Merge tag '2023.03' into update-block-control

.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 <http://www.gnu.org/licenses/>.
+#***********************************************************************
+# 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"

.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, --disable-setting-flags, --with-mpi=no, --disable-r8-defaults]
+        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' }}

.github/workflows/intel_pr.yml → .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:2022.2-devel-ubuntu20.04
+      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
@@ -22,7 +25,7 @@ jobs:
         path: /libs
         key: ${{ runner.os }}-intel-libs
     - name: Install packages for building
-      run: apt update && apt install -y autoconf libtool automake zlibc zlib1g-dev
+      run: apt-get update && apt-get install -y autoconf libtool automake zlibc zlib1g-dev
     - if: steps.cache.outputs.cache-hit != 'true'
       name: Build netcdf
       run: |
@@ -50,4 +53,4 @@ jobs:
     - name: Compile
       run: make -j || make
     - name: Run test suite
-      run: make check LD_LIBRARY_PATH="/libs/lib:$LD_LIBRARY_PATH" SKIP_TESTS="$SKIP_TESTS" VERBOSE=1
+      run: make check LD_LIBRARY_PATH="/libs/lib:$LD_LIBRARY_PATH" TEST_VERBOSE=1

.github/workflows/build_cmake_gnu.yml → .github/workflows/github_cmake_gnu.yml

@@ -9,10 +9,11 @@ jobs:
       matrix:
         omp-flags: [ -DOPENMP=on, -DOPENMP=off ]
         libyaml-flag: [ "", -DWITH_YAML=on ]
+        io-flag: [ "", -DUSE_DEPRECATED_IO=on ]
     container:
       image: noaagfdl/hpc-me.ubuntu-minimal:cmake
       env:
-        CMAKE_FLAGS: "${{ matrix.omp-flags }} ${{ matrix.libyaml-flag }} -D64BIT=on"
+        CMAKE_FLAGS: "${{ matrix.omp-flags }} ${{ matrix.io-flag  }} ${{ matrix.libyaml-flag }} -D64BIT=on"
     steps:
     - name: Checkout code
       uses: actions/checkout@v2

.github/workflows/coupler.yml → .github/workflows/github_coupler_gnu.yml

@@ -5,14 +5,16 @@ jobs:
   coupler-build:
     runs-on: ubuntu-latest
     container:
-      image: ryanmulhall/hpc-me.ubuntu-minimal:coupler
+      image: ghcr.io/noaa-gfdl/fms/fms-ci-rocky-gnu:12.3.0
+      credentials:
+        username: ${{ github.actor }}
+        password: ${{ secrets.github_token }}
       env:
         CC: mpicc
         FC: mpif90
-        CPPFLAGS: '-I/usr/include -Duse_LARGEFILE -DMAXFIELDMETHODS_=500'
-        FCFLAGS: '-fcray-pointer -fdefault-double-8 -fdefault-real-8 -Waliasing -ffree-line-length-none -fno-range-check -I/usr/include'
-        LDFLAGS: '-L/usr/lib'
-        VERBOSE: 1
+        CPPFLAGS: '-I/opt/view/include'
+        FFLAGS: '-fallow-argument-mismatch' # mkmf uses FFLAGS instead of FC
+        LDFLAGS: '-L/opt/view/lib'
     steps:
     - name: Checkout FMS
       uses: actions/checkout@v2

.github/workflows/update_docs.yml → .github/workflows/github_doc_site.yml

@@ -6,7 +6,7 @@ on:
     types: [published]
   workflow_dispatch:
 jobs:
-  update_docs:
+  build:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code
@@ -23,8 +23,26 @@ jobs:
         run: |
           sudo apt -y install doxygen graphviz
           doxygen gen_docs/Doxyfile
-      - name: Deploy
-        uses: peaceiris/actions-gh-pages@v3
+      - name: Upload Pages Artifact
+        uses: actions/upload-pages-artifact@v1
         with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: ./gen_docs/html
+          path: 'gen_docs/html'
+  deploy:
+    needs: build
+
+    # Grant GITHUB_TOKEN the permissions required to make a Pages deployment
+    permissions:
+      pages: write      # to deploy to Pages
+      id-token: write   # to verify the deployment originates from an appropriate source
+
+    # Deploy to the github-pages environment
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    # Specify runner + deployment step
+    runs-on: ubuntu-latest
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v1

.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

.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.

CHANGELOG.md

@@ -6,6 +6,81 @@ 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`).
 
+## [2023.03] - 2023-10-27
+### Known Issues
+- GCC 9 and below as well as GCC 11.1.0 are unsupported due to compilation issues. See prior releases for more details.
+- `NO_QUAD_PRECISION` macro is no longer set by FMS, the `ENABLE_QUAD_PRECISION` macro has replaced prior usage of `NO_QUAD_PRECISION`. `-DENABLE_QUAD_PRECISION` should be set if quad precision is to be used, otherwise FMS will not use quad precision reals where applicable.
+
+### Added
+- UNIT_TESTS: New unit tests have been created or and existing ones expanded on for any modules utilizing mixed precision support.
+
+### Changed
+- MIXED PRECISION: Most subroutines and functions in FMS have been updated to simultaneously accept both 4 byte and 8 byte reals as arguments. This deprecates the `--enable-mixed-mode` option, which enabled similar functionality but was limited to certain directories and was not enabled by default. To facilitate easier testing of these code changes, the CMake precision options for default real size were left in (along with an equivalent `--disable-r8-default` flag for autotools). The resulting libraries will support mixed-precision real kinds regardless of default real size. It should also be noted that many routines that accept real arguments have been moved to include files along with headers in order to be compiled with both kinds. Most module level variables were explicitly declared as r8_kind for these updates.
+- Some type/module changes were made to facilitate mixed precision support. They are **intended** to have minimal impact to other codebases:
+  - COUPLER_TYPES: In coupler_types.F90,  `coupler_nd_field_type` and `coupler_nd_values_type` have been renamed to indicate real kind value: `coupler_nd_real4/8_field_type` and `coupler_nd_real4/8_values_type`. The `bc` field within `coupler_nd_bc_type` was modified to use r8_kind within the value and field types, and an additional field added `bc_r4` to use r4_kind values.
+  - TRIDIAGONAL: Module state between r4 and r8 calls are distinct (ie. subsequent calls will only be affected by calls of the same precision). This behaviour can be changed via the `save_both_kinds` optional argument to `tri_invert`.
+- CODE_STYLE: has been updated to reflect the formatting used for the mixed precision support updates.
+
+### Fixed
+- DIAG_MANAGER: Tile number (ie. tileX) will now be added to filenames for sub-regional diagnostics.
+- MPP: Bug affecting non-intel compilers coming from uninitialized pointer in the `nest_domain_type`
+- MPP: Bug fix for unallocated field causing seg faults in `mpp_check_field`
+- FMS2_IO: Fixed segfault occuring from use of cray pointer remapping along with mpp_scatter/gather
+- TEST_FMS: Added various fixes for different compilers within test programs for fms2_io, mpp, diag_manager, parser, and sat_vapor_pres.
+- INTERPOLATOR: Deallocates fields in the type that were previously left out in `interpolator_end`
+
+### Removed
+- CPP MACROS:
+  - `no_4byte_reals` was removed and will not set any additional macros if used. `no_8byte_integers` is still functional.
+  - `NO_QUAD_PRECISION` was removed. It was conditionally set if ENABLE_QUAD_PRECISION was undefined. ENABLE_QUAD_PRECISION should be used in model components instead (logic is flipped)
+  - `use_netCDF` was set by autotools previously but wasn't consistently used in the code. FMS should always be compiled with netcdf installed so this was removed with the exception of its use in deprecated IO modules.
+- DRIFTERS: The drifters subdirectory has been deprecated. It will only be compiled if using the `-Duse_drifters` CPP flag.
+
+### Tag Commit Hashes
+- 2023.03-beta1  06b94a7f574e7794684b8584391744ded68e2989
+- 2023.03-alpha3 b25a7c52a27dfd52edc10bc0ebe12776af0f03df
+- 2023.03-alpha2 9983ce308e62e9f7215b04c227cebd30fd75e784
+- 2023.03-alpha1 a46bd94fd8dd1f6f021501e29179003ff28180ec
+
+## [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: