Merge develop to feature/sparse_data (#5154)

.autom4te.cfg

@@ -3,7 +3,7 @@
 #
 # This file is part of HDF5.  The full HDF5 copyright notice, including
 # terms governing use, modification, and redistribution, is contained in
-# the COPYING file, which can be found at the root of the source code
+# the LICENSE file, which can be found at the root of the source code
 # distribution tree, or in https://www.hdfgroup.org/licenses.
 # If you do not have access to either file, you may request a copy from
 # help@hdfgroup.org.

.gitattributes

@@ -72,7 +72,6 @@ hl/tools/gif2h5/testfiles/ex_image2.h5 -text
 hl/tools/gif2h5/testfiles/h52giftst.h5 -text
 hl/tools/gif2h5/testfiles/image1.gif -text
 java/CMakeLists.txt -text
-java/COPYING -text
 java/Makefile.am -text
 java/examples/CMakeLists.txt -text
 java/examples/Makefile.am -text

.github/workflows/abi-report.yml

@@ -51,15 +51,15 @@ jobs:
       - name: Get published binary (Linux)
         uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16 # v4.1.8
         with:
-            name: tgz-ubuntu-2204_gcc-binary
+            name: tgz-ubuntu-2404_gcc-binary
             path: ${{ github.workspace }}
 
       - name: List files for the space (Linux)
         run: |
           ls -l ${{ github.workspace }}
 
       - name: Uncompress gh binary (Linux)
-        run: tar -zxvf ${{ github.workspace }}/${{ inputs.file_base }}-ubuntu-2204_gcc.tar.gz
+        run: tar -zxvf ${{ github.workspace }}/${{ inputs.file_base }}-ubuntu-2404_gcc.tar.gz
 
       - name: Uncompress hdf5 binary (Linux)
         run:  |
@@ -84,8 +84,8 @@ jobs:
         run: |
           mkdir "${{ github.workspace }}/hdf5R"
           cd "${{ github.workspace }}/hdf5R"
-          wget -q https://github.com/HDFGroup/hdf5/releases/download/hdf5_${{ inputs.file_ref }}/hdf5-${{ steps.convert-hdf5lib-refname.outputs.HDF5R_DOTS }}-ubuntu-2204_gcc.tar.gz
-          tar zxf hdf5-${{ steps.convert-hdf5lib-refname.outputs.HDF5R_DOTS }}-ubuntu-2204_gcc.tar.gz
+          wget -q https://github.com/HDFGroup/hdf5/releases/download/hdf5_${{ inputs.file_ref }}/hdf5-${{ steps.convert-hdf5lib-refname.outputs.HDF5R_DOTS }}-ubuntu-2404_gcc.tar.gz
+          tar zxf hdf5-${{ steps.convert-hdf5lib-refname.outputs.HDF5R_DOTS }}-ubuntu-2404_gcc.tar.gz
 
       - name: List files for the space (Linux)
         run: |

.github/workflows/autotools.yml

@@ -12,7 +12,7 @@ on:
       - 'doc/**'
       - 'release_docs/**'
       - 'ACKNOWLEDGEMENTS'
-      - 'COPYING**'
+      - 'LICENSE**'
       - '**.md'
 
 # Using concurrency to cancel any in-progress job or run
@@ -90,21 +90,15 @@ jobs:
       with:
             build_mode: "production"
 
-    call-release-auto-cygwin:
-      name: "Autotools Cygwin Workflows"
-      uses: ./.github/workflows/cygwin-auto.yml
-      with:
-            build_mode: "production"
-
     call-release-auto-xpr:
         name: "Autotools TestExpress Workflows"
         uses: ./.github/workflows/testxpr-auto.yml
 
-    call-release-auto-julia:
-        name: "Autotools Julia Workflows"
-        uses: ./.github/workflows/julia-auto.yml
-        with:
-          build_mode: "production"
+#    call-release-auto-julia:
+#        name: "Autotools Julia Workflows"
+#        uses: ./.github/workflows/julia-auto.yml
+#        with:
+#          build_mode: "production"
 
 #  workflow-msys2-autotools:
 #    name: "CMake msys2 Workflows"

.github/workflows/build_mpich_source.yml

@@ -0,0 +1,95 @@
+# Build MPICH from source using the latest commit on the
+# 'main' branch and cache the results. The result is compressed
+# into a 'mpich.tar' archive to preserve permissions and
+# then is uploaded as the artifact 'mpich' which can later
+# be downloaded with 'actions/download-artifact' and then
+# uncompressed with 'tar xvf mpich.tar -C <directory>'
+
+# Triggers the workflow on a call from another workflow
+on:
+  workflow_call:
+    inputs:
+      build_mode:
+        description: "Release vs. Debug build"
+        required: true
+        type: string
+
+permissions:
+  contents: read
+
+jobs:
+  ubuntu_gcc_build_and_test:
+    name: "Build MPICH ${{ inputs.build_mode }} (GCC)"
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Install Linux dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install build-essential libtool libtool-bin
+
+      - name: Get MPICH source
+        uses: actions/checkout@v4.1.7
+        with:
+          repository: 'pmodels/mpich'
+          path: 'mpich'
+          submodules: recursive
+
+      - name: Get MPICH commit hash
+        shell: bash
+        id: get-sha
+        run: |
+          cd $GITHUB_WORKSPACE/mpich
+          export MPICH_SHA=$(git rev-parse HEAD)
+          echo "MPICH_SHA=$MPICH_SHA" >> $GITHUB_ENV
+          echo "sha=$MPICH_SHA" >> $GITHUB_OUTPUT
+          # Output SHA for debugging
+          echo "MPICH_SHA=$MPICH_SHA"
+
+      - name: Cache MPICH (GCC) installation
+        id: cache-mpich-ubuntu-gcc
+        uses: actions/cache@v4
+        with:
+          path: ${{ runner.workspace }}/mpich
+          key: ${{ runner.os }}-${{ runner.arch }}-gcc-mpich-${{ steps.get-sha.outputs.sha }}-${{ inputs.build_mode }}
+
+      # Enable threads=multiple for testing with Subfiling and
+      # VOL connectors that require MPI_THREAD_MULTIPLE
+      - name: Install MPICH (GCC) (Release)
+        if: ${{ steps.cache-mpich-ubuntu-gcc.outputs.cache-hit != 'true' && (inputs.build_mode == 'Release') }}
+        run: |
+          cd $GITHUB_WORKSPACE/mpich
+          ./autogen.sh
+          ./configure \
+            CC=gcc \
+            --prefix=${{ runner.workspace }}/mpich \
+            --enable-threads=multiple
+          make -j2
+          make install
+
+      # Enable threads=multiple for testing with Subfiling and
+      # VOL connectors that require MPI_THREAD_MULTIPLE
+      - name: Install MPICH (GCC) (Debug)
+        if: ${{ steps.cache-mpich-ubuntu-gcc.outputs.cache-hit != 'true' && (inputs.build_mode == 'Debug') }}
+        run: |
+          cd $GITHUB_WORKSPACE/mpich
+          ./autogen.sh
+          ./configure \
+            CC=gcc \
+            --prefix=${{ runner.workspace }}/mpich \
+            --enable-g=most \
+            --enable-debuginfo \
+            --enable-threads=multiple
+          make -j2
+          make install
+
+      - name: Tar MPICH installation to preserve permissions for artifact
+        run: tar -cvf mpich.tar -C ${{ runner.workspace }} mpich
+
+      - name: Save MPICH installation artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: mpich
+          path: mpich.tar
+          if-no-files-found: error # 'warn' or 'ignore' are also available, defaults to `warn`

.github/workflows/build_openmpi_source.yml

@@ -0,0 +1,88 @@
+# Build OpenMPI from source using the latest commit on the
+# 'main' branch and cache the results. The result is compressed
+# into a 'openmpi.tar' archive to preserve permissions and
+# then is uploaded as the artifact 'openmpi' which can later
+# be downloaded with 'actions/download-artifact' and then
+# uncompressed with 'tar xvf openmpi.tar -C <directory>'
+
+# Triggers the workflow on a call from another workflow
+on:
+  workflow_call:
+    inputs:
+      build_mode:
+        description: "Release vs. Debug build"
+        required: true
+        type: string
+
+permissions:
+  contents: read
+
+jobs:
+  ubuntu_gcc_build_and_test:
+    name: "Build OpenMPI ${{ inputs.build_mode }} (GCC)"
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Install Linux dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install build-essential libtool libtool-bin
+
+      - name: Get OpenMPI source
+        uses: actions/checkout@v4.1.7
+        with:
+          repository: 'open-mpi/ompi'
+          path: 'ompi'
+          submodules: recursive
+
+      - name: Get OpenMPI commit hash
+        shell: bash
+        id: get-sha
+        run: |
+          cd $GITHUB_WORKSPACE/ompi
+          export OPENMPI_SHA=$(git rev-parse HEAD)
+          echo "OPENMPI_SHA=$OPENMPI_SHA" >> $GITHUB_ENV
+          echo "sha=$OPENMPI_SHA" >> $GITHUB_OUTPUT
+          # Output SHA for debugging
+          echo "OPENMPI_SHA=$OPENMPI_SHA"
+
+      - name: Cache OpenMPI (GCC) installation
+        id: cache-openmpi-ubuntu-gcc
+        uses: actions/cache@v4
+        with:
+          path: ${{ runner.workspace }}/openmpi
+          key: ${{ runner.os }}-${{ runner.arch }}-gcc-openmpi-${{ steps.get-sha.outputs.sha }}-${{ inputs.build_mode }}
+
+      - name: Install OpenMPI (GCC) (Release)
+        if: ${{ steps.cache-openmpi-ubuntu-gcc.outputs.cache-hit != 'true' && (inputs.build_mode == 'Release') }}
+        run: |
+          cd $GITHUB_WORKSPACE/ompi
+          ./autogen.pl
+          ./configure \
+            CC=gcc \
+            --prefix=${{ runner.workspace }}/openmpi
+          make -j2
+          make install
+
+      - name: Install OpenMPI (GCC) (Debug)
+        if: ${{ steps.cache-openmpi-ubuntu-gcc.outputs.cache-hit != 'true' && (inputs.build_mode == 'Debug') }}
+        run: |
+          cd $GITHUB_WORKSPACE/ompi
+          ./autogen.pl
+          ./configure \
+            CC=gcc \
+            --prefix=${{ runner.workspace }}/openmpi \
+            --enable-debug
+          make -j2
+          make install
+
+      - name: Tar OpenMPI installation to preserve permissions for artifact
+        run: tar -cvf openmpi.tar -C ${{ runner.workspace }} openmpi
+
+      - name: Save OpenMPI installation artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: openmpi
+          path: openmpi.tar
+          if-no-files-found: error # 'warn' or 'ignore' are also available, defaults to `warn`