Merge pull request #4025 from lrknox/1_14_dev_sync3_lrk

Sync more develop changes to hdf5_1_14

.github/workflows/cmake-ctest.yml

@@ -79,7 +79,7 @@ jobs:
           Copy-Item -Path ${{ runner.workspace }}/hdf5/hdfsrc/COPYING -Destination ${{ runner.workspace }}/build114/hdf5/
           Copy-Item -Path ${{ runner.workspace }}/hdf5/hdfsrc/COPYING_LBNL_HDF5 -Destination ${{ runner.workspace }}/build114/hdf5/
           Copy-Item -Path ${{ runner.workspace }}/hdf5/hdfsrc/README.md -Destination ${{ runner.workspace }}/build114/hdf5/
-          Copy-Item -Path ${{ runner.workspace }}/hdf5/build114/ci-StdShar-MSVC/* -Destination ${{ runner.workspace }}/build114/hdf5/ -Include *.zip
+          Copy-Item -Path ${{ runner.workspace }}/hdf5/build114/${{ inputs.preset_name }}-MSVC/* -Destination ${{ runner.workspace}}/build114/hdf5/ -Include *.zip
           cd "${{ runner.workspace }}/build114"
           7z a -tzip ${{ steps.set-file-base.outputs.FILE_BASE }}-win-vs2022_cl.zip hdf5
         shell: pwsh
@@ -147,7 +147,7 @@ jobs:
           cp ${{ runner.workspace }}/hdf5/hdfsrc/COPYING ${{ runner.workspace }}/build114/hdf5
           cp ${{ runner.workspace }}/hdf5/hdfsrc/COPYING_LBNL_HDF5 ${{ runner.workspace }}/build114/hdf5
           cp ${{ runner.workspace }}/hdf5/hdfsrc/README.md ${{ runner.workspace }}/build114/hdf5
-          cp ${{ runner.workspace }}/hdf5/build114/ci-StdShar-GNUC/*.tar.gz ${{ runner.workspace }}/build114/hdf5
+          cp ${{ runner.workspace }}/hdf5/build114/${{ inputs.preset_name }}-GNUC/*.tar.gz ${{ runner.workspace }}/build114/hdf5
           cd "${{ runner.workspace }}/build114"
           tar -zcvf ${{ steps.set-file-base.outputs.FILE_BASE }}-ubuntu-2204_gcc.tar.gz hdf5
         shell: bash
@@ -170,7 +170,7 @@ jobs:
         uses: actions/upload-artifact@v4
         with:
               name: docs-doxygen
-              path: ${{ runner.workspace }}/hdf5/build114/ci-StdShar-GNUC/hdf5lib_docs/html
+              path: ${{ runner.workspace }}/hdf5/build114/${{ inputs.preset_name }}-GNUC/hdf5lib_docs/html
               if-no-files-found: error # 'warn' or 'ignore' are also available, defaults to `warn`
 
   build_and_test_mac:
@@ -232,7 +232,7 @@ jobs:
           cp ${{ runner.workspace }}/hdf5/hdfsrc/COPYING ${{ runner.workspace }}/build114/hdf5
           cp ${{ runner.workspace }}/hdf5/hdfsrc/COPYING_LBNL_HDF5 ${{ runner.workspace }}/build114/hdf5
           cp ${{ runner.workspace }}/hdf5/hdfsrc/README.md ${{ runner.workspace }}/build114/hdf5
-          cp ${{ runner.workspace }}/hdf5/build114/ci-StdShar-Clang/*.tar.gz ${{ runner.workspace }}/build114/hdf5
+          cp ${{ runner.workspace }}/hdf5/build114/${{ inputs.preset_name }}-Clang/*.tar.gz ${{ runner.workspace }}/build114/hdf5
           cd "${{ runner.workspace }}/build114"
           tar -zcvf ${{ steps.set-file-base.outputs.FILE_BASE }}-osx12.tar.gz hdf5
         shell: bash

.github/workflows/daily-build.yml

@@ -12,6 +12,26 @@ permissions:
 # A workflow run is made up of one or more jobs that can run sequentially or
 # in parallel.
 jobs:
+  get-old-names:
+    runs-on: ubuntu-latest
+    outputs:
+      hdf5-name: ${{ steps.gethdf5base.outputs.HDF5_NAME_BASE }}
+
+    steps:
+    - uses: actions/[email protected]
+
+    - name: Get hdf5 release base name
+      uses: dsaltares/fetch-gh-release-asset@master
+      with:
+        version: 'tags/snapshot-1.14'
+        file: 'last-file.txt'
+
+    - name: Read base-name file
+      id: gethdf5base
+      run: echo "HDF5_NAME_BASE=$(cat last-file.txt)" >> $GITHUB_OUTPUT
+
+    - run: echo "hdf5 base name is ${{ steps.gethdf5base.outputs.HDF5_NAME_BASE }}."
+
   call-workflow-tarball:
     uses: ./.github/workflows/tarball.yml
     with:
@@ -23,6 +43,7 @@ jobs:
     uses: ./.github/workflows/cmake-ctest.yml
     with:
       file_base: ${{ needs.call-workflow-tarball.outputs.file_base }}
+      preset_name: ci-StdShar
       #use_tag: snapshot-1.14
       #use_environ: snapshots
     if: ${{ needs.call-workflow-tarball.outputs.has_changes == 'true' }}
@@ -50,3 +71,14 @@ jobs:
       use_environ: snapshots
     if: ${{ needs.call-workflow-tarball.outputs.has_changes == 'true' }}
 
+  call-workflow-remove:
+    needs: [get-old-names, call-workflow-tarball, call-workflow-ctest, call-workflow-abi, call-workflow-release]
+    permissions:
+      contents: write # In order to allow file deletion
+    uses: ./.github/workflows/remove-files.yml
+    with:
+      file_base: ${{ needs.get-old-names.outputs.hdf5-name }}
+      use_tag: snapshot-1.14
+      use_environ: snapshots
+    if: ${{ needs.call-workflow-tarball.outputs.has_changes == 'true' }}
+

.github/workflows/release.yml

@@ -96,7 +96,6 @@ jobs:
       use_environ: release
 
   call-workflow-release:
-    #needs: [call-workflow-tarball, call-workflow-ctest]
     needs: [log-the-inputs, create-files-ctest, call-workflow-ctest, call-workflow-abi]
     permissions:
       contents: write # In order to allow tag creation

.github/workflows/remove-files.yml

@@ -0,0 +1,60 @@
+name: hdf5 dev remove-files
+
+# Controls when the action will run. Triggers the workflow on a schedule
+on:
+  workflow_call:
+    inputs:
+      use_tag:
+        description: 'Release version tag'
+        type: string
+        required: false
+        default: snapshot
+      use_environ:
+        description: 'Environment to locate files'
+        type: string
+        required: true
+        default: snapshots
+      file_base:
+        description: "The common base name of the source tarballs"
+        required: true
+        type: string
+
+# Minimal permissions to be inherited by any job that doesn't declare its own permissions
+permissions:
+  contents: read
+
+# Previous workflows must pass to get here so tag the commit that created the files
+jobs:
+  PreRelease-delfiles:
+    runs-on: ubuntu-latest
+    environment: ${{ inputs.use_environ }}
+    permissions:
+        contents: write
+    steps:
+      - name: Get file base name
+        id: get-file-base
+        run: |
+          FILE_NAME_BASE=$(echo "${{ inputs.file_base }}")
+          echo "FILE_BASE=$FILE_NAME_BASE" >> $GITHUB_OUTPUT
+
+      - name: PreRelease delete from tag
+        id: delete_prerelease
+        if: ${{ (inputs.use_environ == 'snapshots') }}
+        uses: mknejp/delete-release-assets@v1
+        with:
+          token: ${{ github.token }}
+          tag: "${{ inputs.use_tag }}"
+          assets: |
+              ${{ steps.get-file-base.outputs.FILE_BASE }}-hdf5_compat_report.html
+              ${{ steps.get-file-base.outputs.FILE_BASE }}-hdf5_hl_compat_report.html
+              ${{ steps.get-file-base.outputs.FILE_BASE }}-hdf5_cpp_compat_report.html
+              ${{ steps.get-file-base.outputs.FILE_BASE }}-java_compat_report.html
+              ${{ steps.get-file-base.outputs.FILE_BASE }}.doxygen.zip
+              ${{ steps.get-file-base.outputs.FILE_BASE }}.tar.gz
+              ${{ steps.get-file-base.outputs.FILE_BASE }}.zip
+              ${{ steps.get-file-base.outputs.FILE_BASE }}-osx12.tar.gz
+              ${{ steps.get-file-base.outputs.FILE_BASE }}-ubuntu-2204_gcc.tar.gz
+              ${{ steps.get-file-base.outputs.FILE_BASE }}-ubuntu-2204_gcc_s3.tar.gz
+              ${{ steps.get-file-base.outputs.FILE_BASE }}-win-vs2022_cl.zip
+              ${{ steps.get-file-base.outputs.FILE_BASE }}-ubuntu-2204_intel.tar.gz
+              ${{ steps.get-file-base.outputs.FILE_BASE }}-win-vs2022_intel.zip

HDF5Examples/C/H5PAR/ph5_dataset.c

@@ -53,6 +53,24 @@ main(int argc, char **argv)
     plist_id = H5Pcreate(H5P_FILE_ACCESS);
     H5Pset_fapl_mpio(plist_id, comm, info);
 
+    /*
+     * OPTIONAL: It is generally recommended to set collective
+     *           metadata reads on FAPL to perform metadata reads
+     *           collectively, which usually allows datasets
+     *           to perform better at scale, although it is not
+     *           strictly necessary.
+     */
+    H5Pset_all_coll_metadata_ops(plist_id, true);
+
+    /*
+     * OPTIONAL: It is generally recommended to set collective
+     *           metadata writes on FAPL to perform metadata writes
+     *           collectively, which usually allows datasets
+     *           to perform better at scale, although it is not
+     *           strictly necessary.
+     */
+    H5Pset_coll_metadata_write(plist_id, true);
+
     /*
      * Create a new file collectively and release property list identifier.
      */

HDF5Examples/C/H5PAR/ph5_file_create.c

@@ -36,6 +36,24 @@ main(int argc, char **argv)
     plist_id = H5Pcreate(H5P_FILE_ACCESS);
     H5Pset_fapl_mpio(plist_id, comm, info);
 
+    /*
+     * OPTIONAL: It is generally recommended to set collective
+     *           metadata reads on FAPL to perform metadata reads
+     *           collectively, which usually allows datasets
+     *           to perform better at scale, although it is not
+     *           strictly necessary.
+     */
+    H5Pset_all_coll_metadata_ops(plist_id, true);
+
+    /*
+     * OPTIONAL: It is generally recommended to set collective
+     *           metadata writes on FAPL to perform metadata writes
+     *           collectively, which usually allows datasets
+     *           to perform better at scale, although it is not
+     *           strictly necessary.
+     */
+    H5Pset_coll_metadata_write(plist_id, true);
+
     /*
      * Create a new file collectively.
      */

HDF5Examples/C/H5PAR/ph5_filtered_writes.c

@@ -377,13 +377,23 @@ main(int argc, char **argv)
     H5Pset_fapl_mpio(fapl_id, comm, info);
 
     /*
-     * OPTIONAL: Set collective metadata reads on FAPL to allow
-     *           parallel writes to filtered datasets to perform
-     *           better at scale. While not strictly necessary,
-     *           this is generally recommended.
+     * OPTIONAL: It is generally recommended to set collective
+     *           metadata reads on FAPL to perform metadata reads
+     *           collectively, which usually allows filtered datasets
+     *           to perform better at scale, although it is not
+     *           strictly necessary.
      */
     H5Pset_all_coll_metadata_ops(fapl_id, true);
 
+    /*
+     * OPTIONAL: It is generally recommended to set collective
+     *           metadata writes on FAPL to perform metadata writes
+     *           collectively, which usually allows filtered datasets
+     *           to perform better at scale, although it is not
+     *           strictly necessary.
+     */
+    H5Pset_coll_metadata_write(fapl_id, true);
+
     /*
      * OPTIONAL: Set the latest file format version for HDF5 in
      *           order to gain access to different dataset chunk

HDF5Examples/C/H5PAR/ph5_filtered_writes_no_sel.c

@@ -271,13 +271,23 @@ main(int argc, char **argv)
     H5Pset_fapl_mpio(fapl_id, comm, info);
 
     /*
-     * OPTIONAL: Set collective metadata reads on FAPL to allow
-     *           parallel writes to filtered datasets to perform
-     *           better at scale. While not strictly necessary,
-     *           this is generally recommended.
+     * OPTIONAL: It is generally recommended to set collective
+     *           metadata reads on FAPL to perform metadata reads
+     *           collectively, which usually allows filtered datasets
+     *           to perform better at scale, although it is not
+     *           strictly necessary.
      */
     H5Pset_all_coll_metadata_ops(fapl_id, true);
 
+    /*
+     * OPTIONAL: It is generally recommended to set collective
+     *           metadata writes on FAPL to perform metadata writes
+     *           collectively, which usually allows filtered datasets
+     *           to perform better at scale, although it is not
+     *           strictly necessary.
+     */
+    H5Pset_coll_metadata_write(fapl_id, true);
+
     /*
      * OPTIONAL: Set the latest file format version for HDF5 in
      *           order to gain access to different dataset chunk

HDF5Examples/C/H5PAR/ph5_hyperslab_by_chunk.c

@@ -64,6 +64,24 @@ main(int argc, char **argv)
     plist_id = H5Pcreate(H5P_FILE_ACCESS);
     H5Pset_fapl_mpio(plist_id, comm, info);
 
+    /*
+     * OPTIONAL: It is generally recommended to set collective
+     *           metadata reads on FAPL to perform metadata reads
+     *           collectively, which usually allows datasets
+     *           to perform better at scale, although it is not
+     *           strictly necessary.
+     */
+    H5Pset_all_coll_metadata_ops(plist_id, true);
+
+    /*
+     * OPTIONAL: It is generally recommended to set collective
+     *           metadata writes on FAPL to perform metadata writes
+     *           collectively, which usually allows datasets
+     *           to perform better at scale, although it is not
+     *           strictly necessary.
+     */
+    H5Pset_coll_metadata_write(plist_id, true);
+
     /*
      * Create a new file collectively and release property list identifier.
      */

HDF5Examples/C/H5PAR/ph5_hyperslab_by_col.c

@@ -59,6 +59,24 @@ main(int argc, char **argv)
     plist_id = H5Pcreate(H5P_FILE_ACCESS);
     H5Pset_fapl_mpio(plist_id, comm, info);
 
+    /*
+     * OPTIONAL: It is generally recommended to set collective
+     *           metadata reads on FAPL to perform metadata reads
+     *           collectively, which usually allows datasets
+     *           to perform better at scale, although it is not
+     *           strictly necessary.
+     */
+    H5Pset_all_coll_metadata_ops(plist_id, true);
+
+    /*
+     * OPTIONAL: It is generally recommended to set collective
+     *           metadata writes on FAPL to perform metadata writes
+     *           collectively, which usually allows datasets
+     *           to perform better at scale, although it is not
+     *           strictly necessary.
+     */
+    H5Pset_coll_metadata_write(plist_id, true);
+
     /*
      * Create a new file collectively and release property list identifier.
      */

HDF5Examples/C/H5PAR/ph5_hyperslab_by_pattern.c

@@ -64,6 +64,24 @@ main(int argc, char **argv)
     plist_id = H5Pcreate(H5P_FILE_ACCESS);
     H5Pset_fapl_mpio(plist_id, comm, info);
 
+    /*
+     * OPTIONAL: It is generally recommended to set collective
+     *           metadata reads on FAPL to perform metadata reads
+     *           collectively, which usually allows datasets
+     *           to perform better at scale, although it is not
+     *           strictly necessary.
+     */
+    H5Pset_all_coll_metadata_ops(plist_id, true);
+
+    /*
+     * OPTIONAL: It is generally recommended to set collective
+     *           metadata writes on FAPL to perform metadata writes
+     *           collectively, which usually allows datasets
+     *           to perform better at scale, although it is not
+     *           strictly necessary.
+     */
+    H5Pset_coll_metadata_write(plist_id, true);
+
     /*
      * Create a new file collectively and release property list identifier.
      */

HDF5Examples/C/H5PAR/ph5_hyperslab_by_row.c

@@ -48,6 +48,24 @@ main(int argc, char **argv)
     plist_id = H5Pcreate(H5P_FILE_ACCESS);
     H5Pset_fapl_mpio(plist_id, comm, info);
 
+    /*
+     * OPTIONAL: It is generally recommended to set collective
+     *           metadata reads on FAPL to perform metadata reads
+     *           collectively, which usually allows datasets
+     *           to perform better at scale, although it is not
+     *           strictly necessary.
+     */
+    H5Pset_all_coll_metadata_ops(plist_id, true);
+
+    /*
+     * OPTIONAL: It is generally recommended to set collective
+     *           metadata writes on FAPL to perform metadata writes
+     *           collectively, which usually allows datasets
+     *           to perform better at scale, although it is not
+     *           strictly necessary.
+     */
+    H5Pset_coll_metadata_write(plist_id, true);
+
     /*
      * Create a new file collectively and release property list identifier.
      */

HDF5Examples/C/H5PAR/ph5example.c

@@ -269,6 +269,24 @@ phdf5writeInd(char *filename)
     assert(ret != FAIL);
     MESG("H5Pset_fapl_mpio succeed");
 
+    /*
+     * OPTIONAL: It is generally recommended to set collective
+     *           metadata reads on FAPL to perform metadata reads
+     *           collectively, which usually allows datasets
+     *           to perform better at scale, although it is not
+     *           strictly necessary.
+     */
+    H5Pset_all_coll_metadata_ops(acc_tpl1, true);
+
+    /*
+     * OPTIONAL: It is generally recommended to set collective
+     *           metadata writes on FAPL to perform metadata writes
+     *           collectively, which usually allows datasets
+     *           to perform better at scale, although it is not
+     *           strictly necessary.
+     */
+    H5Pset_coll_metadata_write(acc_tpl1, true);
+
     /* create the file collectively */
     fid1 = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, acc_tpl1);
     assert(fid1 != FAIL);