Merge GDAL interface into ESMF develop.

.gitignore

@@ -23,7 +23,7 @@ PET*.ESMF_LogFile
 /examples/
 /src/Infrastructure/IO/PIO/Build/
 /src/Infrastructure/IO/PIO/Install/
-
+/holding
 # protex generated files #
 ##########################
 *_ccapi.tex

ParallelIO/.github/workflows/autotools.yml

@@ -0,0 +1,66 @@
+name: autotools_ubuntu_latest
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    env:
+      CC: mpicc
+      FC: mpifort
+      CPPFLAGS: "-I/usr/include -I/usr/local/include -I/home/runner/pnetcdf/include"
+      LDFLAGS: "-L/home/runner/pnetcdf/lib"
+      PNETCDF_VERSION: 1.12.3
+      FCFLAGS: "-fallow-argument-mismatch"
+    steps:
+    - uses: actions/checkout@v3
+    - name: Installs
+      run: |
+        set -x
+        #        sudo gem install apt-spy2
+        #        sudo apt-spy2 check
+        #        sudo apt-spy2 fix --commit
+        # after selecting a specific mirror, we need to run 'apt-get update'
+        sudo apt-get update 
+        sudo apt-get install netcdf-bin 
+        sudo apt-get install libnetcdf-dev
+        sudo apt-get install doxygen
+        sudo apt-get install graphviz
+        sudo apt-get install wget
+        sudo apt-get install gfortran
+        sudo apt-get install libjpeg-dev
+        sudo apt-get install libz-dev
+        sudo apt-get install openmpi-bin
+        sudo apt-get install libopenmpi-dev
+    - name: cache-pnetcdf
+      id: cache-pnetcdf
+      uses: actions/cache@v3
+      with:
+        path: ~/pnetcdf
+        key: pnetcdf-${{ runner.os }}-${{ env.PNETCDF_VERSION }}
+
+    - name: build-pnetcdf
+      if: steps.cache-pnetcdf.outputs.cache-hit != 'true'
+      run: |
+        set -x
+        wget https://parallel-netcdf.github.io/Release/pnetcdf-${{ env.PNETCDF_VERSION }}.tar.gz &> /dev/null
+        tar -xzvf pnetcdf-${{ env.PNETCDF_VERSION }}.tar.gz
+        pushd pnetcdf-${{ env.PNETCDF_VERSION }}
+        ./configure --prefix=/home/runner/pnetcdf --enable-shared --disable-cxx
+        make
+        sudo make install
+        popd
+
+    - name: autoreconf
+      run: autoreconf -i
+    - name: configure
+      run: ./configure --enable-fortran  --with-mpiexec='mpiexec --oversubscribe'
+      #run: ./configure --enable-fortran --enable-docs  --with-mpiexec='mpiexec --oversubscribe'
+    - name: make check
+      run: make -j check

ParallelIO/.github/workflows/cmake.yml

@@ -0,0 +1,64 @@
+name: cmake
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    env:
+      CC: mpicc
+      FC: mpifort
+      CPPFLAGS: "-I/usr/include -I/usr/local/include -I/home/runner/pnetcdf/include"
+      LDFLAGS: "-L/home/runner/pnetcdf/lib"
+      LD_LIBRARY_PATH: "/home/runner/pnetcdf/lib"
+      PNETCDF_VERSION: 1.12.3
+      FCFLAGS: "-fallow-argument-mismatch"
+    steps:
+    - uses: actions/checkout@v3
+    - name: Installs
+      run: |
+        set -x
+        #sudo gem install apt-spy2
+        #sudo apt-spy2 check
+        #sudo apt-spy2 fix --commit
+        # after selecting a specific mirror, we need to run 'apt-get update'
+        sudo apt-get update
+        sudo apt-get install netcdf-bin libnetcdf-dev doxygen graphviz wget gfortran libjpeg-dev libz-dev openmpi-bin libopenmpi-dev cmake
+
+    - name: cache-pnetcdf
+      id: cache-pnetcdf
+      uses: actions/cache@v3
+      with:
+        path: ~/pnetcdf
+        key: pnetcdf-${{ runner.os }}-${{ env.PNETCDF_VERSION }}
+
+    - name: build-pnetcdf
+      if: steps.cache-pnetcdf.outputs.cache-hit != 'true'
+      run: |
+        set -x
+        wget https://parallel-netcdf.github.io/Release/pnetcdf-${{ env.PNETCDF_VERSION }}.tar.gz &> /dev/null
+        tar -xzvf pnetcdf-${{ env.PNETCDF_VERSION }}.tar.gz
+        pushd pnetcdf-${{ env.PNETCDF_VERSION }}
+        ./configure --prefix=/home/runner/pnetcdf --enable-shared --disable-cxx
+        make
+        sudo make install
+        popd
+
+    - name: cmake build
+      run: |
+        set -x
+        mkdir build
+        cd build
+        cmake -Wno-dev -DNetCDF_C_LIBRARY=/usr/lib/x86_64-linux-gnu/libnetcdf.so \
+        -DNetCDF_C_INCLUDE_DIR=/usr/include -DPnetCDF_PATH='/home/runner/pnetcdf' \
+        -DPIO_ENABLE_FORTRAN=Off \
+        -DPIO_ENABLE_LOGGING=On -DPIO_ENABLE_TIMING=Off  -DMPIEXEC_PREFLAGS="--oversubscribe" ..
+        make VERBOSE=1
+        make tests VERBOSE=1
+        ctest -VV

ParallelIO/.github/workflows/cmake_ubuntu_latest.yml

@@ -0,0 +1,68 @@
+---   # cmake build without netcdf integration
+name: cmake_ubuntu-latest
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    env:
+      CC: mpicc
+      FC: mpifort
+      CPPFLAGS: "-I/usr/include -I/usr/local/include -I/home/runner/pnetcdf/include"
+      LDFLAGS: "-L/home/runner/pnetcdf/lib"
+      LD_LIBRARY_PATH: "/home/runner/pnetcdf/lib"
+      PNETCDF_VERSION: 1.12.3
+      FCFLAGS: "-fallow-argument-mismatch"
+    steps:
+      - uses: actions/checkout@v3
+      - name: Installs
+        run: |
+          set -x
+          #sudo gem install apt-spy2
+          #sudo apt-spy2 check
+          #sudo apt-spy2 fix --commit
+          # after selecting a specific mirror, we need to run 'apt-get update'
+          sudo apt-get update
+          sudo apt-get install netcdf-bin libnetcdf-dev doxygen graphviz wget gfortran libjpeg-dev libz-dev openmpi-bin libopenmpi-dev
+
+      - name: cache-pnetcdf
+        id: cache-pnetcdf
+        uses: actions/cache@v3
+        with:
+          path: ~/pnetcdf
+          key: pnetcdf-${{ runner.os }}-${{ env.PNETCDF_VERSION }}
+
+      - name: build-pnetcdf
+        if: steps.cache-pnetcdf.outputs.cache-hit != 'true'
+        run: |
+          set -x
+          wget https://parallel-netcdf.github.io/Release/pnetcdf-${{ env.PNETCDF_VERSION }}.tar.gz &> /dev/null
+          tar -xzvf pnetcdf-${{ env.PNETCDF_VERSION }}.tar.gz
+          pushd pnetcdf-${{ env.PNETCDF_VERSION }}
+          ./configure --prefix=/home/runner/pnetcdf --enable-shared --disable-cxx
+          make
+          sudo make install
+          popd
+
+      - name: cmake build
+        run: |
+          set -x
+          mkdir build
+          cd build
+          cmake -Wno-dev -DPIO_ENABLE_NETCDF_INTEGRATION=OFF \
+          -DNetCDF_C_LIBRARY=/usr/lib/x86_64-linux-gnu/libnetcdf.so \
+          -DNetCDF_C_INCLUDE_DIR=/usr/include -DPnetCDF_PATH='/home/runner/pnetcdf' \
+          -DPIO_ENABLE_FORTRAN=OFF \
+          -DPIO_ENABLE_LOGGING=On -DPIO_ENABLE_TIMING=Off -DMPIEXEC_PREFLAGS="--oversubscribe" ..
+          make VERBOSE=1
+          make tests VERBOSE=1
+          ctest -VV

ParallelIO/.github/workflows/netcdf_hdf5_no_pnetcdf_ncint_mpich.yml

@@ -0,0 +1,119 @@
+name: netcdf_hdf5_no_pnetcdf_ncint_mpich
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    env:
+      CPPFLAGS: "-I/home/runner/mpich/include -I/home/runner/hdf5/include -I/home/runner/netcdf-c/include -I/home/runner/netcdf-fortran/include"
+      LDFLAGS: "-L/home/runner/mpich/lib -L/home/runner/hdf5/lib -L/home/runner/netcdf-c/lib -L/home/runner/netcdf-fortran/lib"
+      # Note issue https://github.com/NCAR/ParallelIO/issues/1889 netcdf integration currently only works with netcdf 4.7.4
+      NETCDF_C_VERSION: 4.7.4
+      NETCDF_F_VERSION: 4.5.4
+      MPICH_VERSION: 4.0.3
+      HDF5_VERSION_MAJOR: 1.12
+      HDF5_VERSION_PATCH: 2
+      FFLAGS: "-fallow-argument-mismatch"
+      FCFLAGS: "-fallow-argument-mismatch"
+    steps:
+    - uses: actions/checkout@v3
+    - name: Installs
+      run: |
+        sudo apt-get install doxygen graphviz wget gfortran libjpeg-dev libz-dev
+    - name: cache-mpich
+      id: cache-mpich
+      uses: actions/cache@v3
+      with:
+        path: ~/mpich
+        key: mpich-${{ runner.os }}-${{ env.MPICH_VERSION }}
+
+    - name: build-mpich
+      if: steps.cache-mpich.outputs.cache-hit != 'true'
+      run: |
+        wget http://www.mpich.org/static/downloads/${{ env.MPICH_VERSION }}/mpich-${{ env.MPICH_VERSION }}.tar.gz &> /dev/null
+        tar -xzf mpich-${{ env.MPICH_VERSION }}.tar.gz
+        pushd mpich-${{ env.MPICH_VERSION }}
+        ./configure --prefix=/home/runner/mpich
+        make
+        sudo make install
+        popd
+    - name: cache-hdf5
+      id: cache-hdf5
+      uses: actions/cache@v3
+      with:
+        path: ~/hdf5
+        key: hdf5-${{ runner.os }}-${{ env.HDF5_VERSION_MAJOR }}.${{ env.HDF5_VERSION_PATCH }}-mpich-${{ env.MPICH_VERSION }}
+
+    - name: build-hdf5
+      if: steps.cache-hdf5.outputs.cache-hit != 'true'
+      run: |
+        set -x
+        export PATH="/home/runner/mpich/bin:$PATH"
+        export CC=/home/runner/mpich/bin/mpicc
+        wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${{ env.HDF5_VERSION_MAJOR }}/hdf5-${{ env.HDF5_VERSION_MAJOR }}.${{ env.HDF5_VERSION_PATCH }}/src/hdf5-${{ env.HDF5_VERSION_MAJOR }}.${{ env.HDF5_VERSION_PATCH }}.tar.gz &> /dev/null
+        tar -xzf hdf5-${{ env.HDF5_VERSION_MAJOR }}.${{ env.HDF5_VERSION_PATCH }}.tar.gz
+        pushd hdf5-${{ env.HDF5_VERSION_MAJOR }}.${{ env.HDF5_VERSION_PATCH }}
+        ./configure --prefix=/home/runner/hdf5 --enable-parallel --disable-tools --disable-fortran --disable-cxx --enable-parallel-tests
+        make
+        sudo make install
+        popd
+    - name: cache-netcdf-c
+      id: cache-netcdf-c
+      uses: actions/cache@v3
+      with:
+        path: ~/netcdf-c
+        key: netcdf-c-${{ runner.os }}-${{ env.NETCDF_C_VERSION }}-mpich-${{ env.MPICH_VERSION }}-hdf5-${{ env.HDF5_VERSION_MAJOR }}.${{ env.HDF5_VERSION_PATCH }}
+
+    - name: build-netcdf-c
+      if: steps.cache-netcdf-c.outputs.cache-hit != 'true'
+      run: |
+        set -x
+        export PATH="/home/runner/mpich/bin:$PATH"
+        export CC=/home/runner/mpich/bin/mpicc
+        wget https://github.com/Unidata/netcdf-c/archive/refs/tags/v${{ env.NETCDF_C_VERSION }}.tar.gz
+        tar -xzf v${{ env.NETCDF_C_VERSION }}.tar.gz &> /dev/null
+        pushd netcdf-c-${{ env.NETCDF_C_VERSION }}
+        ./configure --prefix=/home/runner/netcdf-c --disable-dap --disable-utilities
+        make -j
+        sudo make install
+        popd
+
+    - name: cache-netcdf-fortran
+      id: cache-netcdf-fortran
+      uses: actions/cache@v3
+      with:
+        path: ~/netcdf-fortran
+        key: netcdf-fortran-${{ runner.os }}-${{ env.NETCDF_F_VERSION }}-mpich-${{ env.MPICH_VERSION }}-hdf5-${{ env.HDF5_VERSION_MAJOR }}.${{ env.HDF5_VERSION_PATCH }}
+
+    - name: build-netcdf-fortran
+      if: steps.cache-netcdf-fortran.outputs.cache-hit != 'true'
+      run: |
+        set -x
+        export PATH="/home/runner/mpich/bin:$PATH"
+        export CC=/home/runner/mpich/bin/mpicc
+        wget https://github.com/Unidata/netcdf-fortran/archive/refs/tags/v${{ env.NETCDF_F_VERSION }}.tar.gz
+        tar -zxf v${{ env.NETCDF_F_VERSION }}.tar.gz &> /dev/null
+        pushd netcdf-fortran-${{ env.NETCDF_F_VERSION }}
+        ./configure --prefix=/home/runner/netcdf-fortran
+        make -j
+        sudo make install
+        popd
+
+    - name: autotools build
+      run: |
+        set -x
+        gcc --version
+        export PATH=/home/runner/mpich/bin:/home/runner/netcdf-c/bin:$PATH
+        export CC=/home/runner/mpich/bin/mpicc
+        export FC=/home/runner/mpich/bin/mpifort
+        autoreconf -i
+        ./configure --enable-fortran --enable-netcdf-integration --disable-pnetcdf
+        make -j check
+
+