switch to building HDF5 with CMake

.github/codeql-config.yml

@@ -0,0 +1,5 @@
+query-filters:
+  - exclude:
+      id: cpp/toctou-race-condition
+  - exclude:
+      id: cpp/short-global-name

.github/workflows/codeql.yml

@@ -1,14 +1,3 @@
-# For most projects, this workflow file will not need changing; you simply need
-# to commit it to your repository.
-#
-# You may wish to alter this file to override the set of languages analyzed,
-# or to provide custom queries or build logic.
-#
-# ******** NOTE ********
-# We have attempted to detect the languages in your repository. Please check
-# the `language` matrix defined below to confirm you have the correct set of
-# supported CodeQL languages.
-#
 name: "CodeQL Advanced"
 
 on:
@@ -21,13 +10,14 @@ on:
 
 jobs:
   analyze:
-    name: Analyze (${{ matrix.language }})
+    name: Analyze
     # Runner size impacts CodeQL analysis time. To learn more, please see:
     #   - https://gh.io/recommended-hardware-resources-for-running-codeql
     #   - https://gh.io/supported-runners-and-hardware-resources
     #   - https://gh.io/using-larger-runners (GitHub.com only)
     # Consider using larger runners or machines with greater resources for possible analysis time improvements.
-    runs-on: ${{ (matrix.language == 'swift' && 'macos-latest') || 'ubuntu-latest' }}
+    runs-on: ubuntu-latest
+    #runs-on: ${{ (matrix.language == 'swift' && 'macos-latest') || 'ubuntu-latest' }}
     permissions:
       # required for all workflows
       security-events: write
@@ -36,17 +26,15 @@ jobs:
       packages: read
 
       # only required for workflows in private repositories
-      actions: read
-      contents: read
+      #actions: read
+      #contents: read
 
     strategy:
       fail-fast: false
       matrix:
         include:
         - language: c-cpp
-          build-mode: autobuild
-        - language: python
-          build-mode: none
+          build-mode: manual
         # CodeQL supports the following values keywords for 'language': 'c-cpp', 'csharp', 'go', 'java-kotlin', 'javascript-typescript', 'python', 'ruby', 'swift'
         # Use `c-cpp` to analyze code written in C, C++ or both
         # Use 'java-kotlin' to analyze code written in Java, Kotlin or both
@@ -56,39 +44,80 @@ jobs:
         # If you are analyzing a compiled language, you can modify the 'build-mode' for that language to customize how
         # your codebase is analyzed, see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/codeql-code-scanning-for-compiled-languages
     steps:
-    - name: Checkout repository
-      uses: actions/checkout@v4
+      - name: Checkout submodule Argobots
+        uses: actions/[email protected]
+        with:
+          submodules: 'true'
+
+      - name: Checkout HDF5 latest
+        uses: actions/[email protected]
+        with:
+          repository: HDFGroup/hdf5
+          path: hdf5
+
+      - name: Dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install libtool libopenmpi-dev zlib1g-dev python3 cmake
+
+      - name: Configure Async VOL (install dependencies)
+        run: |
+          mydir="$PWD"
+          export HDF5_DIR=$mydir/hdf5/install
+          export ABT_DIR=$mydir/argobots
+          export VOL_DIR=$mydir/vol-async/install
+
+          mkdir $HDF5_DIR
+          # Compile HDF5
+          cd hdf5
+          mkdir build
+          cd build
+          cmake -DCMAKE_INSTALL_PREFIX=$HDF5_DIR -DHDF5_ENABLE_PARALLEL=ON -DHDF5_ENABLE_THREADSAFE=ON \
+            -DALLOW_UNSUPPORTED=ON -DBUILD_TESTING=OFF -DHDF5_BUILD_HL_LIB=OFF \
+            -DHDF5_BUILD_EXAMPLES=OFF -DHDF5_BUILD_FORTRAN=OFF -DCMAKE_C_COMPILER=mpicc ..
+          make -j && make install
+
+          # Compile Argobots
+          cd $ABT_DIR
+          ./autogen.sh
+          ./configure --prefix=$ABT_DIR
+          make && make install
+
+          # Configure Asynchronous VOL connector
+          pwd
+          cd ../
+          mkdir build
+          cd build
+          cmake -DCMAKE_INSTALL_PREFIX=$VOL_DIR -DCMAKE_C_COMPILER=mpicc ..
 
     # Initializes the CodeQL tools for scanning.
-    - name: Initialize CodeQL
-      uses: github/codeql-action/init@v3
-      with:
-        languages: ${{ matrix.language }}
-        build-mode: ${{ matrix.build-mode }}
-        # If you wish to specify custom queries, you can do so here or in a config file.
-        # By default, queries listed here will override any specified in a config file.
-        # Prefix the list here with "+" to use these queries and those in the config file.
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v3
+        with:
+          languages: ${{ matrix.language }}
+          build-mode: ${{ matrix.build-mode }}
+          config-file: ./.github/codeql-config.yml
+          # If you wish to specify custom queries, you can do so here or in a config file.
+          # By default, queries listed here will override any specified in a config file.
+          # Prefix the list here with "+" to use these queries and those in the config file.
 
-        # For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
-        # queries: security-extended,security-and-quality
+          # For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+          queries: +security-extended,security-and-quality
 
-    # If the analyze step fails for one of the languages you are analyzing with
-    # "We were unable to automatically build your code", modify the matrix above
-    # to set the build mode to "manual" for that language. Then modify this step
-    # to build your code.
-    # ℹ️ Command-line programs to run using the OS shell.
-    # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
-    - if: matrix.build-mode == 'manual'
-      shell: bash
-      run: |
-        echo 'If you are using a "manual" build mode for one or more of the' \
-          'languages you are analyzing, replace this with the commands to build' \
-          'your code, for example:'
-        echo '  make bootstrap'
-        echo '  make release'
-        exit 1
+      # If the analyze step fails for one of the languages you are analyzing with
+      # "We were unable to automatically build your code", modify the matrix above
+      # to set the build mode to "manual" for that language. Then modify this step
+      # to build your code.
+      # ℹ️ Command-line programs to run using the OS shell.
+      # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
+      - name: Async VOL,build and test
+        shell: bash
+        run: |
+          cd build
+          make && make install
+          ctest -V -E async_test_parallel5 .
 
-    - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v3
-      with:
-        category: "/language:${{matrix.language}}"
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v3
+        with:
+          category: "/language:${{matrix.language}}"

.github/workflows/linux.yml

@@ -14,7 +14,12 @@ on:
   # Allows to run this workflow manually from the Actions tab
   workflow_dispatch:
 jobs:
-  vol-async-hdf5-latest-Makefile:
+
+###############################################
+# Testing last version of the HDF5 1.14 series
+###############################################
+
+  vol-async-hdf5-1_14-Makefile:
     runs-on: ubuntu-latest
     timeout-minutes: 60
 
@@ -31,9 +36,9 @@ jobs:
 
       - name: Checkout latest HDF5 release
         run: |
-          wget https://github.com/HDFGroup/hdf5/releases/latest/download/hdf5.tar.gz
-          tar xzf hdf5.tar.gz
-          ln -sf hdf5-* hdf5
+          wget https://github.com/HDFGroup/hdf5/releases/download/hdf5_1.14.5/hdf5-1.14.5.tar.gz
+          tar xzf hdf5-1.14.5.tar.gz
+          mv hdf5-1.14.5 hdf5
 
       - name: Installation
         run: |
@@ -101,7 +106,7 @@ jobs:
           make check
           date
 
-  vol-async-hdf5-develop-Makefile:
+  vol-async-hdf5-1_14-cmake:
     runs-on: ubuntu-latest
     timeout-minutes: 30
 
@@ -110,33 +115,34 @@ jobs:
         uses: actions/[email protected]
         with:
           submodules: 'true'
-
-      - name: Checkout HDF5 latest
-        uses: actions/[email protected]
-        with:
-          repository: HDFGroup/hdf5
-          path: hdf5
-
+
       - name: Dependencies
         run: |
           sudo apt-get update
-          sudo apt-get install libtool libopenmpi-dev zlib1g-dev python3
-
+          sudo apt-get install libtool libopenmpi-dev zlib1g-dev python3 cmake
+
+      - name: Checkout latest HDF5 release
+        run: |
+          wget https://github.com/HDFGroup/hdf5/releases/download/hdf5_1.14.5/hdf5-1.14.5.tar.gz
+          tar xzf hdf5-1.14.5.tar.gz
+          mv hdf5-1.14.5 hdf5
+
       - name: Installation
         run: |
           mydir="$PWD"
           export HDF5_DIR=$mydir/hdf5/install
           export ABT_DIR=$mydir/argobots
-          export VOL_DIR=$mydir
+          export VOL_DIR=$mydir/vol-async/install
 
           mkdir $HDF5_DIR
           # Compile HDF5
           cd hdf5
-          export HDF5_LIBTOOL=/usr/bin/libtoolize
-          ./autogen.sh
-          ./configure --prefix=$HDF5_DIR --enable-parallel --enable-threadsafe --enable-unsupported \
-          --disable-tests --disable-hl --disable-fortran --disable-tools
-          make && make install
+          mkdir build
+          cd build
+          cmake -DCMAKE_INSTALL_PREFIX=$HDF5_DIR -DHDF5_ENABLE_PARALLEL=ON -DHDF5_ENABLE_THREADSAFE=ON \
+            -DALLOW_UNSUPPORTED=ON -DBUILD_TESTING=OFF -DHDF5_BUILD_HL_LIB=OFF \
+            -DHDF5_BUILD_EXAMPLES=OFF -DHDF5_BUILD_FORTRAN=OFF -DCMAKE_C_COMPILER=mpicc ..
+          make -j && make install
 
           # Compile Argobots
           cd $ABT_DIR
@@ -145,51 +151,47 @@ jobs:
           make && make install
 
           # Compile Asynchronous VOL connector
-          cd $VOL_DIR/src
-          tail -n 48 Makefile.summit > Makefile
-          make
+          pwd
+          cd ../
+          mkdir build
+          cd build
+          cmake -DCMAKE_INSTALL_PREFIX=$VOL_DIR -DCMAKE_C_COMPILER=mpicc ..
+          make && make install
 
       - name: Compile and Test Vol-Async
         run: |
           # Compile vol-async tests
           mydir="$PWD"
-          cd $mydir
-          cd test
+          echo $PWD
+          cd build
 
           # Set Environmental Variables
-          export H5_DIR=$mydir/hdf5
-          export VOL_DIR=$mydir/
+          export VOL_DIR=$mydir/vol-async/install
           export ABT_DIR=$mydir/argobots
-          export ASYNC_DIR=$mydir/src
           export HDF5_DIR=$mydir/hdf5/install
-          export LD_LIBRARY_PATH=$VOL_DIR/src:$H5_DIR/install/lib:$ABT_DIR/lib:$LD_LIBRARY_PATH
-          export HDF5_PLUGIN_PATH="$VOL_DIR/src"
+          export LD_LIBRARY_PATH=$VOL_DIR/lib:$HDF5_DIR/install/lib:$ABT_DIR/lib:$LD_LIBRARY_PATH
+          export HDF5_PLUGIN_PATH="$VOL_DIR/lib"
           export HDF5_VOL_CONNECTOR="async under_vol=0;under_info={}"
-
-          # Makefile
-          tail -n 47 Makefile.summit > Makefile
           export LD_PRELOAD=$mydir/argobots/lib/libabt.so
-          make
-
-          date
+
           # Run serial and parallel tests
-          make check
+          date
+          ctest -V
           date
 
-          # Test with async VOL double buffering
-          cd ../src
-          sed -i "s/CFLAGS =/CFLAGS = -DENABLE_WRITE_MEMCPY=1 /g" ./Makefile
-          cat Makefile
+          # Test with async VOL write memcopy (double buffering)
+          cmake -DCMAKE_INSTALL_PREFIX=$VOL_DIR -DCMAKE_C_COMPILER=mpicc -DENABLE_WRITE_MEMCPY=ON ..
           make clean
-          make
-          cd ../test
-
+          make && make install
           date
-          make clean
-          make
-          make check
+          ctest -V
           date
 
+#################################################
+# Testing with the HDF5 2.0+ series
+#   * Note: autools support was dropped in HDF5
+#################################################
+
   vol-async-hdf5-latest-cmake:
     runs-on: ubuntu-latest
     timeout-minutes: 30
@@ -271,6 +273,10 @@ jobs:
           ctest -V
           date
 
+#######################################
+# Testing using HDF5's "develop" branch
+#######################################
+
   vol-async-hdf5-develop-cmake:
     runs-on: ubuntu-latest
     timeout-minutes: 30