Merge branch 'develop' into sub_def

brtnfld · May 20, 2024 · c16fbb9 · c16fbb9
2 parents 5b1d943 + baec5ff
commit c16fbb9
Show file tree

Hide file tree

Showing 15 changed files with 111 additions and 39 deletions.
diff --git a/.github/workflows/cmake-bintest.yml b/.github/workflows/cmake-bintest.yml
@@ -163,7 +163,7 @@ jobs:
       - name: Get published binary (MacOS)
         uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7
         with:
-              name: tgz-osx12-${{ inputs.build_mode }}-binary
+              name: tgz-osx-${{ inputs.build_mode }}-binary
               path: ${{ github.workspace }}
 
       - name: Uncompress hdf5 binary (MacOS)
@@ -189,12 +189,12 @@ jobs:
               ls ${{ runner.workspace }}
 
       # symlinks the compiler executables to a common location 
-      - name: Setup GNU Fortran
-        uses: fortran-lang/setup-fortran@v1
-        id: setup-fortran
-        with:
-          compiler: gcc
-          version: 12
+      # - name: Setup GNU Fortran
+      #   uses: fortran-lang/setup-fortran@v1
+      #   id: setup-fortran
+      #   with:
+      #     compiler: gcc
+      #     version: 12
 
       - name: Run ctest (MacOS)
         id: run-ctest

diff --git a/.github/workflows/cmake-ctest.yml b/.github/workflows/cmake-ctest.yml
@@ -308,7 +308,7 @@ jobs:
           cp ${{ runner.workspace }}/hdf5/build/${{ inputs.preset_name }}-Clang/README.md ${{ runner.workspace }}/build/hdf5
           cp ${{ runner.workspace }}/hdf5/build/${{ inputs.preset_name }}-Clang/*.tar.gz ${{ runner.workspace }}/build/hdf5
           cd "${{ runner.workspace }}/build"
-          tar -zcvf ${{ steps.set-file-base.outputs.FILE_BASE }}-osx12.tar.gz hdf5
+          tar -zcvf ${{ steps.set-file-base.outputs.FILE_BASE }}-osx.tar.gz hdf5
         shell: bash
 
       - name: List files in the space (MacOS)
@@ -320,8 +320,8 @@ jobs:
       - name: Save published binary (MacOS)
         uses: actions/upload-artifact@v4
         with:
-              name: tgz-osx12-binary
-              path: ${{ runner.workspace }}/build/${{ steps.set-file-base.outputs.FILE_BASE }}-osx12.tar.gz
+              name: tgz-osx-binary
+              path: ${{ runner.workspace }}/build/${{ steps.set-file-base.outputs.FILE_BASE }}-osx.tar.gz
               if-no-files-found: error # 'warn' or 'ignore' are also available, defaults to `warn`
 
   build_and_test_S3_linux:

diff --git a/.github/workflows/h5py.yml b/.github/workflows/h5py.yml
@@ -11,11 +11,6 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-    - name: Install Fortran
-      uses: fortran-lang/setup-fortran@v1
-      with:
-        compiler: gcc
-        version: 13
     - name: Checkout Spack
       uses: actions/[email protected]
       with:

diff --git a/.github/workflows/main-cmake.yml b/.github/workflows/main-cmake.yml
@@ -261,7 +261,7 @@ jobs:
       - name: Save published binary (Mac)
         uses: actions/upload-artifact@v4
         with:
-              name: tgz-osx12-${{ inputs.build_mode }}-binary
+              name: tgz-osx-${{ inputs.build_mode }}-binary
               path: ${{ runner.workspace }}/build/HDF5-*-Darwin.tar.gz
               if-no-files-found: error # 'warn' or 'ignore' are also available, defaults to `warn`
         if: ${{ (matrix.os == 'macos-13') && (inputs.thread_safety != 'TS') }}
diff --git a/.github/workflows/release-files.yml b/.github/workflows/release-files.yml
@@ -103,7 +103,7 @@ jobs:
       - name: Get published binary (MacOS)
         uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7
         with:
-              name: tgz-osx12-binary
+              name: tgz-osx-binary
               path: ${{ github.workspace }}
 
       - name: Get published binary (Linux)
@@ -148,12 +148,26 @@ jobs:
               name: abi-reports
               path: ${{ github.workspace }}
 
+      - name: Get published nonversioned source (tgz)
+        if: ${{ (inputs.use_environ == 'release') }}
+        uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7
+        with:
+              name: tgz-tarball-nover
+              path: ${{ github.workspace }}
+
+      - name: Get published nonversioned source (zip)
+        if: ${{ (inputs.use_environ == 'release') }}
+        uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7
+        with:
+              name: zip-tarball-nover
+              path: ${{ github.workspace }}
+
       - name: Create sha256 sums for files
         run: |
           sha256sum ${{ steps.get-file-base.outputs.FILE_BASE }}.doxygen.zip > ${{ steps.get-file-base.outputs.FILE_BASE }}.sha256sums.txt
           sha256sum ${{ steps.get-file-base.outputs.FILE_BASE }}.tar.gz >> ${{ steps.get-file-base.outputs.FILE_BASE }}.sha256sums.txt
           sha256sum ${{ steps.get-file-base.outputs.FILE_BASE }}.zip >> ${{ steps.get-file-base.outputs.FILE_BASE }}.sha256sums.txt
-          sha256sum ${{ steps.get-file-base.outputs.FILE_BASE }}-osx12.tar.gz >> ${{ steps.get-file-base.outputs.FILE_BASE }}.sha256sums.txt
+          sha256sum ${{ steps.get-file-base.outputs.FILE_BASE }}-osx.tar.gz >> ${{ steps.get-file-base.outputs.FILE_BASE }}.sha256sums.txt
           sha256sum ${{ steps.get-file-base.outputs.FILE_BASE }}-ubuntu-2204_gcc.tar.gz >> ${{ steps.get-file-base.outputs.FILE_BASE }}.sha256sums.txt
           sha256sum ${{ steps.get-file-base.outputs.FILE_BASE }}-ubuntu-2204_gcc.deb.tar.gz >> ${{ steps.get-file-base.outputs.FILE_BASE }}.sha256sums.txt
           sha256sum ${{ steps.get-file-base.outputs.FILE_BASE }}-ubuntu-2204_gcc.rpm.tar.gz >> ${{ steps.get-file-base.outputs.FILE_BASE }}.sha256sums.txt
@@ -163,6 +177,11 @@ jobs:
           sha256sum ${{ steps.get-file-base.outputs.FILE_BASE }}-win-vs2022_intel.zip >> ${{ steps.get-file-base.outputs.FILE_BASE }}.sha256sums.txt
           sha256sum ${{ steps.get-file-base.outputs.FILE_BASE }}.html.abi.reports.tar.gz >> ${{ steps.get-file-base.outputs.FILE_BASE }}.sha256sums.txt
 
+      - name: Create sha256 sums for files  for nonversioned files
+        run: |
+          sha256sum hdf5.zip >> ${{ steps.get-file-base.outputs.FILE_BASE }}.sha256sums.txt
+          sha256sum hdf5.tar.gz >> ${{ steps.get-file-base.outputs.FILE_BASE }}.sha256sums.txt
+
       - name: Store snapshot name
         run: |
           echo "${{ steps.get-file-base.outputs.FILE_BASE }}" > ./last-file.txt
@@ -190,7 +209,7 @@ jobs:
               ${{ 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 }}-osx.tar.gz
               ${{ steps.get-file-base.outputs.FILE_BASE }}-ubuntu-2204_gcc.tar.gz
               ${{ steps.get-file-base.outputs.FILE_BASE }}-ubuntu-2204_gcc.deb.tar.gz
               ${{ steps.get-file-base.outputs.FILE_BASE }}-ubuntu-2204_gcc.rpm.tar.gz
@@ -214,7 +233,9 @@ jobs:
               ${{ 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
+              hdf5.tar.gz
+              hdf5.zip
+              ${{ steps.get-file-base.outputs.FILE_BASE }}-osx.tar.gz
               ${{ steps.get-file-base.outputs.FILE_BASE }}-ubuntu-2204_gcc.tar.gz
               ${{ steps.get-file-base.outputs.FILE_BASE }}-ubuntu-2204_gcc.deb.tar.gz
               ${{ steps.get-file-base.outputs.FILE_BASE }}-ubuntu-2204_gcc.rpm.tar.gz

diff --git a/.github/workflows/remove-files.yml b/.github/workflows/remove-files.yml
@@ -50,7 +50,7 @@ jobs:
               ${{ 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 }}-osx.tar.gz
               ${{ steps.get-file-base.outputs.FILE_BASE }}-ubuntu-2204_gcc.tar.gz
               ${{ steps.get-file-base.outputs.FILE_BASE }}-ubuntu-2204_gcc.deb.tar.gz
               ${{ steps.get-file-base.outputs.FILE_BASE }}-ubuntu-2204_gcc.rpm.tar.gz

diff --git a/.github/workflows/tarball.yml b/.github/workflows/tarball.yml
@@ -144,6 +144,14 @@ jobs:
           mv hdf5-${{ steps.version.outputs.SOURCE_TAG }}.zip ${{ inputs.use_tag }}.zip
         shell: bash
 
+      - name: Copy the release file source to a non-versioned file name
+        id: cp-to-non-versioned
+        if: ${{ (inputs.use_environ == 'release') }}
+        run: |
+          cp ${{ inputs.use_tag }}.tar.gz hdf5.tar.gz
+          cp ${{ inputs.use_tag }}.zip hdf5.zip
+        shell: bash
+
       - name: List files in the repository
         run: |
               ls -l ${{ github.workspace }}
@@ -164,6 +172,22 @@ jobs:
               path: ${{ steps.set-file-base.outputs.FILE_BASE }}.zip
               if-no-files-found: error # 'warn' or 'ignore' are also available, defaults to `warn`
 
+      - name: Save tgz-tarball-nover
+        if: ${{ (inputs.use_environ == 'release') }}
+        uses: actions/upload-artifact@v4
+        with:
+              name: tgz-tarball-nover
+              path: hdf5.tar.gz
+              if-no-files-found: error # 'warn' or 'ignore' are also available, defaults to `warn`
+
+      - name: Save zip-tarball-nover
+        if: ${{ (inputs.use_environ == 'release') }}
+        uses: actions/upload-artifact@v4
+        with:
+              name: zip-tarball-nover
+              path: hdf5.zip
+              if-no-files-found: error # 'warn' or 'ignore' are also available, defaults to `warn`
+
       - name: Save NEWSLETTER
         uses: actions/upload-artifact@v4
         with:

diff --git a/configure.ac b/configure.ac
@@ -4613,5 +4613,12 @@ if test "X$HDF_FORTRAN" = "Xyes"; then
   esac
 fi
 
+## HDF5 configure code created by autotools with gcc 4.9.2 is adding problematic
+## linker flags:  -l with no library name; -l <libname>, specifically gfortran or m.
+## This sed script corrects "-l <libname>" first and then "-l " with no library name.
+## If the order is not preserved, all instances of "-l " will be removed.
+sed -e '/^postdeps/ s/-l \([a-zA-Z]\)/-l\1/g' -e '/^postdeps/ s/-l //g' libtool > libtool.bak
+mv -- libtool.bak libtool
+
 ## show the configure settings
 cat src/libhdf5.settings
diff --git a/doxygen/dox/VOLConnGuide.dox b/doxygen/dox/VOLConnGuide.dox
@@ -306,6 +306,13 @@ it may be some time before that work is complete.
 \subsection subsecVOLPassthrough Passthrough Connectors
 Coming Soon
 
+Note: 
+Passthrough VOL connectors should avoid doing anything with the file in the open and create 
+callbacks except opening it. If connectors need to do anything else they should use the post 
+open callback (H5VL_NATIVE_FILE_POST_OPEN op_type for the file "optional" callback), 
+making sure to perform operations on the file only after passing the post open call down to 
+the terminal connector.  The post open callback is made for both file open and file create calls.
+
 \subsection subsecVOLAsync Asynchronous Operations
 Coming Soon
 

diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
@@ -1674,6 +1674,22 @@ Bug Fixes since HDF5-1.14.0 release
 
     Configuration
     -------------
+    - Fixed/reverted an Autotools configure hack that causes problems on MacOS
+
+      A sed line in configure.ac was added in the past to paper over some
+      problems with older versions of the Autotools that would add incorrect
+      linker flags. This used the -i option in a way that caused silent
+      errors on MacOS that did not break the build.
+
+      The original fix for this problem (in 1.14.4) removed the sed line
+      entirely, but it turns out that the sed cleanup is still necessary
+      on some systems, where empty -l options will be added to the libtool
+      script.
+
+      This sed line has been restored and reworked to not use -i.
+
+      Fixes GitHub issues #3843 and #4448
+
     - Fixed a list index out of range issue in the runTest.cmake file
 
       Fixed an issue in config/cmake/runTest.cmake where the CMake logic
@@ -1701,16 +1717,6 @@ Bug Fixes since HDF5-1.14.0 release
         * HDF5_ENABLE_DOXY_WARNINGS: ON/OFF (Default: OFF)
         * --enable-doxygen-errors: enable/disable (Default: disable)
 
-    - Removed an Autotools configure hack that causes problems on MacOS
-
-      A sed line in configure.ac was added in the past to paper over some
-      problems with older versions of the Autotools that would add incorrect
-      linker flags. This hack is not needed with recent versions of the
-      Autotools and the sed line errors on MacOS (though this was a silent
-      error that didn't break the build) so the hack has been removed.
-
-      Fixes GitHub issue #3843
-
     - Fixed an issue where the h5tools_test_utils test program was being
       installed on the system for Autotools builds of HDF5
 

diff --git a/src/H5Adense.c b/src/H5Adense.c
@@ -839,6 +839,7 @@ H5A__dense_rename(H5F_t *f, const H5O_ainfo_t *ainfo, const char *old_name, cons
     htri_t              attr_sharable;       /* Flag indicating attributes are shareable */
     htri_t              shared_mesg;         /* Should this message be stored in the Shared Message table? */
     bool                attr_exists;         /* Attribute exists in v2 B-tree */
+    H5O_ainfo_t         tainfo    = *ainfo;  /* Copy of ainfo */
     herr_t              ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_PACKAGE
@@ -977,8 +978,12 @@ H5A__dense_rename(H5F_t *f, const H5O_ainfo_t *ainfo, const char *old_name, cons
     else if (shared_mesg < 0)
         HGOTO_ERROR(H5E_ATTR, H5E_WRITEERROR, FAIL, "error determining if message should be shared");
 
-    /* Delete old attribute from dense storage */
-    if (H5A__dense_remove(f, ainfo, old_name) < 0)
+    /* Deactivate the field so that H5A__dense_remove() won't delete the new renamed attribute
+       that was just added to the creation order index v2 B-tree via H5A__dense_insert() */
+    tainfo.corder_bt2_addr = HADDR_UNDEF;
+
+    /* Only delete the old attribute (before rename) from the name index v2 B-tree */
+    if (H5A__dense_remove(f, (const H5O_ainfo_t *)&tainfo, old_name) < 0)
         HGOTO_ERROR(H5E_ATTR, H5E_CANTDELETE, FAIL, "unable to delete attribute in dense storage");
 
 done:

diff --git a/src/H5Fpkg.h b/src/H5Fpkg.h
@@ -131,6 +131,10 @@
     (H5F_SUPERBLOCK_FIXED_SIZE +                                                                             \
      H5F_SUPERBLOCK_VARLEN_SIZE((s)->super_vers, (s)->sizeof_addr, (s)->sizeof_size))
 
+/* Optimistic read size for superblock */
+/* Size of a v2+ superblock, w/8-byte addresses & lengths */
+#define H5F_SUPERBLOCK_SPEC_READ_SIZE (H5F_SUPERBLOCK_FIXED_SIZE + H5F_SUPERBLOCK_VARLEN_SIZE(2, 8, 8))
+
 /* For superblock version 0 & 1:
    Offset to the file consistency flags (status_flags) in the superblock (excluding H5F_SUPERBLOCK_FIXED_SIZE)
  */

diff --git a/src/H5Fsuper.c b/src/H5Fsuper.c
@@ -416,8 +416,7 @@ H5F__super_read(H5F_t *f, H5P_genplist_t *fa_plist, bool initial_read)
         HGOTO_ERROR(H5E_FILE, H5E_BADTYPE, FAIL, "can't get property list");
 
     /* Make certain we can read the fixed-size portion of the superblock */
-    if (H5F__set_eoa(f, H5FD_MEM_SUPER,
-                     (haddr_t)(H5F_SUPERBLOCK_FIXED_SIZE + H5F_SUPERBLOCK_MINIMAL_VARLEN_SIZE)) < 0)
+    if (H5F__set_eoa(f, H5FD_MEM_SUPER, (haddr_t)H5F_SUPERBLOCK_SPEC_READ_SIZE) < 0)
         HGOTO_ERROR(H5E_FILE, H5E_CANTSET, FAIL, "set end of space allocation request failed");
 
     /* Set up the user data for cache callbacks */

diff --git a/src/H5Fsuper_cache.c b/src/H5Fsuper_cache.c
@@ -306,8 +306,7 @@ H5F__cache_superblock_get_initial_load_size(void H5_ATTR_UNUSED *_udata, size_t
     assert(image_len);
 
     /* Set the initial image length size */
-    *image_len = H5F_SUPERBLOCK_FIXED_SIZE + /* Fixed size of superblock */
-                 H5F_SUPERBLOCK_MINIMAL_VARLEN_SIZE;
+    *image_len = H5F_SUPERBLOCK_SPEC_READ_SIZE;
 
     FUNC_LEAVE_NOAPI(SUCCEED)
 } /* end H5F__cache_superblock_get_initial_load_size() */

diff --git a/test/tattr.c b/test/tattr.c
@@ -2898,6 +2898,11 @@ test_attr_dense_rename(hid_t fcpl, hid_t fapl)
             VERIFY(is_dense, true, "H5O__is_attr_dense_test");
         }
 
+        /* Verify github issue #1388 that the last renamed attribute
+           with/without tracking corder can be deleted */
+        ret = H5Adelete(dataset, new_attrname);
+        CHECK(ret, FAIL, "H5Adelete");
+
         /* Close Dataset */
         ret = H5Dclose(dataset);
         CHECK(ret, FAIL, "H5Dclose");
@@ -2930,8 +2935,8 @@ test_attr_dense_rename(hid_t fcpl, hid_t fapl)
     dataset = H5Dopen2(fid, DSET1_NAME, H5P_DEFAULT);
     CHECK(dataset, H5I_INVALID_HID, "H5Dopen2");
 
-    /* Verify renamed attributes */
-    for (u = 0; u < (max_compact * 2); u++) {
+    /* Verify renamed attributes (the last attribute was deleted) */
+    for (u = 0; u < (max_compact * 2 - 1); u++) {
         unsigned value; /* Attribute value */
 
         /* Open attribute */