2.9 release

CMakeLists.txt

@@ -22,7 +22,7 @@ endif()
 
 message(NOTICE "Compiler: ${CMAKE_Fortran_COMPILER}")
 
-project(tristan-v2 VERSION 2.8
+project(tristan-v2 VERSION 2.9
         DESCRIPTION "Relativistic cartesian particle-in-cell code"
         LANGUAGES Fortran)
 
@@ -178,9 +178,11 @@ add_compile_definitions(NGHOST=${nghosts})
 
 if (${radiation} MATCHES "sync")
   add_compile_definitions(SYNCHROTRON)
+  add_compile_definitions(RADIATION)
 endif()
 if (${radiation} MATCHES "ic")
   add_compile_definitions(INVERSECOMPTON)
+  add_compile_definitions(RADIATION)
 endif()
 
 # select the dimension

Makefile.in

@@ -10,7 +10,7 @@ FFLAGS := @COMPILER_FLAGS@
 PFLAGS := @PREPROCESSOR_FLAGS@
 WARNFLAGS := @WARNING_FLAGS@
 
-#H5OBJ := $(HDF5_INCDIR)
+INC_DIRS := -I $(HDF5_ROOT)/include
 
 PFLAGS += @DEFS@
 # FFLAGS += $(WARNFLAGS)
@@ -53,7 +53,7 @@ $(EXECUTABLE): $(OBJ_FILES)
 
 $(BUILD_DIR)%.o: %.F90
 	${HIDE}mkdir -p $(@D)
-	${HIDE}$(FC) $(FFLAGS) $(PFLAGS) -cpp $(addprefix -I, $(dir $(INC_FILES))) @MODULE@ $(BUILD_DIR) -c $< -o $@
+	${HIDE}$(FC) $(FFLAGS) $(PFLAGS) -cpp $(addprefix -I, $(dir $(INC_FILES))) $(INC_DIRS) -J  $(BUILD_DIR) -c $< -o $@
 	${HIDE}echo [OK]: compiled $<
 
 clean :

README.md

@@ -1,4 +1,4 @@
-# Tristan v2.8
+# Tristan v2.9
 
 [![DOI](https://zenodo.org/badge/234551890.svg)](https://zenodo.org/badge/latestdoi/234551890)
 
@@ -8,38 +8,47 @@ For detailed tutorials and code description please visit our [wiki](https://prin
 
 ### Prerequisites
 
-* MPI (either OpenMPI or Intel-MPI)
+* MPI (either OpenMPI or Intel-MPI; mpich is currently untested)
 * GCC or Intel Fortran compiler
 * (optional) Parallel HDF5 (compiled with either OpenMPI or Intel-MPI)
 
 On clusters typically all you need to do is to load the specific modules see [here](https://princetonuniversity.github.io/tristan-v2/tristanv2-configure.html#cluster-specific-customization). 
 
-If you are, however, running on a local machine make sure to install the following prerequisites (assuming non-Intel compiler and `apt` package manager):
+If you are, however, running on a local machine make sure to install the following prerequisites (assuming non-Intel compiler):
 
+#### `apt` (Debian-like)
 ```sh
 # gcc + openmpi
-sudo apt install build-essential libopenmpi-dev
+sudo apt install build-essential libopenmpi-dev 
 # hdf5
 sudo apt libhdf5-openmpi-dev hdf5-tools
 ```
 
-> Also make sure you have a working `python3` installation to be able to configure the code.
+#### `pacman` (Arch-like)
+```sh
+# gcc + openmpi
+sudo pacman -S base-devel gcc gcc-fortran openmpi 
+# hdf5
+sudo pacman -S hdf5-openmpi
+```
+
+> Also make sure you have a working `python3` (v3.8+) installation to be able to configure the code or `Cmake`.
 
 ### Usage
 
-#### `configure.py` + GNU Make
+#### Compiling with `configure.py` + GNU Make
 
 ```shell
 # to view all configuration options
-python3 configure.py --help
+python3 configure.py -h
 # to configure the code (example)
-python3 configure.py -mpi08 -hdf5 --user=user_2d_rec -2d
+python3 configure.py -mpi08 --user=user_2d_rec -2d
 # compile and link (-j compiles in parallel which is much faster)
-make all -j
+make -j
 # executable will be in the `bin/` directory
 ```
 
-#### Cmake
+#### Compiling with `cmake`
 
 Since `v2.8` we also support `cmake` for the code configuration. 
 
@@ -51,22 +60,13 @@ cmake --build build -j
 # executable will be in the `build/src/` directory (*.xc extension)
 ```
 
-Running:
+#### Running:
 
 ```sh
 # run the code (on clusters need to do `srun`, or `irun` etc. depending on the cluster)
 mpirun -np <NCORES> ./<EXECUTABLE> -input <INPUTFILE> -output <OUTPUTDIR>
 ```
 
-#### `CMake` (experimental support)
-
-```shell
-# preconfigure the code using
-cmake -B build -D user=<USERFILE> -D dim=3 ...
-# compile
-cmake --build build -j $(nproc)
-```
-
 ### Docker
 
 Another way to avoid the tedium of installing libraries (especially for local development) is to use [Docker containers](https://docs.docker.com/get-started/). This approach allows to quickly create an isolated linux environment with all the necessary packages already preinstalled (similar to a VM, but much lighter). The best thing is that VSCode can natively attach to a running container, and all the development can be done there (make sure to install the [appropriate extension](https://code.visualstudio.com/docs/remote/containers)).
@@ -116,17 +116,17 @@ Since `v2.4` code formatting policy is employed. To follow the proper formatting
 
 ```sh
 # create a local pip environment
-python3 -m virtualenv venv
+python3 -m venv .venv
 # activate it
-source venv/bin/activate
+source .venv/bin/activate
 # install required modules
-pip install -r dev-requirements.txt
+pip install fprettify
 ```
 
 After that one can either use the tool in a stand-alone manner:
 
 ```sh
-./venv/bin/fprettify -i 2 -w 4 --whitespace-assignment true --enable-decl --whitespace-decl true --whitespace-relational true --whitespace-logical true --whitespace-plusminus true --whitespace-multdiv true --whitespace-print true --whitespace-type true --whitespace-intrinsics true --enable-replacements -l 1000 [FILENAME.F90]
+.venv/bin/fprettify -i 2 -w 4 --whitespace-assignment true --enable-decl --whitespace-decl true --whitespace-relational true --whitespace-logical true --whitespace-plusminus true --whitespace-multdiv true --whitespace-print true --whitespace-type true --whitespace-intrinsics true --enable-replacements -l 1000 [FILENAME.F90]
 ```
 or in the VSCode environment (see the extension list in the `.vscode/settings.json` of the current repo).
 
@@ -151,6 +151,10 @@ or in the VSCode environment (see the extension list in the `.vscode/settings.js
 __@TODO__
 
 ## Latest Releases
+* `v2.9` __Dec 2024__
+  * removed `tristanVis` (see [`graph-et`](https://pypi.org/project/graph-et/))
+  * cleanups & updated instructions
+  * minor bugfixes
 * `v2.8` __Apr 2024__
   * cmake support
   * minor reformatting + bugfixes
@@ -225,11 +229,3 @@ __@TODO__
   * Slice outputs for 3d added
   * Particle momentum binning improved for downsampling
   * Minor bugs fixed
-
----
-
-We employ [semantic versioning](https://semver.org/) for this code. Given a version number `v<MAJOR>.<MINOR>.<PATCH>r<CANDIDATE>`, increment the:
-- `MAJOR` version when you make incompatible changes,
-- `MINOR` version when you add functionality in a backwards compatible manner, and
-- `PATCH` version when you make backwards compatible bug fixes.
-- `CANDIDATE`: release candidate for "nightly" builds

configure.py

@@ -1,5 +1,11 @@
-#! /usr/bin/env python
+#!/usr/bin/env python3
 # -----------------------------------------------------------------------------------------
+
+import sys
+
+if sys.version_info[0] < 3 or sys.version_info[1] < 8:
+    raise Exception("Must be using python 3.8+")
+
 import argparse
 import glob
 import re
@@ -21,7 +27,7 @@
 flags_choices = ["intel", "generic"]
 
 rad_choices = ["no", "sync", "ic", "sync+ic"]
-clusters = ["frontera", "zaratan", "stellar", "ginsburg"]
+clusters = ["frontera", "zaratan", "stellar", "ginsburg", "rusty"]
 
 # system
 parser.add_argument(
@@ -39,16 +45,15 @@
 )
 
 parser.add_argument(
-    "--vector",
+    "--vectorization",
     default=None,
     required=False,
     choices=["avx2", "avx512"],
     help="choose the vectorization option.",
 )
 
-parser.add_argument(
-    "-hdf5", action="store_true", default=False, help="enable HDF5 & use h5pfc compiler"
-)
+parser.add_argument("-nohdf5", action="store_true", default=False, help="disable HDF5")
+
 parser.add_argument(
     "-serial", action="store_true", default=False, help="enable serial output"
 )
@@ -59,14 +64,6 @@
     help="enable non-blocking mpi calls (faster simulation but non-reproducible)",
 )
 
-# vec_group = parser.add_mutually_exclusive_group(required=False)
-# vec_group.add_argument(
-#     "-avx2", action="store_true", default=False, help="enable avx2 vectorization"
-# )
-# vec_group.add_argument(
-#     "-avx512", action="store_true", default=False, help="enable avx512 vectorization"
-# )
-
 parser.add_argument(
     "-lowmem", action="store_true", default=False, help="enable low memory regime"
 )
@@ -213,39 +210,43 @@
 makefile_options["COMPILER_FLAGS"] = ""
 makefile_options["PREPROCESSOR_FLAGS"] = ""
 makefile_options["WARNING_FLAGS"] = ""
-makefile_options[
-    "DEFS"
-] = "-DSTR_MAX=280 -DTINYXYZ=1e-6 -DTINYREAL=1e-3 -DTINYFLD=1e-8 -DTINYWEI=1e-6 -DM_PI=3.141592653589793 -DVEC_LEN=16 "
+makefile_options["DEFS"] = (
+    "-DSTR_MAX=280 -DTINYXYZ=1e-6 -DTINYREAL=1e-3 -DTINYFLD=1e-8 -DTINYWEI=1e-6 -DM_PI=3.141592653589793 -DVEC_LEN=16 "
+)
 makefile_options["ADD_INCLUDES"] = ""
 
 # specific cluster:
 specific_cluster = False
+clustername = ""
 if args["cluster"] is not None:
     specific_cluster = True
     clustername = args["cluster"].capitalize()
     args["ifport"] = True
     if args["cluster"] == "frontera":
         args["flags"] = "intel"
-        args["vector"] = "avx512"
+        args["vectorization"] = "avx512"
         args["lowmem"] = True
     elif args["cluster"] == "stellar":
         args["flags"] = "intel"
-        args["vector"] = "avx512"
+        args["vectorization"] = "avx512"
     elif args["cluster"] == "zaratan":
         args["flags"] = "generic"
-        args["vector"] = "avx2"
+        args["vectorization"] = "avx2"
         makefile_options["ADD_INCLUDES"] = "$(HDF5_INCDIR)"
     elif args["cluster"] == "ginsburg":
         args["flags"] = "intel"
-        args["vector"] = "avx512"
+        args["vectorization"] = "avx512"
+    elif args["cluster"] == "rusty":
+        args["flags"] = "intel"
+        args["vectorization"] = "avx512"
 
 # compilation command
-if args["hdf5"]:
+if not args["nohdf5"]:
     makefile_options["COMPILER_COMMAND"] += "h5pfc "
     makefile_options["PREPROCESSOR_FLAGS"] += "-DHDF5 "
 else:
     makefile_options["COMPILER_COMMAND"] += (
-        "mpif90 " if not args["compiler"] == "intel" else "mpiifort "
+        "mpif90 " if not args["flags"] == "intel" else "mpiifort "
     )
 if args["ifport"]:
     makefile_options["PREPROCESSOR_FLAGS"] += "-DIFPORT "
@@ -277,13 +278,13 @@
                 "COMPILER_FLAGS"
             ] += "-fbacktrace -ffpe-trap=invalid,zero,overflow,underflow,denormal "
         # @TODO: add aocc
-    if int(args["debug"]) >= 2 and (args["compiler"] == "intel"):
+    if int(args["debug"]) >= 2 and (args["flags"] == "intel"):
         makefile_options["COMPILER_FLAGS"] += "-check all -check noarg_temp_created "
 else:
     makefile_options["COMPILER_FLAGS"] += "-Ofast "
 
 if args["double"]:
-    if args["compiler"] == "intel":
+    if args["flags"] == "intel":
         makefile_options["COMPILER_FLAGS"] += "-r8 "
     else:
         makefile_options["COMPILER_FLAGS"] += "-fdefault-real-8 "
@@ -306,17 +307,17 @@
     ] += (
         "-diag-disable 10397 -diag-disable 10346 -diag-disable 8100 -diag-disable 6178 "
     )
-    if args["vector"] is not None:
-        if args["vector"] == "avx2":
+    if args["vectorization"] is not None:
+        if args["vectorization"] == "avx2":
             makefile_options["COMPILER_FLAGS"] += "-xCORE-AVX2 "
-        elif args["vector"] == "avx512":
+        elif args["vectorization"] == "avx512":
             makefile_options["COMPILER_FLAGS"] += "-xCORE-AVX512 -qopt-zmm-usage:high "
-        elif args["vector"] == "amd-avx2":
+        elif args["vectorization"] == "amd-avx2":
             makefile_options["COMPILER_FLAGS"] += "-mavx2 "
 else:
     makefile_options["MODULE"] = "-J "
     makefile_options["COMPILER_FLAGS"] += "-O3 -DSoA -ffree-line-length-512 "
-    if args["vector"] is not None:
+    if args["vectorization"] is not None:
         makefile_options["COMPILER_FLAGS"] += "-mavx "
 
 if args["1d"]:
@@ -436,7 +437,7 @@
 
 print("TECHNICAL ....................................................................")
 
-print("  Flag types [vec.]:       " + f'{args["flags"]} [{args["vector"]}]')
+print("  Flag types [vec.]:       " + f'{args["flags"]} [{args["vectorization"]}]')
 print("  Precision:               " + ("double" if args["double"] else "single"))
 print(
     "  Debug mode:              "
@@ -448,7 +449,7 @@
     "  Output:                  "
     + (
         ("HDF5" + (" (serial)" if args["serial"] else " (parallel)"))
-        if args["hdf5"]
+        if not args["nohdf5"]
         else "N/A"
     )
 )