Merge branch 'main' into H5Sselect_hyperslab

Unidata · Dec 12, 2023 · 1947e4a · 1947e4a
2 parents 64d3f2b + 0603c98
commit 1947e4a
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diff --git a/.github/workflows/run_tests_cdash.yml b/.github/workflows/run_tests_cdash.yml
@@ -0,0 +1,179 @@
+###
+# Build hdf5 dependencies and cache them in a combined directory.
+###
+
+name: Run CDash Ubuntu/Linux netCDF Tests
+
+on: workflow_dispatch
+
+concurrency:  
+  group: ${{ github.workflow}}-${{ github.head_ref }}  
+  cancel-in-progress: true
+
+jobs:
+
+  build-deps-cdash:
+
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        hdf5: [ 1.10.8, 1.12.2, 1.14.0 ]
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Install System dependencies
+        shell: bash -l {0}
+        run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev doxygen openssl
+
+        ###
+        # Installing libhdf5
+        ###
+      - name: Cache libhdf5-${{ matrix.hdf5 }}
+        id: cache-hdf5
+        uses: actions/cache@v3
+        with:
+          path: ~/environments/${{ matrix.hdf5 }}
+          key: hdf5-${{ runner.os }}-${{ matrix.hdf5 }}
+
+
+      - name: Build libhdf5-${{ matrix.hdf5 }}
+        if: steps.cache-hdf5.outputs.cache-hit != 'true'
+        run: |
+          set -x
+
+          wget https://support.hdfgroup.org/ftp/HDF/releases/HDF4.2.15/src/hdf-4.2.15.tar.bz2
+          tar -jxf hdf-4.2.15.tar.bz2
+          pushd hdf-4.2.15
+          ./configure --prefix=${HOME}/environments/${{ matrix.hdf5 }} --disable-static --enable-shared --disable-fortran --disable-netcdf --with-szlib --enable-hdf4-xdr
+          make -j
+          make install -j
+          popd
+
+          wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-$(echo ${{ matrix.hdf5 }} | cut -d. -f 1,2)/hdf5-${{ matrix.hdf5 }}/src/hdf5-${{ matrix.hdf5 }}.tar.bz2
+          tar -jxf hdf5-${{ matrix.hdf5 }}.tar.bz2
+          pushd hdf5-${{ matrix.hdf5 }}
+          ./configure --disable-static --enable-shared --prefix=${HOME}/environments/${{ matrix.hdf5 }} --enable-hl --with-szlib
+          make -j
+          make install -j
+          popd
+          
+
+  build-deps-parallel:
+
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        hdf5: [ 1.14.0 ]
+
+    steps:
+
+      - uses: actions/checkout@v3
+
+      - name: Install System dependencies
+        shell: bash -l {0}
+        run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev mpich libmpich-dev 
+
+        ###
+        # Installing libhdf5
+        ###
+      - name: Cache libhdf5-parallel-${{ matrix.hdf5 }}
+        id: cache-hdf5
+        uses: actions/cache@v3
+        with:
+          path: ~/environments/${{ matrix.hdf5 }}
+          key: hdf5-parallel-${{ runner.os }}-${{ matrix.hdf5 }}
+
+
+      - name: Build libhdf5-${{ matrix.hdf5 }}-pnetcdf-1.12.3
+        if: steps.cache-hdf5.outputs.cache-hit != 'true'
+        run: |
+          set -x
+
+          wget https://support.hdfgroup.org/ftp/HDF/releases/HDF4.2.15/src/hdf-4.2.15.tar.bz2
+          tar -jxf hdf-4.2.15.tar.bz2
+          pushd hdf-4.2.15
+          CC=mpicc ./configure --prefix=${HOME}/environments/${{ matrix.hdf5 }} --disable-static --enable-shared --disable-fortran --disable-netcdf --with-szlib --enable-parallel --enable-hdf4-xdr
+          make -j
+          make install -j
+          popd
+
+          wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-$(echo ${{ matrix.hdf5 }} | cut -d. -f 1,2)/hdf5-${{ matrix.hdf5 }}/src/hdf5-${{ matrix.hdf5 }}.tar.bz2
+          tar -jxf hdf5-${{ matrix.hdf5 }}.tar.bz2
+          pushd hdf5-${{ matrix.hdf5 }}
+          CC=mpicc ./configure --disable-static --enable-shared --prefix=${HOME}/environments/${{ matrix.hdf5 }} --enable-hl --with-szlib --enable-parallel
+          make -j
+          make install -j
+          popd
+          wget https://parallel-netcdf.github.io/Release/pnetcdf-1.12.3.tar.gz
+          tar -zxf pnetcdf-1.12.3.tar.gz
+          pushd pnetcdf-1.12.3
+          CC=mpicc ./configure --disable-static --enable-shared --prefix=${HOME}/environments/${{ matrix.hdf5 }} 
+          make -j
+          make install -j
+          popd
+
+
+      ###
+      # Run CTest Serial Script
+      ###
+  nc-ctest-serial:
+      needs: build-deps-cdash
+      runs-on: ubuntu-latest
+      environment: CDashCI
+
+      strategy:
+        matrix:
+          hdf5: [ 1.10.8, 1.12.2, 1.14.0 ]
+
+      steps:          
+        - uses: actions/checkout@v3
+          with:
+            CDASH_TOKEN: ${{ secrets.CDASH_TOKEN }}
+          env:
+            CDASH_TOKEN: ${{ secrets.CDASH_TOKEN }}
+
+        - name: Install System dependencies
+          shell: bash -l {0}
+          run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev
+
+        ###
+        # Set Environmental Variables
+        ###
+
+        - run: echo "CMAKE_PREFIX_PATH=${HOME}/environments/${{ matrix.hdf5 }}/" >> $GITHUB_ENV
+        - run: echo "LD_LIBRARY_PATH=${HOME}/environments/${{ matrix.hdf5 }}/lib" >> $GITHUB_ENV
+        - run: echo "CTEST_OUTPUT_ON_FAILURE=1" >> $GITHUB_ENV
+
+        ###
+        # Fetch Cache
+        ###
+
+        - name: Fetch HDF Cache
+          id: cache-hdf5
+          uses: actions/cache@v3
+          with:
+            path: ~/environments/${{ matrix.hdf5 }}
+            key: hdf5-${{ runner.os }}-${{ matrix.hdf5 }}
+
+        - name: Check Cache
+          shell: bash -l {0}
+          run: ls ${HOME}/environments/${{ matrix.hdf5 }} && ls ${HOME}/environments/${{ matrix.hdf5}}/lib
+
+        - name: Run ctest serial script
+          shell: bash -l {0}
+          env: 
+            CDASH_TOKEN: ${{ secrets.CDASH_TOKEN }}
+          run: |
+            mkdir build
+            cd build
+            LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ctest -j 12 -V -S ../ctest_scripts/ctest_serial.ctest
+
+        - name: Verbose Output if CTest Failure
+          shell: bash -l {0}
+          run: |
+            cd build
+            LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ctest -j 12 --rerun-failed --output-on-failure -VV
+          if: ${{ failure() }}
diff --git a/.github/workflows/run_tests_osx.yml b/.github/workflows/run_tests_osx.yml
@@ -6,8 +6,11 @@
 
 name: Run macOS-based netCDF Tests
 
+on: [pull_request,workflow_dispatch]
 
-on: [pull_request, workflow_dispatch]
+concurrency:  
+  group: ${{ github.workflow}}-${{ github.head_ref }}  
+  cancel-in-progress: true
 
 jobs:
 
@@ -17,18 +20,18 @@ jobs:
 
     strategy:
       matrix:
-        hdf5: [ 1.12.1 ]
+        hdf5: [ 1.12.2, 1.14.0 ]
 
     steps:
 
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
         ###
         # libhdf5
         ###
       - name: Cache libhdf5-${{ runner.os }}-${{ matrix.hdf5 }}
         id: cache-hdf5-osx
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: ~/environments/${{ matrix.hdf5 }}
           key: hdf5-${{ runner.os }}-${{ matrix.hdf5 }}
@@ -54,14 +57,13 @@ jobs:
 
     strategy:
       matrix:
-        hdf5: [ 1.12.1 ]
-        #hdf5: [ 1.8.21, 1.10.1, 1.10.7, 1.12.1 ]
+        hdf5: [ 1.12.2, 1.14.0 ]
         use_nc4: [ nc3, nc4 ]
         use_dap: [ dap_off, dap_on ]
         use_nczarr: [ nczarr_off, nczarr_on ]
     steps:
 
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
 ###
 # Set Environmental Variables
@@ -93,7 +95,7 @@ jobs:
 
       - name: Fetch HDF Cache
         id: cache-hdf-osx
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: ~/environments/${{ matrix.hdf5 }}
           key: hdf5-${{ runner.os }}-${{ matrix.hdf5 }}
@@ -161,13 +163,13 @@ jobs:
 
     strategy:
       matrix:
-        hdf5: [ 1.12.1 ]
+        hdf5: [ 1.12.2, 1.14.0 ]
         use_nc4: [ nc3, nc4 ]
         use_dap: [ dap_off, dap_on ]
         use_nczarr: [ nczarr_off, nczarr_on ]
     steps:
 
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
 ###
 # Set Environmental Variables
@@ -199,7 +201,7 @@ jobs:
 
       - name: Fetch HDF Cache
         id: cache-hdf5-osx
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: ~/environments/${{ matrix.hdf5 }}
           key: hdf5-${{ runner.os }}-${{ matrix.hdf5 }}
@@ -257,10 +259,10 @@ jobs:
 
     strategy:
       matrix:
-        hdf5: [ 1.12.1 ]
+        hdf5: [ 1.12.2, 1.14.0 ]
     steps:
 
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
 ###
 # Set Environmental Variables
@@ -277,7 +279,7 @@ jobs:
 
       - name: Fetch HDF Cache
         id: cache-hdf-osx
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: ~/environments/${{ matrix.hdf5 }}
           key: hdf5-${{ runner.os }}-${{ matrix.hdf5 }}
@@ -300,7 +302,7 @@ jobs:
 
       - name: Configure
         shell: bash -l {0}
-        run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ./configure --enable-hdf5 --enable-dap --disable-dap-remote-tests
+        run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ./configure --enable-hdf5 --enable-dap --disable-dap-remote-tests --disable-xml2
         if: ${{ success() }}
 
       - name: Look at config.log if error
@@ -338,11 +340,11 @@ jobs:
 
     strategy:
       matrix:
-        hdf5: [ 1.12.1 ]
+        hdf5: [ 1.12.2, 1.14.0 ]
 
     steps:
 
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
 ###
 # Set Environmental Variables
@@ -357,7 +359,7 @@ jobs:
 
       - name: Fetch HDF Cache
         id: cache-hdf5-osx
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: ~/environments/${{ matrix.hdf5 }}
           key: hdf5-${{ runner.os }}-${{ matrix.hdf5 }}
@@ -375,7 +377,7 @@ jobs:
         run: |
           mkdir build
           cd build
-          LD_LIBRARY_PATH=${LD_LIBRARY_PATH} cmake .. -DCMAKE_PREFIX_PATH=${CMAKE_PREFIX_PATH} -DENABLE_DAP=TRUE -DENABLE_HDF5=TRUE -DENABLE_NCZARR=TRUE -D ENABLE_DAP_LONG_TESTS=TRUE
+          LD_LIBRARY_PATH=${LD_LIBRARY_PATH} cmake .. -DCMAKE_PREFIX_PATH=${CMAKE_PREFIX_PATH} -DENABLE_DAP=TRUE -DENABLE_HDF5=TRUE -DENABLE_NCZARR=TRUE -D ENABLE_DAP_LONG_TESTS=TRUE -DENABLE_XML2=FALSE
 
       - name: Print Summary
         shell: bash -l {0}