diff --git a/.github/workflows/Dockerfile.gnu b/.github/workflows/Dockerfile.gnu new file mode 100644 index 0000000000..3506c2b9ee --- /dev/null +++ b/.github/workflows/Dockerfile.gnu @@ -0,0 +1,68 @@ +#*********************************************************************** +#* GNU Lesser General Public License +#* +#* This file is part of the GFDL Flexible Modeling System (FMS). +#* +#* FMS is free software: you can redistribute it and/or modify it under +#* the terms of the GNU Lesser General Public License as published by +#* the Free Software Foundation, either version 3 of the License, or (at +#* your option) any later version. +#* +#* FMS is distributed in the hope that it will be useful, but WITHOUT +#* ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or +#* FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License +#* for more details. +#* +#* You should have received a copy of the GNU Lesser General Public +#* License along with FMS. If not, see . +#*********************************************************************** +# FMS CI image recipefile for GNU +# Runs on centos stream (builder has same base from redhat registry) +# +# arguments to specify versions to build can be given to docker or changed here (--build-arg name=val) +FROM spack/rockylinux9:latest as builder + +ARG gcc_version=12.3.0 +ARG netcdfc_version=4.9.0 +ARG netcdff_version=4.6.0 +ARG libyaml_version=0.2.5 +ARG mpich_version=4.0.2 + +COPY spack.env /opt/deps/spack.env + +# perl's download kept timing out +RUN sed -i 's/connect_timeout: 10/connect_timeout: 600/' /opt/spack/etc/spack/defaults/config.yaml && \ + spack install gcc@${gcc_version} && \ + source /opt/spack/share/spack/setup-env.sh && \ + spack load gcc@${gcc_version} && \ + spack compiler find && \ + sed "s/COMPILER/gcc@$gcc_version/" /opt/deps/spack.env > spack.yaml && \ + sed -i "s/NETCDF_C_VERSION/$netcdfc_version/" spack.yaml && \ + sed -i "s/NETCDF_F_VERSION/$netcdff_version/" spack.yaml && \ + sed -i "s/LIBYAML_VERSION/$libyaml_version/" spack.yaml && \ + sed -i "s/MPI_LIB/mpich@$mpich_version/" spack.yaml && \ + spack env activate -d . && \ + spack -e . concretize -f > /opt/deps/deps.log && \ + spack install --fail-fast + +# copy built software to base from first image +FROM rockylinux:9 + +COPY --from=builder /opt/view/ /opt/view/ +COPY --from=builder /opt/deps/ /opt/deps/ + +# input files used with --enable-input-tests +# need to be on the dev boxes if building +COPY ./fms_test_input /home/unit_tests_input + +RUN dnf install -y autoconf make automake m4 libtool pkg-config zip + +ENV FC="mpifort" +ENV CC="mpicc" +ENV MPICH_FC="/opt/view/bin/gfortran" +ENV MPICH_CC="/opt/view/bin/gcc" +ENV FCFLAGS="-I/opt/view/include" +ENV CFLAGS="-I/opt/view/include" +ENV LDFLAGS="-L/opt/view/lib" +ENV LD_LIBRARY_PATH="/opt/view/lib:/opt/view/lib64:/usr/local/lib:/usr/local/lib64" +ENV PATH="/opt/view/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin" diff --git a/.github/workflows/github_autotools_gnu.yml b/.github/workflows/github_autotools_gnu.yml new file mode 100644 index 0000000000..b7008a0814 --- /dev/null +++ b/.github/workflows/github_autotools_gnu.yml @@ -0,0 +1,39 @@ +# 'main' required ci, does a distcheck (builds, tests, check install) +# image created off dockerfile in repo, compile/link flags are set there +name: Build libFMS test with autotools + +on: [push, pull_request] + +jobs: + build: + runs-on: ubuntu-latest + strategy: + matrix: + conf-flag: [ --disable-openmp, --enable-mixed-mode, --disable-setting-flags, --with-mpi=no] + input-flag: [--with-yaml, --enable-test-input=/home/unit_tests_input] + exclude: + - conf-flag: --with-mpi=no + input-flag: --enable-test-input=/home/unit_tests_input + container: + image: noaagfdl/fms-ci-rocky-gnu:12.3.0 + env: + TEST_VERBOSE: 1 + DISTCHECK_CONFIGURE_FLAGS: "${{ matrix.conf-flag }} ${{ matrix.input-flag }} ${{ matrix.io-flag }}" + SKIP_TESTS: "test_yaml_parser.5" # temporary till fixes are in + steps: + - name: Checkout code + uses: actions/checkout@v2 + - name: Prepare GNU autoconf for build + run: autoreconf -if + - name: Configure the build + if: ${{ matrix.conf-flag != '--disable-setting-flags' }} + run: ./configure ${DISTCHECK_CONFIGURE_FLAGS} || cat config.log + - name: Configure the build with compiler flags + if: ${{ matrix.conf-flag == '--disable-setting-flags' }} + run: ./configure ${DISTCHECK_CONFIGURE_FLAGS} FCFLAGS="-fdefault-real-8 -fdefault-double-8 -fcray-pointer -ffree-line-length-none -I/usr/include $FCFLAGS" || cat config.log + - name: Build the library + run: make distcheck + if: ${{ matrix.conf-flag != '--with-mpi=no' }} + - name: Build the library (without test suite for serial build) + run: make + if: ${{ matrix.conf-flag == '--with-mpi=no' }} diff --git a/.github/workflows/intel_pr.yml b/.github/workflows/github_autotools_intel.yml similarity index 92% rename from .github/workflows/intel_pr.yml rename to .github/workflows/github_autotools_intel.yml index 62a15361ea..851ad71520 100644 --- a/.github/workflows/intel_pr.yml +++ b/.github/workflows/github_autotools_intel.yml @@ -2,13 +2,16 @@ on: pull_request jobs: intel-autotools: runs-on: ubuntu-latest + strategy: + matrix: + io-flag: ["--disable-deprecated-io", "--enable-deprecated-io"] container: image: intel/oneapi-hpckit:2023.1.0-devel-ubuntu20.04 env: CC: mpiicc FC: mpiifort CFLAGS: "-I/libs/include" - FCFLAGS: "-I/libs/include -g -traceback" + FCFLAGS: "-I/libs/include -g -traceback ${{ matrix.io-flag }}" LDFLAGS: "-L/libs/lib" TEST_VERBOSE: 1 I_MPI_FABRICS: "shm" # needed for mpi in image diff --git a/.github/workflows/build_cmake_gnu.yml b/.github/workflows/github_cmake_gnu.yml similarity index 100% rename from .github/workflows/build_cmake_gnu.yml rename to .github/workflows/github_cmake_gnu.yml diff --git a/.github/workflows/coupler.yml b/.github/workflows/github_coupler_gnu.yml similarity index 100% rename from .github/workflows/coupler.yml rename to .github/workflows/github_coupler_gnu.yml diff --git a/.github/workflows/update_docs.yml b/.github/workflows/github_doc_site.yml similarity index 100% rename from .github/workflows/update_docs.yml rename to .github/workflows/github_doc_site.yml diff --git a/.github/workflows/lint_fms.yml b/.github/workflows/github_linter.yml similarity index 100% rename from .github/workflows/lint_fms.yml rename to .github/workflows/github_linter.yml diff --git a/.github/workflows/am4_regression_parallelWorks_intel_tag.yml b/.github/workflows/parallelworks_am4_intel.yml similarity index 100% rename from .github/workflows/am4_regression_parallelWorks_intel_tag.yml rename to .github/workflows/parallelworks_am4_intel.yml diff --git a/.github/workflows/spack.env b/.github/workflows/spack.env new file mode 100644 index 0000000000..69a3bdcbd0 --- /dev/null +++ b/.github/workflows/spack.env @@ -0,0 +1,17 @@ +# template for spack environment yaml +# uppercase words get replaced before activating +spack: + specs: + - COMPILER + - MPI_LIB + - netcdf-c@NETCDF_C_VERSION ^MPI_LIB + - netcdf-fortran@NETCDF_F_VERSION + - libyaml@LIBYAML_VERSION + concretizer: + unify: true + packages: + all: + compiler: [ COMPILER ] + config: + install_tree: /opt/deps + view: /opt/view diff --git a/.github/workflows/version.yml b/.github/workflows/version.yml index 1e71236386..31641aea69 100644 --- a/.github/workflows/version.yml +++ b/.github/workflows/version.yml @@ -1,3 +1,5 @@ +# appends -dev to the version upon release and opens pr +# CI won't run on generated PR, easiest workaround is to close + reopen on: release: types: [published] @@ -16,4 +18,4 @@ jobs: branch-suffix: timestamp # add a timestamp to branch name delete-branch: true # delete afer merge title: Append dev to version number post-release - body: automated change, adds '-dev' to the version number upon releases + body: automated change, adds '-dev' to the version number upon releases. This PR will need to be closed and reopened to run CI testing. diff --git a/CHANGELOG.md b/CHANGELOG.md index 0cc9802f8f..2c616e647d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,6 +6,45 @@ and this project uses `yyyy.rr[.pp]`, where `yyyy` is the year a patch is releas `rr` is a sequential release number (starting from `01`), and an optional two-digit sequential patch number (starting from `01`). +## [2023.02] - 2023-07-27 +### Known Issues +- GCC 11.1.0 is unsupported due to compilation issues with select type. The issue is resolved in later GCC releases. +- When outputting sub-region diagnostics, the current diag_manager does not add "tileX" to the filename when using a cube sphere. This leads to trouble when trying to combine the files and regrid them (if the region is in two different tiles) +- GCC 10 and greater causing io issues when compiled using O2 optimization flags +- GNU compilers prior to the GCC 9.0 release are unsupported for this release due to lack of support for the findloc intrinsic function. This will result in an error saying 'findloc' has no IMPLICIT type and can be resolved by compiling with gcc version 9.0 or greater. + +### Added +- MPP/EXCHANGE: Adds association checks before pointer deallocations in mpp includes and xgrid + +### Changed +- LIBFMS: The libFMS.F90 file (module name `fms`) meant to provide global access has been updated to include 'fms' and it's module/subdirectory name as prefixes for all names. This will only affect external codes that are already using the global module (via `use fms`) and not individual modules. +- MIXED PRECISION: Updates the axis_utils2, horiz_interp, sat_vapor_pressure, and axis_utils subdirectories to support mixed precision real values. +- FMS2_IO: Added in mpp_scatter and mpp_gather performance changes from the 2023.01.01 patch. See below for more details. +- FMS2_IO: Improved error messages to give more debugging information +- FMS_MOD: Changed fms_init to include a system call to set the stack size to unlimited, removed previously added stack size fixes +- MONIN_OBUKHOV: Restructures the subroutines in `stable_mix` interface so that 1d calls the underlying implementation, and 2 and 3d call it on 1d slices of the data as opposed to passing in mismatched arrays. +- MPP: Updates from JEDI for ajoint version the mpp halo filling (mpp_do_update_ad.fh), adds checkpoint for forward buffer information. + +### Fixed +- MPP: mpp_broadcast causing an unintended error message due to checking the wrong pe value +- MPP: Added workaround for GCC 12 issues causing errors with string lengths in fms2_io +- FMS2_IO: Fixed support for 'packed' data when using NF_SHORT variables. Scale_factor and add_offset attributes will now be applied if present. +- DOCS: Improved doxygen comments for tranlon, updated deployment action for site +- TESTS: Workaround added for ICE coming from mpp_alltoall test with intel 2022.3, and fixes for any test scripts missing input.nml creation. Fixes for mpp/test_global_array failures. +- TIME_INTERP: Fixes crashes when calling with a non-existant field +- DIAG_MANAGER: Fixes a module dependency issue causing failures during parallel builds +- AXIS_UTILS2: Fixes an out of bounds memory index + +### Removed +- FMS_IO/MPP_IO: The two older io modules, fms_io_mod and mpp_io_mod, have been deprecated and will not be compiled by default. If you wish to compile these modules, you must use the -Duse_deprecated_io CPP flag or the --enable-deprecated-io configure option if building with autotools. + +### Tag Commit Hashes +- 2023.02-beta1 2be8aa452ad3e5f43e92c38a64f12d1ae6c43fb8 +- 2023.02-alpha3 8c73bd18dc1d580f2ee524c37cf903ff54d40501 +- 2023.02-alpha2 783019fdec89a8db2b26247c2f63d4782e1495c0 +- 2023.02-alpga1 419c66be31f82ebb13a91ea5e837c707eb54473b + + ## [2023.01.01] - 2023-06-06 ### Changed - FMS2_IO: Performance changes for domain_reads_2d and domain_reads_3d: diff --git a/CI.md b/CI.md index 225b25129b..89b4db256e 100644 --- a/CI.md +++ b/CI.md @@ -8,24 +8,30 @@ Required CI for pull requests are listed first. ## Pull Request CI and checks ### Build libFMS with autotools + Required GNU build test for all pull requests/pushes. Runs `make distcheck` after configuring via GNU autotools. +Runs on a container image with spack installed dependencies, on top a rocky linux base. + +Dockerfile for image is stored at .github/workflows/Dockerfile.gnu for more specific information on the CI environment. + Container environment: -gcc v7.3.0 -mpich v3.3a2 -netcdf v4.6.0 -netcdf-fortran v4.4.4 +gcc v12.3.0 +mpich v4.0.2 +netcdf v4.9.0 +netcdf-fortran v4.6.0 autoconf v2.69 +libyaml v0.2.5 -container hosted at [noaagfdl/ubuntu_libfms_gnu:latest](https://hub.docker.com/r/noaagfdl/ubuntu_libfms_gnu) - -`./configure` flags: -- `--enable-openmp` +`./configure` flags tested: - `--disable-openmp` - `--enable-mixed-mode` +- `--with-mpi=no` (disables unit testing) - `--disable-setting-flags` - `--with-yaml` +- `--enable-test-input=/home/unit_tests_input` + ### Build libfms with cmake Required GNU build test for all pull requests/pushes. diff --git a/CMakeLists.txt b/CMakeLists.txt index 61fccf9c62..338dfb8f18 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -26,7 +26,7 @@ set(CMAKE_Fortran_FLAGS_DEBUG) # Define the CMake project project(FMS - VERSION 2023.01.0 + VERSION 2023.02.0 DESCRIPTION "GFDL FMS Library" HOMEPAGE_URL "https://www.gfdl.noaa.gov/fms" LANGUAGES C Fortran) @@ -196,6 +196,7 @@ list(APPEND fms_fortran_src_files # Collect FMS C source files list(APPEND fms_c_src_files affinity/affinity.c + fms/fms_stacksize.c mosaic/create_xgrid.c mosaic/gradient_c2l.c mosaic/interp.c @@ -314,9 +315,12 @@ foreach(kind ${kinds}) constants topography/include axis_utils/include + constants + astronomy/include field_manager/include time_interp/include - tracer_manager/include) + tracer_manager/include + interpolator/include) target_compile_definitions(${libTgt}_f PRIVATE "${fms_defs}") target_compile_definitions(${libTgt}_f PRIVATE "${${kind}_defs}") @@ -353,6 +357,7 @@ foreach(kind ${kinds}) $ $ $ + $ $ $ $ @@ -363,7 +368,10 @@ foreach(kind ${kinds}) $ $ $ - $) + $ + $ + $ + $) target_include_directories(${libTgt} INTERFACE diff --git a/astronomy/Makefile.am b/astronomy/Makefile.am index 33d4acaf3c..50a1449412 100644 --- a/astronomy/Makefile.am +++ b/astronomy/Makefile.am @@ -23,14 +23,23 @@ # Ed Hartnett 2/22/19 # Include .h and .mod files. -AM_CPPFLAGS = -I$(top_srcdir)/include +AM_CPPFLAGS = -I$(top_srcdir)/include -I$(top_srcdir)/astronomy/include AM_FCFLAGS = $(FC_MODINC). $(FC_MODOUT)$(MODDIR) # Build this uninstalled convenience library. noinst_LTLIBRARIES = libastronomy.la # The convenience library depends on its source. -libastronomy_la_SOURCES = astronomy.F90 +libastronomy_la_SOURCES = \ + astronomy.F90 \ + include/astronomy_r4.fh \ + include/astronomy_r8.fh \ + include/astronomy.inc + +astronomy.$(FC_MODEXT): \ +include/astronomy_r4.fh \ +include/astronomy_r8.fh \ +include/astronomy.inc BUILT_SOURCES = astronomy_mod.$(FC_MODEXT) nodist_include_HEADERS = astronomy_mod.$(FC_MODEXT) diff --git a/astronomy/astronomy.F90 b/astronomy/astronomy.F90 index 192fc8f22a..0a7af2cc6e 100644 --- a/astronomy/astronomy.F90 +++ b/astronomy/astronomy.F90 @@ -29,296 +29,320 @@ module astronomy_mod -use fms_mod, only: fms_init, & - mpp_pe, mpp_root_pe, stdlog, & - write_version_number, & - check_nml_error, error_mesg, & - FATAL, NOTE, WARNING -use time_manager_mod, only: time_type, set_time, get_time, & - get_date_julian, set_date_julian, & - set_date, length_of_year, & - time_manager_init, & - operator(-), operator(+), & - operator( // ), operator(<) -use constants_mod, only: constants_init, PI -use mpp_mod, only: input_nml_file - -!-------------------------------------------------------------------- - -implicit none -private - -!--------------------------------------------------------------------- -!----------- version number for this module -------------------------- + use fms_mod, only: fms_init, & + mpp_pe, mpp_root_pe, stdlog, & + write_version_number, & + check_nml_error, error_mesg, & + FATAL, NOTE, WARNING + use time_manager_mod, only: time_type, set_time, get_time, & + get_date_julian, set_date_julian, & + set_date, length_of_year, & + time_manager_init, & + operator(-), operator(+), & + operator( // ), operator(<) + use constants_mod, only: constants_init, PI + use mpp_mod, only: input_nml_file + use platform_mod, only: r4_kind, r8_kind, i4_kind, i8_kind + + !-------------------------------------------------------------------- + + implicit none + private + + !--------------------------------------------------------------------- + !----------- version number for this module -------------------------- ! Include variable "version" to be written to log file. #include -!--------------------------------------------------------------------- -!------- interfaces -------- - -public & - astronomy_init, get_period, set_period, & - set_orbital_parameters, get_orbital_parameters, & - set_ref_date_of_ae, get_ref_date_of_ae, & - diurnal_solar, daily_mean_solar, annual_mean_solar, & - astronomy_end, universal_time, orbital_time - -!> @} - -!> @brief Calculates solar information for the given location(lat & lon) and time -!! -!> ~~~~~~~~~~{.f90} -!! call diurnal_solar (lat, lon, time, cosz, fracday, rrsun, dt_time) -!! call diurnal_solar (lat, lon, gmt, time_since_ae, cosz, fracday, rrsun, dt) -!! ~~~~~~~~~~ -!! -!! The first option (used in conjunction with time_manager_mod) -!! generates the real variables gmt and time_since_ae from the -!! time_type input, and then calls diurnal_solar with these real inputs. -!! -!! The time of day is set by -!! ~~~~~~~~~~{.f90} -!! real, intent(in) :: gmt -!! ~~~~~~~~~~ -!! The time of year is set by -!! ~~~~~~~~~~{.f90} -!! real, intent(in) :: time_since_ae -!! ~~~~~~~~~~ -!! with time_type input, both of these are extracted from -!! ~~~~~~~~~~{.f90} -!! type(time_type), intent(in) :: time -!! ~~~~~~~~~~ -!! -!! Separate routines exist within this interface for scalar, -!! 1D or 2D input and output fields: -!! -!! ~~~~~~~~~~{.f90} -!! real, intent(in), dimension(:,:) :: lat, lon -!! real, intent(in), dimension(:) :: lat, lon -!! real, intent(in) :: lat, lon -!! -!! real, intent(out), dimension(:,:) :: cosz, fracday -!! real, intent(out), dimension(:) :: cosz, fracday -!! real, intent(out) :: cosz, fracday -!! ~~~~~~~~~~ -!! -!! One may also average the output fields over the time interval -!! between gmt and gmt + dt by including the optional argument dt (or -!! dt_time). dt is measured in radians and must be less than pi -!! (1/2 day). This average is computed analytically, and should be -!! exact except for the fact that changes in earth-sun distance over -!! the time interval dt are ignored. In the context of a diurnal GCM, -!! this option should always be employed to insure that the total flux -!! at the top of the atmosphere is not modified by time truncation error. -!! -!! ~~~~~~~~~~{.f90} -!! real, intent(in), optional :: dt -!! type(time_type), optional :: dt_time -!! ~~~~~~~~~~ -!! -!! @param [in] Latitudes of model grid points [radians] -!! @param [in] Longitudes of model grid points [radians] -!! @param [in] Time of day at longitude 0.0; midnight = 0.0, one day = 2 * pi [radians] -!! @param [in] Time of year; autumnal equinox = 0.0, one year = 2 * pi [radians] -!! @param [in]