatDB(name=args.statsfile) # List tests if only listing if args.list_tests: @@ -70,7 +70,7 @@ test_list = [t for t in args.test if t in testdb.getdb()] # Analyze test input, if requested (overwrite forces re-analysis) - statdb.analyze(test_list, force=args.overwrite) + statdb.analyze(testdb, tests=test_list, force=args.overwrite) # Save to the stats file statdb.save_statistics(name=args.statsfile) diff --git a/tests/yellowstone/mktimings.py b/tests/yellowstone/mktimings.py index 6090fcb..1c73505 100755 --- a/tests/yellowstone/mktimings.py +++ b/tests/yellowstone/mktimings.py @@ -12,7 +12,6 @@ import glob import datetime import argparse -import json # Package Modules from utilities import testtools as tt @@ -27,9 +26,6 @@ _PARSER_.add_argument('-i', '--infofile', default='testinfo.json', type=str, help='Location of the testinfo.json database file ' '[Default: testinfo.json]') -_PARSER_.add_argument('-s', '--statsfile', default='teststats.json', type=str, - help='Location of the teststats.json database file ' - '[Default: teststats.json]') _PARSER_.add_argument('-t', '--timefile', default='timings.json', type=str, help='Location of the timings.json database file ' '[Default: timings.json]') @@ -55,17 +51,7 @@ def find_shortest_str(strng, left, right=os.linesep, loc=0): # Create/read the testing info and stats files testdb = tt.TestDB(name=args.infofile).getdb() - statdb = tt.StatsDB(testdb, name=args.statsfile).getdb() - - # Get the timings.json data file - timefn = os.path.abspath(args.timefile) - - # Open JSON file - timedb = {} - if (os.path.isfile(timefn)): - json_file = open(timefn) - timedb = dict(json.load(json_file)) - json_file.close() + timedb = tt.TimeDB(name=args.timefile) # Current working directory cwd = os.getcwd() @@ -74,6 +60,7 @@ def find_shortest_str(strng, left, right=os.linesep, loc=0): for rundir in glob.iglob(os.path.join('results.d', '*', '[ser,par]*', '*')): print print 'Extracting times from test dir:', rundir + print root, ncfmt = os.path.split(rundir) root, run_type = os.path.split(root) root, test_name = os.path.split(root) @@ -95,14 +82,6 @@ def find_shortest_str(strng, left, right=os.linesep, loc=0): elif ncfmt == 'netcdf4': method_name = 'pyreshaper4' - # Check for this test in the timing database - if common_name not in timedb: - timedb[common_name] = {'results': {}} - - # Check for method in results - if method_name not in timedb[common_name]['results']: - timedb[common_name]['results'][method_name] = {} - # Get the number of cores and nodes from the run type num_cores = 1 num_nodes = 0 @@ -174,41 +153,19 @@ def find_shortest_str(strng, left, right=os.linesep, loc=0): print ' Elapsed time (INTERNAL):', elapsed, 'sec' # Write the JSON data - if job_num in timedb[common_name]['results'][method_name]: - print ' Job already exists in database. Skipping.' - else: - print ' Adding new job to timings database.' - timedb[common_name]['results'][method_name][job_num] = {} - - timedb[common_name]['results'][ - method_name][job_num]['sys'] = "yellowstone" - timedb[common_name]['results'][ - method_name][job_num]['cores'] = num_cores - timedb[common_name]['results'][ - method_name][job_num]['nodes'] = num_nodes - timedb[common_name]['results'][ - method_name][job_num]['real'] = elapsed - timedb[common_name]['results'][ - method_name][job_num]['metadata'] = True - timedb[common_name]['results'][ - method_name][job_num]['once'] = used_once_file - timedb[common_name]['results'][ - method_name][job_num]['actual'] = float(actual_str) - timedb[common_name]['results'][ - method_name][job_num]['request'] = float(requested_str) - timedb[common_name]['results'][ - method_name][job_num]['openi'] = float(openi_str) - timedb[common_name]['results'][ - method_name][job_num]['openo'] = float(openo_str) - timedb[common_name]['results'][ - method_name][job_num]['metaTI'] = float(metaTI_str) - timedb[common_name]['results'][ - method_name][job_num]['metaTV'] = float(metaTV_str) - timedb[common_name]['results'][ - method_name][job_num]['TS'] = float(TS_str) + print ' Adding job result to timings database.' + timedb.add_result(common_name, method_name, job_num, + tser_write=float(TS_str), + tim_write=float(metaTI_str), + tvm_write=float(metaTV_str), + metadata=True, once=used_once_file, + cores=num_cores, nodes=num_nodes, + input_open=float(openi_str), + output_open=float(openo_str), + total=elapsed, + actual_mb=float(actual_str), + requested_mb=float(requested_str), + system='yellowstone') # Write the JSON data file - json_file = open(timefn, 'w') - json_file.write(json.dumps(timedb, sort_keys=True, - indent=4, separators=(',', ': '))) - json_file.close() + timedb.save(args.timefile) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index 2941d0f..58d72c0 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -11,6 +11,7 @@ import os import glob import json +import datetime import textwrap # Third-Party Modules @@ -58,7 +59,7 @@ def _nbyte_str(n, exp=0): #============================================================================== class TestDB(object): - def __init__(self, name=None): + def __init__(self, name='testinfo.json'): """ Initializer @@ -70,13 +71,8 @@ def __init__(self, name=None): ValueError: If the test database file cannot be opened and/or read. """ - # See if there is a user-defined testinfo file, - # otherwise look for default - abs_path = '' - if name: - abs_path = os.path.abspath(name) - else: - abs_path = os.path.join(os.getcwd(), 'testinfo.json') + # Get the path to the testinfo file + abs_path = os.path.abspath(name) # Try opening and reading the testinfo file self._database = {} @@ -172,16 +168,15 @@ def create_specifier(self, test_name, ncfmt='netcdf4c', #============================================================================== -# StatsDB - Statistics Database +# StatDB - Statistics Database #============================================================================== -class StatsDB(object): +class StatDB(object): - def __init__(self, tdb, name=None): + def __init__(self, name=None): """ Initializer Parameters: - tdb (TestDB): A testing database for which to associate statistics name (str): The name of the test statistics file. Defaults to 'teststats.json'. @@ -190,14 +185,6 @@ def __init__(self, tdb, name=None): read. """ - # Check type of testing db object - if not isinstance(tdb, TestDB): - err_msg = "Testing database must be of TestDB type" - raise TypeError(err_msg) - - # Initialize the testing database - self._database = tdb.getdb() - # Initialize test statistics self._statistics = {} @@ -222,17 +209,26 @@ def getdb(self): """ return self._statistics - def analyze(self, tests=None, force=False): + def analyze(self, database, tests=None, force=False): """ Analyze the test database to determine test statistics Parameters: + database (TestDB): The testing database to analyze tests (list): A list of string names of tests in the database to analyze. If None, assume all tests. force (bool): Whether to force reanalysis of tests that have already been analyzed """ + # Check type of testing db object + if not isinstance(database, TestDB): + err_msg = "Testing database must be of TestDB type" + raise TypeError(err_msg) + + # Get the testing database dictionary + dbdict = database.getdb() + # Check type if tests is not None and not isinstance(tests, (list, tuple)): err_msg = "Test name list must be of list or tuple type" @@ -240,10 +236,10 @@ def analyze(self, tests=None, force=False): # Assume all tests to be analyzed if None input elif tests is None: - tests = self._database.keys() + tests = dbdict.keys() # Error if tests not in database - bad_names = [t for t in tests if t not in self._database] + bad_names = [t for t in tests if t not in dbdict] if len(bad_names) > 0: err_msg = "Tests not found in database: " + ", ".join(bad_names) raise ValueError(err_msg) @@ -259,7 +255,7 @@ def analyze(self, tests=None, force=False): print "Analyzing Test: {0!s}".format(test_name) # Create a specifier for this test - spec = self.create_specifier(str(test_name), ncfmt='netcdf') + spec = database.create_specifier(str(test_name), ncfmt='netcdf') # Validate the test information spec.validate() @@ -529,31 +525,6 @@ def save(self, name="teststats.json"): # Close the file fp.close() - def load(self, name="teststats.json"): - """ - Load the statistics information from a JSON data file - - Parameters: - name (str): The name of the JSON data file to read - """ - - # Check types - if isinstance(name, str): - fp = open(name, 'r') - else: - err_msg = "Statistics filename must be a string" - raise TypeError(err_msg) - - # Try reading the statistics - try: - self._statistics = dict(json.load(fp)) - except: - err_msg = "Failed to read statistics file" - raise RuntimeError(err_msg) - - # Close the file - fp.close() - #============================================================================== # TimeDB - Database for Timing Data @@ -566,7 +537,7 @@ def __init__(self, name=None): Parameters: name (str): The name of the timing database file. Defaults - to 'timing.json'. + to 'timings.json'. Raises: ValueError: If the timing database file cannot be opened and/or @@ -574,11 +545,7 @@ def __init__(self, name=None): """ # See if there is a user-defined testinfo file, # otherwise look for default - abs_path = '' - if name: - abs_path = os.path.abspath(name) - else: - abs_path = os.path.join(os.getcwd(), 'testinfo.json') + abs_path = os.path.abspath('timings.json') # Try opening and reading the testinfo file self._timings = {} @@ -593,20 +560,201 @@ def __init__(self, name=None): def getdb(self): """ - Return the testing database as a dictionary + Return the timings database as a dictionary Returns: - dict: The testing database + dict: The timings database dictionary """ return self._timings - def display(self): + def test_has_method(self, test, method): + """ + Check if given test was done with the given method + + Parameters: + test (str): The name of the test to query + method (str): The name of the method to query + + Returns: + bool: True, if the test was performed with the given method, + False, otherwise. + """ + + # checking + if test not in self._timings: + err_msg = "Given test '{0!s}' not in timings database".format(test) + raise ValueError(err_msg) + + # Start looking for the method + if 'results' not in self._timings[test]: + return False + return method in self._timings[test]['results'] + + def tests_with_methods(self, methods=None): + """ + Return the list of tests that use the given methods + + If no methods are given, then returns all tests + + Parameters: + methods (list, tuple): The list of methods to query + """ + if not methods: + return [str(t) for t in self._timings.keys()] + + test_set = set() + for method in methods: + test_set.update(set(str(t) for t in self._timings + if self.test_has_method(t, method))) + return list(test_set) + + def methods_in_tests(self, tests=None): + """ + Return the list of methods that are used by all of the given tests + + If no tests given, return list of all methods found. + + Parameters: + tests (list, tuple): The list of tests to query + """ + if tests: + tests_to_search = tests + else: + tests_to_search = self._timings.keys() + + method_set = set() + for test in tests_to_search: + if 'results' in self._timings[test]: + method_set.update(set(str(t) for t in self._timings[test]['results'].keys())) + return list(method_set) + + def display_tests(self, methods=None): """ List the tests in the test database. + + If methods are given, then only the tests using these methods will be + displayed. + + Parameters: + methods (list, tuple): A method names to query """ print - print 'Tests found in the Test Database are:' + print "Tests", + if methods: + print "with methods {0!s}".format(methods), + print "in the Timings Database:" print - for test_name in self._timings: - print ' {0!s}'.format(test_name) - return + for test in self.tests_with_methods(methods): + print ' {0!s}'.format(test) + + def display_methods(self, tests=None): + """ + List the methods in the test database. + + If tests are given, then only the methods used by these tests will be + displayed. + + Parameters: + tests (list, tuple): A test names to query + """ + print + print "Methods", + if tests: + print "used by tests {0!s}".format(tests), + print "in the Timings Database:" + print + for method in self.methods_in_tests(tests): + print ' {0!s}'.format(method) + + def add_result(self, test, method, job, + tser_write=0.0, tim_write=0.0, tvm_write=0.0, + metadata=True, once=False, cores=1, nodes=0, + input_open=0.0, output_open=0.0, total=0.0, + actual_mb=0.0, requested_mb=0.0, system='yellowstone'): + """ + Add new timing results to the timings database + + All times are in seconds. + + Parameters: + test (str): Name of the test associated with the result + method (str): Name of the method used by the test result + job (str): Individual job ID string to associate with the result + tser_write (float): Time to write Time-Series data + tim_write (float): Time to write Time-Invariant Metadata (TIM) + tvm_write (float): Time to write Time-Variant Metadata (TVM) + metadata (bool): Whether all metadata was written + once (bool): Whether metadata was written to a "once" file + cores (int): Number of cores used for the job + nodes (int): Number of nodes used for the job + input_open (float): Time to open all input files + output_open (float): Time to open all output files + total (float): Total time for the entire conversion process + actual_mb (float): Number of MB actually read (assuming a given + block size) from input files + requested_mb (float): Number of MB requested + system (str): Name of the system on which the test was run + """ + + if test not in self._timings: + self._timings[test] = {'results': {}} + if method not in self._timings[test]['results']: + self._timings[test]['results'][method] = {} + + if job not in self._timings[test]['results'][method]: + self._timings[test]['results'][method][job] = {} + self._timings[test]['results'][method][job]['sys'] = system + self._timings[test]['results'][method][job]['cores'] = cores + self._timings[test]['results'][method][job]['nodes'] = nodes + self._timings[test]['results'][method][job]['real'] = total + self._timings[test]['results'][method][job]['metadata'] = metadata + self._timings[test]['results'][method][job]['once'] = once + self._timings[test]['results'][method][job]['actual'] = actual_mb + self._timings[test]['results'][method][job]['request'] = requested_mb + self._timings[test]['results'][method][job]['openi'] = input_open + self._timings[test]['results'][method][job]['openo'] = output_open + self._timings[test]['results'][method][job]['metaTI'] = tim_write + self._timings[test]['results'][method][job]['metaTV'] = tvm_write + self._timings[test]['results'][method][job]['TS'] = tser_write + + def get_results(self, test, method): + """ + Get timings results as a dictionary for a given test and method. + + Parameters: + test (str): Name of the test + method (str); Name of the method + """ + if test not in self._timings: + err_msg = "Test {0!s} not in timings database".format(test) + raise KeyError(err_msg) + if self.test_has_method(test, method): + return self._timings[test]['results'][method] + else: + err_msg = "Method {0!s} not in test {1!s} database".format(method, test) + raise KeyError(err_msg) + + def save(self, name="timings.json"): + """ + Save the timing information to a JSON data file + + Parameters: + name (str): The name of the JSON timings file to write + """ + + # Check types + if isinstance(name, str): + fp = open(name, 'w') + else: + err_msg = "Statistics filename must be a string" + raise TypeError(err_msg) + + # Dump JSON data to file + try: + json.dump(self._timings, fp) + except: + err_msg = "Failed to write statistics file" + raise RuntimeError(err_msg) + + # Close the file + fp.close() From ea180c7562db779271d2099b57a8c9591257f7f2 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Tue, 22 Sep 2015 12:32:57 -0600 Subject: [PATCH 190/250] Removing unused import --- tests/yellowstone/utilities/testtools.py | 1 - 1 file changed, 1 deletion(-) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index 58d72c0..fdd5086 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -11,7 +11,6 @@ import os import glob import json -import datetime import textwrap # Third-Party Modules From 066b5f3e6a28fa17524c3391602551b663585ee5 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Tue, 29 Sep 2015 09:26:40 -0600 Subject: [PATCH 191/250] Adding test info for high-frequency (or variable-frequency) tests --- tests/yellowstone/testinfo.json | 81 +++++++++++++++++++++++++++++++++ 1 file changed, 81 insertions(+) diff --git a/tests/yellowstone/testinfo.json b/tests/yellowstone/testinfo.json index 0f9542c..a5f529d 100644 --- a/tests/yellowstone/testinfo.json +++ b/tests/yellowstone/testinfo.json @@ -163,6 +163,87 @@ "time_written" ] }, + "camhf—monthly-1deg":{ + "common_name":"CAMHF-MONTHLY-1.0”, + "input_dir":"/glade/u/tdd/asap/bakeoff/hist/camhf-monthly-1.0”, + "results_dir":"/glade/u/tdd/asap/bakeoff/tseries/camhf—monthly-1.0”, + "input_globs":[ + “b.e11.BDP.f09_g16.1958-11.002.cam.h0.19*.nc” + ], + "output_prefix":"b.e11.BDP.f09_g16.1958-11.002.cam.h0.", + "output_suffix":".195811-196810.nc", + "metadata":[ + "ch4vmr", + "co2vmr", + "date", + "date_written", + "datesec", + "f11vmr", + "f12vmr", + "n2ovmr", + "ndcur", + "nscur", + "nsteph", + "sol_tsi", + "time", + "time_bnds", + "time_written" + ] + }, + "camhf—daily-1deg":{ + "common_name":"CAMHF-DAILY-1.0”, + "input_dir":"/glade/u/tdd/asap/bakeoff/hist/camhf-daily-1.0”, + "results_dir":"/glade/u/tdd/asap/bakeoff/tseries/camhf—daily-1.0”, + "input_globs":[ + “b.e11.BDP.f09_g16.1958-11.002.cam.h1.19*.nc” + ], + "output_prefix":"b.e11.BDP.f09_g16.1958-11.002.cam.h1.”, + "output_suffix":".195811-196810.nc", + "metadata":[ + "ch4vmr", + "co2vmr", + "date", + "date_written", + "datesec", + "f11vmr", + "f12vmr", + "n2ovmr", + "ndcur", + "nscur", + "nsteph", + "sol_tsi", + "time", + "time_bnds", + "time_written" + ] + }, + "camhf—6hourly-1deg":{ + "common_name":"CAMHF-6HOURLY-1.0”, + "input_dir":"/glade/u/tdd/asap/bakeoff/hist/camhf-6hourly-1.0”, + "results_dir":"/glade/u/tdd/asap/bakeoff/tseries/camhf—6hourly-1.0”, + "input_globs":[ + “b.e11.BDP.f09_g16.1958-11.002.cam.h2.19*.nc” + ], + "output_prefix":"b.e11.BDP.f09_g16.1958-11.002.cam.h2.”, + "output_suffix":".195811-196810.nc", + "metadata":[ + "ch4vmr", + "co2vmr", + "date", + "date_written", + "datesec", + "f11vmr", + "f12vmr", + "n2ovmr", + "ndcur", + "nscur", + "nsteph", + "sol_tsi", + "time", + "time_bnds", + "time_written" + ] + }, "clmse-1deg":{ "common_name":"CLM-1.0", "input_dir":"/glade/u/tdd/asap/bakeoff/hist/clmse-1.0", From 3d75c5096805ef1c006fba05ee70613d573f5b5c Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Tue, 29 Sep 2015 10:42:02 -0600 Subject: [PATCH 192/250] Updating metadata list for tests --- tests/yellowstone/testinfo.json | 60 ++++++++++++++++----------------- 1 file changed, 30 insertions(+), 30 deletions(-) diff --git a/tests/yellowstone/testinfo.json b/tests/yellowstone/testinfo.json index a5f529d..3d2db88 100644 --- a/tests/yellowstone/testinfo.json +++ b/tests/yellowstone/testinfo.json @@ -174,20 +174,20 @@ "output_suffix":".195811-196810.nc", "metadata":[ "ch4vmr", - "co2vmr", - "date", + "f12vmr", + "time_written", + "time_bnds", + "nsteph", "date_written", + "co2vmr", + "sol_tsi", "datesec", - "f11vmr", - "f12vmr", - "n2ovmr", + "date", "ndcur", + "n2ovmr", + "f11vmr", "nscur", - "nsteph", - "sol_tsi", - "time", - "time_bnds", - "time_written" + "time" ] }, "camhf—daily-1deg":{ @@ -201,20 +201,20 @@ "output_suffix":".195811-196810.nc", "metadata":[ "ch4vmr", - "co2vmr", - "date", + "f12vmr", + "time_written", + "time_bnds", + "nsteph", "date_written", + "co2vmr", + "sol_tsi", "datesec", - "f11vmr", - "f12vmr", - "n2ovmr", + "date", "ndcur", + "n2ovmr", + "f11vmr", "nscur", - "nsteph", - "sol_tsi", - "time", - "time_bnds", - "time_written" + "time" ] }, "camhf—6hourly-1deg":{ @@ -228,20 +228,20 @@ "output_suffix":".195811-196810.nc", "metadata":[ "ch4vmr", - "co2vmr", - "date", + "f12vmr", + "time_written", + "time_bnds", + "nsteph", "date_written", + "co2vmr", + "sol_tsi", "datesec", - "f11vmr", - "f12vmr", - "n2ovmr", + "date", "ndcur", + "n2ovmr", + "f11vmr", "nscur", - "nsteph", - "sol_tsi", - "time", - "time_bnds", - "time_written" + "time" ] }, "clmse-1deg":{ From 553fb305658cf1170b5e4d90e91ebea04f7e0da8 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Tue, 29 Sep 2015 15:14:11 -0600 Subject: [PATCH 193/250] Attempting multi-step read/write for time-variant data --- source/pyreshaper/reshaper.py | 107 +++++++++++++++++++--------------- 1 file changed, 60 insertions(+), 47 deletions(-) diff --git a/source/pyreshaper/reshaper.py b/source/pyreshaper/reshaper.py index 9a68a5f..eef5df4 100644 --- a/source/pyreshaper/reshaper.py +++ b/source/pyreshaper/reshaper.py @@ -645,6 +645,9 @@ def convert(self, output_limit=0): self._timer.reset('Create Time-Invariant Metadata') self._timer.reset('Create Time-Variant Metadata') self._timer.reset('Create Time-Series Variables') + self._timer.reset('Read Time-Invariant Metadata') + self._timer.reset('Read Time-Variant Metadata') + self._timer.reset('Read Time-Series Variables') self._timer.reset('Write Time-Invariant Metadata') self._timer.reset('Write Time-Variant Metadata') self._timer.reset('Write Time-Series Variables') @@ -705,7 +708,7 @@ def _get_once_info(vname): self._timer.stop('Open Output Files') # Create the time-invariant metadata variables - if (write_meta): + if write_meta: self._timer.start('Create Time-Invariant Metadata') for name in self._time_invariant_metadata: in_var = ref_infile.variables[name] @@ -757,14 +760,20 @@ def _get_once_info(vname): # Write the time-invariant metadata if write_meta: - self._timer.start('Write Time-Invariant Metadata') for name in self._time_invariant_metadata: in_meta = ref_infile.variables[name] out_meta = out_file.variables[name] + self._timer.start('Read Time-Invariant Metadata') + if in_meta.rank > 0: + tmp_data = in_meta[:] + else: + tmp_data = in_meta.get_value() + self._timer.stop('Read Time-Invariant Metadata') + self._timer.start('Write Time-Invariant Metadata') if in_meta.rank > 0: - out_meta[:] = in_meta[:] + out_meta[:] = tmp_data else: - out_meta.assign_value(in_meta.get_value()) + out_meta.assign_value(tmp_data) self._timer.stop('Write Time-Invariant Metadata') # Write each time-variant variable @@ -774,55 +783,59 @@ def _get_once_info(vname): # Get the number of time steps in this slice file num_steps = in_file.dimensions[self._unlimited_dim] - # Loop over the time steps in this slice file - for slice_step_index in range(num_steps): - - # Write the time-varient metadata - if write_meta: - self._timer.start('Write Time-Variant Metadata') - for name in self._time_variant_metadata: - in_meta = in_file.variables[name] - out_meta = out_file.variables[name] - ndims = len(in_meta.dimensions) - udidx = in_meta.dimensions.index( - self._unlimited_dim) - in_slice = [slice(None)] * ndims - in_slice[udidx] = slice_step_index - out_slice = [slice(None)] * ndims - out_slice[udidx] = series_step_index - out_meta[tuple(out_slice)] = in_meta[ - tuple(in_slice)] - - requested_nbytes = in_meta[:].nbytes - self._byte_counts[ - 'Requested Data'] += requested_nbytes - actual_nbytes = self.assumed_block_size \ - * numpy.ceil(requested_nbytes / self.assumed_block_size) - self._byte_counts['Actual Data'] += actual_nbytes - self._timer.stop('Write Time-Variant Metadata') - - # Write the time-series variables - if write_tser: - self._timer.start('Write Time-Series Variables') - in_var = in_file.variables[out_name] - ndims = len(in_var.dimensions) - udidx = in_var.dimensions.index(self._unlimited_dim) + # Write the time-varient metadata + if write_meta: + for name in self._time_variant_metadata: + in_meta = in_file.variables[name] + out_meta = out_file.variables[name] + ndims = len(in_meta.dimensions) + udidx = in_meta.dimensions.index(self._unlimited_dim) in_slice = [slice(None)] * ndims - in_slice[udidx] = slice_step_index + in_slice[udidx] = slice(0, num_steps) out_slice = [slice(None)] * ndims - out_slice[udidx] = series_step_index - out_var[tuple(out_slice)] = in_var[tuple(in_slice)] + out_slice[udidx] = slice(series_step_index, + series_step_index + num_steps) + self._timer.start('Read Time-Variant Metadata') + tmp_data = in_meta[tuple(in_slice)] + self._timer.stop('Read Time-Variant Metadata') + self._timer.start('Write Time-Variant Metadata') + out_meta[tuple(out_slice)] = tmp_data + self._timer.stop('Write Time-Variant Metadata') - requested_nbytes = in_file.variables[ - out_name][:].nbytes - self._byte_counts['Requested Data'] += requested_nbytes + requested_nbytes = in_meta[:].nbytes + self._byte_counts[ + 'Requested Data'] += requested_nbytes actual_nbytes = self.assumed_block_size \ * numpy.ceil(requested_nbytes / self.assumed_block_size) self._byte_counts['Actual Data'] += actual_nbytes - self._timer.stop('Write Time-Series Variables') - - # Increment the time-series step index - series_step_index += 1 + self._timer.stop('Write Time-Variant Metadata') + + # Write the time-series variables + if write_tser: + in_var = in_file.variables[out_name] + ndims = len(in_var.dimensions) + udidx = in_var.dimensions.index(self._unlimited_dim) + in_slice = [slice(None)] * ndims + in_slice[udidx] = slice(0, num_steps) + out_slice = [slice(None)] * ndims + out_slice[udidx] = slice(series_step_index, + series_step_index + num_steps) + self._timer.start('Read Time-Series Variables') + tmp_data = in_var[tuple(in_slice)] + self._timer.stop('Read Time-Series Variables') + self._timer.start('Write Time-Series Variables') + out_var[tuple(out_slice)] = tmp_data + self._timer.stop('Write Time-Series Variables') + + requested_nbytes = in_file.variables[ + out_name][:].nbytes + self._byte_counts['Requested Data'] += requested_nbytes + actual_nbytes = self.assumed_block_size \ + * numpy.ceil(requested_nbytes / self.assumed_block_size) + self._byte_counts['Actual Data'] += actual_nbytes + + # Increment the time-series step index + series_step_index += 1 # Close the output file self._timer.start('Close Output Files') From 597d41413bd2cffc295d7f584fa80128f6d42cbe Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Tue, 29 Sep 2015 15:23:41 -0600 Subject: [PATCH 194/250] Debugging output. --- source/pyreshaper/reshaper.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/source/pyreshaper/reshaper.py b/source/pyreshaper/reshaper.py index eef5df4..0b0079e 100644 --- a/source/pyreshaper/reshaper.py +++ b/source/pyreshaper/reshaper.py @@ -822,6 +822,8 @@ def _get_once_info(vname): series_step_index + num_steps) self._timer.start('Read Time-Series Variables') tmp_data = in_var[tuple(in_slice)] + print numpy.shape(tmp_data) + print out_slice self._timer.stop('Read Time-Series Variables') self._timer.start('Write Time-Series Variables') out_var[tuple(out_slice)] = tmp_data From ce9d4d8af6952821e9640c6d65734b163b51571a Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Tue, 29 Sep 2015 15:26:21 -0600 Subject: [PATCH 195/250] More debugging output. --- source/pyreshaper/reshaper.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/source/pyreshaper/reshaper.py b/source/pyreshaper/reshaper.py index 0b0079e..d26f64b 100644 --- a/source/pyreshaper/reshaper.py +++ b/source/pyreshaper/reshaper.py @@ -797,6 +797,8 @@ def _get_once_info(vname): series_step_index + num_steps) self._timer.start('Read Time-Variant Metadata') tmp_data = in_meta[tuple(in_slice)] + print numpy.shape(tmp_data) + print out_slice self._timer.stop('Read Time-Variant Metadata') self._timer.start('Write Time-Variant Metadata') out_meta[tuple(out_slice)] = tmp_data From 68cd99079f2e9d8e1129496124dd4a62cdaac147 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Tue, 29 Sep 2015 15:28:15 -0600 Subject: [PATCH 196/250] Typo --- source/pyreshaper/reshaper.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/source/pyreshaper/reshaper.py b/source/pyreshaper/reshaper.py index d26f64b..960fdf4 100644 --- a/source/pyreshaper/reshaper.py +++ b/source/pyreshaper/reshaper.py @@ -839,7 +839,7 @@ def _get_once_info(vname): self._byte_counts['Actual Data'] += actual_nbytes # Increment the time-series step index - series_step_index += 1 + series_step_index += num_steps # Close the output file self._timer.start('Close Output Files') From 3db19aeb9f8e457a522011005ab62409ded028f3 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Tue, 29 Sep 2015 16:10:38 -0600 Subject: [PATCH 197/250] Move back to explicit loop over time. PyNIO can't do it. --- source/pyreshaper/reshaper.py | 108 ++++++++++++++++++---------------- 1 file changed, 56 insertions(+), 52 deletions(-) diff --git a/source/pyreshaper/reshaper.py b/source/pyreshaper/reshaper.py index 960fdf4..ded2284 100644 --- a/source/pyreshaper/reshaper.py +++ b/source/pyreshaper/reshaper.py @@ -774,7 +774,14 @@ def _get_once_info(vname): out_meta[:] = tmp_data else: out_meta.assign_value(tmp_data) - self._timer.stop('Write Time-Invariant Metadata') + self._timer.stop('Write Time-Invariant Metadata') + + requested_nbytes = in_meta[:].nbytes + self._byte_counts[ + 'Requested Data'] += requested_nbytes + actual_nbytes = self.assumed_block_size \ + * numpy.ceil(requested_nbytes / self.assumed_block_size) + self._byte_counts['Actual Data'] += actual_nbytes # Write each time-variant variable series_step_index = 0 @@ -783,63 +790,60 @@ def _get_once_info(vname): # Get the number of time steps in this slice file num_steps = in_file.dimensions[self._unlimited_dim] - # Write the time-varient metadata - if write_meta: - for name in self._time_variant_metadata: - in_meta = in_file.variables[name] - out_meta = out_file.variables[name] - ndims = len(in_meta.dimensions) - udidx = in_meta.dimensions.index(self._unlimited_dim) - in_slice = [slice(None)] * ndims - in_slice[udidx] = slice(0, num_steps) - out_slice = [slice(None)] * ndims - out_slice[udidx] = slice(series_step_index, - series_step_index + num_steps) - self._timer.start('Read Time-Variant Metadata') - tmp_data = in_meta[tuple(in_slice)] - print numpy.shape(tmp_data) - print out_slice - self._timer.stop('Read Time-Variant Metadata') - self._timer.start('Write Time-Variant Metadata') - out_meta[tuple(out_slice)] = tmp_data + # Loop over time steps (PyNIO can't read but 1 step at a time) + for slice_step_index in xrange(num_steps): + + # Write the time-varient metadata + if write_meta: + for name in self._time_variant_metadata: + in_meta = in_file.variables[name] + out_meta = out_file.variables[name] + ndims = len(in_meta.dimensions) + udidx = in_meta.dimensions.index( + self._unlimited_dim) + in_slice = [slice(None)] * ndims + in_slice[udidx] = slice_step_index + out_slice = [slice(None)] * ndims + out_slice[udidx] = series_step_index + self._timer.start('Read Time-Variant Metadata') + tmp_data = in_meta[tuple(in_slice)] + self._timer.stop('Read Time-Variant Metadata') + self._timer.start('Write Time-Variant Metadata') + out_meta[tuple(out_slice)] = tmp_data + self._timer.stop('Write Time-Variant Metadata') + + requested_nbytes = in_meta[tuple(in_slice)].nbytes + self._byte_counts[ + 'Requested Data'] += requested_nbytes + actual_nbytes = self.assumed_block_size \ + * numpy.ceil(requested_nbytes / self.assumed_block_size) + self._byte_counts['Actual Data'] += actual_nbytes self._timer.stop('Write Time-Variant Metadata') - requested_nbytes = in_meta[:].nbytes - self._byte_counts[ - 'Requested Data'] += requested_nbytes + # Write the time-series variables + if write_tser: + in_var = in_file.variables[out_name] + ndims = len(in_var.dimensions) + udidx = in_var.dimensions.index(self._unlimited_dim) + in_slice = [slice(None)] * ndims + in_slice[udidx] = slice_step_index + out_slice = [slice(None)] * ndims + out_slice[udidx] = series_step_index + self._timer.start('Read Time-Series Variables') + tmp_data = in_var[tuple(in_slice)] + self._timer.stop('Read Time-Series Variables') + self._timer.start('Write Time-Series Variables') + out_var[tuple(out_slice)] = tmp_data + self._timer.stop('Write Time-Series Variables') + + requested_nbytes = in_var[tuple(in_slice)].nbytes + self._byte_counts['Requested Data'] += requested_nbytes actual_nbytes = self.assumed_block_size \ * numpy.ceil(requested_nbytes / self.assumed_block_size) self._byte_counts['Actual Data'] += actual_nbytes - self._timer.stop('Write Time-Variant Metadata') - - # Write the time-series variables - if write_tser: - in_var = in_file.variables[out_name] - ndims = len(in_var.dimensions) - udidx = in_var.dimensions.index(self._unlimited_dim) - in_slice = [slice(None)] * ndims - in_slice[udidx] = slice(0, num_steps) - out_slice = [slice(None)] * ndims - out_slice[udidx] = slice(series_step_index, - series_step_index + num_steps) - self._timer.start('Read Time-Series Variables') - tmp_data = in_var[tuple(in_slice)] - print numpy.shape(tmp_data) - print out_slice - self._timer.stop('Read Time-Series Variables') - self._timer.start('Write Time-Series Variables') - out_var[tuple(out_slice)] = tmp_data - self._timer.stop('Write Time-Series Variables') - - requested_nbytes = in_file.variables[ - out_name][:].nbytes - self._byte_counts['Requested Data'] += requested_nbytes - actual_nbytes = self.assumed_block_size \ - * numpy.ceil(requested_nbytes / self.assumed_block_size) - self._byte_counts['Actual Data'] += actual_nbytes - # Increment the time-series step index - series_step_index += num_steps + # Increment the time-series step index + series_step_index += 1 # Close the output file self._timer.start('Close Output Files') From 2d033024bc7ab464d61e31094292ee687ea4a436 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Tue, 29 Sep 2015 16:11:45 -0600 Subject: [PATCH 198/250] Timer bugfix. --- source/pyreshaper/reshaper.py | 1 - 1 file changed, 1 deletion(-) diff --git a/source/pyreshaper/reshaper.py b/source/pyreshaper/reshaper.py index ded2284..bfaf531 100644 --- a/source/pyreshaper/reshaper.py +++ b/source/pyreshaper/reshaper.py @@ -818,7 +818,6 @@ def _get_once_info(vname): actual_nbytes = self.assumed_block_size \ * numpy.ceil(requested_nbytes / self.assumed_block_size) self._byte_counts['Actual Data'] += actual_nbytes - self._timer.stop('Write Time-Variant Metadata') # Write the time-series variables if write_tser: From 38bf30a474a02db84551722cb3c6a135b012325f Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Tue, 29 Sep 2015 16:15:39 -0600 Subject: [PATCH 199/250] Can't reliably get time-invariant metadata sizes --- source/pyreshaper/reshaper.py | 7 ------- 1 file changed, 7 deletions(-) diff --git a/source/pyreshaper/reshaper.py b/source/pyreshaper/reshaper.py index bfaf531..1a1607a 100644 --- a/source/pyreshaper/reshaper.py +++ b/source/pyreshaper/reshaper.py @@ -776,13 +776,6 @@ def _get_once_info(vname): out_meta.assign_value(tmp_data) self._timer.stop('Write Time-Invariant Metadata') - requested_nbytes = in_meta[:].nbytes - self._byte_counts[ - 'Requested Data'] += requested_nbytes - actual_nbytes = self.assumed_block_size \ - * numpy.ceil(requested_nbytes / self.assumed_block_size) - self._byte_counts['Actual Data'] += actual_nbytes - # Write each time-variant variable series_step_index = 0 for in_file in self._input_files: From 9b97f88f10bbd7673747fa488779a392fc8c0f29 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Wed, 30 Sep 2015 08:46:17 -0600 Subject: [PATCH 200/250] Some cleanup. Adds get_bytesize function to get metadata sizes safely. --- source/pyreshaper/reshaper.py | 52 +++++++++++++++++++++++------------ 1 file changed, 34 insertions(+), 18 deletions(-) diff --git a/source/pyreshaper/reshaper.py b/source/pyreshaper/reshaper.py index 1a1607a..b089cc7 100644 --- a/source/pyreshaper/reshaper.py +++ b/source/pyreshaper/reshaper.py @@ -11,12 +11,14 @@ # Built-in imports import abc -import os -import itertools +from os import linesep, remove +from os.path import exists, isfile +from itertools import chain # Third-party imports -import Nio import numpy +from Nio import open_file as nio_open_file +from Nio import options as nio_options from asaptools.simplecomm import create_comm, SimpleComm from asaptools.timekeeper import TimeKeeper from asaptools.partition import WeightBalanced @@ -141,8 +143,8 @@ def _pprint_dictionary(title, dictionary, order=None): print_order.append(item) # Header line with Title - hline = '-' * 50 + os.linesep - ostr = hline + ' ' + title.upper() + ':' + os.linesep + hline + hline = '-' * 50 + linesep + ostr = hline + ' ' + title.upper() + ':' + linesep + hline # Determine the longest timer name # and thus computer the column to line up values @@ -156,7 +158,7 @@ def _pprint_dictionary(title, dictionary, order=None): for name in print_order: spacer = ' ' * (valcol - len(str(name))) ostr += str(name) + ':' + spacer - ostr += str(dictionary[name]) + os.linesep + ostr += str(dictionary[name]) + linesep ostr += hline return ostr @@ -287,7 +289,7 @@ def __init__(self, specifier, serial=False, verbosity=1, self._vprint('Specifier validated', verbosity=1) # Setup PyNIO options (including disabling the default PreFill option) - opt = Nio.options() + opt = nio_options() opt.PreFill = False # Determine the Format and CompressionLevel options @@ -308,7 +310,7 @@ def __init__(self, specifier, serial=False, verbosity=1, self._timer.start('Open Input Files') self._input_files = [] for filename in specifier.input_file_list: - self._input_files.append(Nio.open_file(filename, "r")) + self._input_files.append(nio_open_file(filename, "r")) self._timer.stop('Open Input Files') if self._simplecomm.is_manager(): self._vprint('Input files opened', verbosity=2) @@ -404,7 +406,7 @@ def _validate_input_files(self, specifier): missing_vars.update(var_names - var_names_next) if len(missing_vars) != 0: warning = "WARNING: The first input file has variables that are " \ - + "not in all input files:" + os.linesep + ' ' + + "not in all input files:" + linesep + ' ' for var in missing_vars: warning += ' ' + str(var) self._vprint(warning, header=True, verbosity=1) @@ -474,8 +476,7 @@ def _sort_input_files_by_time(self, specifier): # Now that this is validated, let's string together the numpy array # of all times (using the new_values array) self._all_time_values = \ - numpy.fromiter(itertools.chain.from_iterable(new_values), - dtype='float') + numpy.fromiter(chain.from_iterable(new_values), dtype='float') def _sort_variables(self, specifier): """ @@ -566,7 +567,7 @@ def _validate_output_files(self, specifier, # Find which files already exist existing = [] for variable, filename in self._time_series_filenames.items(): - if os.path.isfile(filename): + if isfile(filename): existing.append(variable) # If overwrite is enabled, delete all existing files first @@ -576,7 +577,7 @@ def _validate_output_files(self, specifier, 'time-series variables: ' + str(existing), verbosity=1) for variable in existing: - os.remove(self._time_series_filenames[variable]) + remove(self._time_series_filenames[variable]) # Or, if skip_existing is set, remove the existing time-series # variables from the list of time-series variables to convert @@ -669,6 +670,14 @@ def _get_once_info(vname): write_tser = not is_once_file return is_once_file, write_meta, write_tser + # Defining a simple helper function to determine the bytes size of + # a variable given to it, whether an NDArray or not + def _get_bytesize(data): + if hasattr(data, 'nbytes'): + return data.nbytes + else: + return 0 + # NOTE: In the prototype, we check for the existance of the output # directory at this point. If it does not exist, we create it (but # only from the master rank). This requires synchronization with @@ -693,10 +702,10 @@ def _get_once_info(vname): # Open each output file and create the dimensions and attributes # NOTE: If the output file already exists, abort! self._timer.start('Open Output Files') - if os.path.exists(out_filename): + if exists(out_filename): err_msg = 'Found existing output file: ' + out_filename raise OSError(err_msg) - out_file = Nio.open_file(out_filename, 'w', + out_file = nio_open_file(out_filename, 'w', options=self._nio_options) for att_name, att_val in common_atts.iteritems(): setattr(out_file, att_name, att_val) @@ -776,6 +785,13 @@ def _get_once_info(vname): out_meta.assign_value(tmp_data) self._timer.stop('Write Time-Invariant Metadata') + requested_nbytes = _get_bytesize(tmp_data) + self._byte_counts[ + 'Requested Data'] += requested_nbytes + actual_nbytes = self.assumed_block_size \ + * numpy.ceil(requested_nbytes / self.assumed_block_size) + self._byte_counts['Actual Data'] += actual_nbytes + # Write each time-variant variable series_step_index = 0 for in_file in self._input_files: @@ -805,7 +821,7 @@ def _get_once_info(vname): out_meta[tuple(out_slice)] = tmp_data self._timer.stop('Write Time-Variant Metadata') - requested_nbytes = in_meta[tuple(in_slice)].nbytes + requested_nbytes = _get_bytesize(tmp_data) self._byte_counts[ 'Requested Data'] += requested_nbytes actual_nbytes = self.assumed_block_size \ @@ -828,7 +844,7 @@ def _get_once_info(vname): out_var[tuple(out_slice)] = tmp_data self._timer.stop('Write Time-Series Variables') - requested_nbytes = in_var[tuple(in_slice)].nbytes + requested_nbytes = _get_bytesize(tmp_data) self._byte_counts['Requested Data'] += requested_nbytes actual_nbytes = self.assumed_block_size \ * numpy.ceil(requested_nbytes / self.assumed_block_size) @@ -1032,7 +1048,7 @@ def convert(self, output_limit=0): if self._simplecomm.is_manager(): self._vprint('--- Finished converting Specifier: ' + - str(spec_name) + os.linesep, verbosity=0) + str(spec_name) + linesep, verbosity=0) self._simplecomm.sync() def print_diagnostics(self): From c6065a481a8923ef40156943e1137829c3488afe Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Wed, 30 Sep 2015 15:24:46 -0600 Subject: [PATCH 201/250] Removed unnecessary variable dictionary --- source/pyreshaper/reshaper.py | 17 ++++++++--------- 1 file changed, 8 insertions(+), 9 deletions(-) diff --git a/source/pyreshaper/reshaper.py b/source/pyreshaper/reshaper.py index b089cc7..5e90d50 100644 --- a/source/pyreshaper/reshaper.py +++ b/source/pyreshaper/reshaper.py @@ -11,6 +11,7 @@ # Built-in imports import abc +import time from os import linesep, remove from os.path import exists, isfile from itertools import chain @@ -688,7 +689,6 @@ def _get_bytesize(data): # For each time-series variable, create the corresponding output file # (Also defines the header info for each output file) out_files = {} - out_tvm_vars = {} for out_name in tsv_names_loc: is_once_file, write_meta, write_tser = _get_once_info(out_name) @@ -721,9 +721,8 @@ def _get_bytesize(data): self._timer.start('Create Time-Invariant Metadata') for name in self._time_invariant_metadata: in_var = ref_infile.variables[name] - out_var = out_file.create_variable(name, - in_var.typecode(), - in_var.dimensions) + out_var = out_file.create_variable( + name, in_var.typecode(), in_var.dimensions) for att_name, att_val in in_var.attributes.iteritems(): setattr(out_var, att_name, att_val) self._timer.stop('Create Time-Invariant Metadata') @@ -733,18 +732,18 @@ def _get_bytesize(data): self._timer.start('Create Time-Variant Metadata') for name in self._time_variant_metadata: in_var = ref_infile.variables[name] - out_tvm_vars[name] = out_file.create_variable(name, - in_var.typecode(), in_var.dimensions) + out_var = out_file.create_variable( + name, in_var.typecode(), in_var.dimensions) for att_name, att_val in in_var.attributes.iteritems(): - setattr(out_tvm_vars[name], att_name, att_val) + setattr(out_var, att_name, att_val) self._timer.stop('Create Time-Variant Metadata') # Create the time-series variable itself if write_tser: self._timer.start('Create Time-Series Variables') in_var = ref_infile.variables[out_name] - out_var = out_file.create_variable(out_name, - in_var.typecode(), in_var.dimensions) + out_var = out_file.create_variable( + out_name, in_var.typecode(), in_var.dimensions) self._timer.stop('Create Time-Series Variables') # Append the output file to list From 7e52cb96e8c70955ffde33054907a9a4a7d4444b Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 1 Oct 2015 10:03:34 -0600 Subject: [PATCH 202/250] Renaming results directory --- tests/yellowstone/checkresults.py | 2 +- tests/yellowstone/mktimings.py | 2 +- tests/yellowstone/runtests.py | 4 ++-- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index 39353de..14f7e53 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -148,7 +148,7 @@ def compare(self, nc1, nc2, outfile=None, alltimes=True, verbose=False): if len(args.rundir) > 0: rundirs = args.rundir else: - rundirs = glob.glob(os.path.join('results.d', '*', '[ser,par]*', '*')) + rundirs = glob.glob(os.path.join('results', '*', '[ser,par]*', '*')) # Get the list of valid run names and the output directory pattern if args.multispec: diff --git a/tests/yellowstone/mktimings.py b/tests/yellowstone/mktimings.py index 1c73505..2a4fa1a 100755 --- a/tests/yellowstone/mktimings.py +++ b/tests/yellowstone/mktimings.py @@ -57,7 +57,7 @@ def find_shortest_str(strng, left, right=os.linesep, loc=0): cwd = os.getcwd() # Extract each possible test - for rundir in glob.iglob(os.path.join('results.d', '*', '[ser,par]*', '*')): + for rundir in glob.iglob(os.path.join('results', '*', '[ser,par]*', '*')): print print 'Extracting times from test dir:', rundir print diff --git a/tests/yellowstone/runtests.py b/tests/yellowstone/runtests.py index 83296ef..2b33906 100755 --- a/tests/yellowstone/runtests.py +++ b/tests/yellowstone/runtests.py @@ -179,7 +179,7 @@ def runmultitest(tests, nodes=0, tiling=16, minutes=120, else: runtype = 'ser' testdir = os.path.abspath( - os.path.join('results.d', 'multitest', runtype, ncformat)) + os.path.join('results', 'multitest', runtype, ncformat)) # If the test directory doesn't exist, make it and move into it cwd = os.getcwd() @@ -266,7 +266,7 @@ def runindivtests(tests, nodes=0, tiling=16, minutes=120, else: runtype = 'ser' testdir = os.path.abspath( - os.path.join('results.d', str(test_name), runtype, ncformat)) + os.path.join('results', str(test_name), runtype, ncformat)) # If the test directory doesn't exist, make it and move into it if os.path.exists(testdir): From 75172bc65f39146dd857229198f5f8fe6bed19c7 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 1 Oct 2015 10:14:22 -0600 Subject: [PATCH 203/250] Fixed unrecognized characters in JSON data --- tests/yellowstone/testinfo.json | 34 ++++++++++++++++----------------- 1 file changed, 17 insertions(+), 17 deletions(-) diff --git a/tests/yellowstone/testinfo.json b/tests/yellowstone/testinfo.json index 3d2db88..8fd2c22 100644 --- a/tests/yellowstone/testinfo.json +++ b/tests/yellowstone/testinfo.json @@ -163,12 +163,12 @@ "time_written" ] }, - "camhf—monthly-1deg":{ - "common_name":"CAMHF-MONTHLY-1.0”, - "input_dir":"/glade/u/tdd/asap/bakeoff/hist/camhf-monthly-1.0”, - "results_dir":"/glade/u/tdd/asap/bakeoff/tseries/camhf—monthly-1.0”, + "camhf-monthly-1deg":{ + "common_name":"CAMHF-MONTHLY-1.0", + "input_dir":"/glade/u/tdd/asap/bakeoff/hist/camhf-monthly-1.0", + "results_dir":"/glade/u/tdd/asap/bakeoff/tseries/camhf-monthly-1.0", "input_globs":[ - “b.e11.BDP.f09_g16.1958-11.002.cam.h0.19*.nc” + "b.e11.BDP.f09_g16.1958-11.002.cam.h0.19*.nc" ], "output_prefix":"b.e11.BDP.f09_g16.1958-11.002.cam.h0.", "output_suffix":".195811-196810.nc", @@ -190,14 +190,14 @@ "time" ] }, - "camhf—daily-1deg":{ - "common_name":"CAMHF-DAILY-1.0”, - "input_dir":"/glade/u/tdd/asap/bakeoff/hist/camhf-daily-1.0”, - "results_dir":"/glade/u/tdd/asap/bakeoff/tseries/camhf—daily-1.0”, + "camhf-daily-1deg":{ + "common_name":"CAMHF-DAILY-1.0", + "input_dir":"/glade/u/tdd/asap/bakeoff/hist/camhf-daily-1.0", + "results_dir":"/glade/u/tdd/asap/bakeoff/tseries/camhf-daily-1.0", "input_globs":[ - “b.e11.BDP.f09_g16.1958-11.002.cam.h1.19*.nc” + "b.e11.BDP.f09_g16.1958-11.002.cam.h1.19*.nc" ], - "output_prefix":"b.e11.BDP.f09_g16.1958-11.002.cam.h1.”, + "output_prefix":"b.e11.BDP.f09_g16.1958-11.002.cam.h1.", "output_suffix":".195811-196810.nc", "metadata":[ "ch4vmr", @@ -217,14 +217,14 @@ "time" ] }, - "camhf—6hourly-1deg":{ - "common_name":"CAMHF-6HOURLY-1.0”, - "input_dir":"/glade/u/tdd/asap/bakeoff/hist/camhf-6hourly-1.0”, - "results_dir":"/glade/u/tdd/asap/bakeoff/tseries/camhf—6hourly-1.0”, + "camhf-6hourly-1deg":{ + "common_name":"CAMHF-6HOURLY-1.0", + "input_dir":"/glade/u/tdd/asap/bakeoff/hist/camhf-6hourly-1.0", + "results_dir":"/glade/u/tdd/asap/bakeoff/tseries/camhf-6hourly-1.0", "input_globs":[ - “b.e11.BDP.f09_g16.1958-11.002.cam.h2.19*.nc” + "b.e11.BDP.f09_g16.1958-11.002.cam.h2.19*.nc" ], - "output_prefix":"b.e11.BDP.f09_g16.1958-11.002.cam.h2.”, + "output_prefix":"b.e11.BDP.f09_g16.1958-11.002.cam.h2.", "output_suffix":".195811-196810.nc", "metadata":[ "ch4vmr", From 4e009c7f3c2f69d364d27a6ded16e2dc9e7d7867 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 1 Oct 2015 11:01:44 -0600 Subject: [PATCH 204/250] Changing "save_statistics" call to just "save" --- tests/yellowstone/mkstats.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/mkstats.py b/tests/yellowstone/mkstats.py index 968f3e9..4fc0b04 100755 --- a/tests/yellowstone/mkstats.py +++ b/tests/yellowstone/mkstats.py @@ -73,4 +73,4 @@ statdb.analyze(testdb, tests=test_list, force=args.overwrite) # Save to the stats file - statdb.save_statistics(name=args.statsfile) + statdb.save(name=args.statsfile) From ed41a14a7a1ba60f295a7b914bc59d97f6c09435 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 1 Oct 2015 11:10:36 -0600 Subject: [PATCH 205/250] Changing the JSON save format to something human-readable --- tests/yellowstone/utilities/testtools.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index fdd5086..a1eb6d7 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -516,7 +516,8 @@ def save(self, name="teststats.json"): # Dump JSON data to file try: - json.dump(self._statistics, fp) + json.dump(self._statistics, fp, sort_keys=True, + indent=3, separators=(',', ': ')) except: err_msg = "Failed to write statistics file" raise RuntimeError(err_msg) @@ -750,7 +751,8 @@ def save(self, name="timings.json"): # Dump JSON data to file try: - json.dump(self._timings, fp) + json.dump(self._timings, fp, sort_keys=True, + indent=3, separators=(',', ': ')) except: err_msg = "Failed to write statistics file" raise RuntimeError(err_msg) From 5d50481a006cc3bd997d81d23046e00785bcbea3 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 1 Oct 2015 11:17:30 -0600 Subject: [PATCH 206/250] Adding updated statistics file --- tests/yellowstone/teststats.json | 28483 ++++++++++++++++------------- 1 file changed, 15666 insertions(+), 12817 deletions(-) diff --git a/tests/yellowstone/teststats.json b/tests/yellowstone/teststats.json index c790731..64baa47 100644 --- a/tests/yellowstone/teststats.json +++ b/tests/yellowstone/teststats.json @@ -1,16662 +1,19520 @@ { - "clmse-0.25deg":{ - "maxsizes":{ - "tseries":5598734400, - "tinvariant":46656120, - "tvariant":1920 + "camfv-1deg": { + "counts": { + "other": 0, + "tinvariant": 26, + "tseries": 122, + "tvariant": 15 }, - "variables":{ - "URBAN_AC":{ - "xshape":[ - 777602 + "length": 120, + "maxsizes": { + "tinvariant": 2304, + "tseries": 716636160, + "tvariant": 1920 + }, + "names": { + "other": [], + "tinvariant": [ + "gw", + "nbdate", + "ntrm", + "ntrn", + "nsbase", + "slon", + "ndbase", + "hybi", + "mdt", + "P0", + "ilev", + "lev", + "hybm", + "wnummax", + "lat", + "lon", + "nbsec", + "w_stag", + "slat", + "isccp_prs", + "isccp_prstau", + "ntrk", + "hyai", + "hyam", + "isccp_tau", + "nlon" + ], + "tseries": [ + "cb_sulf_c", + "ODV_bcar2", + "FSNTOAC", + "TS", + "ODV_SSLTC", + "ODV_SSLTA", + "QREFHT", + "FSNS", + "FSNT", + "CLDLIQ", + "DCQ", + "ODV_dust4", + "PRECSC", + "ODV_dust1", + "ODV_dust3", + "ODV_dust2", + "PRECSH", + "PRECSL", + "ODV_bcar1", + "CMFDQ", + "CLDMED", + "FSDS", + "FSNTOA", + "CLDLOW", + "SWCF", + "SFCLDICE", + "DTV", + "PS", + "CLDTOT", + "CMFMCDZM", + "FLDSC", + "TAUX", + "TAUY", + "SRFRAD", + "Z3", + "TREFMXAV", + "SHFLX", + "FLNSC", + "RELHUM", + "TROP_P", + "QFLX", + "PSL", + "UU", + "LCLOUD", + "LANDFRAC", + "FLNT", + "US", + "PRECT", + "TROP_Z", + "ICEFRAC", + "PRECL", + "PRECC", + "TROP_T", + "ODV_VOLC_MMR", + "FLNTC", + "VU", + "TMQ", + "NDROPCOL", + "CMFDQR", + "FREQZM", + "LWCF", + "FLDS", + "VD01", + "TGCLDIWP", + "AEROD_v", + "SNOWHLND", + "TREFMNAV", + "PHIS", + "FSUTOA", + "OMEGA", + "FLUT", + "PBLH", + "TREFHT", + "FICE", + "NDROPSNK", + "FSDSC", + "ICLDTWP", + "V", + "CONCLD", + "NDROPMIX", + "WTKE", + "CLDHGH", + "ICLDIWP", + "cb_ozone_c", + "SFCLDLIQ", + "QC", + "RHREFHT", + "FLNS", + "PCONVT", + "SOLIN", + "DTCOND", + "PCONVB", + "GCLDLWP", + "NDROPSRC", + "FSNTC", + "U", + "ODV_ocar1", + "ODV_ocar2", + "OCNFRAC", + "QRL", + "FLUTC", + "QRS", + "OMEGAT", + "TGCLDLWP", + "CLOUD", + "LHFLX", + "TSMN", + "PRECCDZM", + "ODV_sulf", + "Q", + "VQ", + "VS", + "VT", + "FREQSH", + "VV", + "FSNSC", + "TSMX", + "CMFDT", + "SNOWHICE", + "T", + "CLDICE", + "CMFMC" + ], + "tvariant": [ + "ch4vmr", + "time_bnds", + "nsteph", + "co2vmr", + "date_written", + "datesec", + "f11vmr", + "time_written", + "n2ovmr", + "ndcur", + "f12vmr", + "sol_tsi", + "date", + "nscur", + "time" + ] + }, + "totalsizes": { + "tinvariant": 14088, + "tseries": 29829703680, + "tvariant": 11040 + }, + "variables": { + "AEROD_v": { + "meta": false, + "tvariant": true, + "xshape": [ + 192, + 288 ], - "meta":false, - "xsize":3110408, - "tvariant":true + "xsize": 221184 }, - "QSOIL":{ - "xshape":[ - 777602 + "CLDHGH": { + "meta": false, + "tvariant": true, + "xshape": [ + 192, + 288 ], - "meta":false, - "xsize":3110408, - "tvariant":true + "xsize": 221184 }, - "WA":{ - "xshape":[ - 777602 + "CLDICE": { + "meta": false, + "tvariant": true, + "xshape": [ + 26, + 192, + 288 ], - "meta":false, - "xsize":3110408, - "tvariant":true + "xsize": 5750784 }, - "ZBOT":{ - "xshape":[ - 777602 + "CLDLIQ": { + "meta": false, + "tvariant": true, + "xshape": [ + 26, + 192, + 288 ], - "meta":false, - "xsize":3110408, - "tvariant":true + "xsize": 5750784 }, - "WT":{ - "xshape":[ - 777602 + "CLDLOW": { + "meta": false, + "tvariant": true, + "xshape": [ + 192, + 288 ], - "meta":false, - "xsize":3110408, - "tvariant":true + "xsize": 221184 }, - "GC_HEAT1":{ - "xshape":[ - 777602 + "CLDMED": { + "meta": false, + "tvariant": true, + "xshape": [ + 192, + 288 ], - "meta":false, - "xsize":3110408, - "tvariant":true + "xsize": 221184 }, - "nstep":{ - "xshape":[ - + "CLDTOT": { + "meta": false, + "tvariant": true, + "xshape": [ + 192, + 288 ], - "meta":true, - "xsize":4, - "tvariant":true + "xsize": 221184 }, - "DSTDEP":{ - "xshape":[ - 777602 + "CLOUD": { + "meta": false, + "tvariant": true, + "xshape": [ + 26, + 192, + 288 ], - "meta":false, - "xsize":3110408, - "tvariant":true + "xsize": 5750784 }, - "SNOOCMSL":{ - "xshape":[ - 777602 + "CMFDQ": { + "meta": false, + "tvariant": true, + "xshape": [ + 26, + 192, + 288 ], - "meta":false, - "xsize":3110408, - "tvariant":true + "xsize": 5750784 }, - "FSNO":{ - "xshape":[ - 777602 + "CMFDQR": { + "meta": false, + "tvariant": true, + "xshape": [ + 26, + 192, + 288 ], - "meta":false, - "xsize":3110408, - "tvariant":true + "xsize": 5750784 }, - "FGR":{ - "xshape":[ - 777602 + "CMFDT": { + "meta": false, + "tvariant": true, + "xshape": [ + 26, + 192, + 288 ], - "meta":false, - "xsize":3110408, - "tvariant":true + "xsize": 5750784 }, - "FSDSVDLN":{ - "xshape":[ - 777602 + "CMFMC": { + "meta": false, + "tvariant": true, + "xshape": [ + 27, + 192, + 288 ], - "meta":false, - "xsize":3110408, - "tvariant":true + "xsize": 5971968 }, - "QBOT":{ - "xshape":[ - 777602 + "CMFMCDZM": { + "meta": false, + "tvariant": true, + "xshape": [ + 27, + 192, + 288 ], - "meta":false, - "xsize":3110408, - "tvariant":true + "xsize": 5971968 }, - "FSRNDLN":{ - "xshape":[ - 777602 + "CONCLD": { + "meta": false, + "tvariant": true, + "xshape": [ + 26, + 192, + 288 ], - "meta":false, - "xsize":3110408, - "tvariant":true + "xsize": 5750784 }, - "SNOW_SOURCES":{ - "xshape":[ - 777602 + "DCQ": { + "meta": false, + "tvariant": true, + "xshape": [ + 26, + 192, + 288 ], - "meta":false, - "xsize":3110408, - "tvariant":true + "xsize": 5750784 }, - "FSM_R":{ - "xshape":[ - 777602 + "DTCOND": { + "meta": false, + "tvariant": true, + "xshape": [ + 26, + 192, + 288 ], - "meta":false, - "xsize":3110408, - "tvariant":true + "xsize": 5750784 }, - "TSOI":{ - "xshape":[ - 15, - 777602 + "DTV": { + "meta": false, + "tvariant": true, + "xshape": [ + 26, + 192, + 288 ], - "meta":false, - "xsize":46656120, - "tvariant":true + "xsize": 5750784 }, - "TBOT":{ - "xshape":[ - 777602 + "FICE": { + "meta": false, + "tvariant": true, + "xshape": [ + 26, + 192, + 288 ], - "meta":false, - "xsize":3110408, - "tvariant":true + "xsize": 5750784 }, - "QRGWL":{ - "xshape":[ - 777602 + "FLDS": { + "meta": false, + "tvariant": true, + "xshape": [ + 192, + 288 ], - "meta":false, - "xsize":3110408, - "tvariant":true + "xsize": 221184 }, - "TG":{ - "xshape":[ - 777602 + "FLDSC": { + "meta": false, + "tvariant": true, + "xshape": [ + 192, + 288 ], - "meta":false, - "xsize":3110408, - "tvariant":true + "xsize": 221184 }, - "OCDEP":{ - "xshape":[ - 777602 + "FLNS": { + "meta": false, + "tvariant": true, + "xshape": [ + 192, + 288 ], - "meta":false, - "xsize":3110408, - "tvariant":true + "xsize": 221184 }, - "SoilAlpha_U":{ - "xshape":[ - 777602 + "FLNSC": { + "meta": false, + "tvariant": true, + "xshape": [ + 192, + 288 ], - "meta":false, - "xsize":3110408, - "tvariant":true + "xsize": 221184 }, - "TAUX":{ - "xshape":[ - 777602 + "FLNT": { + "meta": false, + "tvariant": true, + "xshape": [ + 192, + 288 ], - "meta":false, - "xsize":3110408, - "tvariant":true + "xsize": 221184 }, - "levgrnd":{ - "xshape":[ - 15 + "FLNTC": { + "meta": false, + "tvariant": true, + "xshape": [ + 192, + 288 ], - "meta":true, - "xsize":60, - "tvariant":false + "xsize": 221184 }, - "FSDSNDLN":{ - "xshape":[ - 777602 - ], - "meta":false, - "xsize":3110408, - "tvariant":true - }, - "TREFMXAV_U":{ - "xshape":[ - 777602 + "FLUT": { + "meta": false, + "tvariant": true, + "xshape": [ + 192, + 288 ], - "meta":false, - "xsize":3110408, - "tvariant":true + "xsize": 221184 }, - "QRUNOFF_NODYNLNDUSE":{ - "xshape":[ - 777602 + "FLUTC": { + "meta": false, + "tvariant": true, + "xshape": [ + 192, + 288 ], - "meta":false, - "xsize":3110408, - "tvariant":true + "xsize": 221184 }, - "mdcur":{ - "xshape":[ - + "FREQSH": { + "meta": false, + "tvariant": true, + "xshape": [ + 192, + 288 ], - "meta":true, - "xsize":4, - "tvariant":true + "xsize": 221184 }, - "TLAI":{ - "xshape":[ - 777602 + "FREQZM": { + "meta": false, + "tvariant": true, + "xshape": [ + 192, + 288 ], - "meta":false, - "xsize":3110408, - "tvariant":true + "xsize": 221184 }, - "FIRA_R":{ - "xshape":[ - 777602 + "FSDS": { + "meta": false, + "tvariant": true, + "xshape": [ + 192, + 288 ], - "meta":false, - "xsize":3110408, - "tvariant":true + "xsize": 221184 }, - "FSDS":{ - "xshape":[ - 777602 + "FSDSC": { + "meta": false, + "tvariant": true, + "xshape": [ + 192, + 288 ], - "meta":false, - "xsize":3110408, - "tvariant":true + "xsize": 221184 }, - 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false, + "xshape": [], + "xsize": 8 + }, + "sound": { + "meta": true, + "tvariant": false, + "xshape": [], + "xsize": 8 + }, + "stefan_boltzmann": { + "meta": true, + "tvariant": false, + "xshape": [], + "xsize": 8 + }, + "time": { + "meta": true, + "tvariant": true, + "xshape": [], + "xsize": 8 + }, + "time_bound": { + "meta": true, + "tvariant": true, + "xshape": [ + 2 ], - "meta":true, - "xsize":8, - "tvariant":true + "xsize": 16 }, - "dzw":{ - "xshape":[ - 60 - ], - "meta":true, - "xsize":240, - "tvariant":false + "vonkar": { + "meta": true, + "tvariant": false, + "xshape": [], + "xsize": 8 }, - "z_w_bot":{ - "xshape":[ + "z_t": { + "meta": true, + "tvariant": false, + "xshape": [ 60 ], - "meta":true, - "xsize":240, - "tvariant":false + "xsize": 240 }, - "salt_to_Svppt":{ - "xshape":[ - + "z_t_150m": { + "meta": true, + "tvariant": false, + "xshape": [ + 15 ], - "meta":true, - "xsize":8, - "tvariant":false + "xsize": 60 }, - "TAREA":{ - "xshape":[ - 384, - 320 + "z_w": { + "meta": true, + "tvariant": false, + "xshape": [ + 60 ], - "meta":true, - "xsize":983040, - "tvariant":false + "xsize": 240 }, - "UAREA":{ - "xshape":[ - 384, - 320 + "z_w_bot": { + "meta": true, + "tvariant": false, + "xshape": [ + 60 ], - "meta":true, - "xsize":983040, - "tvariant":false + "xsize": 240 }, - "days_in_norm_year":{ - "xshape":[ - + "z_w_top": { + "meta": true, + "tvariant": false, + "xshape": [ + 60 ], - "meta":true, - "xsize":8, - "tvariant":false + "xsize": 240 } }, - "xcoords":{ - "z_t":60, - "z_w":60, - "nlat":384, - "z_t_150m":15, - "z_w_top":60, - "z_w_bot":60, - "d2":2, - "nlon":320 - }, - "length":3285, - "names":{ - "other":[ - - ], - "tseries":[ - "SST2", - "XMXL_2", - "HMXL_2", - "SST" - ], - "tinvariant":[ - "latent_heat_fusion", - "DXT", - "REGION_MASK", - "hflux_factor", - "HT", - "z_w_top", - "ANGLET", - "KMU", - "KMT", - "radius", - "ANGLE", - "cp_sw", - "mass_to_Sv", - "rho_fw", - "z_t", - "ULONG", - "z_w", - "DYT", - "DYU", - "fwflux_factor", - "HUW", - "salt_to_ppt", - "HUS", - "TLONG", - "sea_ice_salinity", - "salt_to_mmday", - "rho_sw", - "nsurface_t", - "rho_air", - "z_t_150m", - "nsurface_u", - "sflux_factor", - "stefan_boltzmann", - "dz", - "cp_air", - "momentum_factor", - "ULAT", - "HU", - "omega", - "sound", - "HTE", - "TLAT", - "latent_heat_vapor", - "heat_to_PW", - "vonkar", - "HTN", - "DXU", - "salinity_factor", - "ocn_ref_salinity", - "grav", - "T0_Kelvin", - "ppt_to_salt", - "dzw", - "z_w_bot", - "salt_to_Svppt", - "TAREA", - "UAREA", - "days_in_norm_year" - ], - "tvariant":[ - "time_bound", - "time" - ] + "xcoords": { + "d2": 2, + "nlat": 384, + "nlon": 320, + "z_t": 60, + "z_t_150m": 15, + "z_w": 60, + "z_w_bot": 60, + "z_w_top": 60 }, - "xshapes":{ - "tseries":[ - [ - 384, - 320 - ] - ], - "tinvariant":[ + "xshapes": { + "tinvariant": [ [ 384, 320 @@ -16664,32 +19522,23 @@ [ 15 ], - [ - - ], + [], [ 60 ] ], - "tvariant":[ + "tseries": [ + [ + 384, + 320 + ] + ], + "tvariant": [ [ 2 ], - [ - - ] + [] ] - }, - "counts":{ - "other":0, - "tseries":4, - "tinvariant":58, - "tvariant":2 - }, - "totalsizes":{ - "tseries":6458572800, - "tinvariant":19171020, - "tvariant":78840 } } } \ No newline at end of file From 8791cf74b4600e89cb7f3ecb3a5157c2a07ddb29 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 1 Oct 2015 11:46:34 -0600 Subject: [PATCH 207/250] Adding to CHANGE log new features --- CHANGES.rst | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/CHANGES.rst b/CHANGES.rst index a62f2b1..ffc67b7 100644 --- a/CHANGES.rst +++ b/CHANGES.rst @@ -85,3 +85,8 @@ VERSION 0.9.4 29 June 2015: - Newly automated versioning information + +1 October 2015: + - Bugfixes, performance improvements + - New yellowstone testing code + \ No newline at end of file From 0f47c11186f8c53e9d8d29cab975d0a56225632a Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 1 Oct 2015 12:04:53 -0600 Subject: [PATCH 208/250] Updating metadata names for new high-frequency datasets --- tests/yellowstone/testinfo.json | 126 ++++++++++++++++++++++++-------- 1 file changed, 96 insertions(+), 30 deletions(-) diff --git a/tests/yellowstone/testinfo.json b/tests/yellowstone/testinfo.json index 8fd2c22..e86e687 100644 --- a/tests/yellowstone/testinfo.json +++ b/tests/yellowstone/testinfo.json @@ -174,20 +174,42 @@ "output_suffix":".195811-196810.nc", "metadata":[ "ch4vmr", - "f12vmr", - "time_written", - "time_bnds", - "nsteph", - "date_written", "co2vmr", - "sol_tsi", - "datesec", "date", - "ndcur", - "n2ovmr", + "datesec", "f11vmr", + "f12vmr", + "n2ovmr", + "ndcur", "nscur", - "time" + "nsteph", + "sol_tsi", + "time", + "time_bnds", + "time_written", + "gw", + "hyai", + "hyam", + "hybi", + "hybm", + "ilev", + "lat", + "lev", + "lon", + "nlon", + "slat", + "slon", + "w_stag", + "wnummax", + "P0", + "mdt", + "nbdate", + "nbsec", + "ndbase", + "nsbase", + "ntrk", + "ntrm", + "ntrn" ] }, "camhf-daily-1deg":{ @@ -201,20 +223,42 @@ "output_suffix":".195811-196810.nc", "metadata":[ "ch4vmr", - "f12vmr", - "time_written", - "time_bnds", - "nsteph", - "date_written", "co2vmr", - "sol_tsi", - "datesec", "date", - "ndcur", - "n2ovmr", + "datesec", "f11vmr", + "f12vmr", + "n2ovmr", + "ndcur", "nscur", - "time" + "nsteph", + "sol_tsi", + "time", + "time_bnds", + "time_written", + "gw", + "hyai", + "hyam", + "hybi", + "hybm", + "ilev", + "lat", + "lev", + "lon", + "nlon", + "slat", + "slon", + "w_stag", + "wnummax", + "P0", + "mdt", + "nbdate", + "nbsec", + "ndbase", + "nsbase", + "ntrk", + "ntrm", + "ntrn" ] }, "camhf-6hourly-1deg":{ @@ -228,20 +272,42 @@ "output_suffix":".195811-196810.nc", "metadata":[ "ch4vmr", - "f12vmr", - "time_written", - "time_bnds", - "nsteph", - "date_written", "co2vmr", - "sol_tsi", - "datesec", "date", - "ndcur", - "n2ovmr", + "datesec", "f11vmr", + "f12vmr", + "n2ovmr", + "ndcur", "nscur", - "time" + "nsteph", + "sol_tsi", + "time", + "time_bnds", + "time_written", + "gw", + "hyai", + "hyam", + "hybi", + "hybm", + "ilev", + "lat", + "lev", + "lon", + "nlon", + "slat", + "slon", + "w_stag", + "wnummax", + "P0", + "mdt", + "nbdate", + "nbsec", + "ndbase", + "nsbase", + "ntrk", + "ntrm", + "ntrn" ] }, "clmse-1deg":{ From 7de6c875cb0ab114fb5f5d9bab97a700cf814ec0 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 1 Oct 2015 13:06:23 -0600 Subject: [PATCH 209/250] Setting better default for test info file name --- tests/yellowstone/checkresults.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index 14f7e53..1a4d058 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -28,9 +28,9 @@ help='The name of the project code for charging in ' 'parallel runs (ignored if running in serial) ' '[Default: STDD0002]') -_PARSER_.add_argument('-i', '--infofile', default=None, +_PARSER_.add_argument('-i', '--infofile', default='testinfo.json', help='Location of the testinfo.json file ' - '[Default: None]') + '[Default: testinfo.json]') _PARSER_.add_argument('-l', '--list', default=False, action='store_true', dest='list_tests', help='True or False, indicating whether to list all ' From 5a15b5d365bc3a6a803ed493d2cc9775d5eee44c Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 1 Oct 2015 13:11:12 -0600 Subject: [PATCH 210/250] Adding code to list tests only --- tests/yellowstone/checkresults.py | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index 1a4d058..9f554b7 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -207,6 +207,16 @@ def compare(self, nc1, nc2, outfile=None, alltimes=True, verbose=False): tests_to_check[test_name]['old'] = olddir tests_to_check[test_name]['cpr'] = cprncdir + # List and quit, if just listing + if args.list_tests: + print + print "Tests for checking:" + print + for test_name in tests_to_check: + print " {}".format(test_name) + print + sys.exit(0) + # Expand the test directories into individual file-test dictionaries items_to_check = [] unchecked_new_items = [] From 1351e2f1b5a32e2ec9772e408d02e4442f82bc06 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 1 Oct 2015 13:19:12 -0600 Subject: [PATCH 211/250] Adding debugging info --- tests/yellowstone/checkresults.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index 9f554b7..c8dc89c 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -322,6 +322,8 @@ def compare(self, nc1, nc2, outfile=None, alltimes=True, verbose=False): for i in range(comm.get_size() - 1): results.extend(comm.collect()) + print results + for test_name, test_info in tests_to_check.items(): summfile = os.path.join(test_info['run'], test_name + '.cprnc') sfile = open(summfile, 'w') From e2c45e85dc562b60e39778d6e84fa976c981d7fb Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 1 Oct 2015 13:31:23 -0600 Subject: [PATCH 212/250] Add collected data only (ignore rank info) --- tests/yellowstone/checkresults.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index c8dc89c..6a9c732 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -320,7 +320,7 @@ def compare(self, nc1, nc2, outfile=None, alltimes=True, verbose=False): if comm.is_manager(): results = local_results for i in range(comm.get_size() - 1): - results.extend(comm.collect()) + results.extend(comm.collect()[1]) print results From 8f5bc1a30847575578b03753deb9ef95ab8dcc4a Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 1 Oct 2015 13:35:43 -0600 Subject: [PATCH 213/250] Remove debugging output --- tests/yellowstone/checkresults.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index 6a9c732..782a234 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -322,8 +322,6 @@ def compare(self, nc1, nc2, outfile=None, alltimes=True, verbose=False): for i in range(comm.get_size() - 1): results.extend(comm.collect()[1]) - print results - for test_name, test_info in tests_to_check.items(): summfile = os.path.join(test_info['run'], test_name + '.cprnc') sfile = open(summfile, 'w') From 750073163419c87e9c225458486729e3a3e071c2 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 1 Oct 2015 14:27:03 -0600 Subject: [PATCH 214/250] Printing more information when listing tests --- tests/yellowstone/checkresults.py | 12 +----------- 1 file changed, 1 insertion(+), 11 deletions(-) diff --git a/tests/yellowstone/checkresults.py b/tests/yellowstone/checkresults.py index 782a234..23ffa00 100755 --- a/tests/yellowstone/checkresults.py +++ b/tests/yellowstone/checkresults.py @@ -207,16 +207,6 @@ def compare(self, nc1, nc2, outfile=None, alltimes=True, verbose=False): tests_to_check[test_name]['old'] = olddir tests_to_check[test_name]['cpr'] = cprncdir - # List and quit, if just listing - if args.list_tests: - print - print "Tests for checking:" - print - for test_name in tests_to_check: - print " {}".format(test_name) - print - sys.exit(0) - # Expand the test directories into individual file-test dictionaries items_to_check = [] unchecked_new_items = [] @@ -245,7 +235,7 @@ def compare(self, nc1, nc2, outfile=None, alltimes=True, verbose=False): unchecked_old_items.append(item_dict) # Get a basic MPI comm - comm = create_comm(serial=args.serial) + comm = create_comm(serial=(args.serial or args.list_tests)) # Print tests that will be checked if comm.is_manager(): From 2251402a3b2cccc61456a24038fc5d6001cc42ab Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 1 Oct 2015 14:48:06 -0600 Subject: [PATCH 215/250] Removing LSF batch script (not really needed) --- tests/yellowstone/checkresults.lsf | 15 --------------- 1 file changed, 15 deletions(-) delete mode 100644 tests/yellowstone/checkresults.lsf diff --git a/tests/yellowstone/checkresults.lsf b/tests/yellowstone/checkresults.lsf deleted file mode 100644 index 77f3e77..0000000 --- a/tests/yellowstone/checkresults.lsf +++ /dev/null @@ -1,15 +0,0 @@ -#!/bin/bash -# -# LSF batch script to run an MPI application -# -#BSUB -P STDD0002 # project code -#BSUB -W 02:00 # wall-clock time (hrs:mins) -#BSUB -n 80 # number of tasks in job -#BSUB -x # exclusive nodes -#BSUB -R "span[ptile=40]" # run 16 MPI tasks per node -#BSUB -J checkresults # job name -#BSUB -o checkresults.%J.out # output file name in which %J is replaced by the job ID -#BSUB -q bigmem # queue - -#run the executable -mpirun.lsf ./checkresults.py From 90d8486021d55ba9a92f543d33e7345ec707d290 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Thu, 1 Oct 2015 15:59:20 -0600 Subject: [PATCH 216/250] Adding new timing data --- tests/yellowstone/timings.json | 8744 ++++++++++++++++---------------- 1 file changed, 4372 insertions(+), 4372 deletions(-) diff --git a/tests/yellowstone/timings.json b/tests/yellowstone/timings.json index 8905d0b..aea2145 100644 --- a/tests/yellowstone/timings.json +++ b/tests/yellowstone/timings.json @@ -1,4384 +1,4384 @@ { - "CAMFV-1.0": { - "baseline": "/glade/u/tdd/asap/bakeoff/tseries/camfv-1.0", - "endYear": "1859", - "input": "/glade/u/tdd/asap/bakeoff/hist/camfv-1.0", - "isize": 28447.744, - "n2dVars": 82, - "n3dVars": 40, - "nVars": 122, - "osize": 28525.4, - "results": { - "cdo": { - "??????-??????": { - "cores": 1, - "correct": "pass", - "metadata": true, - "nodes": 1, - "real": 1940.0, - "sys": "caldera" - } - }, - "ncl": { - "140226-105745": { - "cores": 1, - "correct": "fail", - "kernel": 120.93, - "metadata": false, - "nodes": 1, - "real": 1767.76, - "sys": "geyser", - "user": 153.4 - } - }, - "nco": { - "??????-??????": { - "cores": 1, - "correct": "pass", - "metadata": true, - "nodes": 1, - "real": 1768.0, - "sys": "geyser" - } - }, - "ncr": { - "140226-173803": { - "cores": 4, - "correct": "fail", - "metadata": true, - "nodes": 1, - "real": 3353.0, - "sys": "caldera" - }, - "140303-175041": { - "cores": 4, - "correct": "pass", - "metadata": true, - "nodes": 1, - "real": 3251.0, - "sys": "caldera" - }, - "140312-182909": { - "TS": 732.7, - "cores": 16, - "correct": "pass", - "metaTI": 1.27, - "metaTV": 164.81, - "metadata": true, - "nodes": 4, - "real": 936.0, - "sys": "caldera" - } - }, - "pagoda": { - "??????-??????": { - "cores": 4, - "correct": "pass", - "metadata": true, - "nodes": 1, - "real": 1236.0, - "sys": "caldera" - } - }, - "pynio": { - "140305-193740": { - "cores": 1, - "correct": "fail", - "kernel": 32.6, - "metadata": false, - "nodes": 1, - "real": 1523.02, - "sys": "geyser", - "user": 112.72 - }, - "140307-113151": { - "TS": 1463.81, - "actual": 84000.0, - "cores": 1, - "correct": false, - "kernel": 31.82, - "metaTI": 6.29, - "metaTV": 50.86, - "metadata": false, - "nodes": 1, - "openi": 6.65, - "openo": 0.78, - "real": 1542.99, - "request": 28447.83, - "sys": "geyser", - "user": 114.6 - }, - "140307-120707": { - "TS": 1824.31, - "actual": 77760.0, - "cores": 1, - "correct": false, - "kernel": 46.61, - "metaTI": 7.74, - "metaTV": 82.0, - "metadata": true, - "nodes": 1, - "openi": 6.19, - "openo": 0.44, - "real": 1933.83, - "request": 28447.83, - "sys": "geyser", - "user": 141.55 - } - }, - "pynio4_0": { - "140317-232104": { - "TS": 1900.95, - "actual": 956160.0, - "cores": 1, - "correct": false, - "kernel": 64.18, - "metaTI": 2.7, - "metaTV": 161.9, - "metadata": true, - "nodes": 1, - "openi": 6.46, - "openo": 0.26, - "real": 2077.05, - "request": 28447.83, - "sys": "geyser", - "user": 498.48 - } - }, - "pynio4_1": { - "140318-114642": { - "TS": 2706.45, - "actual": 956160.0, - "cores": 1, - "correct": false, - "kernel": 62.85, - "metaTI": 3.59, - "metaTV": 291.47, - "metadata": true, - "nodes": 1, - "openi": 7.08, - "openo": 0.91, - "real": 3020.34, - "request": 28447.83, - "sys": "geyser", 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192163.858337, + "sys": "yellowstone" + }, + "140911-115433": { + "TS": 1125.10803962, + "actual": 352320.0, + "cores": 16, + "metaTI": 15.5659887791, + "metaTV": 24.7654159069, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 15.9480159283, + "openo": 0.308713436127, + "real": 1188.0, + "request": 192163.858337, + "sys": "yellowstone" + }, + "150918-141526": { + "TS": 1033.53211641, + "actual": 352320.0, + "cores": 16, + "metaTI": 13.9353010654, + "metaTV": 26.8450388908, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 9.45551896095, + "openo": 0.459881305695, + "real": 1052.35365105, + "request": 192163.858337, + "sys": "yellowstone" + } + } + }, + "startYear": "0001" + }, + "POP-DAILY-1.0": { + "baseline": "/glade/u/tdd/asap/bakeoff/tseries/pop-daily-1.0", + "endYear": "0010", + "input": "/glade/u/tdd/asap/bakeoff/hist/pop-daily-1.0", + "isize": 6859.776, + "n2dVars": 0, + "n3dVars": 4, + "nVars": 4, + "osize": 6963.2, + "results": { + "pyreshaper": { + "140911-111816": { + "TS": 202.800698996, + "actual": 350304.0, + "cores": 16, + "metaTI": 0.725324869156, + "metaTV": 82.8588526249, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 83.4460978508, + "openo": 0.0272371768951, + "real": 398.0, + "request": 208227.04184, + "sys": "yellowstone" + }, + "140911-114043": { + "TS": 384.075725555, + "actual": 350304.0, + "cores": 16, + "metaTI": 1.36809396744, + "metaTV": 219.417865038, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 130.947030067, + "openo": 0.145795822144, + "real": 745.0, + "request": 208227.04184, + "sys": "yellowstone" + } + }, + "pyreshaper4": { + "140911-111815": { + "TS": 213.01793766, + "actual": 350304.0, + "cores": 16, + "metaTI": 0.641710042953, + "metaTV": 73.404512167, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 66.3904781342, + "openo": 0.183240890503, + "real": 376.0, + "request": 208227.04184, + "sys": "yellowstone" + }, + "140911-114834": { + "TS": 334.502142906, + "actual": 350304.0, + "cores": 16, + "metaTI": 2.75354886055, + "metaTV": 189.406442404, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 286.188698053, + "openo": 0.625742197037, + "real": 829.0, + "request": 208227.04184, + "sys": "yellowstone" + } + }, + "pyreshaper4c": { + "140911-111815": { + "TS": 241.960571527, + "actual": 350304.0, + "cores": 16, + "metaTI": 0.735607147217, + "metaTV": 43.8486521244, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 65.7884709835, + "openo": 0.218874931335, + "real": 376.0, + "request": 208227.04184, + "sys": "yellowstone" + }, + "140911-114804": { + "TS": 364.382410526, + "actual": 350304.0, + "cores": 16, + "metaTI": 3.3417840004, + "metaTV": 155.952032328, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 286.188265085, + "openo": 0.610445976257, + "real": 799.0, + "request": 208227.04184, + "sys": "yellowstone" + }, + "150918-140809": { + "TS": 344.406491041, + "actual": 315360.0, + "cores": 16, + "metaTI": 2.29843902588, + "metaTV": 142.575973034, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 165.554438829, + "openo": 0.451182126999, + "real": 484.280472994, + "request": 187507.280182, + "sys": "yellowstone" } - }, - "startYear": "0001" - } + } + }, + "startYear": "0001" + } } \ No newline at end of file From 6299185fe4c64adc05842fa2074abc337cab175c Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 2 Oct 2015 11:05:45 -0600 Subject: [PATCH 217/250] Adding new timings --- tests/yellowstone/timings.json | 200 ++++++++++++++++++++++++++++++++- 1 file changed, 199 insertions(+), 1 deletion(-) diff --git a/tests/yellowstone/timings.json b/tests/yellowstone/timings.json index aea2145..b56d777 100644 --- a/tests/yellowstone/timings.json +++ b/tests/yellowstone/timings.json @@ -503,11 +503,89 @@ "real": 329.733877182, "request": 28449.3301392, "sys": "yellowstone" + }, + "151002-091959": { + "TS": 60.2626390457, + "actual": 968848.0, + "cores": 16, + "metaTI": 0.261739492416, + "metaTV": 10.9838540554, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 5.89429616928, + "openo": 0.257526159286, + "real": 190.701400042, + "request": 28450.9692535, + "sys": "yellowstone" } } }, "startYear": "1850" }, + "CAMHF-6HOURLY-1.0": { + "results": { + "pyreshaper4c": { + "151002-105208": { + "TS": 3164.16029859, + "actual": 16880504.0, + "cores": 16, + "metaTI": 0.070193529129, + "metaTV": 302.568546534, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 224.951442003, + "openo": 0.540024995804, + "real": 4717.14768195, + "request": 412733.208378, + "sys": "yellowstone" + } + } + } + }, + "CAMHF-DAILY-1.0": { + "results": { + "pyreshaper4c": { + "151002-094928": { + "TS": 106.482156515, + "actual": 11395904.0, + "cores": 16, + "metaTI": 0.0740783214569, + "metaTV": 146.638347387, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 45.2218770981, + "openo": 0.418075799942, + "real": 1020.13037086, + "request": 39295.5901566, + "sys": "yellowstone" + } + } + } + }, + "CAMHF-MONTHLY-1.0": { + "results": { + "pyreshaper4c": { + "151002-093524": { + "TS": 84.0484206676, + "actual": 1023964.0, + "cores": 16, + "metaTI": 0.197278022766, + "metaTV": 8.23391604424, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 19.332545042, + "openo": 0.158255577087, + "real": 325.792993069, + "request": 41617.1186371, + "sys": "yellowstone" + } + } + } + }, "CAMSE-0.25": { "baseline": "/glade/u/tdd/asap/bakeoff/tseries/camse-0.25", "endYear": "0010", @@ -1017,6 +1095,21 @@ "real": 2787.62379503, "request": 1074995.44647, "sys": "yellowstone" + }, + "151002-100638": { + "TS": 1835.60106206, + "actual": 2561592.0, + "cores": 16, + "metaTI": 6.68212819099, + "metaTV": 10.6226089001, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 10.9332418442, + "openo": 0.649513483047, + "real": 2207.67511892, + "request": 1078519.71414, + "sys": "yellowstone" } } }, @@ -1525,6 +1618,21 @@ "real": 377.197709084, "request": 30681.9406128, "sys": "yellowstone" + }, + "151002-091617": { + "TS": 65.0861947536, + "actual": 1043904.0, + "cores": 16, + "metaTI": 0.534062385559, + "metaTV": 15.8530282974, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 7.89265394211, + "openo": 0.417589902878, + "real": 198.518553019, + "request": 30828.9682617, + "sys": "yellowstone" } } }, @@ -2032,6 +2140,21 @@ "real": 1004.08923078, "request": 442968.903809, "sys": "yellowstone" + }, + "151002-092925": { + "TS": 376.300118208, + "actual": 715008.0, + "cores": 16, + "metaTI": 70.3662366867, + "metaTV": 0.59819149971, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 11.5092349052, + "openo": 0.235598564148, + "real": 785.061555147, + "request": 561093.903809, + "sys": "yellowstone" } } }, @@ -2468,6 +2591,21 @@ "real": 125.465778112, "request": 6581.41067505, "sys": "yellowstone" + }, + "151002-093114": { + "TS": 7.29186058044, + "actual": 177840.0, + "cores": 16, + "metaTI": 1.62267613411, + "metaTV": 0.319401979446, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 9.7917881012, + "openo": 0.256956577301, + "real": 85.7960050106, + "request": 8336.41067505, + "sys": "yellowstone" } } }, @@ -2923,6 +3061,21 @@ "real": 307.761037111, "request": 81515.3311157, "sys": "yellowstone" + }, + "151002-093416": { + "TS": 64.9041206837, + "actual": 798360.0, + "cores": 16, + "metaTI": 42.5193638802, + "metaTV": 3.18136024475, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 10.3529610634, + "openo": 0.151391983032, + "real": 261.155253887, + "request": 124675.246468, + "sys": "yellowstone" } } }, @@ -3404,6 +3557,21 @@ "real": 264.768231869, "request": 8678.71307373, "sys": "yellowstone" + }, + "151002-093313": { + "TS": 10.7341187, + "actual": 1443420.0, + "cores": 16, + "metaTI": 5.90268445015, + "metaTV": 10.5968191624, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 9.87163710594, + "openo": 0.614326238632, + "real": 204.401623964, + "request": 14019.9852104, + "sys": "yellowstone" } } }, @@ -4252,6 +4420,21 @@ "real": 1052.35365105, "request": 192163.858337, "sys": "yellowstone" + }, + "151002-094524": { + "TS": 341.83474493, + "actual": 381048.0, + "cores": 16, + "metaTI": 4.18152046204, + "metaTV": 1.73612046242, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 14.1330201626, + "openo": 0.300295114517, + "real": 908.396248817, + "request": 194248.586632, + "sys": "yellowstone" } } }, @@ -4376,9 +4559,24 @@ "real": 484.280472994, "request": 187507.280182, "sys": "yellowstone" + }, + "151002-094206": { + "TS": 44.544624567, + "actual": 158608.0, + "cores": 16, + "metaTI": 0.416500329971, + "metaTV": 4.26540613174, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 125.451020956, + "openo": 0.415581941605, + "real": 293.116672993, + "request": 6232.80738831, + "sys": "yellowstone" } } }, "startYear": "0001" } -} \ No newline at end of file +} From 264e71cfef524f417ce92c6b50ca0aa68c5dbb87 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 2 Oct 2015 11:21:04 -0600 Subject: [PATCH 218/250] Moving time-series attribute creation to before data write loop --- source/pyreshaper/reshaper.py | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/source/pyreshaper/reshaper.py b/source/pyreshaper/reshaper.py index 5e90d50..658d656 100644 --- a/source/pyreshaper/reshaper.py +++ b/source/pyreshaper/reshaper.py @@ -744,6 +744,8 @@ def _get_bytesize(data): in_var = ref_infile.variables[out_name] out_var = out_file.create_variable( out_name, in_var.typecode(), in_var.dimensions) + for att_name, att_val in in_var.attributes.iteritems(): + setattr(out_var, att_name, att_val) self._timer.stop('Create Time-Series Variables') # Append the output file to list @@ -759,13 +761,6 @@ def _get_bytesize(data): dbg_msg = 'Writing "once" file.' self._vprint(dbg_msg, header=True, verbosity=1) - # Create the attributes of the time-series variable - if write_tser: - in_var = ref_infile.variables[out_name] - out_var = out_file.variables[out_name] - for att_name, att_val in in_var.attributes.iteritems(): - setattr(out_var, att_name, att_val) - # Write the time-invariant metadata if write_meta: for name in self._time_invariant_metadata: From a1d542e67644f9e1f4b25b24f3698b2e791a7cc9 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 2 Oct 2015 11:21:45 -0600 Subject: [PATCH 219/250] Adding splitting read and write timing data --- tests/yellowstone/mktimings.py | 30 ++++++++++++++++++------ tests/yellowstone/utilities/testtools.py | 22 ++++++++++++----- 2 files changed, 39 insertions(+), 13 deletions(-) diff --git a/tests/yellowstone/mktimings.py b/tests/yellowstone/mktimings.py index 2a4fa1a..2304d9d 100755 --- a/tests/yellowstone/mktimings.py +++ b/tests/yellowstone/mktimings.py @@ -114,11 +114,18 @@ def find_shortest_str(strng, left, right=os.linesep, loc=0): # order so that you only need to search through it once... loc = 0 + # Look for the successful completion message + success_str, success_loc = find_shortest_str( + log_str, 'Successfully completed.', loc=0) + if success_loc < 0: + print ' Unsuccessful job. Skipping.' + continue + # Look for the use of a metadata "once" file... once_file_str, once_loc = find_shortest_str( log_str, 'Closed "once" ', loc=0) used_once_file = False - if (once_loc > 0): + if once_loc > 0: used_once_file = True # Find the internal timing data from the run output: @@ -128,11 +135,17 @@ def find_shortest_str(strng, left, right=os.linesep, loc=0): log_str, 'Complete Conversion Process: ', loc=loc) openo_str, loc = find_shortest_str( log_str, 'Open Output Files: ', loc=loc) - metaTI_str, loc = find_shortest_str( + rmetaTI_str, loc = find_shortest_str( + log_str, 'Read Time-Invariant Metadata: ', loc=loc) + rmetaTV_str, loc = find_shortest_str( + log_str, 'Read Time-Variant Metadata: ', loc=loc) + rTS_str, loc = find_shortest_str( + log_str, 'Read Time-Series Variables: ', loc=loc) + wmetaTI_str, loc = find_shortest_str( log_str, 'Write Time-Invariant Metadata: ', loc=loc) - metaTV_str, loc = find_shortest_str( + wmetaTV_str, loc = find_shortest_str( log_str, 'Write Time-Variant Metadata: ', loc=loc) - TS_str, loc = find_shortest_str( + wTS_str, loc = find_shortest_str( log_str, 'Write Time-Series Variables: ', loc=loc) # Get read/write size amounts @@ -155,9 +168,12 @@ def find_shortest_str(strng, left, right=os.linesep, loc=0): # Write the JSON data print ' Adding job result to timings database.' timedb.add_result(common_name, method_name, job_num, - tser_write=float(TS_str), - tim_write=float(metaTI_str), - tvm_write=float(metaTV_str), + tser_read=float(rTS_str), + tim_read=float(rmetaTI_str), + tvm_read=float(rmetaTV_str), + tser_write=float(wTS_str), + tim_write=float(wmetaTI_str), + tvm_write=float(wmetaTV_str), metadata=True, once=used_once_file, cores=num_cores, nodes=num_nodes, input_open=float(openi_str), diff --git a/tests/yellowstone/utilities/testtools.py b/tests/yellowstone/utilities/testtools.py index a1eb6d7..7f05407 100644 --- a/tests/yellowstone/utilities/testtools.py +++ b/tests/yellowstone/utilities/testtools.py @@ -625,7 +625,8 @@ def methods_in_tests(self, tests=None): method_set = set() for test in tests_to_search: if 'results' in self._timings[test]: - method_set.update(set(str(t) for t in self._timings[test]['results'].keys())) + method_set.update( + set(str(t) for t in self._timings[test]['results'].keys())) return list(method_set) def display_tests(self, methods=None): @@ -667,6 +668,7 @@ def display_methods(self, tests=None): print ' {0!s}'.format(method) def add_result(self, test, method, job, + tser_read=0.0, tim_read=0.0, tvm_read=0.0, tser_write=0.0, tim_write=0.0, tvm_write=0.0, metadata=True, once=False, cores=1, nodes=0, input_open=0.0, output_open=0.0, total=0.0, @@ -680,6 +682,9 @@ def add_result(self, test, method, job, test (str): Name of the test associated with the result method (str): Name of the method used by the test result job (str): Individual job ID string to associate with the result + tser_read (float): Time to read Time-Series data + tim_read (float): Time to read Time-Invariant Metadata (TIM) + tvm_read (float): Time to read Time-Variant Metadata (TVM) tser_write (float): Time to write Time-Series data tim_write (float): Time to write Time-Invariant Metadata (TIM) tvm_write (float): Time to write Time-Variant Metadata (TVM) @@ -710,12 +715,16 @@ def add_result(self, test, method, job, self._timings[test]['results'][method][job]['metadata'] = metadata self._timings[test]['results'][method][job]['once'] = once self._timings[test]['results'][method][job]['actual'] = actual_mb - self._timings[test]['results'][method][job]['request'] = requested_mb + self._timings[test]['results'][method][ + job]['request'] = requested_mb self._timings[test]['results'][method][job]['openi'] = input_open self._timings[test]['results'][method][job]['openo'] = output_open - self._timings[test]['results'][method][job]['metaTI'] = tim_write - self._timings[test]['results'][method][job]['metaTV'] = tvm_write - self._timings[test]['results'][method][job]['TS'] = tser_write + self._timings[test]['results'][method][job]['metaTIr'] = tim_read + self._timings[test]['results'][method][job]['metaTVr'] = tvm_read + self._timings[test]['results'][method][job]['TSr'] = tser_read + self._timings[test]['results'][method][job]['metaTIw'] = tim_write + self._timings[test]['results'][method][job]['metaTVw'] = tvm_write + self._timings[test]['results'][method][job]['TSw'] = tser_write def get_results(self, test, method): """ @@ -731,7 +740,8 @@ def get_results(self, test, method): if self.test_has_method(test, method): return self._timings[test]['results'][method] else: - err_msg = "Method {0!s} not in test {1!s} database".format(method, test) + err_msg = "Method {0!s} not in test {1!s} database".format( + method, test) raise KeyError(err_msg) def save(self, name="timings.json"): From 34009fef70e58a3132b5fba8ea358c2b56fd162a Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 2 Oct 2015 11:23:19 -0600 Subject: [PATCH 220/250] Adding new timing data with read/write split --- tests/yellowstone/timings.json | 20 +++++++++++++++++++- 1 file changed, 19 insertions(+), 1 deletion(-) diff --git a/tests/yellowstone/timings.json b/tests/yellowstone/timings.json index b56d777..a6f9487 100644 --- a/tests/yellowstone/timings.json +++ b/tests/yellowstone/timings.json @@ -4002,6 +4002,24 @@ "real": 7504.10058808, "request": 3029589.93713, "sys": "yellowstone" + }, + "151002-111249": { + "TSr": 1027.95776629, + "TSw": 5291.65748668, + "actual": 3121360.0, + "cores": 16, + "metaTIr": 104.953143358, + "metaTIw": 87.6997177601, + "metaTVr": 12.7391045094, + "metaTVw": 1.22518730164, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 16.252808094, + "openo": 0.1517329216, + "real": 6153.10157013, + "request": 3073293.60839, + "sys": "yellowstone" } } }, @@ -4579,4 +4597,4 @@ }, "startYear": "0001" } -} +} \ No newline at end of file From c33807a7e87a71f06d63d386a077e331fc79a294 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 2 Oct 2015 11:55:28 -0600 Subject: [PATCH 221/250] Bugfix: Output variable not retrieved before access. --- source/pyreshaper/reshaper.py | 1 + 1 file changed, 1 insertion(+) diff --git a/source/pyreshaper/reshaper.py b/source/pyreshaper/reshaper.py index 658d656..1d7270f 100644 --- a/source/pyreshaper/reshaper.py +++ b/source/pyreshaper/reshaper.py @@ -825,6 +825,7 @@ def _get_bytesize(data): # Write the time-series variables if write_tser: in_var = in_file.variables[out_name] + out_var = out_file.variables[out_name] ndims = len(in_var.dimensions) udidx = in_var.dimensions.index(self._unlimited_dim) in_slice = [slice(None)] * ndims From 8ae77aa58f0af43416cc0a2d2ca856b49aebcbc0 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 2 Oct 2015 11:58:38 -0600 Subject: [PATCH 222/250] Updating change log with new features. --- CHANGES.rst | 3 +++ 1 file changed, 3 insertions(+) diff --git a/CHANGES.rst b/CHANGES.rst index ffc67b7..062935b 100644 --- a/CHANGES.rst +++ b/CHANGES.rst @@ -89,4 +89,7 @@ VERSION 0.9.4 1 October 2015: - Bugfixes, performance improvements - New yellowstone testing code + +2 October 2015: + - Now measures read/write times separately in diagnostic data \ No newline at end of file From 91107bc557cb934d42e028febd8e8fcadde88163 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 2 Oct 2015 12:15:11 -0600 Subject: [PATCH 223/250] Adding feature to skip logs that do not show successful completion --- tests/yellowstone/mktimings.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/mktimings.py b/tests/yellowstone/mktimings.py index 2304d9d..bca70d6 100755 --- a/tests/yellowstone/mktimings.py +++ b/tests/yellowstone/mktimings.py @@ -117,7 +117,7 @@ def find_shortest_str(strng, left, right=os.linesep, loc=0): # Look for the successful completion message success_str, success_loc = find_shortest_str( log_str, 'Successfully completed.', loc=0) - if success_loc < 0: + if success_str < 0: print ' Unsuccessful job. Skipping.' continue From 79673a6f20bdef3aae405ec80a01b8d9e8236b2b Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 2 Oct 2015 12:18:48 -0600 Subject: [PATCH 224/250] Bugfix: check for successful completion --- tests/yellowstone/mktimings.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/mktimings.py b/tests/yellowstone/mktimings.py index bca70d6..3119aff 100755 --- a/tests/yellowstone/mktimings.py +++ b/tests/yellowstone/mktimings.py @@ -117,7 +117,7 @@ def find_shortest_str(strng, left, right=os.linesep, loc=0): # Look for the successful completion message success_str, success_loc = find_shortest_str( log_str, 'Successfully completed.', loc=0) - if success_str < 0: + if success_loc <= 0: print ' Unsuccessful job. Skipping.' continue From e15973b451be8825156f9659fc42784fed3a1fa3 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 2 Oct 2015 12:33:48 -0600 Subject: [PATCH 225/250] Better output message. --- tests/yellowstone/mktimings.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/yellowstone/mktimings.py b/tests/yellowstone/mktimings.py index 3119aff..812f9c8 100755 --- a/tests/yellowstone/mktimings.py +++ b/tests/yellowstone/mktimings.py @@ -118,7 +118,7 @@ def find_shortest_str(strng, left, right=os.linesep, loc=0): success_str, success_loc = find_shortest_str( log_str, 'Successfully completed.', loc=0) if success_loc <= 0: - print ' Unsuccessful job. Skipping.' + print ' Unsuccessful or incomplete job. Skipping.' continue # Look for the use of a metadata "once" file... From 805c8991cb9f733e5c1dafa1655a31793ba55465 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 2 Oct 2015 12:43:36 -0600 Subject: [PATCH 226/250] Removing explicit loop over timesteps in history files (using slices) --- source/pyreshaper/reshaper.py | 91 +++++++++++++++++------------------ 1 file changed, 44 insertions(+), 47 deletions(-) diff --git a/source/pyreshaper/reshaper.py b/source/pyreshaper/reshaper.py index 1d7270f..fa45fd9 100644 --- a/source/pyreshaper/reshaper.py +++ b/source/pyreshaper/reshaper.py @@ -787,66 +787,63 @@ def _get_bytesize(data): self._byte_counts['Actual Data'] += actual_nbytes # Write each time-variant variable - series_step_index = 0 + series_start_index = 0 for in_file in self._input_files: # Get the number of time steps in this slice file num_steps = in_file.dimensions[self._unlimited_dim] - # Loop over time steps (PyNIO can't read but 1 step at a time) - for slice_step_index in xrange(num_steps): - - # Write the time-varient metadata - if write_meta: - for name in self._time_variant_metadata: - in_meta = in_file.variables[name] - out_meta = out_file.variables[name] - ndims = len(in_meta.dimensions) - udidx = in_meta.dimensions.index( - self._unlimited_dim) - in_slice = [slice(None)] * ndims - in_slice[udidx] = slice_step_index - out_slice = [slice(None)] * ndims - out_slice[udidx] = series_step_index - self._timer.start('Read Time-Variant Metadata') - tmp_data = in_meta[tuple(in_slice)] - self._timer.stop('Read Time-Variant Metadata') - self._timer.start('Write Time-Variant Metadata') - out_meta[tuple(out_slice)] = tmp_data - self._timer.stop('Write Time-Variant Metadata') - - requested_nbytes = _get_bytesize(tmp_data) - self._byte_counts[ - 'Requested Data'] += requested_nbytes - actual_nbytes = self.assumed_block_size \ - * numpy.ceil(requested_nbytes / self.assumed_block_size) - self._byte_counts['Actual Data'] += actual_nbytes - - # Write the time-series variables - if write_tser: - in_var = in_file.variables[out_name] - out_var = out_file.variables[out_name] - ndims = len(in_var.dimensions) - udidx = in_var.dimensions.index(self._unlimited_dim) + # Write the time-varient metadata + if write_meta: + for name in self._time_variant_metadata: + in_meta = in_file.variables[name] + out_meta = out_file.variables[name] + ndims = len(in_meta.dimensions) + udidx = in_meta.dimensions.index( + self._unlimited_dim) in_slice = [slice(None)] * ndims - in_slice[udidx] = slice_step_index + in_slice[udidx] = slice(0, num_steps) out_slice = [slice(None)] * ndims - out_slice[udidx] = series_step_index - self._timer.start('Read Time-Series Variables') - tmp_data = in_var[tuple(in_slice)] - self._timer.stop('Read Time-Series Variables') - self._timer.start('Write Time-Series Variables') - out_var[tuple(out_slice)] = tmp_data - self._timer.stop('Write Time-Series Variables') + out_slice[udidx] = slice(series_start_index, None) + self._timer.start('Read Time-Variant Metadata') + tmp_data = in_meta[tuple(in_slice)] + self._timer.stop('Read Time-Variant Metadata') + self._timer.start('Write Time-Variant Metadata') + out_meta[tuple(out_slice)] = tmp_data + self._timer.stop('Write Time-Variant Metadata') requested_nbytes = _get_bytesize(tmp_data) - self._byte_counts['Requested Data'] += requested_nbytes + self._byte_counts[ + 'Requested Data'] += requested_nbytes actual_nbytes = self.assumed_block_size \ * numpy.ceil(requested_nbytes / self.assumed_block_size) self._byte_counts['Actual Data'] += actual_nbytes - # Increment the time-series step index - series_step_index += 1 + # Write the time-series variables + if write_tser: + in_var = in_file.variables[out_name] + out_var = out_file.variables[out_name] + ndims = len(in_var.dimensions) + udidx = in_var.dimensions.index(self._unlimited_dim) + in_slice = [slice(None)] * ndims + in_slice[udidx] = slice(0, num_steps) + out_slice = [slice(None)] * ndims + out_slice[udidx] = slice(series_start_index, None) + self._timer.start('Read Time-Series Variables') + tmp_data = in_var[tuple(in_slice)] + self._timer.stop('Read Time-Series Variables') + self._timer.start('Write Time-Series Variables') + out_var[tuple(out_slice)] = tmp_data + self._timer.stop('Write Time-Series Variables') + + requested_nbytes = _get_bytesize(tmp_data) + self._byte_counts['Requested Data'] += requested_nbytes + actual_nbytes = self.assumed_block_size \ + * numpy.ceil(requested_nbytes / self.assumed_block_size) + self._byte_counts['Actual Data'] += actual_nbytes + + # Increment the time-series step index + series_start_index += num_steps # Close the output file self._timer.start('Close Output Files') From 9466a8ada42b32489c492c05139dd8f466357e2e Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 2 Oct 2015 14:10:05 -0600 Subject: [PATCH 227/250] Adding newest timings --- tests/yellowstone/timings.json | 234 +++++++++++++++++++++++++++++++++ 1 file changed, 234 insertions(+) diff --git a/tests/yellowstone/timings.json b/tests/yellowstone/timings.json index a6f9487..7cb8ef9 100644 --- a/tests/yellowstone/timings.json +++ b/tests/yellowstone/timings.json @@ -518,6 +518,24 @@ "real": 190.701400042, "request": 28450.9692535, "sys": "yellowstone" + }, + "151002-120211": { + "TSr": 267.074586868, + "TSw": 60.4137539864, + "actual": 968848.0, + "cores": 16, + "metaTIr": 0.212244749069, + "metaTIw": 0.262345075607, + "metaTVr": 13.3320331573, + "metaTVw": 11.3042991161, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 4.30114293098, + "openo": 0.335148334503, + "real": 324.800256014, + "request": 28450.9692535, + "sys": "yellowstone" } } }, @@ -540,6 +558,24 @@ "real": 4717.14768195, "request": 412733.208378, "sys": "yellowstone" + }, + "151002-132743": { + "TSr": 2102.44257331, + "TSw": 3221.23370409, + "actual": 16880504.0, + "cores": 16, + "metaTIr": 1.16329169273, + "metaTIw": 0.0410597324371, + "metaTVr": 578.328157187, + "metaTVw": 324.140898943, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 319.565881968, + "openo": 0.560957193375, + "real": 5139.13690186, + "request": 412733.208378, + "sys": "yellowstone" } } } @@ -561,6 +597,24 @@ "real": 1020.13037086, "request": 39295.5901566, "sys": "yellowstone" + }, + "151002-121835": { + "TSr": 718.967712879, + "TSw": 109.465676069, + "actual": 11395904.0, + "cores": 16, + "metaTIr": 3.48129415512, + "metaTIw": 0.316914319992, + "metaTVr": 327.981246948, + "metaTVw": 163.808205605, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 51.1060910225, + "openo": 0.799788951874, + "real": 1241.54569411, + "request": 39295.5901566, + "sys": "yellowstone" } } } @@ -582,6 +636,24 @@ "real": 325.792993069, "request": 41617.1186371, "sys": "yellowstone" + }, + "151002-120324": { + "TSr": 303.185502052, + "TSw": 84.3467159271, + "actual": 1023964.0, + "cores": 16, + "metaTIr": 2.37086200714, + "metaTIw": 0.221300363541, + "metaTVr": 10.6845979691, + "metaTVw": 8.21553111076, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 24.5326368809, + "openo": 0.497053861618, + "real": 375.913740158, + "request": 41617.1186371, + "sys": "yellowstone" } } } @@ -1110,6 +1182,24 @@ "real": 2207.67511892, "request": 1078519.71414, "sys": "yellowstone" + }, + "151002-123613": { + "TSr": 520.182231903, + "TSw": 1827.02842641, + "actual": 2561592.0, + "cores": 16, + "metaTIr": 2.53915166855, + "metaTIw": 6.77962827682, + "metaTVr": 40.9809556007, + "metaTVw": 12.277674675, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 9.0326859951, + "openo": 0.439650297165, + "real": 2362.43693519, + "request": 1078519.71414, + "sys": "yellowstone" } } }, @@ -1633,6 +1723,24 @@ "real": 198.518553019, "request": 30828.9682617, "sys": "yellowstone" + }, + "151002-120250": { + "TSr": 292.098123789, + "TSw": 64.9243013859, + "actual": 1043904.0, + "cores": 16, + "metaTIr": 0.472710609436, + "metaTIw": 0.53111410141, + "metaTVr": 14.7551693916, + "metaTVw": 16.2517373562, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 6.55523085594, + "openo": 0.544054508209, + "real": 370.380084991, + "request": 30828.9682617, + "sys": "yellowstone" } } }, @@ -2155,6 +2263,24 @@ "real": 785.061555147, "request": 561093.903809, "sys": "yellowstone" + }, + "151002-121023": { + "TSr": 317.063103914, + "TSw": 378.894732237, + "actual": 715008.0, + "cores": 16, + "metaTIr": 48.0411641598, + "metaTIw": 70.4985556602, + "metaTVr": 9.33440876007, + "metaTVw": 0.652191162109, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 9.04424095154, + "openo": 0.267147064209, + "real": 811.08354497, + "request": 561093.903809, + "sys": "yellowstone" } } }, @@ -2606,6 +2732,24 @@ "real": 85.7960050106, "request": 8336.41067505, "sys": "yellowstone" + }, + "151002-115913": { + "TSr": 131.842990875, + "TSw": 7.56044721603, + "actual": 177840.0, + "cores": 16, + "metaTIr": 1.72517442703, + "metaTIw": 1.63546466827, + "metaTVr": 6.24339962006, + "metaTVw": 0.316979408264, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 8.83018398285, + "openo": 0.647891044617, + "real": 141.086723089, + "request": 8336.41067505, + "sys": "yellowstone" } } }, @@ -3076,6 +3220,24 @@ "real": 261.155253887, "request": 124675.246468, "sys": "yellowstone" + }, + "151002-120117": { + "TSr": 121.410551786, + "TSw": 64.8986198902, + "actual": 798360.0, + "cores": 16, + "metaTIr": 24.5644390583, + "metaTIw": 42.7191648483, + "metaTVr": 19.7610211372, + "metaTVw": 3.1215763092, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 11.1755421162, + "openo": 0.393360853195, + "real": 262.587915897, + "request": 124675.246468, + "sys": "yellowstone" } } }, @@ -3572,6 +3734,24 @@ "real": 204.401623964, "request": 14019.9852104, "sys": "yellowstone" + }, + "151002-120140": { + "TSr": 255.788938046, + "TSw": 9.34615063667, + "actual": 1443420.0, + "cores": 16, + "metaTIr": 1.61454749107, + "metaTIw": 5.90498423576, + "metaTVr": 8.47008776665, + "metaTVw": 10.5631215572, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 9.37232899666, + "openo": 0.265953063965, + "real": 287.702008009, + "request": 14019.9852104, + "sys": "yellowstone" } } }, @@ -4020,6 +4200,24 @@ "real": 6153.10157013, "request": 3073293.60839, "sys": "yellowstone" + }, + "151002-134134": { + "TSr": 1017.69567513, + "TSw": 5369.47686791, + "actual": 3121360.0, + "cores": 16, + "metaTIr": 110.276347637, + "metaTIw": 88.3693189621, + "metaTVr": 15.7053070068, + "metaTVw": 19.1175069809, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 12.0257339478, + "openo": 0.108300924301, + "real": 6260.71265197, + "request": 3073293.60839, + "sys": "yellowstone" } } }, @@ -4453,6 +4651,24 @@ "real": 908.396248817, "request": 194248.586632, "sys": "yellowstone" + }, + "151002-121349": { + "TSr": 732.107361078, + "TSw": 340.210021734, + "actual": 381048.0, + "cores": 16, + "metaTIr": 4.61803150177, + "metaTIw": 4.13230228424, + "metaTVr": 16.138954401, + "metaTVw": 1.73543787003, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 10.0871970654, + "openo": 0.285751581192, + "real": 1015.06130505, + "request": 194248.586632, + "sys": "yellowstone" } } }, @@ -4592,6 +4808,24 @@ "real": 293.116672993, "request": 6232.80738831, "sys": "yellowstone" + }, + "151002-120613": { + "TSr": 288.929755926, + "TSw": 45.5107212067, + "actual": 158608.0, + "cores": 16, + "metaTIr": 1.99480342865, + "metaTIw": 0.461429834366, + "metaTVr": 125.482697725, + "metaTVw": 4.67854905128, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 208.385211945, + "openo": 0.543105840683, + "real": 341.90487504, + "request": 6232.80738831, + "sys": "yellowstone" } } }, From 10f339b595d0718860e5a9da76297d5e1704a7e2 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 2 Oct 2015 14:10:39 -0600 Subject: [PATCH 228/250] Updating the changelog --- CHANGES.rst | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/CHANGES.rst b/CHANGES.rst index 062935b..3407dac 100644 --- a/CHANGES.rst +++ b/CHANGES.rst @@ -92,4 +92,6 @@ VERSION 0.9.4 2 October 2015: - Now measures read/write times separately in diagnostic data - \ No newline at end of file + - Performance improvement (no explicit loop over time-steps in a time-slice + file needed) + \ No newline at end of file From 627d48f3ec295948ddb37a8a2eec7d4b18fee174 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 2 Oct 2015 14:15:56 -0600 Subject: [PATCH 229/250] Removing unused import --- source/pyreshaper/reshaper.py | 1 - 1 file changed, 1 deletion(-) diff --git a/source/pyreshaper/reshaper.py b/source/pyreshaper/reshaper.py index fa45fd9..5fd2ddc 100644 --- a/source/pyreshaper/reshaper.py +++ b/source/pyreshaper/reshaper.py @@ -11,7 +11,6 @@ # Built-in imports import abc -import time from os import linesep, remove from os.path import exists, isfile from itertools import chain From fcbf8a035eaec195e9e351ac04c166a6942fc7a3 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 2 Oct 2015 14:21:47 -0600 Subject: [PATCH 230/250] Simplifying use of slices (none needed for reading) --- source/pyreshaper/reshaper.py | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/source/pyreshaper/reshaper.py b/source/pyreshaper/reshaper.py index 5fd2ddc..0db36d0 100644 --- a/source/pyreshaper/reshaper.py +++ b/source/pyreshaper/reshaper.py @@ -800,12 +800,10 @@ def _get_bytesize(data): ndims = len(in_meta.dimensions) udidx = in_meta.dimensions.index( self._unlimited_dim) - in_slice = [slice(None)] * ndims - in_slice[udidx] = slice(0, num_steps) out_slice = [slice(None)] * ndims out_slice[udidx] = slice(series_start_index, None) self._timer.start('Read Time-Variant Metadata') - tmp_data = in_meta[tuple(in_slice)] + tmp_data = in_meta[:] self._timer.stop('Read Time-Variant Metadata') self._timer.start('Write Time-Variant Metadata') out_meta[tuple(out_slice)] = tmp_data @@ -824,12 +822,10 @@ def _get_bytesize(data): out_var = out_file.variables[out_name] ndims = len(in_var.dimensions) udidx = in_var.dimensions.index(self._unlimited_dim) - in_slice = [slice(None)] * ndims - in_slice[udidx] = slice(0, num_steps) out_slice = [slice(None)] * ndims out_slice[udidx] = slice(series_start_index, None) self._timer.start('Read Time-Series Variables') - tmp_data = in_var[tuple(in_slice)] + tmp_data = in_var[:] self._timer.stop('Read Time-Series Variables') self._timer.start('Write Time-Series Variables') out_var[tuple(out_slice)] = tmp_data From 68c8833d798cb97a842e0b824027458b18eb7dca Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 2 Oct 2015 14:26:07 -0600 Subject: [PATCH 231/250] Adding debugging output --- source/pyreshaper/reshaper.py | 1 + 1 file changed, 1 insertion(+) diff --git a/source/pyreshaper/reshaper.py b/source/pyreshaper/reshaper.py index 0db36d0..75077ae 100644 --- a/source/pyreshaper/reshaper.py +++ b/source/pyreshaper/reshaper.py @@ -828,6 +828,7 @@ def _get_bytesize(data): tmp_data = in_var[:] self._timer.stop('Read Time-Series Variables') self._timer.start('Write Time-Series Variables') + print out_slice, numpy.shape(tmp_data) out_var[tuple(out_slice)] = tmp_data self._timer.stop('Write Time-Series Variables') From 9336b387fce800cfa291bbf12d112ff4f48d3bb5 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 2 Oct 2015 14:37:53 -0600 Subject: [PATCH 232/250] Have to deal with single time-steps differently --- source/pyreshaper/reshaper.py | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/source/pyreshaper/reshaper.py b/source/pyreshaper/reshaper.py index 75077ae..b486769 100644 --- a/source/pyreshaper/reshaper.py +++ b/source/pyreshaper/reshaper.py @@ -786,7 +786,7 @@ def _get_bytesize(data): self._byte_counts['Actual Data'] += actual_nbytes # Write each time-variant variable - series_start_index = 0 + series_step_index = 0 for in_file in self._input_files: # Get the number of time steps in this slice file @@ -801,7 +801,10 @@ def _get_bytesize(data): udidx = in_meta.dimensions.index( self._unlimited_dim) out_slice = [slice(None)] * ndims - out_slice[udidx] = slice(series_start_index, None) + if num_steps > 1: + out_slice[udidx] = slice(series_step_index, None) + else: + out_slice[udidx] = series_step_index self._timer.start('Read Time-Variant Metadata') tmp_data = in_meta[:] self._timer.stop('Read Time-Variant Metadata') @@ -823,7 +826,10 @@ def _get_bytesize(data): ndims = len(in_var.dimensions) udidx = in_var.dimensions.index(self._unlimited_dim) out_slice = [slice(None)] * ndims - out_slice[udidx] = slice(series_start_index, None) + if num_steps > 1: + out_slice[udidx] = slice(series_step_index, None) + else: + out_slice[udidx] = series_step_index self._timer.start('Read Time-Series Variables') tmp_data = in_var[:] self._timer.stop('Read Time-Series Variables') @@ -839,7 +845,7 @@ def _get_bytesize(data): self._byte_counts['Actual Data'] += actual_nbytes # Increment the time-series step index - series_start_index += num_steps + series_step_index += num_steps # Close the output file self._timer.start('Close Output Files') From 1ba0970974988afaa5a1e380f285a2577dd0b176 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 2 Oct 2015 14:39:16 -0600 Subject: [PATCH 233/250] Removing debugging output --- source/pyreshaper/reshaper.py | 1 - 1 file changed, 1 deletion(-) diff --git a/source/pyreshaper/reshaper.py b/source/pyreshaper/reshaper.py index b486769..206e76c 100644 --- a/source/pyreshaper/reshaper.py +++ b/source/pyreshaper/reshaper.py @@ -834,7 +834,6 @@ def _get_bytesize(data): tmp_data = in_var[:] self._timer.stop('Read Time-Series Variables') self._timer.start('Write Time-Series Variables') - print out_slice, numpy.shape(tmp_data) out_var[tuple(out_slice)] = tmp_data self._timer.stop('Write Time-Series Variables') From a69439d8c72b067779780cae3bbcd8404a528281 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 2 Oct 2015 14:59:09 -0600 Subject: [PATCH 234/250] Remove unrecognized characters from LICENSE --- LICENSE.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/LICENSE.rst b/LICENSE.rst index a0c4596..b9eb5a3 100644 --- a/LICENSE.rst +++ b/LICENSE.rst @@ -11,7 +11,7 @@ Corporation for Atmospheric Research ("UCAR"). 1. **License Grant to Technology.** UCAR grants to Licensee a restricted, royalty-free, perpetual, nonexclusive, nontransferable, noncommercial license to copy, modify, enhance, improve and use the NCAR PyReshaper code set for - transforming NetCDF time-slice datasets into NetCDF time-series format provided in source code format (“Technology”) + transforming NetCDF time-slice datasets into NetCDF time-series format provided in source code format (**Technology**) for research purposes and for collaborating with UCAR only; provided, however, that Licensee does not commercialize, sell, license, distribute, or transfer the Technology, or any work that contains the Technology. Licensee may freely use the data and results from the Technology. Licensee shall note in all publications of data or results that this @@ -30,7 +30,7 @@ Corporation for Atmospheric Research ("UCAR"). Technology, sublicense, display, and distribute your Contributions. You represent that you are legally entitled to grant the above license. If your employer(s) has rights to intellectual property that you create that includes your Contributions, you acknowledge that you are allowed to make Contributions on behalf of that employer. -5. **Disclaimer of Warranty/Noninfringement.** THE TECHNOLOGY IS SUPPLIED “AS IS” WITHOUT WARRANTY OF ANY KIND. UCAR DISCLAIMS +5. **Disclaimer of Warranty/Noninfringement.** THE TECHNOLOGY IS SUPPLIED **AS IS** WITHOUT WARRANTY OF ANY KIND. UCAR DISCLAIMS ALL WARRANTIES, EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION, ANY IMPLIED WARRANTIES OF NONINFRINGEMENT, ORIGINALITY, MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE WITH REGARD TO THE TECHNOLOGY PROVIDED HEREUNDER. UCAR MAKES NO REPRESENTATIONS THAT THE USE, OPERATION, SALE, PERFORMANCE, MODIFICATION, REPRODUCTION, DISPLAY OF THE TECHNOLOGY WILL @@ -45,7 +45,7 @@ Corporation for Atmospheric Research ("UCAR"). intended for use in any operational activities including activities or hazardous environments requiring fail-safe performance, such as in aircraft navigation or communication systems, air traffic control, weapons systems, nuclear power plants or critical 24/7 operations, in which the failure of the Technology could lead directly to death, personal - injury, or severe physical or environmental damage (“High Risk Activities”). Accordingly, UCAR specifically disclaims + injury, or severe physical or environmental damage (**High Risk Activities**). Accordingly, UCAR specifically disclaims any express or implied warranties of fitness for High Risk Activities. You agree that UCAR shall not be liable for any claims or damages arising from High Risk Activities. 8. **Controlling Law.** This Agreement shall be governed by the laws of the State of Colorado and of the United States. From 8524ef46960273aee612fdb07e20637159da4139 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 2 Oct 2015 15:16:40 -0600 Subject: [PATCH 235/250] Updating the LICENSE copy file --- source/pyreshaper/LICENSE.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/source/pyreshaper/LICENSE.rst b/source/pyreshaper/LICENSE.rst index a0c4596..b9eb5a3 100644 --- a/source/pyreshaper/LICENSE.rst +++ b/source/pyreshaper/LICENSE.rst @@ -11,7 +11,7 @@ Corporation for Atmospheric Research ("UCAR"). 1. **License Grant to Technology.** UCAR grants to Licensee a restricted, royalty-free, perpetual, nonexclusive, nontransferable, noncommercial license to copy, modify, enhance, improve and use the NCAR PyReshaper code set for - transforming NetCDF time-slice datasets into NetCDF time-series format provided in source code format (“Technology”) + transforming NetCDF time-slice datasets into NetCDF time-series format provided in source code format (**Technology**) for research purposes and for collaborating with UCAR only; provided, however, that Licensee does not commercialize, sell, license, distribute, or transfer the Technology, or any work that contains the Technology. Licensee may freely use the data and results from the Technology. Licensee shall note in all publications of data or results that this @@ -30,7 +30,7 @@ Corporation for Atmospheric Research ("UCAR"). Technology, sublicense, display, and distribute your Contributions. You represent that you are legally entitled to grant the above license. If your employer(s) has rights to intellectual property that you create that includes your Contributions, you acknowledge that you are allowed to make Contributions on behalf of that employer. -5. **Disclaimer of Warranty/Noninfringement.** THE TECHNOLOGY IS SUPPLIED “AS IS” WITHOUT WARRANTY OF ANY KIND. UCAR DISCLAIMS +5. **Disclaimer of Warranty/Noninfringement.** THE TECHNOLOGY IS SUPPLIED **AS IS** WITHOUT WARRANTY OF ANY KIND. UCAR DISCLAIMS ALL WARRANTIES, EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION, ANY IMPLIED WARRANTIES OF NONINFRINGEMENT, ORIGINALITY, MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE WITH REGARD TO THE TECHNOLOGY PROVIDED HEREUNDER. UCAR MAKES NO REPRESENTATIONS THAT THE USE, OPERATION, SALE, PERFORMANCE, MODIFICATION, REPRODUCTION, DISPLAY OF THE TECHNOLOGY WILL @@ -45,7 +45,7 @@ Corporation for Atmospheric Research ("UCAR"). intended for use in any operational activities including activities or hazardous environments requiring fail-safe performance, such as in aircraft navigation or communication systems, air traffic control, weapons systems, nuclear power plants or critical 24/7 operations, in which the failure of the Technology could lead directly to death, personal - injury, or severe physical or environmental damage (“High Risk Activities”). Accordingly, UCAR specifically disclaims + injury, or severe physical or environmental damage (**High Risk Activities**). Accordingly, UCAR specifically disclaims any express or implied warranties of fitness for High Risk Activities. You agree that UCAR shall not be liable for any claims or damages arising from High Risk Activities. 8. **Controlling Law.** This Agreement shall be governed by the laws of the State of Colorado and of the United States. From b4d5bfc05bfed92b51a4f2ec8aae1671e5906cfd Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 2 Oct 2015 15:27:17 -0600 Subject: [PATCH 236/250] Updating the README in preparation for release --- README.rst | 31 ++++++++++++++++++------------- 1 file changed, 18 insertions(+), 13 deletions(-) diff --git a/README.rst b/README.rst index 4a1c9a8..ed7673b 100644 --- a/README.rst +++ b/README.rst @@ -52,8 +52,8 @@ so problems might occur if an earlier versions of these packages have been installed. -Easy Installation ------------------ +Easy Installation with PIP +-------------------------- The easiest way to install the ASAP Python Toolbox is from the Python Package Index (PyPI) with the pip package manager:: @@ -64,32 +64,37 @@ The optional '--user' argument can be used to install the package in the local user's directory, which is useful if the user doesn't have root privileges. +One should be careful, however, as the PyPI packages may not always be up +to date. We recommend obtaining the most recent versions of the PyReshaper +from the GitHub site shown in the section below. + Obtaining the Source Code ------------------------- -Currently, the most up-to-date development source code is available via git from the site:: +Currently, the most up-to-date development source code is available +via git from the site:: https://github.com/NCAR-CISL-ASAP/PyReshaper -Check out the most recent stable tag. The source is available in read-only mode to -everyone, but special permissions can be given to those to make changes to the source. +Check out the most recent stable tag. The source is available in +read-only mode to everyone. Developers are welcome to update the source +and submit Pull Requests via GitHub. -Building & Installation ------------------------ +Building & Installing from Source +--------------------------------- Installation of the PyReshaper is very simple. After checking out the source from the above svn link, via:: $ git clone https://github.com/NCAR-CISL-ASAP/PyReshaper -Enter the newly cloned directory and check out the most recent stable tag:: +Enter the newly cloned directory:: $ cd PyReshaper - $ git checkout [latest tag] -Then, run the Python distutils setup. On unix, this involves:: +Then, run the Python setuptools setup script. On unix, this involves:: $ python setup.py install [--prefix=/path/to/install/location] @@ -97,7 +102,7 @@ The prefix is optional, as the default prefix is typically /usr/local on linux machines. However, you must have permissions to write to the prefix location, so you may want to choose a prefix location where you have write permissions. Like most distutils installations, you can alternatively -install the pyReshaper with the --user option, which will automatically +install the PyReshaper with the '--user' option, which will automatically select (and create if it does not exist) the $HOME/.local directory in which to install. To do this, type (on unix machines):: @@ -150,6 +155,6 @@ Instructions & Use ------------------ Please see the more detailed instructions found in the docs/ directory for -usage and examples. See the 'Building & Installation' section for how to -build the documentation with Sphinx. +usage and examples. See the 'Building & Installing from Source' section +for how to build the documentation with Sphinx. From 01ee6c2fdcaabf5055d3d71a8c409506e15f5efc Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 2 Oct 2015 15:28:23 -0600 Subject: [PATCH 237/250] Updating version number --- docs/source/conf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index f5aa3ba..f9b0d6d 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -61,7 +61,7 @@ # The short X.Y version. version = '0.9' # The full version, including alpha/beta/rc tags. -release = '0.9.3' +release = '0.9.4' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. From 8d312113a968ecbc4001b9e51aec80c0ac9cdcb4 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 2 Oct 2015 15:44:48 -0600 Subject: [PATCH 238/250] Updates to the manual for new features --- docs/source/manual.rst | 22 +++++++++++++--------- 1 file changed, 13 insertions(+), 9 deletions(-) diff --git a/docs/source/manual.rst b/docs/source/manual.rst index 88a91a5..e26f661 100644 --- a/docs/source/manual.rst +++ b/docs/source/manual.rst @@ -30,17 +30,21 @@ How can I get it? ================= The best way to obtain the PyReshaper code is to check it out from the -UCAR subversion site, as shown below. +GitHub site, as shown below. :: $ git clone https://github.com/NCAR-CISL-ASAP/PyReshaper $ cd PyReshaper - $ git checkout v0.9.2 -This is the most recent stable version of the source code. The trunk is -also available for download, if you choose to have the most up-to-date -version. +This will download the most recent stable version of the source code. If +the most recent version of the non-stable source is desired, you may switch +to the development branch. + +:: + + $ git checkout devel + How do I set it up? =================== @@ -74,12 +78,11 @@ shown below. $ git clone https://github.com/NCAR-CISL-ASAP/PyReshaper -Enter into the newly created directory and check out the stable tag. +Enter into the newly created directory. :: $ cd PyReshaper - $ git checkout [latest release] The contents of the repository will look like the following. @@ -89,7 +92,7 @@ The contents of the repository will look like the following. CHANGES.rst README.rst docs/ setup.py tests/ LICENSE.rst bin/ setup.cfg source/ -To install in package, type the following command from this directory. +To install the package, type the following command from this directory. :: @@ -253,7 +256,8 @@ format. specifier.time_variant_metadata = ["time", "time_bounds", ...] # Create the Reshaper object - rshpr = reshaper.create_reshaper(specifier, serial=False, verbosity=1) + rshpr = reshaper.create_reshaper(specifier, serial=False, verbosity=1, + skip_existing=True, overwrite=False) # Run the conversion (slice-to-series) process rshpr.convert() From 06bb60ae7a85c76d128004dfdc6008dd690f2c9d Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 2 Oct 2015 15:45:34 -0600 Subject: [PATCH 239/250] Adding Eclipse settings folder to ignored items --- .gitignore | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index 01fc523..685c4fe 100644 --- a/.gitignore +++ b/.gitignore @@ -1,4 +1,5 @@ *.pyc dist/ build/ -PyReshaper.egg-info/ \ No newline at end of file +PyReshaper.egg-info/ +/.settings/ From facb5e601e02b7ae7b0b0c2395b7f8510bd8fab6 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 2 Oct 2015 16:11:38 -0600 Subject: [PATCH 240/250] Putting the compression level in the specifier --- CHANGES.rst | 1 + docs/source/manual.rst | 10 ++++++++-- source/pyreshaper/reshaper.py | 10 +++++----- source/pyreshaper/specification.py | 24 +++++++++++++++++++++++- 4 files changed, 37 insertions(+), 8 deletions(-) diff --git a/CHANGES.rst b/CHANGES.rst index 3407dac..e21a3f3 100644 --- a/CHANGES.rst +++ b/CHANGES.rst @@ -94,4 +94,5 @@ VERSION 0.9.4 - Now measures read/write times separately in diagnostic data - Performance improvement (no explicit loop over time-steps in a time-slice file needed) + - Enabling user-defined compression level for NetCDF4 output \ No newline at end of file diff --git a/docs/source/manual.rst b/docs/source/manual.rst index e26f661..50a7b2f 100644 --- a/docs/source/manual.rst +++ b/docs/source/manual.rst @@ -291,8 +291,14 @@ In the above example, NetCDF4 with level-1 compression is requested. Acceptable Options are: - ``"netcdf"``: NetCDF3 -- ``"netcdf4"``: NetCDF4 uncompressed -- ``"netcdf4c"``: NetCDF4 compressed (level 1) +- ``"netcdf4"``: NetCDF4 +- ``"netcdf4c"``: NetCDF4 with level 1 compression + +- ``compression_level``: This is an integer specifying the level of + compression to use when writing the output files. This can be a number + from 0 to 9, where 0 means no compression (default) and 9 mean the + highest level of compression. This is overridden when the ``"netcdf4c"`` + format is used. - ``output_file_prefix``: This is a string specifying the common output (time-series) filename prefix. It is assumed that each time-series diff --git a/source/pyreshaper/reshaper.py b/source/pyreshaper/reshaper.py index 206e76c..ef4b22a 100644 --- a/source/pyreshaper/reshaper.py +++ b/source/pyreshaper/reshaper.py @@ -64,6 +64,9 @@ def create_reshaper(specifier, serial=False, verbosity=1, write all metadata to a 'once' file (separately). simplecomm (SimpleComm): A SimpleComm object to handle the parallel communication, if necessary + compressionlevel (int): An integer specifying the level of + compression to be used for the output files, if compression + is allowed by the NetCDF format Returns: Reshaper: An instance of the Reshaper object requested @@ -296,12 +299,9 @@ def __init__(self, specifier, serial=False, verbosity=1, # from the NetCDF format string in the Specifier if specifier.netcdf_format == 'netcdf': opt.Format = 'Classic' - elif specifier.netcdf_format == 'netcdf4': + elif specifier.netcdf_format in ['netcdf4', 'netcdf4c']: opt.Format = 'NetCDF4Classic' - opt.CompressionLevel = 0 - elif specifier.netcdf_format == 'netcdf4c': - opt.Format = 'NetCDF4Classic' - opt.CompressionLevel = 1 + opt.CompressionLevel = specifier.compression_level self._nio_options = opt if self._simplecomm.is_manager(): self._vprint('PyNIO options set', verbosity=2) diff --git a/source/pyreshaper/specification.py b/source/pyreshaper/specification.py index bf3d722..09d82e8 100644 --- a/source/pyreshaper/specification.py +++ b/source/pyreshaper/specification.py @@ -45,7 +45,8 @@ class Specifier(object): def __init__(self, infiles=[], - ncfmt='netcdf4c', + ncfmt='netcdf4', + compression=0, prefix='tseries.', suffix='.nc', metadata=[], @@ -64,6 +65,8 @@ def __init__(self, infiles (list): List of full-path input filenames ncfmt (str): String specifying the NetCDF data format ('netcdf','netcdf4','netcdf4c') + compression (int): Compression level to use for NetCDF4 + formatted data (overridden by the 'netcdf4c' format) prefix (str): String specifying the full-path prefix common to all time-series output files suffix (str): String specifying the suffix common @@ -81,6 +84,9 @@ def __init__(self, # The string specifying the NetCDF file format for output self.netcdf_format = ncfmt + # The string specifying the NetCDF file format for output + self.compression_level = compression + # The common prefix to all output files (following the rule: # prefix + variable_name + suffix) self.output_file_prefix = prefix @@ -130,6 +136,11 @@ def validate_types(self): err_msg = "NetCDF format must be given as a string" raise TypeError(err_msg) + # Validate the netcdf compression level + if not isinstance(self.compression_level, int): + err_msg = "NetCDF compression level must be given as an int" + raise TypeError(err_msg) + # Validate the output file prefix if not isinstance(self.output_file_prefix, str): err_msg = "Output file prefix must be given as a string" @@ -187,6 +198,17 @@ def validate_values(self): + " is not valid" raise ValueError(err_msg) + # Forcefully set the compression level if 'netcdf4c' format + if self.netcdf_format == 'netcdf4c': + self.compression_level = 1 + + # Validate the value of the compression level integer + if self.compression_level < 0 or self.compression_level > 9: + err_msg = "Output NetCDF compression level " \ + + str(self.compression_level) \ + + " is not in the valid range (0-9)" + raise ValueError(err_msg) + # Validate the output file directory abs_output_prefix = ospath.abspath(self.output_file_prefix) abs_output_dir = ospath.dirname(abs_output_prefix) From 530e5c3d61a51a1ae99b33047fb9891c3a03d8a7 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Fri, 2 Oct 2015 16:32:34 -0600 Subject: [PATCH 241/250] Adding new timings to the database --- tests/yellowstone/timings.json | 216 +++++++++++++++++++++++++++++++++ 1 file changed, 216 insertions(+) diff --git a/tests/yellowstone/timings.json b/tests/yellowstone/timings.json index 7cb8ef9..0431f01 100644 --- a/tests/yellowstone/timings.json +++ b/tests/yellowstone/timings.json @@ -536,6 +536,24 @@ "real": 324.800256014, "request": 28450.9692535, "sys": "yellowstone" + }, + "151002-144720": { + "TSr": 267.789553165, + "TSw": 62.3434591293, + "actual": 968848.0, + "cores": 16, + "metaTIr": 0.148299455643, + "metaTIw": 0.26377415657, + "metaTVr": 15.7539906502, + "metaTVw": 10.9335258007, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 4.0840959549, + "openo": 0.172574281693, + "real": 323.57800293, + "request": 28450.9692535, + "sys": "yellowstone" } } }, @@ -615,6 +633,24 @@ "real": 1241.54569411, "request": 39295.5901566, "sys": "yellowstone" + }, + "151002-145049": { + "TSr": 240.105856419, + "TSw": 94.4298458099, + "actual": 77864.0, + "cores": 16, + "metaTIr": 3.07635235786, + "metaTIw": 0.10428237915, + "metaTVr": 244.117375135, + "metaTVw": 7.25943517685, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 37.4065859318, + "openo": 0.587407112122, + "real": 469.319635868, + "request": 39295.5901566, + "sys": "yellowstone" } } } @@ -654,6 +690,24 @@ "real": 375.913740158, "request": 41617.1186371, "sys": "yellowstone" + }, + "151002-144915": { + "TSr": 300.091548204, + "TSw": 86.8913040161, + "actual": 1023964.0, + "cores": 16, + "metaTIr": 3.63008785248, + "metaTIw": 0.239748716354, + "metaTVr": 10.3928160667, + "metaTVw": 9.76353907585, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 26.914000988, + "openo": 0.475345373154, + "real": 384.981215954, + "request": 41617.1186371, + "sys": "yellowstone" } } } @@ -1200,6 +1254,24 @@ "real": 2362.43693519, "request": 1078519.71414, "sys": "yellowstone" + }, + "151002-152949": { + "TSr": 1009.50953722, + "TSw": 1854.70439887, + "actual": 2561592.0, + "cores": 16, + "metaTIr": 1.82785892487, + "metaTIw": 8.34366703033, + "metaTVr": 54.4348504543, + "metaTVw": 17.7780208588, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 13.8072900772, + "openo": 0.825301170349, + "real": 2840.41509485, + "request": 1078519.71414, + "sys": "yellowstone" } } }, @@ -1741,6 +1813,24 @@ "real": 370.380084991, "request": 30828.9682617, "sys": "yellowstone" + }, + "151002-144824": { + "TSr": 300.078349829, + "TSw": 107.732641459, + "actual": 1043904.0, + "cores": 16, + "metaTIr": 0.865505695343, + "metaTIw": 0.587111234665, + "metaTVr": 12.9958343506, + "metaTVw": 31.3837080002, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 2.28778886795, + "openo": 1.09594678879, + "real": 389.049459934, + "request": 30828.9682617, + "sys": "yellowstone" } } }, @@ -2281,6 +2371,24 @@ "real": 811.08354497, "request": 561093.903809, "sys": "yellowstone" + }, + "151002-150144": { + "TSr": 619.917356491, + "TSw": 379.453398466, + "actual": 715008.0, + "cores": 16, + "metaTIr": 102.077307701, + "metaTIw": 78.5123889446, + "metaTVr": 23.8168251514, + "metaTVw": 2.38540887833, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 21.7854847908, + "openo": 0.407775163651, + "real": 1168.82769799, + "request": 561093.903809, + "sys": "yellowstone" } } }, @@ -2750,6 +2858,24 @@ "real": 141.086723089, "request": 8336.41067505, "sys": "yellowstone" + }, + "151002-144535": { + "TSr": 164.895143509, + "TSw": 8.39152407646, + "actual": 177840.0, + "cores": 16, + "metaTIr": 2.69702959061, + "metaTIw": 1.62958669662, + "metaTVr": 6.13357424736, + "metaTVw": 0.329475164413, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 12.0156641006, + "openo": 2.29768490791, + "real": 177.504949093, + "request": 8336.41067505, + "sys": "yellowstone" } } }, @@ -3238,6 +3364,24 @@ "real": 262.587915897, "request": 124675.246468, "sys": "yellowstone" + }, + "151002-145027": { + "TSr": 257.785825014, + "TSw": 95.3491647243, + "actual": 798360.0, + "cores": 16, + "metaTIr": 49.3381197453, + "metaTIw": 55.4652349949, + "metaTVr": 50.4830415249, + "metaTVw": 4.86789798737, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 21.76009202, + "openo": 0.745949745178, + "real": 462.231551886, + "request": 124675.246468, + "sys": "yellowstone" } } }, @@ -3752,6 +3896,24 @@ "real": 287.702008009, "request": 14019.9852104, "sys": "yellowstone" + }, + "151002-144726": { + "TSr": 269.169423342, + "TSw": 13.1295950413, + "actual": 1443420.0, + "cores": 16, + "metaTIr": 1.14924407005, + "metaTIw": 5.88382959366, + "metaTVr": 4.54588770866, + "metaTVw": 10.5600767136, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 10.0409920216, + "openo": 1.07933664322, + "real": 300.97479105, + "request": 14019.9852104, + "sys": "yellowstone" } } }, @@ -4218,6 +4380,24 @@ "real": 6260.71265197, "request": 3073293.60839, "sys": "yellowstone" + }, + "151002-162705": { + "TSr": 1008.87791133, + "TSw": 5330.33792472, + "actual": 3121360.0, + "cores": 16, + "metaTIr": 107.638655424, + "metaTIw": 88.9155454636, + "metaTVr": 14.8814268112, + "metaTVw": 2.1268658638, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 11.387442112, + "openo": 0.150990962982, + "real": 6270.88925004, + "request": 3073293.60839, + "sys": "yellowstone" } } }, @@ -4669,6 +4849,24 @@ "real": 1015.06130505, "request": 194248.586632, "sys": "yellowstone" + }, + "151002-145908": { + "TSr": 727.685482979, + "TSw": 344.882488966, + "actual": 381048.0, + "cores": 16, + "metaTIr": 4.81376791, + "metaTIw": 5.70712137222, + "metaTVr": 16.7337415218, + "metaTVw": 3.95496964455, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 12.9056642056, + "openo": 0.517478704453, + "real": 991.616967916, + "request": 194248.586632, + "sys": "yellowstone" } } }, @@ -4826,6 +5024,24 @@ "real": 341.90487504, "request": 6232.80738831, "sys": "yellowstone" + }, + "151002-145228": { + "TSr": 222.422555923, + "TSw": 42.7405705452, + "actual": 11296.0, + "cores": 16, + "metaTIr": 1.67179584503, + "metaTIw": 0.42426276207, + "metaTVr": 131.151450157, + "metaTVw": 1.62547826767, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 210.754734993, + "openo": 0.479517936707, + "real": 392.414848089, + "request": 6232.80738831, + "sys": "yellowstone" } } }, From 9497772f4d7770871f7bc989eae860923242e557 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 5 Oct 2015 11:24:02 -0600 Subject: [PATCH 242/250] Cleaning up validation/inspection routines --- source/pyreshaper/reshaper.py | 284 +++++++++++++--------------------- 1 file changed, 110 insertions(+), 174 deletions(-) diff --git a/source/pyreshaper/reshaper.py b/source/pyreshaper/reshaper.py index ef4b22a..ba32c13 100644 --- a/source/pyreshaper/reshaper.py +++ b/source/pyreshaper/reshaper.py @@ -291,6 +291,16 @@ def __init__(self, specifier, serial=False, verbosity=1, if self._simplecomm.is_manager(): self._vprint('Specifier validated', verbosity=1) + # Store the input file names + self._input_filenames = specifier.input_file_list + + # Initialize the dictionary of variable names for each category + # (Keys are variable names, Values are variable sizes) + self._time_variant_metadata = dict( + [(v, 0) for v in specifier.time_variant_metadata]) + self._time_invariant_metadata = {} + self._time_series_variables = {} + # Setup PyNIO options (including disabling the default PreFill option) opt = nio_options() opt.PreFill = False @@ -306,44 +316,23 @@ def __init__(self, specifier, serial=False, verbosity=1, if self._simplecomm.is_manager(): self._vprint('PyNIO options set', verbosity=2) - # Open all of the input files - self._timer.start('Open Input Files') - self._input_files = [] - for filename in specifier.input_file_list: - self._input_files.append(nio_open_file(filename, "r")) - self._timer.stop('Open Input Files') - if self._simplecomm.is_manager(): - self._vprint('Input files opened', verbosity=2) - # Validate the input files themselves - self._timer.start('Input File Validation') - self._validate_input_files(specifier) - self._timer.stop('Input File Validation') - if self._simplecomm.is_manager(): - self._vprint('Input files validated', verbosity=2) - - # Sort the input files by time - self._timer.start('Sort Input Files') - self._sort_input_files_by_time(specifier) - self._timer.stop('Sort Input Files') if self._simplecomm.is_manager(): - self._vprint('Input files sorted', verbosity=2) - - # Retrieve and sort the variables in each time-slice file - # (To determine if it is time-invariant metadata, time-variant - # metadata, or if it is a time-series variable) - self._timer.start('Sort Variables') - self._sort_variables(specifier) - self._timer.stop('Sort Variables') + self._vprint('Inspecting input files...', verbosity=1) + self._timer.start('Inspect Input Files') + self._inspect_input_files() + self._timer.stop('Inspect Input Files') if self._simplecomm.is_manager(): - self._vprint('Variables sorted', verbosity=2) + self._vprint('Input files inspected.', verbosity=1) # Validate the output files - self._timer.start('Output File Validation') - self._validate_output_files(specifier, skip_existing, overwrite) - self._timer.stop('Output File Validation') if self._simplecomm.is_manager(): - self._vprint('Output files validated', verbosity=2) + self._vprint('Checking output file status...', verbosity=1) + self._timer.start('Check Output File Status') + self._check_output_file_status(specifier, skip_existing, overwrite) + self._timer.stop('Check Output File Status') + if self._simplecomm.is_manager(): + self._vprint('Output file status checked.', verbosity=1) # Helpful debugging message if self._simplecomm.is_manager(): @@ -352,171 +341,118 @@ def __init__(self, specifier, serial=False, verbosity=1, # Sync before continuing.. self._simplecomm.sync() - def _validate_input_files(self, specifier): + def _inspect_input_files(self): """ - Perform validation of input data files themselves. - - We check the file contents here, assuming that the files are already - open. + Inspect the input data files themselves. - Parameters: - specifier (Specifier): The reshaper specifier object + We check the file contents here. """ - # Helpful debugging message - if self._simplecomm.is_manager(): - self._vprint('Validating input files', verbosity=1) - - # In the first file, look for the 'unlimited' dimension - ifile = self._input_files[0] - self._unlimited_dim = None - for dim in ifile.dimensions: - if ifile.unlimited(dim): - self._unlimited_dim = dim - continue # There can only be 1! - if self._unlimited_dim is None: - err_msg = 'Unlimited dimension not identified.' + #===== INSPECT FIRST INPUT FILE ===== + + # Open first file + ifile = nio_open_file(self._input_filenames[0]) + + # Look for the 'unlimited' dimension + try: + self._unlimited_dim = next(dim for dim in ifile.dimensions + if ifile.unlimited(dim)) + except StopIteration: + err_msg = 'Unlimited dimension not found.' raise LookupError(err_msg) - # Make a pass through each file and: + # Get the time values + time_values = [ifile.variables[self._unlimited_dim].get_value()] + + # Get the list of variable names and missing variables + var_names = set(ifile.variables.keys()) + missing_vars = set() + + # Categorize each variable (only looking at first file) + for var_name, var in ifile.variables.iteritems(): + size = numpy.dtype(var.typecode()).itemsize + size = size * numpy.prod(var.shape) + if self._unlimited_dim not in var.dimensions: + self._time_invariant_metadata[var_name] = size + elif var_name in self._time_variant_metadata: + self._time_variant_metadata[var_name] = size + else: + self._time_series_variables[var_name] = size + + # Close the first file + ifile.close() + + #===== INSPECT REMAINING INPUT FILES ===== + + # Make a pass through remaining files and: # (1) Make sure it has the 'unlimited' dimension # (2) Make sure this dimension is truely 'unlimited' # (3) Check that this dimension has a corresponding variable - for i in range(len(self._input_files)): - ifile = self._input_files[i] + # (4) Check if there are any missing variables + # (5) Get the time values from the files + for ifilename in self._input_filenames[1:]: + ifile = nio_open_file(ifilename) + + # Determine the unlimited dimension if self._unlimited_dim not in ifile.dimensions: - err_msg = 'Unlimited dimension not found in file (' \ - + specifier.input_file_list[i] + ')' + err_msg = ('Unlimited dimension not found ' + 'in file "{}"').format(ifilename) raise LookupError(err_msg) if not ifile.unlimited(self._unlimited_dim): - err_msg = 'Unlimited dimension not unlimited in file (' \ - + specifier.input_file_list[i] + ')' + err_msg = ('Dimension "{}" not unlimited in file ' + '"{}"').format(self._unlimited_dim, ifilename) raise LookupError(err_msg) if self._unlimited_dim not in ifile.variables: - err_msg = 'Unlimited dimension variable not found in file (' \ - + specifier.input_file_list[i] + ')' + err_msg = ('Unlimited dimension variable not found in file ' + '"{}"').format(ifilename) raise LookupError(err_msg) - # Make sure that the list of variables in each file is the same - variables = self._input_files[0].variables - var_names = set(variables.keys()) - missing_vars = set() - for ifile in self._input_files[1:]: + # Get the time values (list of NDArrays) + time_values.append( + ifile.variables[self._unlimited_dim].get_value()) + + # Get the missing variables var_names_next = set(ifile.variables.keys()) missing_vars.update(var_names - var_names_next) + + # Close the file + ifile.close() + + #===== CHECK FOR MISSING VARIABLES ===== + + # Make sure that the list of variables in each file is the same if len(missing_vars) != 0: - warning = "WARNING: The first input file has variables that are " \ - + "not in all input files:" + linesep + ' ' + warning = ("WARNING: The first input file has variables that are " + "not in all input files:{}{}").format(linesep, ' ') for var in missing_vars: - warning += ' ' + str(var) + warning += ' {}'.format(var) self._vprint(warning, header=True, verbosity=1) - def _sort_input_files_by_time(self, specifier): - """ - Internal method for sorting the input files by time - - This assumes that 'time' is the unlimited dimension, and it checks - to make sure that all of the times spanning across each file do not - overlap with each other (i.e., that the times across all files are - monotonicly increasing). - - Currently, this method assumes that all of the input files - have the same 'time:units' attribute, such that all time variable - values are measured from the same date-time. When this is true, - we do not need to consider the value of the 'time:units' - attribute itself. If this assumption is not true, then we need - to consider the 'time:units" attribute of each file, together - with that file's time variable values. To do that properly, - however, one should use UDUNITS to do the comparisons. - - Parameters: - specifier (Specifier): The reshaper specifier object - """ - - # Helpful debugging message - if self._simplecomm.is_manager(): - self._vprint('Sorting input files', verbosity=1) - - # Get the time attributes (for convenience) and, for each file, - # add the times to a list. (Each file will have an array of times - # associated with it. Each array will be added to a list, such - # that the outer-most list contains an array for each input file) - time_values = [] - for ifile in self._input_files: - time_values.append( - ifile.variables[self._unlimited_dim].get_value()) + #===== SORT INPUT FILES BY TIME ===== # Determine the sort order based on the first time in the time values - order = range(len(self._input_files)) - new_order = sorted(order, key=lambda i: time_values[i][0]) - - # Re-order the list of input files and filenames - new_file_list = [None] * len(new_order) - new_filenames = [None] * len(new_order) - new_values = [None] * len(new_order) - for i in order: - new_file_list[i] = self._input_files[new_order[i]] - new_filenames[i] = specifier.input_file_list[new_order[i]] - new_values[i] = time_values[new_order[i]] - - # Save this data in the new orders - self._input_files = new_file_list - self._input_filenames = new_filenames + old_order = range(len(self._input_filenames)) + new_order = sorted(old_order, key=lambda i: time_values[i][0]) + + # Re-order the list of input filenames and time values + new_filenames = [self._input_file_list[i] for i in new_order] + new_values = [time_values[i] for i in new_order] # Now, check that the largest time in each file is less than the # smallest time in the next file (so that the time spans of each file # do not overlap) - for i in order[:-1]: - if new_values[i][-1] >= new_values[i + 1][0]: - err_msg = 'Times in input files ' + str(new_filenames[i]) \ - + ' and ' + str(new_filenames[i + 1]) + ' appear to ' \ - + 'overlap.' + for i in xrange(1, len(new_values)): + if new_values[i - 1][-1] >= new_values[i][0]: + err_msg = ('Times in input files {} and {} appear ' + 'to overlap').format(new_filenames[i - 1], + new_filenames[i]) raise ValueError(err_msg) - # Now that this is validated, let's string together the numpy array - # of all times (using the new_values array) - self._all_time_values = \ - numpy.fromiter(chain.from_iterable(new_values), dtype='float') - - def _sort_variables(self, specifier): - """ - Internal method for sorting the variables in each time-slice file - - This method determines if each variable is to be treated as - time-invariant metadata, time-variant metadata (user defined), or - time-series variables. All metadata is written to every time-series - file, and any time-series variable is written to its own file. - The time-variant metadata variables are determined by user input, - and are contained in the Specifier data member: - - Specifier.time_variant_metadata. - - Parameters: - specifier (Specifier): The reshaper specifier object - """ - - # Helpful debugging message - if self._simplecomm.is_manager(): - self._vprint('Sorting variables', verbosity=1) - - # Initialize the dictionary of variable names for each category - # (Keys are variable names, Values are variable sizes) - self._time_variant_metadata = {} - self._time_invariant_metadata = {} - self._time_series_variables = {} + # Now that this is validated, save the time values and filename in + # the new order + self._input_filenames = new_filenames - # Categorize each variable (only looking at first file) - variables = self._input_files[0].variables - for var_name in variables.keys(): - var = variables[var_name] - size = numpy.dtype(var.typecode()).itemsize - size = size * numpy.prod(var.shape) - if self._unlimited_dim not in var.dimensions: - self._time_invariant_metadata[var_name] = size - elif var_name in specifier.time_variant_metadata: - self._time_variant_metadata[var_name] = size - else: - self._time_series_variables[var_name] = size + #===== FINALIZING OUTPUT ===== # Debug output if self._simplecomm.is_manager(): @@ -533,8 +469,8 @@ def _sort_variables(self, specifier): if self._use_once_file: self._time_series_variables['once'] = 1 - def _validate_output_files(self, specifier, - skip_existing=False, overwrite=False): + def _check_output_file_status(self, specifier, + skip_existing=False, overwrite=False): """ Perform validation of output data files themselves. @@ -574,7 +510,7 @@ def _validate_output_files(self, specifier, if overwrite: if self._simplecomm.is_manager(): self._vprint('WARNING: Deleting existing output files for ' - 'time-series variables: ' + str(existing), + 'time-series variables: {}'.format(existing), verbosity=1) for variable in existing: remove(self._time_series_filenames[variable]) @@ -584,15 +520,15 @@ def _validate_output_files(self, specifier, elif skip_existing: if self._simplecomm.is_manager(): self._vprint('WARNING: Skipping time-series variables with ' - 'existing output files: ' + str(existing), + 'existing output files: {}'.format(existing), verbosity=1) for variable in existing: self._time_series_variables.pop(variable) # Otherwise, throw an exception if any existing output files are found elif len(existing) > 0: - err_msg = "Found existing output files for time-series " + \ - "variables:" + str(existing) + err_msg = ("Found existing output files for time-series " + "variables: {}").format(existing) raise RuntimeError(err_msg) def convert(self, output_limit=0): @@ -622,7 +558,7 @@ def convert(self, output_limit=0): self._vprint('Converting time-slices to time-series', verbosity=1) # For data common to all input files, we reference only the first - ref_infile = self._input_files[0] + ref_infile = self._input_filenames[0] # Store the common dimensions and attributes for each file # (taken from the first input file in the list) @@ -787,7 +723,7 @@ def _get_bytesize(data): # Write each time-variant variable series_step_index = 0 - for in_file in self._input_files: + for in_file in self._input_filenames: # Get the number of time steps in this slice file num_steps = in_file.dimensions[self._unlimited_dim] From 5cc4fe378d1114635de9f685e36c430b98971cab Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 5 Oct 2015 11:33:44 -0600 Subject: [PATCH 243/250] Removed unnecessary import --- source/pyreshaper/reshaper.py | 1 - 1 file changed, 1 deletion(-) diff --git a/source/pyreshaper/reshaper.py b/source/pyreshaper/reshaper.py index ba32c13..7a3d2e6 100644 --- a/source/pyreshaper/reshaper.py +++ b/source/pyreshaper/reshaper.py @@ -13,7 +13,6 @@ import abc from os import linesep, remove from os.path import exists, isfile -from itertools import chain # Third-party imports import numpy From 0615e124cb35049fbec0079d01cd6bc408576198 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 5 Oct 2015 12:51:18 -0600 Subject: [PATCH 244/250] First pass at opening/closing input files in loop over output files --- source/pyreshaper/reshaper.py | 248 ++++++++++++++++------------------ 1 file changed, 116 insertions(+), 132 deletions(-) diff --git a/source/pyreshaper/reshaper.py b/source/pyreshaper/reshaper.py index 7a3d2e6..203b3e0 100644 --- a/source/pyreshaper/reshaper.py +++ b/source/pyreshaper/reshaper.py @@ -556,28 +556,23 @@ def convert(self, output_limit=0): if self._simplecomm.is_manager(): self._vprint('Converting time-slices to time-series', verbosity=1) - # For data common to all input files, we reference only the first - ref_infile = self._input_filenames[0] - - # Store the common dimensions and attributes for each file - # (taken from the first input file in the list) - common_dims = ref_infile.dimensions - common_atts = ref_infile.attributes - # Partition the time-series variables across all processors - tsv_names_loc = self._simplecomm.partition(self._time_series_variables.items(), - func=WeightBalanced(), - involved=True) + tsv_names_loc = self._simplecomm.partition( + self._time_series_variables.items(), func=WeightBalanced(), + involved=True) if output_limit > 0: tsv_names_loc = tsv_names_loc[0:output_limit] # Print partitions for all ranks - dbg_msg = 'Local time-series variables are ' + str(tsv_names_loc) + dbg_msg = 'Local time-series variables are {}'.format(tsv_names_loc) self._vprint(dbg_msg, header=True, verbosity=2) # Reset all of the timer values (as it is possible that there are no # time-series variables in the local list procuded above) self._timer.reset('Open Output Files') + self._timer.reset('Close Output Files') + self._timer.reset('Open Input Files') + self._timer.reset('Close Input Files') self._timer.reset('Create Time-Invariant Metadata') self._timer.reset('Create Time-Variant Metadata') self._timer.reset('Create Time-Series Variables') @@ -587,24 +582,11 @@ def convert(self, output_limit=0): self._timer.reset('Write Time-Invariant Metadata') self._timer.reset('Write Time-Variant Metadata') self._timer.reset('Write Time-Series Variables') - self._timer.reset('Close Output Files') # Initialize the byte count dictionary self._byte_counts['Requested Data'] = 0 self._byte_counts['Actual Data'] = 0 - # Defining a simple helper function to determine whether to - # write time-series data and/or write metadata. This is useful - # for adding the ability to write a "once" file - def _get_once_info(vname): - is_once_file = (vname == 'once') - write_meta = True - write_tser = True - if self._use_once_file: - write_meta = is_once_file - write_tser = not is_once_file - return is_once_file, write_meta, write_tser - # Defining a simple helper function to determine the bytes size of # a variable given to it, whether an NDArray or not def _get_bytesize(data): @@ -613,127 +595,121 @@ def _get_bytesize(data): else: return 0 - # NOTE: In the prototype, we check for the existance of the output - # directory at this point. If it does not exist, we create it (but - # only from the master rank). This requires synchronization with - # the decomp utility. Instead, we assume the output directory - # already exists (and is checked by the Specifier's validation). No - # synchronization is needed. + #===== LOOP OVER TIME_SERIES VARIABLES ===== - # For each time-series variable, create the corresponding output file - # (Also defines the header info for each output file) - out_files = {} + # Loop over all time-series variables for out_name in tsv_names_loc: - is_once_file, write_meta, write_tser = _get_once_info(out_name) # Determine the output file name for this variable out_filename = self._time_series_filenames[out_name] - dbg_msg = 'Creating output file for variable: ' + out_name - if is_once_file: + dbg_msg = 'Creating output file for variable: {}'.format(out_name) + if out_name == 'once': dbg_msg = 'Creating "once" file.' self._vprint(dbg_msg, header=True, verbosity=1) - # Open each output file and create the dimensions and attributes + # Open the output file # NOTE: If the output file already exists, abort! self._timer.start('Open Output Files') if exists(out_filename): - err_msg = 'Found existing output file: ' + out_filename + err_msg = 'Found existing output file: {}'.format(out_filename) raise OSError(err_msg) out_file = nio_open_file(out_filename, 'w', options=self._nio_options) - for att_name, att_val in common_atts.iteritems(): - setattr(out_file, att_name, att_val) - for dim_name, dim_val in common_dims.iteritems(): - if dim_name == self._unlimited_dim: - out_file.create_dimension(dim_name, None) - else: - out_file.create_dimension(dim_name, dim_val) self._timer.stop('Open Output Files') - # Create the time-invariant metadata variables - if write_meta: - self._timer.start('Create Time-Invariant Metadata') - for name in self._time_invariant_metadata: - in_var = ref_infile.variables[name] - out_var = out_file.create_variable( - name, in_var.typecode(), in_var.dimensions) - for att_name, att_val in in_var.attributes.iteritems(): - setattr(out_var, att_name, att_val) - self._timer.stop('Create Time-Invariant Metadata') - - # Create the time-variant metadata variables - if write_meta: - self._timer.start('Create Time-Variant Metadata') - for name in self._time_variant_metadata: - in_var = ref_infile.variables[name] - out_var = out_file.create_variable( - name, in_var.typecode(), in_var.dimensions) - for att_name, att_val in in_var.attributes.iteritems(): - setattr(out_var, att_name, att_val) - self._timer.stop('Create Time-Variant Metadata') - - # Create the time-series variable itself - if write_tser: - self._timer.start('Create Time-Series Variables') - in_var = ref_infile.variables[out_name] - out_var = out_file.create_variable( - out_name, in_var.typecode(), in_var.dimensions) - for att_name, att_val in in_var.attributes.iteritems(): - setattr(out_var, att_name, att_val) - self._timer.stop('Create Time-Series Variables') - - # Append the output file to list - out_files[out_name] = out_file - - # Now that each output file has been created, start writing the data - # (Looping over output file index, which is common in name lists) - for out_name, out_file in out_files.iteritems(): - is_once_file, write_meta, write_tser = _get_once_info(out_name) - - dbg_msg = 'Writing output file for variable: ' + out_name - if is_once_file: - dbg_msg = 'Writing "once" file.' - self._vprint(dbg_msg, header=True, verbosity=1) - - # Write the time-invariant metadata - if write_meta: - for name in self._time_invariant_metadata: - in_meta = ref_infile.variables[name] - out_meta = out_file.variables[name] - self._timer.start('Read Time-Invariant Metadata') - if in_meta.rank > 0: - tmp_data = in_meta[:] - else: - tmp_data = in_meta.get_value() - self._timer.stop('Read Time-Invariant Metadata') - self._timer.start('Write Time-Invariant Metadata') - if in_meta.rank > 0: - out_meta[:] = tmp_data - else: - out_meta.assign_value(tmp_data) - self._timer.stop('Write Time-Invariant Metadata') - - requested_nbytes = _get_bytesize(tmp_data) - self._byte_counts[ - 'Requested Data'] += requested_nbytes - actual_nbytes = self.assumed_block_size \ - * numpy.ceil(requested_nbytes / self.assumed_block_size) - self._byte_counts['Actual Data'] += actual_nbytes - - # Write each time-variant variable + # Start the loop over input files (i.e., time-steps) series_step_index = 0 - for in_file in self._input_filenames: + for in_filename in self._input_filenames: + + # Open the input file + self._timer.start('Open Input Files') + in_file = nio_open_file(in_filename, 'r') + self._timer.stop('Open Input Files') + + # Create header info, if this is the first input file + if in_filename == self._input_filenames[0]: + + # Copy file attributes and dimensions to output file + for name, val in in_file.attributes.iteritems(): + setattr(out_file, name, val) + for name, val in in_file.dimensions.iteritems(): + if name == self._unlimited_dim: + out_file.create_dimension(name, None) + else: + out_file.create_dimension(name, val) + + # Create the metadata variables + if not (self._use_once_file and out_name != 'once'): + + # Time-invariant metadata variables + self._timer.start('Create Time-Invariant Metadata') + for name in self._time_invariant_metadata: + in_var = in_file.variables[name] + out_var = out_file.create_variable( + name, in_var.typecode(), in_var.dimensions) + for att_name, att_val in in_var.attributes.iteritems(): + setattr(out_var, att_name, att_val) + self._timer.stop('Create Time-Invariant Metadata') + + # Time-variant metadata variables + self._timer.start('Create Time-Variant Metadata') + for name in self._time_variant_metadata: + in_var = in_file.variables[name] + out_var = out_file.create_variable( + name, in_var.typecode(), in_var.dimensions) + for att_name, att_val in in_var.attributes.iteritems(): + setattr(out_var, att_name, att_val) + self._timer.stop('Create Time-Variant Metadata') + + # Create the time-series variable + if not (self._use_once_file and out_name == 'once'): + + # Time-series variable + self._timer.start('Create Time-Series Variables') + in_var = in_file.variables[out_name] + out_var = out_file.create_variable( + out_name, in_var.typecode(), in_var.dimensions) + for att_name, att_val in in_var.attributes.iteritems(): + setattr(out_var, att_name, att_val) + self._timer.stop('Create Time-Series Variables') + + dbg_msg = ('Writing output file for variable: ' + '{}').format(out_name) + if out_name == 'once': + dbg_msg = 'Writing "once" file.' + self._vprint(dbg_msg, header=True, verbosity=1) + + # Copy the time-invariant metadata + if not (self._use_once_file and out_name != 'once'): + + for name in self._time_invariant_metadata: + in_var = in_file.variables[name] + out_var = out_file.variables[name] + self._timer.start('Read Time-Invariant Metadata') + tmp_data = in_var.get_value() + self._timer.stop('Read Time-Invariant Metadata') + self._timer.start('Write Time-Invariant Metadata') + out_var.assign_value(tmp_data) + self._timer.stop('Write Time-Invariant Metadata') + + requested_nbytes = _get_bytesize(tmp_data) + self._byte_counts[ + 'Requested Data'] += requested_nbytes + actual_nbytes = self.assumed_block_size \ + * numpy.ceil(requested_nbytes / self.assumed_block_size) + self._byte_counts['Actual Data'] += actual_nbytes # Get the number of time steps in this slice file num_steps = in_file.dimensions[self._unlimited_dim] - # Write the time-varient metadata - if write_meta: + # Copy the time-varient metadata + if not (self._use_once_file and out_name != 'once'): + for name in self._time_variant_metadata: - in_meta = in_file.variables[name] - out_meta = out_file.variables[name] - ndims = len(in_meta.dimensions) - udidx = in_meta.dimensions.index( + in_var = in_file.variables[name] + out_var = out_file.variables[name] + ndims = len(in_var.dimensions) + udidx = in_var.dimensions.index( self._unlimited_dim) out_slice = [slice(None)] * ndims if num_steps > 1: @@ -741,10 +717,10 @@ def _get_bytesize(data): else: out_slice[udidx] = series_step_index self._timer.start('Read Time-Variant Metadata') - tmp_data = in_meta[:] + tmp_data = in_var[:] self._timer.stop('Read Time-Variant Metadata') self._timer.start('Write Time-Variant Metadata') - out_meta[tuple(out_slice)] = tmp_data + out_var[tuple(out_slice)] = tmp_data self._timer.stop('Write Time-Variant Metadata') requested_nbytes = _get_bytesize(tmp_data) @@ -754,8 +730,9 @@ def _get_bytesize(data): * numpy.ceil(requested_nbytes / self.assumed_block_size) self._byte_counts['Actual Data'] += actual_nbytes - # Write the time-series variables - if write_tser: + # Copy the time-series variables + if not (self._use_once_file and out_name == 'once'): + in_var = in_file.variables[out_name] out_var = out_file.variables[out_name] ndims = len(in_var.dimensions) @@ -781,20 +758,27 @@ def _get_bytesize(data): # Increment the time-series step index series_step_index += num_steps + # Close the input file + self._timer.start('Close Input Files') + in_file.close() + self._timer.stop('Close Input Files') + # Close the output file self._timer.start('Close Output Files') out_file.close() self._timer.stop('Close Output Files') - dbg_msg = 'Closed output file for variable: ' + out_name - if is_once_file: + + # Output message to user + dbg_msg = 'Closed output file for variable: {}'.format(out_name) + if out_name == 'once': dbg_msg = 'Closed "once" file.' self._vprint(dbg_msg, header=True, verbosity=1) # Information self._simplecomm.sync() if self._simplecomm.is_manager(): - self._vprint( - 'Finished converting time-slices to time-series.', verbosity=1) + self._vprint(('Finished converting time-slices ' + 'to time-series.'), verbosity=1) # Finish clocking the entire convert procedure self._timer.stop('Complete Conversion Process') From c8b59b80c7ef3f9a81ad285ae80dd767f1bc9131 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 5 Oct 2015 13:11:02 -0600 Subject: [PATCH 245/250] FIX: Attribute name typo --- source/pyreshaper/reshaper.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/source/pyreshaper/reshaper.py b/source/pyreshaper/reshaper.py index 203b3e0..fa49a37 100644 --- a/source/pyreshaper/reshaper.py +++ b/source/pyreshaper/reshaper.py @@ -434,7 +434,7 @@ def _inspect_input_files(self): new_order = sorted(old_order, key=lambda i: time_values[i][0]) # Re-order the list of input filenames and time values - new_filenames = [self._input_file_list[i] for i in new_order] + new_filenames = [self._input_filenames[i] for i in new_order] new_values = [time_values[i] for i in new_order] # Now, check that the largest time in each file is less than the From bbe1681a940a3d661d1902c5de2c6c3513d48057 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 5 Oct 2015 13:21:46 -0600 Subject: [PATCH 246/250] Only display warning if necessary --- source/pyreshaper/reshaper.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/source/pyreshaper/reshaper.py b/source/pyreshaper/reshaper.py index fa49a37..a1e8725 100644 --- a/source/pyreshaper/reshaper.py +++ b/source/pyreshaper/reshaper.py @@ -488,10 +488,6 @@ def _check_output_file_status(self, specifier, output files if they already exist. Default is False. """ - # Helpful debugging message - if self._simplecomm.is_manager(): - self._vprint('Validating output files', verbosity=1) - # Loop through the time-series variables and generate output filenames prefix = specifier.output_file_prefix suffix = specifier.output_file_suffix @@ -505,6 +501,10 @@ def _check_output_file_status(self, specifier, if isfile(filename): existing.append(variable) + # Return if no existing files found + if len(existing) == 0: + return + # If overwrite is enabled, delete all existing files first if overwrite: if self._simplecomm.is_manager(): @@ -525,7 +525,7 @@ def _check_output_file_status(self, specifier, self._time_series_variables.pop(variable) # Otherwise, throw an exception if any existing output files are found - elif len(existing) > 0: + else: err_msg = ("Found existing output files for time-series " "variables: {}").format(existing) raise RuntimeError(err_msg) From 0287d9c97db8d3e3477eeba040479f7c9bb721ca Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 5 Oct 2015 13:29:17 -0600 Subject: [PATCH 247/250] Make sure variables names are only in 1 category (t-var, t-inv, etc) --- source/pyreshaper/reshaper.py | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/source/pyreshaper/reshaper.py b/source/pyreshaper/reshaper.py index a1e8725..6ea88df 100644 --- a/source/pyreshaper/reshaper.py +++ b/source/pyreshaper/reshaper.py @@ -295,8 +295,7 @@ def __init__(self, specifier, serial=False, verbosity=1, # Initialize the dictionary of variable names for each category # (Keys are variable names, Values are variable sizes) - self._time_variant_metadata = dict( - [(v, 0) for v in specifier.time_variant_metadata]) + self._time_variant_metadata = {} self._time_invariant_metadata = {} self._time_series_variables = {} @@ -319,7 +318,7 @@ def __init__(self, specifier, serial=False, verbosity=1, if self._simplecomm.is_manager(): self._vprint('Inspecting input files...', verbosity=1) self._timer.start('Inspect Input Files') - self._inspect_input_files() + self._inspect_input_files(specifier.time_variant_metadata) self._timer.stop('Inspect Input Files') if self._simplecomm.is_manager(): self._vprint('Input files inspected.', verbosity=1) @@ -340,11 +339,15 @@ def __init__(self, specifier, serial=False, verbosity=1, # Sync before continuing.. self._simplecomm.sync() - def _inspect_input_files(self): + def _inspect_input_files(self, metadata_names=[]): """ Inspect the input data files themselves. We check the file contents here. + + Parameters: + metadata_names (list): List of string names. If a variable with + one of these names is found, assume it is metadata. """ #===== INSPECT FIRST INPUT FILE ===== @@ -373,7 +376,7 @@ def _inspect_input_files(self): size = size * numpy.prod(var.shape) if self._unlimited_dim not in var.dimensions: self._time_invariant_metadata[var_name] = size - elif var_name in self._time_variant_metadata: + elif var_name in metadata_names: self._time_variant_metadata[var_name] = size else: self._time_series_variables[var_name] = size From d97c61f610b58c9de6b133835d09d23146553690 Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 5 Oct 2015 13:40:54 -0600 Subject: [PATCH 248/250] Correct read order to get timing info --- tests/yellowstone/mktimings.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/tests/yellowstone/mktimings.py b/tests/yellowstone/mktimings.py index 812f9c8..af4e183 100755 --- a/tests/yellowstone/mktimings.py +++ b/tests/yellowstone/mktimings.py @@ -129,12 +129,16 @@ def find_shortest_str(strng, left, right=os.linesep, loc=0): used_once_file = True # Find the internal timing data from the run output: - openi_str, loc = find_shortest_str( - log_str, 'Open Input Files: ', loc=loc) tot_timing_str, loc = find_shortest_str( log_str, 'Complete Conversion Process: ', loc=loc) openo_str, loc = find_shortest_str( log_str, 'Open Output Files: ', loc=loc) + closeo_str, loc = find_shortest_str( + log_str, 'Close Output Files: ', loc=loc) + openi_str, loc = find_shortest_str( + log_str, 'Open Input Files: ', loc=loc) + closei_str, loc = find_shortest_str( + log_str, 'Close Input Files: ', loc=loc) rmetaTI_str, loc = find_shortest_str( log_str, 'Read Time-Invariant Metadata: ', loc=loc) rmetaTV_str, loc = find_shortest_str( From 91e5b3cf78527aefc4e6497f39316478e6f4c03f Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 5 Oct 2015 14:01:46 -0600 Subject: [PATCH 249/250] Explicit loop over time steps to control memory use --- source/pyreshaper/reshaper.py | 90 +++++++++++++++++------------------ 1 file changed, 45 insertions(+), 45 deletions(-) diff --git a/source/pyreshaper/reshaper.py b/source/pyreshaper/reshaper.py index 6ea88df..851f543 100644 --- a/source/pyreshaper/reshaper.py +++ b/source/pyreshaper/reshaper.py @@ -705,61 +705,61 @@ def _get_bytesize(data): # Get the number of time steps in this slice file num_steps = in_file.dimensions[self._unlimited_dim] - # Copy the time-varient metadata - if not (self._use_once_file and out_name != 'once'): + # Explicitly loop over time steps (to control memory use) + for slice_step_index in xrange(num_steps): - for name in self._time_variant_metadata: - in_var = in_file.variables[name] - out_var = out_file.variables[name] + # Copy the time-varient metadata + if not (self._use_once_file and out_name != 'once'): + + for name in self._time_variant_metadata: + in_var = in_file.variables[name] + out_var = out_file.variables[name] + ndims = len(in_var.dimensions) + udidx = in_var.dimensions.index(self._unlimited_dim) + in_slice = [slice(None)] * ndims + in_slice[udidx] = slice_step_index + out_slice = [slice(None)] * ndims + out_slice[udidx] = series_step_index + self._timer.start('Read Time-Variant Metadata') + tmp_data = in_var[tuple(in_slice)] + self._timer.stop('Read Time-Variant Metadata') + self._timer.start('Write Time-Variant Metadata') + out_var[tuple(out_slice)] = tmp_data + self._timer.stop('Write Time-Variant Metadata') + + requested_nbytes = _get_bytesize(tmp_data) + self._byte_counts[ + 'Requested Data'] += requested_nbytes + actual_nbytes = self.assumed_block_size \ + * numpy.ceil(requested_nbytes / self.assumed_block_size) + self._byte_counts['Actual Data'] += actual_nbytes + + # Copy the time-series variables + if not (self._use_once_file and out_name == 'once'): + + in_var = in_file.variables[out_name] + out_var = out_file.variables[out_name] ndims = len(in_var.dimensions) - udidx = in_var.dimensions.index( - self._unlimited_dim) + udidx = in_var.dimensions.index(self._unlimited_dim) + in_slice = [slice(None)] * ndims + in_slice[udidx] = slice_step_index out_slice = [slice(None)] * ndims - if num_steps > 1: - out_slice[udidx] = slice(series_step_index, None) - else: - out_slice[udidx] = series_step_index - self._timer.start('Read Time-Variant Metadata') - tmp_data = in_var[:] - self._timer.stop('Read Time-Variant Metadata') - self._timer.start('Write Time-Variant Metadata') + out_slice[udidx] = series_step_index + self._timer.start('Read Time-Series Variables') + tmp_data = in_var[tuple(in_slice)] + self._timer.stop('Read Time-Series Variables') + self._timer.start('Write Time-Series Variables') out_var[tuple(out_slice)] = tmp_data - self._timer.stop('Write Time-Variant Metadata') + self._timer.stop('Write Time-Series Variables') requested_nbytes = _get_bytesize(tmp_data) - self._byte_counts[ - 'Requested Data'] += requested_nbytes + self._byte_counts['Requested Data'] += requested_nbytes actual_nbytes = self.assumed_block_size \ * numpy.ceil(requested_nbytes / self.assumed_block_size) self._byte_counts['Actual Data'] += actual_nbytes - # Copy the time-series variables - if not (self._use_once_file and out_name == 'once'): - - in_var = in_file.variables[out_name] - out_var = out_file.variables[out_name] - ndims = len(in_var.dimensions) - udidx = in_var.dimensions.index(self._unlimited_dim) - out_slice = [slice(None)] * ndims - if num_steps > 1: - out_slice[udidx] = slice(series_step_index, None) - else: - out_slice[udidx] = series_step_index - self._timer.start('Read Time-Series Variables') - tmp_data = in_var[:] - self._timer.stop('Read Time-Series Variables') - self._timer.start('Write Time-Series Variables') - out_var[tuple(out_slice)] = tmp_data - self._timer.stop('Write Time-Series Variables') - - requested_nbytes = _get_bytesize(tmp_data) - self._byte_counts['Requested Data'] += requested_nbytes - actual_nbytes = self.assumed_block_size \ - * numpy.ceil(requested_nbytes / self.assumed_block_size) - self._byte_counts['Actual Data'] += actual_nbytes - - # Increment the time-series step index - series_step_index += num_steps + # Increment the time-series step index + series_step_index += 1 # Close the input file self._timer.start('Close Input Files') From fbc1f1a89cc9be061e9a5072534fbfe8f8481ebb Mon Sep 17 00:00:00 2001 From: Kevin Paul Date: Mon, 5 Oct 2015 15:52:32 -0600 Subject: [PATCH 250/250] Most recent timings, in preparation for release. --- tests/yellowstone/timings.json | 414 +++++++++++++++++++++++++++++++++ 1 file changed, 414 insertions(+) diff --git a/tests/yellowstone/timings.json b/tests/yellowstone/timings.json index 0431f01..513b3b0 100644 --- a/tests/yellowstone/timings.json +++ b/tests/yellowstone/timings.json @@ -554,6 +554,42 @@ "real": 323.57800293, "request": 28450.9692535, "sys": "yellowstone" + }, + "151005-133333": { + "TSr": 124.339257717, + "TSw": 61.037047863, + "actual": 968848.0, + "cores": 16, + "metaTIr": 0.0115587711334, + "metaTIw": 0.292886972427, + "metaTVr": 1.04787969589, + "metaTVw": 11.0901486874, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 20.3761889935, + "openo": 0.308133363724, + "real": 205.250231981, + "request": 28450.9692535, + "sys": "yellowstone" + }, + "151005-141124": { + "TSr": 251.438382626, + "TSw": 60.7321989536, + "actual": 968848.0, + "cores": 16, + "metaTIr": 0.0118687152863, + "metaTIw": 0.33265209198, + "metaTVr": 1.06335258484, + "metaTVw": 10.987541914, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 31.2857921124, + "openo": 0.316594362259, + "real": 336.083908081, + "request": 28450.9692535, + "sys": "yellowstone" } } }, @@ -594,6 +630,24 @@ "real": 5139.13690186, "request": 412733.208378, "sys": "yellowstone" + }, + "151005-153203": { + "TSr": 1839.39458537, + "TSw": 3156.90317488, + "actual": 16880504.0, + "cores": 16, + "metaTIr": 1.22540211678, + "metaTIw": 0.101293802261, + "metaTVr": 568.625186205, + "metaTVw": 333.683583498, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 350.77940321, + "openo": 0.798895120621, + "real": 4755.39894795, + "request": 412733.208378, + "sys": "yellowstone" } } } @@ -651,6 +705,42 @@ "real": 469.319635868, "request": 39295.5901566, "sys": "yellowstone" + }, + "151005-134305": { + "TSr": 258.39025259, + "TSw": 91.9618022442, + "actual": 77864.0, + "cores": 16, + "metaTIr": 2.48077702522, + "metaTIw": 0.102338075638, + "metaTVr": 67.0126914978, + "metaTVw": 6.04324865341, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 136.388954163, + "openo": 0.433568954468, + "real": 479.639178038, + "request": 39295.5901566, + "sys": "yellowstone" + }, + "151005-142821": { + "TSr": 725.420089722, + "TSw": 107.214648724, + "actual": 11395904.0, + "cores": 16, + "metaTIr": 3.11352205276, + "metaTIw": 0.195004463196, + "metaTVr": 163.349392653, + "metaTVw": 165.829848766, + "metadata": true, + "nodes": 4, + "once": false, + "openi": 148.906975985, + "openo": 1.03988480568, + "real": 1210.8861711, + "request": 39295.5901566, + "sys": "yellowstone" } } } @@ -708,6 +798,42 @@ "real": 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