check test failures from skipped tests

.editorconfig

@@ -1,21 +1,20 @@
 #***********************************************************************
-#                   GNU Lesser General Public License
-#
-# This file is part of the GFDL FRE NetCDF tools package (FRE NCtools).
-#
-# FRE NCtools 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.
-#
-# FRE NCtools 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/>.
-#**********************************************************************/
+#*                             Apache License 2.0
+#*
+#* This file is part of the GFDL Flexible Modeling System (FMS).
+#*
+#* Licensed under the Apache License, Version 2.0 (the "License");
+#* you may not use this file except in compliance with the License.
+#* You may obtain a copy of the License at
+#*
+#*     http://www.apache.org/licenses/LICENSE-2.0
+#*
+#* FMS is distributed in the hope that it will be useful, but WITHOUT
+#* WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied;
+#* without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+#* PARTICULAR PURPOSE. See the License for the specific language
+#* governing permissions and limitations under the License.
+#***********************************************************************
 
 # This is the preferred settings for files in the FRE NetCDF package
 # Please visit https://editorconfig.org for information on how to

.github/CODEOWNERS

@@ -1,20 +1,19 @@
 #***********************************************************************
-#*                   GNU Lesser General Public License
+#*                             Apache License 2.0
 #*
 #* 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.
+#* Licensed under the Apache License, Version 2.0 (the "License");
+#* you may not use this file except in compliance with the License.
+#* You may obtain a copy of the License at
 #*
-#* 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.
+#*     http://www.apache.org/licenses/LICENSE-2.0
 #*
-#* 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 is distributed in the hope that it will be useful, but WITHOUT
+#* WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied;
+#* without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+#* PARTICULAR PURPOSE. See the License for the specific language
+#* governing permissions and limitations under the License.
 #***********************************************************************
 #
 # Each line is a file pattern followed by one or more owners.  The owner
@@ -25,43 +24,4 @@
 # These owners will be the default owners for all the files in the
 # repository.  Unless a later match is found, these owners
 # will be requested for a review when a PR is opened.
-*          @uramirez8707 @bensonr @rem1776 @vithikashah001
-
-# GNU autotools files
-Makefile.am      @uramirez8707 @rem1776
-/configure.ac    @uramirez8707 @rem1776
-/m4/             @uramirez8707 @rem1776
-*.m4             @uramirez8707 @rem1776
-
-# cmake files
-CM*              @mlee03 @rem1776 @vithikashah001
-cmake            @mlee03 @rem1776 @vithikashah001
-
-# Files specific to GitHub or GitLab
-/.github/        @rem1776 @vithikashah001
-
-# Testing files
-/test_fms/       @uramirez8707 @mlee03 @bensonr @rem1776 @vithikashah001
-
-# Specific component directories
-/affinity/          @bensonr
-/test_fms/affinity/ @bensonr @rem1776
-
-/block_control/          @bensonr
-/test_fms/block_control/ @bensonr @rem1776
-
-#/data_override/ Currently no code owner
-/test_fms/data_override/ @rem1776
-
-/diag_manager            @uramirez8707
-/test_fms/diag_manager/  @uramirez8707
-
-/fms/             @uramirez8707 @rem1776
-/test_fms/fms/    @uramirez8707 @rem1776
-/fms2/            @uramirez8707
-/test_fms/fms2/   @uramirez8707
-
-/libFMS/           @uramirez8707 @rem1776
-
-/mpp/              @uramirez8707 @bensonr
-/test_fms/mpp/     @uramirez8707 @bensonr @rem1776
+*          @uramirez8707 @bensonr @rem1776 @vithikashah001

.github/workflows/github_autotools_gnu.yml

@@ -24,7 +24,6 @@ jobs:
       env:
         TEST_VERBOSE: 1
         DISTCHECK_CONFIGURE_FLAGS: "${{ matrix.conf-flag }} ${{ matrix.input-flag }} ${{ matrix.io-flag }}"
-        SKIP_TESTS: "test_horiz_interp2.[23-24]" # TODO (couldn't reproduce outside CI)
         DEBUG_FLAGS: "-O0 -g -fbounds-check -ffpe-trap=invalid,zero,overflow" # debug compiler flags taken from the mkmf template
     steps:
     - name: Checkout code

.github/workflows/github_autotools_intel.yml → .github/workflows/github_autotools_intel_classic.yml

@@ -1,4 +1,7 @@
-on: pull_request
+on:
+  schedule:
+    - cron: '0 0 * * 0' # sundays @ midnight
+
 
 # cancel running jobs if theres a newer push
 concurrency:
@@ -18,15 +21,13 @@ jobs:
         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@v4.2.0
       with:
         path: /libs
-        key: ${{ runner.os }}-intel-libs
+        key: intel-libs
     - name: Install packages for building
       run: apt-get update && apt-get install -y autoconf libtool automake zlibc zlib1g-dev
     - if: steps.cache.outputs.cache-hit != 'true'

.github/workflows/github_autotools_intel_oneapi.yml

@@ -0,0 +1,66 @@
+on: pull_request
+
+# cancel running jobs if theres a newer push
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  intel-oneapi-2025-3:
+    runs-on: ubuntu-latest
+    container:
+      image: intel/oneapi-hpckit:2025.3.0-0-devel-ubuntu22.04
+      env:
+        CC: "mpiicx"
+        FC: "mpiifx"
+        CFLAGS:  "-I/libs/include"
+        FCFLAGS: "-I/libs/include -g -traceback"
+        LDFLAGS: "-L/libs/lib"
+        TEST_VERBOSE: 1
+        I_MPI_FABRICS: "shm" # needed for mpi in image
+    steps:
+    - name: Cache dependencies
+      id: cache
+      uses: actions/cache@v4.2.0
+      with:
+        path: /libs
+        key: intel-libs
+    - name: Install packages for building
+      run: apt-get update && apt-get install -y autoconf libtool automake zlib1g zlib1g-dev libcurl4-openssl-dev
+    - if: steps.cache.outputs.cache-hit != 'true'
+      name: Build netcdf
+      run: |
+        # install everything to /libs
+        export LD_LIBRARY_PATH="/libs/lib:$LD_LIBRARY_PATH"
+        mkdir /libs
+        # hdf5
+        wget https://support.hdfgroup.org/releases/hdf5/v1_14/v1_14_6/downloads/hdf5-1.14.6.tar.gz
+        tar xf hdf5-1.14.6.tar.gz && cd hdf5-1.14.6
+        ./configure --prefix=/libs
+        make -j install && cd ..
+        # netcdf-c
+        wget https://github.com/Unidata/netcdf-c/archive/refs/tags/v4.9.3.tar.gz
+        tar xf v4.9.3.tar.gz && cd netcdf-c-4.9.3
+        ./configure --prefix=/libs --disable-libxml2 --enable-netcdf-4 --enable-shared
+        make -j install && cd ..
+        # netcdf-fortran
+        wget https://github.com/Unidata/netcdf-fortran/archive/refs/tags/v4.6.2.tar.gz
+        tar xf v4.6.2.tar.gz && cd netcdf-fortran-4.6.2
+        ./configure --prefix=/libs
+        make -j install && cd ..
+        # libyaml
+        wget https://github.com/yaml/libyaml/releases/download/0.2.5/yaml-0.2.5.tar.gz
+        tar xf yaml-0.2.5.tar.gz && cd yaml-0.2.5
+        ./configure --prefix=/libs
+        make -j install && cd ..
+    - name: checkout
+      uses: actions/checkout@v4.2.2
+    - name: Configure
+      run: |
+        autoreconf -if ./configure.ac
+        export LD_LIBRARY_PATH="/libs/lib:$LD_LIBRARY_PATH"
+        ./configure --with-yaml
+    - name: Compile
+      run: make -j || make
+    - name: Run test suite
+      run: make check LD_LIBRARY_PATH="/libs/lib:$LD_LIBRARY_PATH" TEST_VERBOSE=1

.github/workflows/github_cmake_gnu.yml

@@ -18,25 +18,18 @@ jobs:
     container:
       image: ghcr.io/noaa-gfdl/fms/fms-ci-rocky-gnu:13.2.0
       env:
-        CMAKE_FLAGS: "${{ matrix.build-type }} ${{ matrix.omp-flags }} ${{ matrix.libyaml-flag }} -D64BIT=on"
+        CMAKE_FLAGS: "${{ matrix.build-type }} ${{ matrix.omp-flags }} ${{ matrix.libyaml-flag }}"
+        PKG_CONFIG_PATH: "/opt/views/view/lib64/pkgconfig:/opt/views/view/lib/pkgconfig:/opt/views/view/share/pkgconfig"
     steps:
     - name: Checkout code
       uses: actions/checkout@v4.2.2
     - name: Generate makefiles with CMake
-      run: cmake $CMAKE_FLAGS -DNetCDF_ROOT=/opt/view -DLIBYAML_ROOT=/opt/view
-    - 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
+        mkdir build
+        cd build
+        cmake $CMAKE_FLAGS -DNetCDF_ROOT=/opt/view ..
+    - name: Build the library
+      run: make -C build
 
   build_arm:
     runs-on: ubuntu-24.04-arm
@@ -48,22 +41,15 @@ jobs:
     container:
       image: ghcr.io/noaa-gfdl/fms/fms-ci-rocky-gnu:13.2.0-arm
       env:
-        CMAKE_FLAGS: "${{ matrix.build-type }} ${{ matrix.omp-flags }} ${{ matrix.libyaml-flag }} -D64BIT=on"
+        CMAKE_FLAGS: "${{ matrix.build-type }} ${{ matrix.omp-flags }} ${{ matrix.libyaml-flag }}"
+        PKG_CONFIG_PATH: "/opt/views/view/lib64/pkgconfig:/opt/views/view/lib/pkgconfig:/opt/views/view/share/pkgconfig"
     steps:
     - name: Checkout code
       uses: actions/checkout@v4.2.2
     - name: Generate makefiles with CMake
-      run: cmake $CMAKE_FLAGS -DNetCDF_ROOT=/opt/view -DLIBYAML_ROOT=/opt/view
-    - 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
+        mkdir build
+        cd build
+        cmake $CMAKE_FLAGS -DNetCDF_ROOT=/opt/view ..
+    - name: Build the library
+      run: make -C build

.gitignore

@@ -1,20 +1,19 @@
 #***********************************************************************
-#*                   GNU Lesser General Public License
+#*                             Apache License 2.0
 #*
 #* 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.
+#* Licensed under the Apache License, Version 2.0 (the "License");
+#* you may not use this file except in compliance with the License.
+#* You may obtain a copy of the License at
 #*
-#* 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.
+#*     http://www.apache.org/licenses/LICENSE-2.0
 #*
-#* 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 is distributed in the hope that it will be useful, but WITHOUT
+#* WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied;
+#* without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+#* PARTICULAR PURPOSE. See the License for the specific language
+#* governing permissions and limitations under the License.
 #***********************************************************************
 # https://github.com/github/gitignore/blob/main/Fortran.gitignore
 # github uses C++ template, this only includes what fms generates