Merge branch 'develop' into FuseFix

brtnfld · Nov 6, 2023 · 9139942 · 9139942
2 parents c4770f0 + 3c07147
commit 9139942
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diff --git a/.github/workflows/autotools.yml b/.github/workflows/autotools.yml
@@ -52,3 +52,9 @@ jobs:
       uses: ./.github/workflows/intel-auto.yml
       with:
             build_mode: "production"
+
+    call-release-auto-nvhpc:
+      name: "Autotools nvhpc Workflows"
+      uses: ./.github/workflows/nvhpc-auto.yml
+      with:
+            build_mode: "production"
diff --git a/.github/workflows/cmake-ctest.yml b/.github/workflows/cmake-ctest.yml
@@ -191,8 +191,12 @@ jobs:
 
       # symlinks the compiler executables to a common location 
       - name: Setup GNU Fortran
-        uses: modflowpy/install-gfortran-action@v1
-
+        uses: fortran-lang/setup-fortran@v1
+        id: setup-fortran
+        with:
+          compiler: gcc
+          version: 12
+
       - name: Run ctest (MacOS)
         id: run-ctest
         run: |

diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
@@ -44,3 +44,9 @@ jobs:
         uses: ./.github/workflows/intel-cmake.yml
         with:
             build_mode: "Release"
+
+    call-release-cmake-nvhpc:
+        name: "CMake nvhpc Workflows"
+        uses: ./.github/workflows/nvhpc-cmake.yml
+        with:
+            build_mode: "Release"
diff --git a/.github/workflows/cve.yml b/.github/workflows/cve.yml
@@ -16,7 +16,7 @@ on:
 
 # Using concurrency to cancel any in-progress job or run
 concurrency:
-  group: ${{ github.workflow }}-${{ github.sha || github.event.pull_request.number }}
+  group: ${{ github.workflow }}-${{ github.head_ref && github.ref || github.run_id }}
   cancel-in-progress: true
 
 permissions:

diff --git a/.github/workflows/h5py.yml b/.github/workflows/h5py.yml
@@ -11,10 +11,11 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-    - name: Install gfortran
-      run: |
-        sudo apt-get update
-        sudo apt-get install -y gfortran-12
+    - name: Install Fortran
+      uses: fortran-lang/setup-fortran@v1
+      with:
+        compiler: gcc
+        version: 13
     - name: Checkout Spack
       uses: actions/checkout@v4
       with:

diff --git a/.github/workflows/hdfeos5.yml b/.github/workflows/hdfeos5.yml
@@ -16,7 +16,7 @@ on:
 
 # Using concurrency to cancel any in-progress job or run
 concurrency:
-  group: ${{ github.workflow }}-${{ github.sha || github.event.pull_request.number }}
+  group: ${{ github.workflow }}-${{ github.head_ref && github.ref || github.run_id }}
   cancel-in-progress: true
 
 permissions:

diff --git a/.github/workflows/intel-auto.yml b/.github/workflows/intel-auto.yml
@@ -13,14 +13,16 @@ permissions:
 
 jobs:
   Intel_build_and_test:
-    name: "Intel ${{ inputs.build_mode }} -Werror (build only)"
+    name: "Intel ${{ inputs.build_mode }}"
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
+
       - name: Install Dependencies
-        run:  |
+        run: |
           sudo apt-get update
           sudo apt-get install autoconf automake libtool libtool-bin libaec-dev
+
       - name: Add oneAPI to apt
         shell: bash
         run: |
@@ -39,9 +41,9 @@ jobs:
           sudo apt install -y intel-oneapi-mpi-devel
           sudo apt-get install doxygen graphviz
           sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
-           echo "CC=icx" >> $GITHUB_ENV
-           echo "CXX=icpx" >> $GITHUB_ENV
-           echo "FC=ifx" >> $GITHUB_ENV
+          echo "CC=icx" >> $GITHUB_ENV
+          echo "CXX=icpx" >> $GITHUB_ENV
+          echo "FC=ifx" >> $GITHUB_ENV
 
       - name: Install oneAPI MKL library
         shell: bash

diff --git a/.github/workflows/intel-cmake.yml b/.github/workflows/intel-cmake.yml
@@ -14,7 +14,7 @@ permissions:
 
 jobs:
   Intel_build_and_test:
-    name: "Intel ${{ inputs.build_mode }} -Werror (build only)"
+    name: "Intel ${{ inputs.build_mode }}"
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
@@ -30,9 +30,9 @@ jobs:
 
       - name: Install Linux Dependencies
         run: |
-           sudo apt update
-           sudo apt-get install ninja-build doxygen graphviz
-           sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
+          sudo apt update
+          sudo apt-get install ninja-build doxygen graphviz
+          sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
 
       - name: install oneAPI dpcpp and fortran compiler
         shell: bash

diff --git a/.github/workflows/linux-auto-aocc-ompi.yml b/.github/workflows/linux-auto-aocc-ompi.yml
@@ -16,12 +16,12 @@ on:
 
 # Using concurrency to cancel any in-progress job or run
 concurrency:
-  group: ${{ github.workflow }}-${{ github.sha || github.event.pull_request.number }}
+  group: ${{ github.workflow }}-${{ github.head_ref && github.ref || github.run_id }}
   cancel-in-progress: true
 
 permissions:
   contents: read
-      
+
 jobs:
   build:
     runs-on: ubuntu-latest
@@ -42,24 +42,31 @@ jobs:
           which clang
           which flang
           clang -v
-      - name: Install OpenMPI 4.1.5
+      - name: Cache OpenMPI 4.1.5 installation
+        id: cache-openmpi-4_1_5
+        uses: actions/cache@v3
+        with:
+          path: /home/runner/work/hdf5/hdf5/openmpi-4.1.5-install
+          key: ${{ runner.os }}-${{ runner.arch }}-openmpi-4_1_5-cache
+      - if: ${{ steps.cache-openmpi-4_1_5.outputs.cache-hit != 'true' }}
+        name: Install OpenMPI 4.1.5
         run: |
           export LD_LIBRARY_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/lib:/usr/local/lib
           wget https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.5.tar.gz
           tar zxvf openmpi-4.1.5.tar.gz
           cd openmpi-4.1.5
-          ./configure CC=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/bin/clang FC=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/bin/flang --prefix=/usr/local
+          ./configure CC=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/bin/clang FC=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/bin/flang --prefix=/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install
           make
-          sudo make install
+          make install
       - name: Install HDF5
         env:
-          NPROCS: 2      
+          NPROCS: 2
         run: |
-          export LD_LIBRARY_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/lib:/usr/local/lib/openmpi:/usr/local/lib
-          export LD_RUN_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/lib:/usr/local/lib/openmpi:/usr/local/lib
-          export PATH=/usr/local/bin:$PATH
+          export LD_LIBRARY_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/lib:/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install/lib:/usr/local/lib
+          export LD_RUN_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/lib:/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install/lib:/usr/local/lib
+          export PATH=/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install/bin:/usr/local/bin:$PATH
           ./autogen.sh
-          ./configure --prefix=/tmp  --enable-parallel --enable-shared CC=/usr/local/bin/mpicc LDFLAGS="-L/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/lib -L/usr/local/lib/openmpi"
+          ./configure --prefix=/tmp  --enable-parallel --enable-shared CC=mpicc LDFLAGS="-L/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/lib -L/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install/lib"
           make -j
           make check -j
           make install

diff --git a/.github/workflows/linux-nvhpc-auto.yml b/.github/workflows/linux-nvhpc-auto.yml
diff --git a/.github/workflows/linux-nvhpc.yml b/.github/workflows/linux-nvhpc.yml
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -17,7 +17,7 @@ on:
 
 # Using concurrency to cancel any in-progress job or run
 concurrency:
-  group: ${{ github.workflow }}-${{ github.sha || github.event.pull_request.number }}
+  group: ${{ github.workflow }}-${{ github.head_ref && github.ref || github.run_id }}
   cancel-in-progress: true
 
 permissions:

diff --git a/.github/workflows/netcdf.yml b/.github/workflows/netcdf.yml
@@ -19,7 +19,7 @@ permissions:
 
 # Using concurrency to cancel any in-progress job or run
 concurrency:
-  group: ${{ github.workflow }}-${{ github.sha || github.event.pull_request.number }}
+  group: ${{ github.workflow }}-${{ github.head_ref && github.ref || github.run_id }}
   cancel-in-progress: true
 
 jobs:

diff --git a/.github/workflows/nvhpc-auto.yml b/.github/workflows/nvhpc-auto.yml
@@ -0,0 +1,87 @@
+name: hdf5 dev autotools nvhpc
+
+on:
+  workflow_call:
+    inputs:
+      build_mode:
+        description: "release vs. debug build"
+        required: true
+        type: string
+
+permissions:
+  contents: read
+
+jobs:
+  nvhpc_build_and_test:
+    name: "nvhpc ${{ inputs.build_mode }}"
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install Dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install autoconf automake libtool libtool-bin libaec-dev
+          sudo apt-get install doxygen graphviz
+          sudo apt install -y zlib1g-dev libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev openssl build-essential
+
+      - name: Install NVHPC
+        shell: bash
+        run: |          
+          curl https://developer.download.nvidia.com/hpc-sdk/ubuntu/DEB-GPG-KEY-NVIDIA-HPC-SDK | sudo gpg --dearmor -o /usr/share/keyrings/nvidia-hpcsdk-archive-keyring.gpg
+          echo 'deb [signed-by=/usr/share/keyrings/nvidia-hpcsdk-archive-keyring.gpg] https://developer.download.nvidia.com/hpc-sdk/ubuntu/amd64 /' | sudo tee /etc/apt/sources.list.d/nvhpc.list
+          sudo apt-get update -y
+          sudo apt-get install -y nvhpc-23-9
+          echo "CC=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/comm_libs/openmpi4/bin/mpicc" >> $GITHUB_ENV
+          echo "FC=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/comm_libs/openmpi4/bin/mpifort" >> $GITHUB_ENV
+          echo "NVHPCSDK=/opt/nvidia/hpc_sdk" >> $GITHUB_ENV
+          echo "OMPI_CXX=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/compilers/bin/nvc++" >> $GITHUB_ENV
+          echo "OMPI_CC=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/compilers/bin/nvc" >> $GITHUB_ENV
+          echo "OMPI_FC=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/compilers/bin/nvfortran" >> $GITHUB_ENV
+          echo "LD_LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/compilers/lib" >> $GITHUB_ENV
+          echo "DESTDIR=/tmp" >> $GITHUB_ENV
+
+      - name: Autotools Configure
+        shell: bash
+        run: |
+          export RUNPARALLEL="mpiexec -np 2"
+          export PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/comm_libs/openmpi4/bin:/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/compilers/bin:$PATH
+          sh ./autogen.sh
+          mkdir "${{ runner.workspace }}/build"
+          cd "${{ runner.workspace }}/build"
+          $GITHUB_WORKSPACE/configure \
+            FCFLAGS="-fPIC -fortranlibs" \
+            --enable-build-mode=${{ inputs.build_mode }} \
+            --enable-fortran \
+            --enable-shared \
+            --enable-parallel
+          #cat config.log
+
+      # BUILD
+      - name: Autotools Build
+        shell: bash
+        run: |
+          export PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/comm_libs/openmpi4/bin:/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/compilers/bin:$PATH
+          make -j3
+        working-directory: ${{ runner.workspace }}/build
+
+      # RUN TESTS
+      # NORMAL
+      - name: Autotools Run Tests
+        run: |
+          export PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/comm_libs/openmpi4/bin:/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/compilers/bin:$PATH
+          make check -j
+        working-directory: ${{ runner.workspace }}/build
+
+      # INSTALL (note that this runs even when we don't run the tests)
+      - name: Autotools Install
+        run: |
+          export PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/comm_libs/openmpi4/bin:/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/compilers/bin:$PATH
+          make install
+        working-directory: ${{ runner.workspace }}/build
+
+#      - name: Autotools Verify Install
+#        run: |
+#          export PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/comm_libs/openmpi4/bin:/opt/nvidia/hpc_sdk/Linux_x86_64/23.9/compilers/bin:$PATH
+#          make check-install
+#        working-directory: ${{ runner.workspace }}/build