Merge remote-tracking branch 'origin/develop' into threading_updates

qkoziol · Apr 2, 2024 · 64851bc · 64851bc
2 parents 13cd597 + f2cf0be
commit 64851bc
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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 doxygen graphviz
+        run: |
+          sudo apt-get update
+          sudo apt-get install ninja-build doxygen graphviz
 
       - name: add oneAPI to env
         uses: fortran-lang/setup-fortran@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
@@ -206,7 +206,7 @@ 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

diff --git a/.github/workflows/release-files.yml b/.github/workflows/release-files.yml
@@ -167,7 +167,7 @@ jobs:
           echo "${{ steps.get-file-base.outputs.FILE_BASE }}" > ./last-file.txt
 
       - name: Get NEWSLETTER
-        uses: actions/download-artifact@6b208ae046db98c579e8a3aa621ab581ff575935 # v4.1.1
+        uses: actions/download-artifact@c850b930e6ba138125429b7e5c93fc707a7f8427 # v4.1.4
         with:
               name: NEWSLETTER
               path: ${{ github.workspace }}
@@ -179,7 +179,7 @@ jobs:
       - name: PreRelease tag
         id: create_prerelease
         if: ${{ (inputs.use_environ == 'snapshots') }}
-        uses: softprops/action-gh-release@de2c0eb89ae2a093876385947365aca7b0e5f844 # v1
+        uses: softprops/action-gh-release@9d7c94cfd0a1f3ed45544c887983e9fa900f0564 # v2.0.4
         with:
           tag_name: "${{ inputs.use_tag }}"
           prerelease: true
@@ -204,7 +204,7 @@ jobs:
       - name: Release tag
         id: create_release
         if: ${{ (inputs.use_environ == 'release') }}
-        uses: softprops/action-gh-release@de2c0eb89ae2a093876385947365aca7b0e5f844 # v1
+        uses: softprops/action-gh-release@9d7c94cfd0a1f3ed45544c887983e9fa900f0564 # v2.0.4
         with:
           tag_name: "${{ inputs.use_tag }}"
           prerelease: false

diff --git a/.github/workflows/scorecard.yml b/.github/workflows/scorecard.yml
@@ -67,6 +67,6 @@ jobs:
 
       # Upload the results to GitHub's code scanning dashboard.
       - name: "Upload to code-scanning"
-        uses: github/codeql-action/upload-sarif@8a470fddafa5cbb6266ee11b37ef4d8aae19c571 # v3.24.6
+        uses: github/codeql-action/upload-sarif@1b1aada464948af03b950897e5eb522f92603cc2 # v3.24.9
         with:
           sarif_file: results.sarif
diff --git a/.github/workflows/testxpr.yml b/.github/workflows/testxpr.yml
@@ -45,7 +45,7 @@ jobs:
     steps:
       - 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/vfd-subfiling.yml b/.github/workflows/vfd-subfiling.yml
@@ -47,7 +47,7 @@ jobs:
     steps:
       - name: Install Linux Dependencies
         run: |
-          sudo apt update
+          sudo apt-get update
           sudo apt-get install automake autoconf libtool libtool-bin
         if: ${{ matrix.os == 'ubuntu-latest' }}
 
@@ -56,14 +56,14 @@ jobs:
       # versions of each, then build and cache those installations
       - name: Install OpenMPI
         run: |
-          sudo apt update
+          sudo apt-get update
           sudo apt-get install libopenmpi-dev
           echo "CC=mpicc" >> $GITHUB_ENV
         if: ${{ matrix.os == 'ubuntu-latest' && matrix.mpi_lib == 'OpenMPI' }}
 
       - name: Install MPICH
         run: |
-          sudo apt update
+          sudo apt-get update
           sudo apt-get install libmpich-dev
           echo "CC=mpicc" >> $GITHUB_ENV
         if: ${{ matrix.os == 'ubuntu-latest' && matrix.mpi_lib == 'MPICH' }}

diff --git a/.github/workflows/vol_adios2.yml b/.github/workflows/vol_adios2.yml
@@ -22,7 +22,7 @@ jobs:
     steps:
       - name: Install dependencies
         run: |
-          sudo apt update
+          sudo apt-get update
           sudo apt-get install automake autoconf libtool libtool-bin libopenmpi-dev
 
       - name: Checkout HDF5

diff --git a/.github/workflows/vol_async.yml b/.github/workflows/vol_async.yml
@@ -18,7 +18,7 @@ jobs:
     steps:
       - name: Install dependencies
         run: |
-          sudo apt update
+          sudo apt-get update
           sudo apt-get install automake autoconf libtool libtool-bin libopenmpi-dev
 
       - name: Checkout HDF5

diff --git a/.github/workflows/vol_cache.yml b/.github/workflows/vol_cache.yml
@@ -31,7 +31,7 @@ jobs:
     steps:
       - name: Install dependencies
         run: |
-          sudo apt update
+          sudo apt-get update
           sudo apt-get install automake autoconf libtool libtool-bin libopenmpi-dev
 
       - name: Checkout HDF5

diff --git a/.github/workflows/vol_ext_passthru.yml b/.github/workflows/vol_ext_passthru.yml
@@ -18,7 +18,7 @@ jobs:
     steps:
       - name: Install dependencies
         run: |
-          sudo apt update
+          sudo apt-get update
           sudo apt-get install automake autoconf libtool libtool-bin libopenmpi-dev
 
       - name: Checkout HDF5

diff --git a/.github/workflows/vol_log.yml b/.github/workflows/vol_log.yml
@@ -18,7 +18,7 @@ jobs:
     steps:
       - name: Install dependencies
         run: |
-          sudo apt update
+          sudo apt-get update
           sudo apt-get install automake autoconf libtool libtool-bin libopenmpi-dev zlib1g-dev
           #mpich
 

diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
@@ -746,6 +746,15 @@ Bug Fixes since HDF5-1.14.0 release
 
     Library
     -------
+    - Fixed a divide-by-zero issue when a corrupt file sets the page size to 0
+
+      If a corrupt file sets the page buffer size in the superblock to zero,
+      the library could attempt to divide by zero when allocating space in
+      the file. The library now checks for valid page buffer sizes when
+      reading the superblock message.
+
+      Fixes oss-fuzz issue 58762
+
     - Fixed a bug when using array datatypes with certain parent types
 
       Array datatype conversion would never use a background buffer, even if the

diff --git a/src/H5Fsuper.c b/src/H5Fsuper.c
@@ -800,8 +800,11 @@ H5F__super_read(H5F_t *f, H5P_genplist_t *fa_plist, bool initial_read)
                         HGOTO_ERROR(H5E_FILE, H5E_CANTSET, FAIL, "unable to set file space strategy");
                 } /* end if */
 
-                assert(f->shared->fs_page_size >= H5F_FILE_SPACE_PAGE_SIZE_MIN);
-                assert(fsinfo.page_size >= H5F_FILE_SPACE_PAGE_SIZE_MIN);
+                if (f->shared->fs_page_size < H5F_FILE_SPACE_PAGE_SIZE_MIN)
+                    HGOTO_ERROR(H5E_FILE, H5E_BADVALUE, FAIL, "file space page size too small");
+                if (fsinfo.page_size < H5F_FILE_SPACE_PAGE_SIZE_MIN)
+                    HGOTO_ERROR(H5E_FILE, H5E_BADVALUE, FAIL, "file space page size too small");
+
                 if (f->shared->fs_page_size != fsinfo.page_size) {
                     f->shared->fs_page_size = fsinfo.page_size;
 

diff --git a/src/H5Gmodule.h b/src/H5Gmodule.h
@@ -775,8 +775,8 @@
  * \image html Groups_fig9_aa.gif "c) A link named dset2 to the same dataset is created in /group2."
  * </td>
  * <td>
- * \image html Groups_fig9_bb.gif "d) The link from /group1 to dset1 is removed. The dataset is
- * still in the file, but can be accessed only as /group2/dset2."
+ * \image html Groups_fig9_bb.gif "d) The link from /group1 to dset1 is removed."
+ * The dataset is still in the file, but can be accessed only as /group2/dset2.
  * </td>
  * </tr>
  * </table>
@@ -811,8 +811,7 @@
  * </tr>
  * <tr>
  * <td>
- * \image html Groups_fig10_c.gif "c) dset1 has three names: /group1/dset1, /group2/dset2, and
- * /group1/GXX/dset2."
+ * \image html Groups_fig10_c.gif "c) dset1 has 3 names: /group1/dset1, /group2/dset2, and /group1/GXX/dset2."
  * </td>
  * <td>
  * \image html Groups_fig10_d.gif "d) dset1 has an infinite number of available path names."