Merge remote-tracking branch 'origin/main' into release/2023.02

.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: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

.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/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

@@ -25,7 +25,7 @@ sequential patch number (starting from `01`).
 - 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 
+- 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.

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.

CMakeLists.txt

@@ -26,7 +26,7 @@ set(CMAKE_Fortran_FLAGS_DEBUG)
 
 # Define the CMake project
 project(FMS
-  VERSION 2023.02.01
+  VERSION 2023.02.0
   DESCRIPTION  "GFDL FMS Library"
   HOMEPAGE_URL "https://www.gfdl.noaa.gov/fms"
   LANGUAGES C Fortran)
@@ -305,12 +305,28 @@ foreach(kind ${kinds})
                                                  fms2_io/include
                                                  string_utils/include
                                                  mpp/include
+                                                 column_diagnostics/include
+                                                 monin_obukhov/include
                                                  sat_vapor_pres/include
                                                  horiz_interp/include
+                                                 diag_integral/include
+                                                 random_numbers/include
                                                  diag_manager/include
                                                  constants4
+                                                 topography/include
+                                                 axis_utils/include
+                                                 mosaic2/include
                                                  constants
-                                                 axis_utils/include)
+                                                 astronomy/include
+                                                 field_manager/include
+                                                 time_interp/include
+                                                 tracer_manager/include
+                                                 tridiagonal/include
+                                                 interpolator/include
+                                                 coupler/include
+                                                 data_override/include
+                                                 amip_interp/include)
+
   target_compile_definitions(${libTgt}_f PRIVATE "${fms_defs}")
   target_compile_definitions(${libTgt}_f PRIVATE "${${kind}_defs}")
 
@@ -346,11 +362,27 @@ foreach(kind ${kinds})
     $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/fms>
     $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/fms/include>
     $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/fms2_io/include>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/column_diagnostics/include>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/astronomy/include>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/monin_obukhov/include>
     $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/sat_vapor_pres/include>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/field_manager/include>
     $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/horiz_interp/include>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/mosaic2/include>
     $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/string_utils/include>
     $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/mpp/include>
-    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/diag_manager/include>)
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/diag_manager/include>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/topography/include>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/random_numbers/include>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/diag_integral/include>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/diag_manager/include>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/tracer_manager/include>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/interpolator/include>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/coupler/include>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/mosaic2/include>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/data_override/include>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/tridiagonal/include>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/amip_interp/include>)
 
   target_include_directories(${libTgt} INTERFACE
     $<BUILD_INTERFACE:${moduleDir}>