Sync develop changes March 28 - April 1 to 1 14 (#4297)

* Relaxed behavior of H5Pset_page_buffer_size() when opening files (#4280) This API call sets the size of a file's page buffer cache. This call was extremely strict about matching its parameters to the file strategy and page size used to create the file, requiring a separate open of the file to obtain these parameters. These requirements have been relaxed when using the fapl to open a previously-created file: * When opening a file that does not use the H5F_FSPACE_STRATEGY_PAGE strategy, the setting is ignored and the file will be opened, but without a page buffer cache. This was previously an error. * When opening a file that has a page size larger than the desired page buffer cache size, the page buffer cache size will be increased to the file's page size. This was previously an error. The behavior when creating a file using H5Pset_page_buffer_size() is unchanged. Fixes GitHub issue #3382 * chore: improve error message (#4287) close #192 * changed to if string contains instead (#4286) * Fix off_t straggers (#4291) Convert off_t to HDoff_t (mainly for Windows): * h5jam * h5unjam * chunk_info test * Add missing foreach for VFD and Pasthrough runs (#4292) * Fixes for file format security issues (#4283) * Add configure options for disabling extension features (#4277) Add configure option to enable or disable extension features in general Add configure option to enable or disable _Float16 support Add new config options to various settings files * Add documentation (H5FD) (#4269) * Use AOCC 4.2 and OpenMPI 4.1.6 (#4290) * Fix problems with background buffers and array datatypes (#4218) * Fix bug in array conversion with strided background buffer. Convert some memmove calls to non-overlapping buffers to memcpy. * Revert inappropriate use of mempy to memmove in H5T__conv_array * Add testing * Add RELEASE.txt note and overwrite test case. * Synch workflows and require apt-get update (#4294) * Fix Figure 9. table format in HDF5 Groups User Guide (#4295) --------- Co-authored-by: Dana Robinson <[email protected]> Co-authored-by: H. Joe Lee <[email protected]> Co-authored-by: Scot Breitenfeld <[email protected]> Co-authored-by: Allen Byrne <[email protected]> Co-authored-by: jhendersonHDF <[email protected]> Co-authored-by: bmribler <[email protected]> Co-authored-by: Neil Fortner <[email protected]>
HDFGroup · Apr 1, 2024 · 9f7b987 · 9f7b987
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diff --git a/.github/workflows/aocc-auto.yml b/.github/workflows/aocc-auto.yml
@@ -28,43 +28,43 @@ jobs:
           sudo apt install -y zlib1g-dev libcurl4-openssl-dev libjpeg-dev wget curl bzip2
           sudo apt install -y m4 flex bison cmake libzip-dev openssl build-essential
 
-      - name: Install AOCC 4.1.0
+      - name: Install AOCC 4.2.0
         shell: bash
         run: |
-          wget https://download.amd.com/developer/eula/aocc/aocc-4-1/aocc-compiler-4.1.0.tar
-          tar -xvf aocc-compiler-4.1.0.tar
-          cd aocc-compiler-4.1.0
+          wget https://download.amd.com/developer/eula/aocc/aocc-4-2/aocc-compiler-4.2.0.tar
+          tar -xvf aocc-compiler-4.2.0.tar
+          cd aocc-compiler-4.2.0
           bash install.sh
           source /home/runner/work/hdf5/hdf5/setenv_AOCC.sh
           which clang
           which flang
           clang -v
 
-      - name: Cache OpenMPI 4.1.5 installation
-        id: cache-openmpi-4_1_5
+      - name: Cache OpenMPI 4.1.6 installation
+        id: cache-openmpi-4_1_6
         uses: actions/cache@v4
         with:
-          path: /home/runner/work/hdf5/hdf5/openmpi-4.1.5-install
-          key: ${{ runner.os }}-${{ runner.arch }}-openmpi-4_1_5-cache
+          path: /home/runner/work/hdf5/hdf5/openmpi-4.1.6-install
+          key: ${{ runner.os }}-${{ runner.arch }}-openmpi-4_1_6-cache
 
-      - name: Install OpenMPI 4.1.5
-        if: ${{ steps.cache-openmpi-4_1_5.outputs.cache-hit != 'true' }}
+      - name: Install OpenMPI 4.1.6
+        if: ${{ steps.cache-openmpi-4_1_6.outputs.cache-hit != 'true' }}
         run: |
-          export LD_LIBRARY_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/lib:/usr/local/lib
-          wget https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.5.tar.gz
-          tar zxvf openmpi-4.1.5.tar.gz
-          cd openmpi-4.1.5
-          ./configure CC=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/bin/clang FC=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/bin/flang --prefix=/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install
+          export LD_LIBRARY_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.2.0/lib:/usr/local/lib
+          wget https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.6.tar.gz
+          tar zxvf openmpi-4.1.6.tar.gz
+          cd openmpi-4.1.6
+          ./configure CC=/home/runner/work/hdf5/hdf5/aocc-compiler-4.2.0/bin/clang FC=/home/runner/work/hdf5/hdf5/aocc-compiler-4.2.0/bin/flang --prefix=/home/runner/work/hdf5/hdf5/openmpi-4.1.6-install
           make
           make install
 
       - name: Autotools Configure
         env:
           NPROCS: 2
         run: |
-          export LD_LIBRARY_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/lib:/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install/lib:/usr/local/lib
-          export LD_RUN_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/lib:/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install/lib:/usr/local/lib
-          export PATH=/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install/bin:/usr/local/bin:$PATH
+          export LD_LIBRARY_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.2.0/lib:/home/runner/work/hdf5/hdf5/openmpi-4.1.6-install/lib:/usr/local/lib
+          export LD_RUN_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.2.0/lib:/home/runner/work/hdf5/hdf5/openmpi-4.1.6-install/lib:/usr/local/lib
+          export PATH=/home/runner/work/hdf5/hdf5/openmpi-4.1.6-install/bin:/usr/local/bin:$PATH
           sh ./autogen.sh
           mkdir "${{ runner.workspace }}/build"
           cd "${{ runner.workspace }}/build"
@@ -73,30 +73,30 @@ jobs:
             --enable-build-mode=${{ inputs.build_mode }} \
             --enable-shared \
             --enable-parallel \
-            LDFLAGS="-L/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/lib \
-            -L/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install/lib"
+            LDFLAGS="-L/home/runner/work/hdf5/hdf5/aocc-compiler-4.2.0/lib \
+            -L/home/runner/work/hdf5/hdf5/openmpi-4.1.6-install/lib"
 
       - name: Autotools Build
         shell: bash
         env:
           NPROCS: 2
         run: |
-          export PATH=/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install/bin:/usr/local/bin:$PATH
+          export PATH=/home/runner/work/hdf5/hdf5/openmpi-4.1.6-install/bin:/usr/local/bin:$PATH
           make -j3
         working-directory: ${{ runner.workspace }}/build
 
       - name: Autotools Run Tests
         env:
           NPROCS: 2
         run: |
-          export PATH=/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install/bin:/usr/local/bin:$PATH
+          export PATH=/home/runner/work/hdf5/hdf5/openmpi-4.1.6-install/bin:/usr/local/bin:$PATH
           make check -j
         working-directory: ${{ runner.workspace }}/build
 
       - name: Autotools Install
         env:
           NPROCS: 2
         run: |
-          export PATH=/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install/bin:/usr/local/bin:$PATH
+          export PATH=/home/runner/work/hdf5/hdf5/openmpi-4.1.6-install/bin:/usr/local/bin:$PATH
           make install
         working-directory: ${{ runner.workspace }}/build
diff --git a/.github/workflows/aocc-cmake.yml b/.github/workflows/aocc-cmake.yml
@@ -28,42 +28,42 @@ jobs:
           sudo apt install -y zlib1g-dev libcurl4-openssl-dev libjpeg-dev wget curl bzip2
           sudo apt install -y m4 flex bison cmake libzip-dev openssl build-essential
 
-      - name: Install AOCC 4.1.0
+      - name: Install AOCC 4.2.0
         shell: bash
         run: |
-          wget https://download.amd.com/developer/eula/aocc/aocc-4-1/aocc-compiler-4.1.0.tar
-          tar -xvf aocc-compiler-4.1.0.tar
-          cd aocc-compiler-4.1.0
+          wget https://download.amd.com/developer/eula/aocc/aocc-4-2/aocc-compiler-4.2.0.tar
+          tar -xvf aocc-compiler-4.2.0.tar
+          cd aocc-compiler-4.2.0
           bash install.sh
           source /home/runner/work/hdf5/hdf5/setenv_AOCC.sh
           which clang
           which flang
           clang -v
 
-      - name: Cache OpenMPI 4.1.5 installation
-        id: cache-openmpi-4_1_5
+      - name: Cache OpenMPI 4.1.6 installation
+        id: cache-openmpi-4_1_6
         uses: actions/cache@v4
         with:
-          path: /home/runner/work/hdf5/hdf5/openmpi-4.1.5-install
-          key: ${{ runner.os }}-${{ runner.arch }}-openmpi-4_1_5-cache
+          path: /home/runner/work/hdf5/hdf5/openmpi-4.1.6-install
+          key: ${{ runner.os }}-${{ runner.arch }}-openmpi-4_1_6-cache
 
-      - name: Install OpenMPI 4.1.5
-        if: ${{ steps.cache-openmpi-4_1_5.outputs.cache-hit != 'true' }}
+      - name: Install OpenMPI 4.1.6
+        if: ${{ steps.cache-openmpi-4_1_6.outputs.cache-hit != 'true' }}
         run: |
-          export LD_LIBRARY_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/lib:/usr/local/lib
-          wget https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.5.tar.gz
-          tar zxvf openmpi-4.1.5.tar.gz
-          cd openmpi-4.1.5
-          ./configure CC=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/bin/clang FC=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/bin/flang --prefix=/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install
+          export LD_LIBRARY_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.2.0/lib:/usr/local/lib
+          wget https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.6.tar.gz
+          tar zxvf openmpi-4.1.6.tar.gz
+          cd openmpi-4.1.6
+          ./configure CC=/home/runner/work/hdf5/hdf5/aocc-compiler-4.2.0/bin/clang FC=/home/runner/work/hdf5/hdf5/aocc-compiler-4.2.0/bin/flang --prefix=/home/runner/work/hdf5/hdf5/openmpi-4.1.6-install
           make
           make install
 
       - name: CMake Configure
         shell: bash
         run: |
-          export LD_LIBRARY_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/lib:/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install/lib:/usr/local/lib
-          export LD_RUN_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/lib:/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install/lib:/usr/local/lib
-          export PATH=/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install/bin:/usr/local/bin:$PATH
+          export LD_LIBRARY_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.2.0/lib:/home/runner/work/hdf5/hdf5/openmpi-4.1.6-install/lib:/usr/local/lib
+          export LD_RUN_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.2.0/lib:/home/runner/work/hdf5/hdf5/openmpi-4.1.6-install/lib:/usr/local/lib
+          export PATH=/home/runner/work/hdf5/hdf5/openmpi-4.1.6-install/bin:/usr/local/bin:$PATH
           mkdir "${{ runner.workspace }}/build"
           cd "${{ runner.workspace }}/build"
           CC=mpicc cmake -C $GITHUB_WORKSPACE/config/cmake/cacheinit.cmake -G Ninja \

diff --git a/.github/workflows/cmake-bintest.yml b/.github/workflows/cmake-bintest.yml
@@ -98,7 +98,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Install CMake Dependencies (Linux)
-        run: sudo apt-get install ninja-build doxygen graphviz
+        run: |
+          sudo apt-get update
+          sudo apt-get install ninja-build doxygen graphviz
 
       - name: Set up JDK 19
         uses: actions/setup-java@v4

diff --git a/.github/workflows/cmake-ctest.yml b/.github/workflows/cmake-ctest.yml
@@ -122,7 +122,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Install CMake Dependencies (Linux)
-        run: sudo apt-get install ninja-build graphviz
+        run: |
+          sudo apt-get update
+          sudo apt-get install ninja-build graphviz
 
       - name: Install Dependencies
         uses: ssciwr/doxygen-install@v1
@@ -330,8 +332,9 @@ jobs:
     steps:
       - name: Install CMake Dependencies (Linux S3)
         run: |
-           sudo apt-get install ninja-build doxygen graphviz
-           sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
+          sudo apt-get update
+          sudo apt-get install ninja-build doxygen graphviz
+          sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
 
       - name: Set file base name (Linux S3)
         id: set-file-base
@@ -493,7 +496,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Install CMake Dependencies (Linux_intel)
-        run: sudo apt-get install ninja-build graphviz
+        run: |
+          sudo apt-get update
+          sudo apt-get install ninja-build doxygen graphviz
 
       - name: Install Dependencies
         uses: ssciwr/doxygen-install@v1

diff --git a/.github/workflows/intel-cmake.yml b/.github/workflows/intel-cmake.yml
@@ -22,7 +22,7 @@ jobs:
       - name: Install Dependencies (Linux)
         shell: bash
         run: |
-           sudo apt update
+           sudo apt-get update
            sudo apt-get install ninja-build doxygen graphviz
            sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
 

diff --git a/.github/workflows/julia-cmake.yml b/.github/workflows/julia-cmake.yml
@@ -22,7 +22,7 @@ jobs:
       - name: Install Dependencies
         shell: bash
         run: |
-          sudo apt update
+          sudo apt-get update
           sudo apt-get install ninja-build doxygen graphviz
           sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
           sudo apt install -y libaec-dev zlib1g-dev wget curl bzip2 flex bison cmake libzip-dev openssl build-essential

diff --git a/.github/workflows/main-auto-par-spc.yml b/.github/workflows/main-auto-par-spc.yml
@@ -28,7 +28,7 @@ jobs:
       # libssl, etc. are needed for the ros3 VFD
       - name: Install Linux Dependencies
         run: |
-           sudo apt update
+           sudo apt-get update
            sudo apt-get install ninja-build doxygen graphviz
            sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
            sudo apt install gcc-12 g++-12 gfortran-12
@@ -86,7 +86,7 @@ jobs:
       # libssl, etc. are needed for the ros3 VFD
       - name: Install Linux Dependencies
         run: |
-           sudo apt update
+           sudo apt-get update
            sudo apt-get install ninja-build doxygen graphviz
            sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
            sudo apt install gcc-12 g++-12 gfortran-12

diff --git a/.github/workflows/main-auto-par.yml b/.github/workflows/main-auto-par.yml
@@ -36,7 +36,7 @@ jobs:
       # SETUP
       - name: Install Linux Dependencies
         run: |
-           sudo apt update
+           sudo apt-get update
            sudo apt-get install ninja-build doxygen graphviz
            sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
            sudo apt install gcc-12 g++-12 gfortran-12

diff --git a/.github/workflows/main-auto-spc.yml b/.github/workflows/main-auto-spc.yml
@@ -28,7 +28,7 @@ jobs:
       # libssl, etc. are needed for the ros3 VFD
       - name: Install Linux Dependencies
         run: |
-           sudo apt update
+           sudo apt-get update
            sudo apt-get install ninja-build doxygen graphviz
            sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
            sudo apt install gcc-12 g++-12 gfortran-12
@@ -89,7 +89,7 @@ jobs:
       # libssl, etc. are needed for the ros3 VFD
       - name: Install Linux Dependencies
         run: |
-           sudo apt update
+           sudo apt-get update
            sudo apt-get install ninja-build doxygen graphviz
            sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
            sudo apt install gcc-12 g++-12 gfortran-12
@@ -150,7 +150,7 @@ jobs:
       # libssl, etc. are needed for the ros3 VFD
       - name: Install Linux Dependencies
         run: |
-           sudo apt update
+           sudo apt-get update
            sudo apt-get install ninja-build doxygen graphviz
            sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
            sudo apt install gcc-12 g++-12 gfortran-12
@@ -211,7 +211,7 @@ jobs:
       # libssl, etc. are needed for the ros3 VFD
       - name: Install Linux Dependencies
         run: |
-           sudo apt update
+           sudo apt-get update
            sudo apt-get install ninja-build doxygen graphviz
            sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
            sudo apt install gcc-12 g++-12 gfortran-12
@@ -272,7 +272,7 @@ jobs:
       # libssl, etc. are needed for the ros3 VFD
       - name: Install Linux Dependencies
         run: |
-           sudo apt update
+           sudo apt-get update
            sudo apt-get install ninja-build doxygen graphviz
            sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
            sudo apt install gcc-12 g++-12 gfortran-12
@@ -333,7 +333,7 @@ jobs:
       # libssl, etc. are needed for the ros3 VFD
       - name: Install Linux Dependencies
         run: |
-           sudo apt update
+           sudo apt-get update
            sudo apt-get install ninja-build doxygen graphviz
            sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
            sudo apt install gcc-12 g++-12 gfortran-12
@@ -394,7 +394,7 @@ jobs:
       # libssl, etc. are needed for the ros3 VFD
       - name: Install Linux Dependencies
         run: |
-           sudo apt update
+           sudo apt-get update
            sudo apt-get install ninja-build doxygen graphviz
            sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
            sudo apt install gcc-12 g++-12 gfortran-12
@@ -457,7 +457,7 @@ jobs:
       # libssl, etc. are needed for the ros3 VFD
       - name: Install Linux Dependencies
         run: |
-           sudo apt update
+           sudo apt-get update
            sudo apt-get install ninja-build doxygen graphviz
            sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
            sudo apt install gcc-12 g++-12 gfortran-12

diff --git a/.github/workflows/main-auto.yml b/.github/workflows/main-auto.yml
@@ -37,7 +37,7 @@ jobs:
       # SETUP
       - name: Install Linux Dependencies
         run: |
-           sudo apt update
+           sudo apt-get update
            sudo apt-get install ninja-build doxygen graphviz
            sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
            sudo apt install gcc-12 g++-12 gfortran-12

diff --git a/.github/workflows/main-cmake-par.yml b/.github/workflows/main-cmake-par.yml
@@ -27,7 +27,7 @@ jobs:
 
       - name: Install Linux Dependencies
         run: |
-           sudo apt update
+           sudo apt-get update
            sudo apt-get install ninja-build doxygen graphviz
            sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
            sudo apt install gcc-12 g++-12 gfortran-12

diff --git a/.github/workflows/main-cmake-spc.yml b/.github/workflows/main-cmake-spc.yml
@@ -26,7 +26,7 @@ jobs:
       # SETUP
       - name: Install Linux Dependencies
         run: |
-           sudo apt update
+           sudo apt-get update
            sudo apt-get install ninja-build doxygen graphviz
            sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
            sudo apt install gcc-12 g++-12 gfortran-12
@@ -86,7 +86,7 @@ jobs:
       # SETUP
       - name: Install Linux Dependencies
         run: |
-           sudo apt update
+           sudo apt-get update
            sudo apt-get install ninja-build doxygen graphviz
            sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
            sudo apt install gcc-12 g++-12 gfortran-12
@@ -146,7 +146,7 @@ jobs:
       # SETUP
       - name: Install Linux Dependencies
         run: |
-           sudo apt update
+           sudo apt-get update
            sudo apt-get install ninja-build doxygen graphviz
            sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
            sudo apt install gcc-12 g++-12 gfortran-12

diff --git a/.github/workflows/main-cmake.yml b/.github/workflows/main-cmake.yml
@@ -124,7 +124,7 @@ jobs:
 
       - name: Install CMake Dependencies (Linux)
         run: |
-           sudo apt update
+           sudo apt-get update
            sudo apt-get install ninja-build graphviz
            sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
            sudo apt install gcc-12 g++-12 gfortran-12

diff --git a/.github/workflows/nvhpc-cmake.yml b/.github/workflows/nvhpc-cmake.yml
@@ -22,7 +22,7 @@ jobs:
       - name: Install Dependencies
         shell: bash
         run: |
-          sudo apt update
+          sudo apt-get update
           sudo apt-get install ninja-build doxygen graphviz
           sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
           sudo apt install -y libaec-dev zlib1g-dev wget curl bzip2 flex bison cmake libzip-dev openssl build-essential