Merge pull request #183 from jedwards4b/jedwards/update_pio_to_262

Update ParallelIO to version 2.6.2

src/Infrastructure/IO/PIO/ParallelIO/.github/actions/buildhdf5/action.yml

@@ -0,0 +1,56 @@
+description: 'Build the HDF5 library'
+inputs:
+  hdf5_version:
+    description: 'Tag in the HDF5 repository to use'
+    default: hdf5-1_12_2
+    required: False
+    type: string
+  enable_logging:
+    description: 'Enable hdf5 logging (for debugging)'
+    default: False
+    required: False
+    type: boolean
+  enable_parallel:
+    description: 'Enable hdf5 parallel build'
+    default: True
+    required: False
+    type: boolean
+  enable_testing:
+    description: 'Build HDF5 tests'
+    default: False
+    required: False
+    type: boolean
+
+  install_prefix:
+    description: 'Install path of hdf5'
+    default: ${GITHUB_WORKSPACE}/hdf5
+    required: False
+    type: string
+  mpi_path:
+    description: 'Path to mpi install'
+    default: /usr
+    required: False
+    type: string
+runs:
+  using: composite
+  steps:
+    - uses: actions/checkout@v3
+      with:
+        repository: HDFGroup/hdf5
+        path: hdf5-src
+        ref: ${{ inputs.hdf5_version }}
+    - id: hdf5-build
+      shell: bash
+      run: |
+        pushd hdf5-src
+        mkdir hdf5-build
+        pushd hdf5-build
+        export PATH=$PATH:${{ inputs.mpi_path }}/bin
+        cmake -DCMAKE_INSTALL_PREFIX=${{ inputs.install_prefix }} \
+        -DHDF5_ENABLE_PARALLEL=${{ inputs.enable_parallel }} \
+        -DHDF5_ENABLE_Z_LIB_SUPPORT=ON \
+        -DBUILD_TESTING=${{ inputs.enable_testing }} \
+        -DHDF5_BUILD_TOOLS=OFF \
+        ../
+        make
+        make install

src/Infrastructure/IO/PIO/ParallelIO/.github/actions/buildmpich/action.yml

@@ -0,0 +1,30 @@
+description: 'Build the MPICH library'
+inputs:
+  mpich_version:
+    description: 'Tag in the MPICH repository to use'
+    default: v4.0.3
+    required: False
+    type: string
+  install_prefix:
+    description: 'Install path of mpich'
+    default: $HOME/mpich
+    required: False
+    type: string
+runs:
+  using: composite
+  steps:
+    - uses: actions/checkout@v3
+      with:
+        repository: pmodels/mpich
+        path: mpich-src
+        ref: ${{ inputs.mpich_version }}
+        submodules: 'recursive'
+    - id: mpich-build
+      shell: bash
+      run: |
+        pushd mpich-src
+        ./autogen.sh
+        ./configure --prefix=${{ inputs.install_prefix }}
+        make -j4
+        make install
+        popd

src/Infrastructure/IO/PIO/ParallelIO/.github/actions/buildnetcdf/action.yml

@@ -0,0 +1,67 @@
+description: 'Build the netcdf fortran library'
+inputs:
+  netcdf_version:
+    description: 'Tag in the netcdf repository to use'
+    default: v4.9.0
+    required: False
+    type: string
+  shared_libraries:
+    description: 'Build shared libraries'
+    default: True
+    required: False
+    type: boolean
+  build_utilities:
+    description: 'Build netcdf utility tools'
+    default: False
+    required: False
+    type: boolean
+  enable_examples:
+    description: 'Build netcdf examples'
+    default: False
+    required: False
+    type: boolean
+  enable_netcdf4:
+    description: 'Build netcdf4 (hdf5) libraries'
+    default: True
+    required: False
+    type: boolean
+  enable_logging:
+    description: 'Enable netcdf logging (for debugging)'
+    default: False
+    required: False
+    type: boolean
+  enable_dap:
+    description: 'Enable netcdf DAP'
+    default: False
+    required: False
+    type: boolean
+
+  install_prefix:
+    description: 'Install path of netcdf'
+    default: $HOME/netcdf-c
+    required: False
+    type: string
+
+runs:
+  using: composite
+  steps:
+    - uses: actions/checkout@v3
+      with:
+        repository: Unidata/netcdf-c
+        path: netcdf-c-src
+        ref: ${{ inputs.NETCDF_VERSION }}
+    - id: netcdf-c-build
+      shell: bash
+      run: |
+        pushd $GITHUB_WORKSPACE/netcdf-c-src
+        autoreconf -i
+        config_args=--prefix=${{ inputs.install_prefix }}
+        if [ "${{ inputs.enable_dap }}" = "false" ];
+        then
+          config_args="$config_args --disable-dap"
+        fi
+        echo "config_args=$config_args"
+        ./configure $config_args
+        make
+        make install
+        popd

src/Infrastructure/IO/PIO/ParallelIO/.github/actions/buildnetcdff/action.yml

@@ -0,0 +1,35 @@
+description: 'Build the netcdf fortran library'
+inputs:
+  netcdf_fortran_version:
+    description: 'Tag in the netcdf fortran repository to use'
+    default: v5.6.0
+    required: False
+    type: string
+  netcdf_c_path:
+    description: 'Path to the installed netcdf c code root'
+    default: /usr
+    required: False
+    type: string
+  install_prefix:
+    description: 'Install path of netcdf-fortran'
+    default: $HOME/netcdf-fortran
+    required: False
+    type: string
+
+runs:
+  using: composite
+  steps:
+    - uses: actions/checkout@v3
+      with:
+        repository: Unidata/netcdf-fortran
+        path: netcdf-fortran-src
+        ref: ${{ inputs.NETCDF_FORTRAN_VERSION }}
+    - id: netcdf-fortran-build
+      shell: bash
+      run: |
+        pushd netcdf-fortran-src
+        export CPPFLAGS="$CPPFLAGS -I${{ inputs.netcdf_c_path }}/include"
+        export LDFLAGS="$LDFLAGS -L${{ inputs.netcdf_c_path }}/lib -lnetcdf"
+        ./configure --prefix=${{ inputs.install_prefix }}
+        make
+        make install

src/Infrastructure/IO/PIO/ParallelIO/.github/actions/buildopenmpi/action.yml

@@ -0,0 +1,30 @@
+description: 'Build the OPENMPI library'
+inputs:
+  openmpi_version:
+    description: 'Tag in the OPENMPI repository to use'
+    default: v4.1.4
+    required: False
+    type: string
+  install_prefix:
+    description: 'Install path of openmpi'
+    default: ${GITHUB_WORKSPACE}/openmpi
+    required: False
+    type: string
+runs:
+  using: composite
+  steps:
+    - uses: actions/checkout@v3
+      with:
+        repository: open-mpi/ompi
+        path: openmpi-src
+        ref: ${{ inputs.openmpi_version }}
+        submodules: 'recursive'
+    - id: openmpi-build
+      shell: bash
+      run: |
+        pushd openmpi-src
+        perl ./autogen.pl
+        ./configure --prefix=${{ inputs.install_prefix }}
+        make -j4
+        make install
+        popd

src/Infrastructure/IO/PIO/ParallelIO/.github/actions/buildpnetcdf/action.yml

@@ -0,0 +1,52 @@
+description: 'Build the pnetcdf library'
+inputs:
+  pnetcdf_version:
+    description: 'Tag in the pnetcdf repository to use'
+    default: checkpoint.1.12.3
+    required: False
+    type: string
+  install_prefix:
+    description: 'Install path of pnetcdf'
+    default: $GITHUB_WORKSPACE/pnetcdf
+    required: False
+    type: string
+  enable_shared:
+    description: 'Enable shared library build'
+    default: True
+    required: False
+    type: boolean
+  enable_fortran:
+    description: "Build the fortran library"
+    default: False
+    required: False
+    type: boolean
+runs:
+  using: composite
+  steps:
+    - uses: actions/checkout@v3
+      with:
+        repository: Parallel-NetCDF/PnetCDF
+        path: pnetcdf-src
+        ref: ${{ inputs.pnetcdf_version }}
+    - id: Build-PnetCDF
+      shell: bash
+      run: |
+        pushd pnetcdf-src
+        config_opts="--prefix=${{ inputs.install_prefix }} --disable-cxx "
+        if [ "${{ inputs.enable_fortran }}" = "false" ];
+        then
+          config_opts="${config_opts} --disable-fortran"
+        fi
+        if [ "${{ inputs.enable_shared }}" = "true" ];
+        then
+          config_opts="${config_opts} --enable-shared=yes"
+        fi
+
+        config_opts="${config_opts}"
+        echo "config_opts=$config_opts"
+        autoreconf -i
+        ./configure $config_opts
+
+        make
+        make install
+        popd

src/Infrastructure/IO/PIO/ParallelIO/.github/actions/intelcompilers/action.yml

@@ -0,0 +1,23 @@
+description: 'Install Intel Compilers'
+runs:
+  using: composite
+  steps:
+    - uses: actions/checkout@v3
+    - name: setup repo
+      shell: bash
+      run: |
+        wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
+        sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
+        rm GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
+        sudo echo "deb https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
+        sudo apt-get update
+    - name: install
+      shell: bash
+      run: |
+        sudo apt-get install -y intel-oneapi-common-vars
+        sudo apt-get install -y intel-oneapi-compiler-fortran
+        sudo apt-get install -y intel-oneapi-mkl
+        sudo apt-get install -y intel-oneapi-mpi
+        sudo apt-get install -y intel-oneapi-mpi-devel
+        source /opt/intel/oneapi/setvars.sh
+        printenv >> $GITHUB_ENV