Merge branch 'HDFGroup:develop' into develop_sel_io_test

HDFGroup · Sep 20, 2023 · 025edfc · 025edfc
2 parents f553c07 + 95907ba
commit 025edfc
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diff --git a/.github/workflows/autotools.yml b/.github/workflows/autotools.yml
@@ -0,0 +1,54 @@
+name: hdf5 dev autools CI
+
+# Controls when the action will run. Triggers the workflow on push or pull request
+on:
+  workflow_call:
+
+permissions:
+  contents: read
+
+# A workflow run is made up of one or more jobs that can run sequentially or
+# in parallel. We just have one job, but the matrix items defined below will
+# run in parallel.
+jobs:
+    call-workflow-special-autotools:
+      name: "Autotools Special Workflows"
+      uses: ./.github/workflows/main-auto-spc.yml
+
+    call-parallel-special-autotools:
+      name: "Autotools Parallel Special Workflows"
+      uses: ./.github/workflows/main-auto-par.yml
+
+    call-debug-thread-autotools:
+      name: "Autotools Debug Thread-Safety Workflows"
+      uses: ./.github/workflows/main-auto.yml
+      with:
+            thread_safety: enable
+            build_mode: "debug"
+
+    call-release-thread-autotools:
+      name: "Autotools Release Thread-Safety Workflows"
+      uses: ./.github/workflows/main-auto.yml
+      with:
+            thread_safety: enable
+            build_mode: "production"
+
+    call-debug-autotools:
+      name: "Autotools Debug Workflows"
+      uses: ./.github/workflows/main-auto.yml
+      with:
+            thread_safety: disable
+            build_mode: "debug"
+
+    call-release-autotools:
+      name: "Autotools Release Workflows"
+      uses: ./.github/workflows/main-auto.yml
+      with:
+            thread_safety: disable
+            build_mode: "production"
+
+    call-release-auto-intel:
+      name: "Autotools Intel Workflows"
+      uses: ./.github/workflows/intel-auto.yml
+      with:
+            build_mode: "production"
diff --git a/.github/workflows/clang-format-check.yml b/.github/workflows/clang-format-check.yml
@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     if: "!contains(github.event.head_commit.message, 'skip-ci')"
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Run clang-format style check for C and Java code
       uses: DoozyX/[email protected]
       with:

diff --git a/.github/workflows/clang-format-fix.yml b/.github/workflows/clang-format-fix.yml
@@ -21,7 +21,7 @@ jobs:
     permissions:
         contents: write # In order to allow EndBug/add-and-commit to commit changes
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Fix C and Java formatting issues detected by clang-format
       uses: DoozyX/[email protected]
       with:

diff --git a/.github/workflows/cmake-ctest.yml b/.github/workflows/cmake-ctest.yml
@@ -1,6 +1,6 @@
 name: hdf5 dev ctest runs
 
-# Controls when the action will run. Triggers the workflow on a schedule
+# Controls when the action will run. Triggers the workflow on a call
 on:
   workflow_call:
     inputs:

diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
@@ -0,0 +1,46 @@
+name: hdf5 dev cmake CI
+
+# Controls when the action will run. Triggers the workflow on push or pull request
+on:
+  workflow_call:
+
+permissions:
+  contents: read
+
+# A workflow run is made up of one or more jobs that can run sequentially or
+# in parallel. We just have one job, but the matrix items defined below will
+# run in parallel.
+jobs:
+    call-debug-thread-cmake:
+        name: "CMake Debug Thread-Safety Workflows"
+        uses: ./.github/workflows/main-cmake.yml
+        with:
+            thread_safety: true
+            build_mode: "Debug"
+
+    call-release-thread-cmake:
+        name: "CMake Release Thread-Safety Workflows"
+        uses: ./.github/workflows/main-cmake.yml
+        with:
+            thread_safety: true
+            build_mode: "Release"
+
+    call-debug-cmake:
+        name: "CMake Debug Workflows"
+        uses: ./.github/workflows/main-cmake.yml
+        with:
+            thread_safety: false
+            build_mode: "Debug"
+
+    call-release-cmake:
+        name: "CMake Release Workflows"
+        uses: ./.github/workflows/main-cmake.yml
+        with:
+            thread_safety: false
+            build_mode: "Release"
+
+    call-release-cmake-intel:
+        name: "CMake Intel Workflows"
+        uses: ./.github/workflows/intel-cmake.yml
+        with:
+            build_mode: "Release"
diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml
@@ -10,7 +10,7 @@ jobs:
     name: Check for spelling errors
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: codespell-project/actions-codespell@master
         with:
           skip: ./.github/workflows/codespell.yml,./bin/trace,./hl/tools/h5watch/h5watch.c,./tools/test/h5jam/tellub.c,./config/sanitizer/LICENSE,./config/sanitizer/sanitizers.cmake,./tools/test/h5repack/testfiles/*.dat,./test/API/driver,./configure,./bin/ltmain.sh,./bin/depcomp,./bin/config.guess,./bin/config.sub,./autom4te.cache,./m4/libtool.m4,./c++/src/*.html

diff --git a/.github/workflows/cve.yml b/.github/workflows/cve.yml
@@ -27,7 +27,7 @@ jobs:
     name: CVE regression
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Install Autotools Dependencies (Linux)
         run: |
@@ -40,7 +40,7 @@ jobs:
           make
           sudo make install
       - name: Checkout CVE test repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           repository: HDFGroup/cve_hdf5
           path: cve_hdf5

diff --git a/.github/workflows/h5py.yml b/.github/workflows/h5py.yml
@@ -16,7 +16,7 @@ jobs:
         sudo apt-get update
         sudo apt-get install -y gfortran-12
     - name: Checkout Spack
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         repository: spack/spack
         path: ./spack

diff --git a/.github/workflows/hdfeos5.yml b/.github/workflows/hdfeos5.yml
@@ -27,7 +27,7 @@ jobs:
     name: Build hdfeos5
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Install Autotools Dependencies (Linux)
         run: |

diff --git a/.github/workflows/intel-auto.yml b/.github/workflows/intel-auto.yml
@@ -0,0 +1,97 @@
+name: hdf5 dev autotools icx CI
+
+on:
+  workflow_call:
+    inputs:
+      build_mode:
+        description: "release vs. debug build"
+        required: true
+        type: string
+
+permissions:
+  contents: read
+
+jobs:
+  Intel_build_and_test:
+    name: "Intel ${{ inputs.build_mode }} -Werror (build only)"
+    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
+      - name: Add oneAPI to apt
+        shell: bash
+        run: |
+          cd /tmp
+          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 add-apt-repository -y "deb https://apt.repos.intel.com/oneapi all main"
+      
+      - name: Install oneAPI dpcpp and fortran compiler
+        shell: bash
+        run: |
+          sudo apt update
+          sudo apt install -y intel-oneapi-compiler-dpcpp-cpp
+          sudo apt install -y intel-oneapi-compiler-fortran
+          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" >> $GITHUB_ENV
+
+      - name: Install oneAPI MKL library
+        shell: bash
+        run: |
+          sudo apt install -y intel-oneapi-mkl-devel
+
+      - name: Autotools Configure
+        shell: bash
+        run: |
+          source /opt/intel/oneapi/setvars.sh
+          export PATH=$PATH:/opt/intel/oneapi/compiler/2023.2.1/linux/bin
+          sh ./autogen.sh
+          mkdir "${{ runner.workspace }}/build"
+          cd "${{ runner.workspace }}/build"
+          $GITHUB_WORKSPACE/configure \
+            --enable-build-mode=${{ inputs.build_mode }} \
+            --enable-shared \
+            --disable-fortran
+
+      # BUILD
+      - name: Autotools Build
+        run: |
+          source /opt/intel/oneapi/setvars.sh
+          export PATH=$PATH:/opt/intel/oneapi/compiler/2023.2.1/linux/bin
+          make -j3
+        working-directory: ${{ runner.workspace }}/build
+
+      # RUN TESTS
+      # NORMAL
+      - name: Autotools Run Tests
+        run: |
+          source /opt/intel/oneapi/setvars.sh
+          export PATH=$PATH:/opt/intel/oneapi/compiler/2023.2.1/linux/bin
+          export SYCL_DEVICE_FILTER=opencl.cpu
+          make check -j2
+        working-directory: ${{ runner.workspace }}/build
+
+      # INSTALL (note that this runs even when we don't run the tests)
+      - name: Autotools Install
+        run: |
+          source /opt/intel/oneapi/setvars.sh
+          export PATH=$PATH:/opt/intel/oneapi/compiler/2023.2.1/linux/bin
+          export SYCL_DEVICE_FILTER=opencl.cpu
+          make install
+        working-directory: ${{ runner.workspace }}/build
+
+      - name: Autotools Verify Install
+        run: |
+          source /opt/intel/oneapi/setvars.sh
+          export PATH=$PATH:/opt/intel/oneapi/compiler/2023.2.1/linux/bin
+          export SYCL_DEVICE_FILTER=opencl.cpu
+          make check-install
+        working-directory: ${{ runner.workspace }}/build
diff --git a/.github/workflows/intel-cmake.yml b/.github/workflows/intel-cmake.yml
@@ -0,0 +1,83 @@
+name: hdf5 dev CMake icx CI
+
+# Controls when the action will run. Triggers the workflow on a call
+on:
+  workflow_call:
+    inputs:
+      build_mode:
+        description: "release vs. debug build"
+        required: true
+        type: string
+
+permissions:
+  contents: read
+
+jobs:
+  Intel_build_and_test:
+    name: "Intel ${{ inputs.build_mode }} -Werror (build only)"
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: add oneAPI to apt
+        shell: bash
+        run: |
+          cd /tmp
+          wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
+          sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
+          rm GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
+          sudo add-apt-repository -y "deb https://apt.repos.intel.com/oneapi all main"
+
+      - name: Install Linux Dependencies
+        run: |
+           sudo apt update
+           sudo apt-get install ninja-build doxygen graphviz
+           sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
+
+      - name: install oneAPI dpcpp and fortran compiler
+        shell: bash
+        run: |
+          sudo apt update
+          sudo apt install -y intel-oneapi-compiler-dpcpp-cpp
+          sudo apt install -y intel-oneapi-compiler-fortran
+
+      - name: install oneAPI MKL library
+        shell: bash
+        run: |
+          sudo apt install -y intel-oneapi-mkl-devel
+
+      - name: CMake Configure with icx
+        shell: bash
+        run: |
+          source /opt/intel/oneapi/setvars.sh
+          export PATH=$PATH:/opt/intel/oneapi/compiler/2023.2.1/linux/bin
+          mkdir "${{ runner.workspace }}/build"
+          cd "${{ runner.workspace }}/build"
+          cmake -C $GITHUB_WORKSPACE/config/cmake/cacheinit.cmake -G Ninja \
+          -DCMAKE_BUILD_TYPE=${{ inputs.build_mode }} \
+          -DCMAKE_TOOLCHAIN_FILE=config/toolchain/intel.cmake \
+          -DMKL_ROOT="/opt/intel/oneapi/mkl/latest" \
+          -DTBB_ROOT="/opt/intel/oneapi/tbb/latest" \
+          -DBUILD_SZIP_WITH_FETCHCONTENT=ON \
+          -DLIBAEC_USE_LOCALCONTENT=OFF \
+          -DBUILD_ZLIB_WITH_FETCHCONTENT=ON \
+          -DZLIB_USE_LOCALCONTENT=OFF \
+          -DHDF5_BUILD_FORTRAN=OFF \
+          $GITHUB_WORKSPACE
+
+      # BUILD
+      - name: CMake Build
+        shell: bash
+        run: |
+          source /opt/intel/oneapi/setvars.sh
+          cmake --build . --parallel 3 --config ${{ inputs.build_mode }}
+        working-directory: ${{ runner.workspace }}/build
+
+      # RUN TESTS
+      - name: CMake Run Tests
+        shell: bash
+        run: |
+          source /opt/intel/oneapi/setvars.sh
+          export SYCL_DEVICE_FILTER=opencl.cpu
+          ctest . --parallel 2 -C ${{ inputs.build_mode }} -V
+        working-directory: ${{ runner.workspace }}/build