1.14 sync with develop

.github/workflows/autotools.yml

@@ -0,0 +1,54 @@
+name: hdf5 1.14 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"

.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:

.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:

.github/workflows/cmake-ctest.yml

@@ -1,6 +1,6 @@
 name: hdf5 1.14 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:

.github/workflows/cmake.yml

@@ -0,0 +1,46 @@
+name: hdf5 1.14 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"

.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

.github/workflows/cve.yml

@@ -0,0 +1,51 @@
+name: cve 1.14
+
+on:
+  workflow_dispatch:
+  push:
+  pull_request:
+    branches: [ hdf5_1_14 ]
+    paths-ignore:
+      - '.github/CODEOWNERS'
+      - '.github/FUNDING.yml'
+      - 'doc/**'
+      - 'release_docs/**'
+      - 'ACKNOWLEDGEMENTS'
+      - 'COPYING**'
+      - '**.md'
+
+# Using concurrency to cancel any in-progress job or run
+concurrency:
+  group: ${{ github.workflow }}-${{ github.sha || github.event.pull_request.number }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    name: CVE regression
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install Autotools Dependencies (Linux)
+        run: |
+          sudo apt update
+          sudo apt install automake autoconf libtool libtool-bin
+      - name: Install HDF5
+        run: |
+          ./autogen.sh
+          ./configure --prefix=/usr/local --disable-tests
+          make
+          sudo make install
+      - name: Checkout CVE test repository
+        uses: actions/checkout@v4
+        with:
+          repository: HDFGroup/cve_hdf5
+          path: cve_hdf5
+      - name: Run regression tests
+        run: |
+          cd cve_hdf5
+          export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/lib"
+          ./test_hdf5_cve.sh /usr/local/bin ./cve_out

.github/workflows/daily-build.yml

@@ -3,6 +3,8 @@ name: hdf5 1.14 daily build
 # Controls when the action will run. Triggers the workflow on a schedule
 on:
   workflow_dispatch:
+  schedule:
+    - cron: "6 0 * * *"
 
 permissions:
   contents: read

.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: |

.github/workflows/intel-auto.yml

@@ -0,0 +1,97 @@
+name: hdf5 1.14 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

.github/workflows/intel-cmake.yml

@@ -0,0 +1,81 @@
+name: hdf5 1.14 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" \
+          -DLIBAEC_USE_LOCALCONTENT=OFF \
+          -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