CI workflow updates and migrate container

.github/workflows/Dockerfile.gnu

@@ -49,13 +49,15 @@ RUN sed -i 's/connect_timeout: 10/connect_timeout: 600/' /opt/spack/etc/spack/de
 FROM rockylinux:9
 
 COPY --from=builder /opt/view/ /opt/view/
-COPY --from=builder /opt/deps/ /opt/deps/
+COPY --from=builder /opt/deps/linux-rocky9-haswell/gcc-12.3.0/ /opt/deps/linux-rocky9-haswell/gcc-12.3.0/
 
+# leaving this out due to storage constraints
+#
 # input files used with --enable-input-tests
 # need to be on the dev boxes if building
-COPY ./fms_test_input /home/unit_tests_input
+#COPY ./fms_test_input /home/unit_tests_input
 
-RUN dnf install -y autoconf make automake m4 libtool pkg-config zip
+RUN dnf install -y autoconf make automake m4 libtool pkg-config zip cmake git
 
 ENV FC="mpifort"
 ENV CC="mpicc"

.github/workflows/github_autotools_gnu.yml

@@ -1,36 +1,47 @@
-# 'main' required ci, does a distcheck (builds, tests, check install)
+# GNU ci run on pull requests, checks more configure options than intel
+# 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]
+on: 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]
+        input-flag: [--with-yaml, ""]
+        target-fcflags: [ "-O2 -fno-expensive-optimizations", "-O0 -g -W -fbounds-check -ffpe-trap=invalid,zero,overflow"] # prod, debug
+        target-cflags: [ "-O2", "-O0"] # prod, debug
         exclude:
           - conf-flag: --with-mpi=no
             input-flag: --enable-test-input=/home/unit_tests_input
+          - target-fcflags: "-O2 -fno-expensive-optimizations"
+            target-cflags: "-O0"
+          - target-fcflags: "-O0 -g -W -fbounds-check -ffpe-trap=invalid,zero,overflow"
+            target-cflags: "-O2"
     container:
-      image: noaagfdl/fms-ci-rocky-gnu:12.3.0
+      image: ghcr.io/noaa-gfdl/fms/fms-ci-rocky-gnu:12.3.0
+      credentials:
+        username: ${{ github.actor }}
+        password: ${{ secrets.github_token }}
       env:
         TEST_VERBOSE: 1
-        DISTCHECK_CONFIGURE_FLAGS: "${{ matrix.conf-flag }} ${{ matrix.input-flag }} ${{ matrix.io-flag }}"
-        SKIP_TESTS: "test_yaml_parser.5" # temporary till fixes are in
+        DISTCHECK_CONFIGURE_FLAGS: "${{ matrix.conf-flag }} ${{ matrix.input-flag }}"
+        TARGET_FLAGS: "${{ matrix.target-fcflags }} ${{ matrix.target-cflags }}"
+        SKIP_TESTS: "test_yaml_parser.5" # TODO
     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
+      run: ./configure ${DISTCHECK_CONFIGURE_FLAGS} FCFLAGS="${TARGET_FLAGS} ${FCFLAGS}"
     - 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
+      run: ./configure ${DISTCHECK_CONFIGURE_FLAGS} FCFLAGS="-fdefault-real-8 -fdefault-double-8 -fcray-pointer -ffree-line-length-none -I/usr/include ${FCFLAGS} ${TARGET_FLAGS}"
     - name: Build the library
       run: make distcheck
       if: ${{ matrix.conf-flag != '--with-mpi=no' }}

.github/workflows/github_autotools_intel.yml

@@ -1,31 +1,24 @@
-on: pull_request
+on: [push, pull_request]
 jobs:
-  intel-autotools:
+  build-dependencies:
     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
+      image: intel/oneapi-hpckit:2022.3.1-devel-ubuntu20.04
       env:
         CC: mpiicc
         FC: mpiifort
         CFLAGS:  "-I/libs/include"
-        FCFLAGS: "-I/libs/include -g -traceback ${{ matrix.io-flag }}"
+        FCFLAGS: "-I/libs/include"
         LDFLAGS: "-L/libs/lib"
-        TEST_VERBOSE: 1
-        I_MPI_FABRICS: "shm" # needed for mpi in image
-        # intel bug causes some failures with shm option(required in container)
-        SKIP_TESTS: "test_mpp_update_domains.1 test_update_domains_performance.1 test_diag_manager2.23"
     steps:
     - name: Cache dependencies
       id: cache
       uses: actions/cache@v3
       with:
         path: /libs
-        key: ${{ runner.os }}-intel-libs
+        key: ${{ runner.os }}-intel-libs${{ matrix.io-flag }}
     - name: Install packages for building
-      run: apt-get update && apt-get install -y autoconf libtool automake zlibc zlib1g-dev
+      run: apt-get update && apt-get install -y autoconf libtool automake
     - if: steps.cache.outputs.cache-hit != 'true'
       name: Build netcdf
       run: |
@@ -46,11 +39,50 @@ jobs:
         tar xf yaml-0.2.5.tar.gz && cd yaml-0.2.5
         ./configure --prefix=/libs
         make -j install && cd
+  make-check-fms:
+    needs: build-dependencies
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        FC: ["ifx", "ifort"]
+        CC: ["icx", "icc"]
+        target-fcflags: [ "-O3 -debug minimal -fp-model source", "-g -O0 -check -check noarg_temp_created -check nopointer -warn noerrors -fpe0 -ftrapuv" ] # prod, debug
+        target-cflags: [ "-O2 -debug minimal", "-O0 -g" ] # prod, debug (-ftrapuv was removed since its incompatible with icx)
+        io-flag: ["--disable-deprecated-io", "--enable-deprecated-io"]
+        exclude:
+          - FC: "ifx"
+            CC: "icc"
+          - target-fcflags: "-O3 -debug minimal -fp-model source"
+            target-cflags: "-O0 -g"
+          - target-fcflags: "-g -O0 -check -check noarg_temp_created -check nopointer -warn noerrors -fpe0 -ftrapuv"
+            target-cflags: "-O2 -debug minimal"
+          - FC: "ifx" # bug with ifx will cause ICE if using -check flag (issue #1348)
+            target-fcflags: "-g -O0 -check -check noarg_temp_created -check nopointer -warn noerrors -fpe0 -ftrapuv"
+    container:
+      image: intel/oneapi-hpckit:2022.3.1-devel-ubuntu20.04
+      env:
+        CC: mpicc -cc=${{ matrix.CC }}
+        FC: mpifc -fc=${{ matrix.FC }}
+        CFLAGS:  "-I/libs/include ${{ matrix.target-cflags }}"
+        FCFLAGS: "-I/libs/include ${{ matrix.target-fcflags }}"
+        LDFLAGS: "-L/libs/lib"
+        TEST_VERBOSE: 1
+        I_MPI_FABRICS: "shm" # needed for mpi in image
+        SKIP_TESTS: "test_fms2_io.2" # TODO compressed writes test fails with ifx
+    steps:
+    - name: Get dependencies from cache
+      id: cache
+      uses: actions/cache@v3
+      with:
+        path: /libs
+        key: ${{ runner.os }}-intel-libs
+    - name: Install packages for building
+      run: apt-get update && apt-get install -y autoconf libtool automake zip
     - name: checkout
       uses: actions/checkout@v2
     - name: Configure
-      run: autoreconf -if ./configure.ac && ./configure --with-yaml
+      run: autoreconf -if ./configure.ac && ./configure --with-yaml ${{ matrix.io-flag }} || cat config.log
     - name: Compile
       run: make -j || make
     - name: Run test suite
-      run: make check LD_LIBRARY_PATH="/libs/lib:$LD_LIBRARY_PATH" TEST_VERBOSE=1
+      run: make distcheck LD_LIBRARY_PATH="/libs/lib:$LD_LIBRARY_PATH" TEST_VERBOSE=1

.github/workflows/github_cmake_gnu.yml

@@ -11,13 +11,28 @@ jobs:
         libyaml-flag: [ "", -DWITH_YAML=on ]
         io-flag: [ "", -DUSE_DEPRECATED_IO=on ]
     container:
-      image: noaagfdl/hpc-me.ubuntu-minimal:cmake
+      image: ghcr.io/noaa-gfdl/fms/fms-ci-rocky-gnu:12.3.0
+      credentials:
+        username: ${{ github.actor }}
+        password: ${{ secrets.github_token }}
       env:
         CMAKE_FLAGS: "${{ matrix.omp-flags }} ${{ matrix.io-flag  }} ${{ matrix.libyaml-flag }} -D64BIT=on"
+        LIBYAML_ROOT: "/opt/deps/linux-rocky9-haswell/gcc-12.3.0/libyaml-0.2.5-fpd3ebh7gulljpolqosg6adfuiqzhwk2/" # TODO should find better way for cmake to find this
     steps:
     - name: Checkout code
       uses: actions/checkout@v2
     - name: Generate makefiles with CMake
-      run: cmake $CMAKE_FLAGS .
+      run: cmake -DNetCDF_INCLUDE_DIR=/opt/view/include/ -DCMAKE_Fortran_FLAGS="-fallow-argument-mismatch" $CMAKE_FLAGS .
     - name: Build the library
       run: make
+    - name: Link with basic executable
+      run: |
+        echo "program test" > test.F90
+        echo "    use fms_mod" >> test.F90
+        echo "    call fms_init" >> test.F90
+        echo "    call fms_end" >> test.F90
+        echo "end program" >> test.F90
+        mpifort -L/opt/view/lib -fopenmp `nf-config --flibs` -Iinclude_r4 -Iinclude_r8 test.F90 libfms_r4.a libfms_r8.a -o test.x
+        touch input.nml
+    - name: Run executable
+      run: ./test.x

.github/workflows/github_coupler_gnu.yml

@@ -5,13 +5,14 @@ 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'
+        CPPFLAGS: '-I/opt/view/include'
+        FFLAGS: '-fallow-argument-mismatch' # mkmf uses FFLAGS instead of FC
+        LDFLAGS: '-L/opt/view/lib'
         VERBOSE: 1
     steps:
     - name: Checkout FMS

parser/fms_yaml_output.F90

@@ -121,7 +121,9 @@ subroutine write_yaml_from_struct_3 (yamlname, a1size, keys, vals, a2size, key2,
                        key3, val3, lvl2keyeach) bind(C, name="write_yaml_from_struct_3")
 use iso_c_binding
 import fmsYamlOutKeys_type, fmsYamlOutValues_type, lvl2_key_parameter
-character (c_char) :: yamlname !< The output yaml file name
+character (c_char) :: yamlname !< The output yaml file name, type is a c char for the binding
+                               !! but seems to only work with a fortran string.
+                               !! Input string should be trimmed to prevent any unwanted characters sneaking in.
 integer (c_int), value :: a1size !< The size of the first yaml array
 type (fmsYamlOutKeys_type) :: keys(a1size) !< Top level yaml keys
 type (fmsYamlOutValues_type) :: vals(a1size) !< Values corresponding to keys

parser/yaml_output_functions.c

@@ -363,7 +363,7 @@ void write_yaml_from_struct_3 (char *yamlname, int asize, struct fmsyamloutkeys
 
   // trim any trailing whitespace
   int ws_ind = strlen(yamlname)-1;
-  while(*(yamlname+ws_ind) == ' ') ws_ind--;
+  while(yamlname[ws_ind] == ' ') ws_ind--;
   if( ws_ind != strlen(yamlname)-1) yamlname[ws_ind+1] = '\0';
 
   /* open the yaml output file. Only 1 core should do this */

test_fms/parser/test_output_yaml.F90

@@ -85,6 +85,7 @@ program test_output_yaml
 character(len=yaml_len) :: yaml_output_read
 character(len=string_len_parameter) :: tmpstr
 integer :: i, io_status !< for looping
+integer :: unum
 call fms_init
 call mpp_init
 
@@ -203,27 +204,29 @@ program test_output_yaml
   call yaml_out_add_level2key( "order 4",k1(1))
   call yaml_out_add_level2key( "sides", k2(1))
   call yaml_out_add_level2key( "specials",  k2(2))
-  call write_yaml_from_struct_3 (filename, 1, k1, v1, a2, k2, v2, a3, (/1, 1, 1, 1, 2, 1/), k3, v3, &
+  call write_yaml_from_struct_3 (trim(filename), 1, k1, v1, a2, k2, v2, a3, (/1, 1, 1, 1, 2, 1/), k3, v3, &
                                & (/ 1, 1, 1 , 1, 0 ,0 ,0 ,0/))
 else
   !> Write the yaml
-  call write_yaml_from_struct_3 (filename, 1, k1, v1, a2, k2, v2, a3, a3each, k3, v3, (/ 3, 0, 0 , 0, 0 ,0 ,0 ,0/))
+  call write_yaml_from_struct_3 (trim(filename), 1, k1, v1, a2, k2, v2, a3, a3each, k3, v3, (/3,0,0,0,0,0,0,0/))
 endif
 
+call mpp_sync()
+
 !> Check yaml output against reference
 if (mpp_pe() == mpp_root_pe() ) then
   do i = 1,yaml_len
     yaml_reference(i:i) = " "
     yaml_output_read(i:i) = " "
   enddo
  write (6,*) "open "//ref_yaml_name
-  open(unit=29, file=ref_yaml_name, status="old", access="stream")
+  open(newunit=unum, file=ref_yaml_name, status="old", access="stream")
  write (6,*) "read "//ref_yaml_name
-  read(29,iostat=i) yaml_reference
+  read(unum,iostat=i) yaml_reference
  write (6,*) "open "//filename
-  open(unit=28, file=filename, status="old", access="stream")
+  open(newunit=unum, file=filename, status="old", access="stream")
  write (6,*) "read "//filename
-  read(28,iostat=i) yaml_output_read
+  read(unum,iostat=i) yaml_output_read
   write(6,*) yaml_reference
   write(6,*) yaml_output_read
   if (trim(yaml_reference) .ne. trim (yaml_output_read)) then