Merge pull request #5 from hpc-io/develop

Add benchmark code, reduce compile warnings, and fix issues with HDF5 1.14.5

Author: houjun

.github/workflows/clang-format-check.yml

@@ -7,12 +7,12 @@ jobs:
     runs-on: ubuntu-latest
     if: "!contains(github.event.head_commit.message, 'skip-ci')"
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/[email protected]
+
     - name: Run clang-format style check for C programs.
-      uses: DoozyX/clang-format-lint-action@v0.11
+      uses: DoozyX/clang-format-lint-action@v0.18.2
       with:
         source: '.'
         extensions: 'c,h,cpp,hpp'
         clangFormatVersion: 10
         style: file
-        # exclude: './config'

.github/workflows/clang-format-fix.yml

@@ -1,26 +1,45 @@
-name: clang-format Commit Chanages
+# NOTE: This action requires write permissions to be set in your GitHub
+#       repo/fork for it to be able to commit changes.
+#
+# This is currently enabled via:
+#
+#   settings > Actions > General > Workflow permissions
+#
+# which you will need to set to "Read and write permissions"
+#
+name: clang-format Commit Changes
 on: 
   workflow_dispatch:
   push:
+    paths-ignore:
+      - '**.md'
+      - '**.txt'
+      - 'docs/**'
+
+permissions:
+  contents: write
+
 jobs:
   formatting-check:
     name: Commit Format Changes
     runs-on: ubuntu-latest
     if: "!contains(github.event.head_commit.message, 'skip-ci')"
     permissions:
-      contents: write # In order to allow EndBug/add-and-commit to commit changes
+        contents: write # In order to allow EndBug/add-and-commit to commit changes
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/[email protected]
+
     - name: Fix C formatting issues detected by clang-format
-      uses: DoozyX/clang-format-lint-action@v0.13
+      uses: DoozyX/clang-format-lint-action@v0.18.2
       with:
         source: '.'
         extensions: 'c,h,cpp,hpp'
         clangFormatVersion: 10
         inplace: True
         style: file
         # exclude: './config '
-    - uses: EndBug/add-and-commit@v9
+
+    - uses: EndBug/add-and-commit@a94899bca583c204427a224a7af87c02f9b325d5 # v9.1.4
       with:
           author_name: github-actions
           author_email: github-actions[bot]@users.noreply.github.com

.github/workflows/linux.yml

@@ -40,12 +40,14 @@ jobs:
         run: |
           sudo apt-get update
           sudo apt-get install libtool
-          sudo apt install cmake
+          sudo apt install cmake uuid-dev
           # hdf5
-          git clone https://github.com/HDFGroup/hdf5.git
-          # libfabric 1.12.1
-          wget https://github.com/ofiwg/libfabric/archive/refs/tags/v1.12.1.tar.gz
-          tar xf v1.12.1.tar.gz
+          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
+          # libfabric 1.20.1
+          wget https://github.com/ofiwg/libfabric/archive/refs/tags/v1.20.1.tar.gz
+          tar xf v1.20.1.tar.gz
           # mercury
           git clone https://github.com/mercury-hpc/mercury.git --recursive
           # mpi
@@ -66,15 +68,14 @@ jobs:
           export HDF5_LIBRARY=$mydir/hdf5/install/lib/libhdf5.so
           export VOL_DIR=$mydir/vol-pdc
           export MERCURY_DIR=$mydir/mercury/install
-          export LIBFABRIC_DIR=$mydir/libfabric-1.12.1/install
+          export LIBFABRIC_DIR=$mydir/libfabric-1.20.1/install
           export PDC_DIR=$mydir/pdc/install
           export LD_LIBRARY_PATH="$LIBFABRIC_DIR/lib:$MERCURY_DIR/lib:$PDC_DIR/lib:$VOL_DIR/install/lib:$LD_LIBRARY_PATH"
           export PATH="$LIBFABRIC_DIR/include:$LIBFABRIC_DIR/lib:$MERCURY_DIR/include:$MERCURY_DIR/lib:$PATH"
           
           # Compile HDF5
           mkdir $HDF5_DIR
           cd hdf5
-          git checkout hdf5-1_14_1-2
           export HDF5_LIBTOOL=/usr/bin/libtoolize
           ./autogen.sh
           ./configure CC=mpicc --prefix=$HDF5_DIR --enable-parallel --disable-tests --disable-hl --disable-fortran 
@@ -92,7 +93,7 @@ jobs:
           # Compile Mercury
           mkdir $MERCURY_DIR
           cd $MERCURY_DIR
-          git checkout v2.1.0
+          git checkout v2.2.0
           cmake ../  -DCMAKE_C_COMPILER=gcc -DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=ON -DNA_USE_OFI=ON -DNA_USE_SM=OFF -DMERCURY_USE_CHECKSUMS=OFF
           make -j2 && sudo make install
           ctest
@@ -117,7 +118,7 @@ jobs:
           
           # Run test
           mpirun -N 1 -n 1 -c 1 $PDC_DIR/bin/pdc_server.exe &
-          mpirun -N 1 -n 1 -c 1 ./bin/h5pdc_vpicio test
+          mpirun -N 1 -n 1 -c 1 ./bin/vpicio test
           mpirun -N 1 -n 1 -c 1 $PDC_DIR/bin/close_server
           
       - name: Setup tmate session

CMakeLists.txt

@@ -224,7 +224,7 @@ add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/src)
 #-----------------------------------------------------------------------------
 # Examples
 #-----------------------------------------------------------------------------
-option(BUILD_EXAMPLES "Build examples." OFF)
+option(BUILD_EXAMPLES "Build examples." ON)
 if(BUILD_EXAMPLES)
   # BuildExamples.cmake builds the examples as a separate project. This ensures
   # that examples can be built by themselves as well as avoiding pollution of
@@ -233,13 +233,15 @@ if(BUILD_EXAMPLES)
   set(examples
     vpicio
     vpicio_open
+    vpicio_batch
+    bdcatsio_batch
   )
 
   foreach (example ${examples})
-    add_executable (h5pdc_${example}
-      ${CMAKE_CURRENT_SOURCE_DIR}/examples/h5pdc_${example}.c
+    add_executable (${example}
+      ${CMAKE_CURRENT_SOURCE_DIR}/examples/${example}.c
     )
-    target_link_libraries(h5pdc_${example} hdf5_vol_pdc)
+    target_link_libraries(${example} hdf5_vol_pdc)
   endforeach()
 endif()
 
@@ -300,8 +302,10 @@ install(
 
 install(
   FILES
-    ${HDF5_VOL_PDC_BINARY_DIR}/bin/h5pdc_vpicio
-    ${HDF5_VOL_PDC_BINARY_DIR}/bin/h5pdc_vpicio_open
+    ${HDF5_VOL_PDC_BINARY_DIR}/bin/vpicio
+    ${HDF5_VOL_PDC_BINARY_DIR}/bin/vpicio_batch
+    ${HDF5_VOL_PDC_BINARY_DIR}/bin/vpicio_open
+    ${HDF5_VOL_PDC_BINARY_DIR}/bin/bdcatsio_batch
   DESTINATION
     ${CMAKE_INSTALL_PREFIX}/bin
 )