Merge branch 'master' into master

.clang-format

@@ -0,0 +1,58 @@
+---
+Language:        Cpp
+BasedOnStyle:  LLVM
+AlignConsecutiveAssignments: true
+#llvm11: AlignConsecutiveBitFields: false
+AlignConsecutiveDeclarations: true
+AlignConsecutiveMacros: true
+#llvm10-11: AlignOperands:   true - Align
+#llvm11: AllowShortEnumsOnASingleLine: true
+AllowShortFunctionsOnASingleLine: None
+AlwaysBreakAfterReturnType: AllDefinitions
+BraceWrapping:
+  AfterFunction:   true
+  #llvm10-11: AfterControlStatement: false - Never
+  BeforeCatch:     true
+  BeforeElse:      true
+  #llvm11:   BeforeLambdaBody: false
+  #llvm11:   BeforeWhile:     false
+BreakBeforeBraces: Stroustrup
+BreakAfterJavaFieldAnnotations: true
+BreakStringLiterals: true
+ColumnLimit:     110    # Update $max_trace_macro_line_len in bin/trace also
+IncludeCategories:
+  - Regex:           '^"(llvm|llvm-c|clang|clang-c)/'
+    Priority:        3
+    SortPriority:    0
+  - Regex:           '^(<|"(gtest|gmock|isl|json)/)'
+    Priority:        4
+    SortPriority:    0
+  - Regex:           '.*'
+    Priority:        0
+    SortPriority:    0
+  - Regex:           '^PDC*.*'
+    Priority:        1
+    SortPriority:    0
+  - Regex:           'private.*'
+    Priority:        2
+    SortPriority:    0
+IncludeIsMainRegex: '(public)?$'
+IndentCaseLabels: true
+#llvm11: IndentCaseBlocks: false
+IndentGotoLabels: false
+#llvm11: IndentExternBlock: AfterExternBlock
+IndentWidth:     4
+#llvm11: InsertTrailingCommas: None
+# MacroBlockBegin: "^BEGIN_FUNC"
+# MacroBlockEnd: "^END_FUNC"
+ObjCBlockIndentWidth: 4
+#llvm11: ObjCBreakBeforeNestedBlockParam: true
+ReflowComments:  true
+SortIncludes:    false
+StatementMacros:
+#llvm10: TypenameMacros:
+#llvm10:   - STACK_OF
+#llvm10:   - LIST
+#llvm11: WhitespaceSensitiveMacros:
+#llvm11:   - STRINGIZE
+#llvm11:   - PP_STRINGIZE

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

@@ -0,0 +1,18 @@
+name: clang-format Check
+on:
+  pull_request:
+jobs:
+  formatting-check:
+    name: Formatting Check
+    runs-on: ubuntu-latest
+    if: "!contains(github.event.head_commit.message, 'skip-ci')"
+    steps:
+    - uses: actions/checkout@v2
+    - name: Run clang-format style check for C programs.
+      uses: DoozyX/clang-format-lint-action@v0.11
+      with:
+        source: '.'
+        extensions: 'c,h,cpp,hpp'
+        clangFormatVersion: 10
+        style: file
+        # exclude: './config'

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

@@ -0,0 +1,25 @@
+name: clang-format Check
+on: 
+  workflow_dispatch:
+  push:
+jobs:
+  formatting-check:
+    name: Formatting Check
+    runs-on: ubuntu-latest
+    if: "!contains(github.event.head_commit.message, 'skip-ci')"
+    steps:
+    - uses: actions/checkout@v2
+    - name: Run clang-format style check for C programs.
+      uses: DoozyX/clang-format-lint-action@v0.11
+      with:
+        source: '.'
+        extensions: 'c,h,cpp,hpp'
+        clangFormatVersion: 10
+        inplace: True
+        style: file
+        # exclude: './config '
+    - uses: EndBug/add-and-commit@v7
+      with:
+          author_name: github-actions
+          author_email: github-actions[bot]@users.noreply.github.com
+          message: 'Committing clang-format changes'

.github/workflows/linux.yml

@@ -0,0 +1,125 @@
+name: linux 
+
+on:
+  pull_request:
+    branches: [ master ]
+
+  # Allows to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  h5bench:
+    runs-on: ubuntu-latest
+    timeout-minutes: 60
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install cmake
+          sudo apt install gcc
+          sudo apt-get install libtool
+          sudo apt-get install zlib1g-dev
+          sudo apt-get install python3
+          sudo apt-get install libopenmpi-dev
+          sudo apt-get install libhdf5-mpi-dev
+          
+          # hdf5
+          git clone https://github.com/HDFGroup/hdf5.git
+          
+          # vol-async
+          git clone --recursive https://github.com/hpc-io/vol-async.git
+          
+      - name: Install VOL-Async
+        run: |
+          mydir="$PWD"
+          export HDF5_DIR=$mydir/hdf5/install
+          export ABT_DIR=$mydir/vol-async/argobots
+          export VOL_DIR=$mydir/vol-async
+          
+          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
+          make && make install
+          
+          # Compile Argobots
+          cd $ABT_DIR
+          ./autogen.sh
+          ./configure --prefix=$ABT_DIR
+          make && make install
+          
+          # Compile Asynchronous VOL connector
+          cd $VOL_DIR
+          cd src
+          tail -n 48 Makefile.summit > Makefile
+          make
+          
+      - name: Compile and Test VOL-Async
+        run: |
+          # Compile vol-async tests
+          mydir="$PWD"
+          cd $mydir/vol-async/test
+          
+          # Set Environmental Variables
+          export H5_DIR=$mydir/hdf5
+          export VOL_DIR=$mydir/vol-async
+          export ABT_DIR=$mydir/vol-async/argobots
+          export ASYNC_DIR=$mydir/vol-async/src
+          export HDF5_DIR=$mydir/hdf5/install
+          export LD_LIBRARY_PATH=$VOL_DIR/src:$H5_DIR/install/lib:$ABT_DIR/lib:$LD_LIBRARY_PATH
+          export HDF5_PLUGIN_PATH="$VOL_DIR/src"
+          export HDF5_VOL_CONNECTOR="async under_vol=0;under_info={}"
+          
+          # Makefile
+          tail -n 47 Makefile.summit > Makefile
+          export LD_PRELOAD=$ABT_DIR/lib/libabt.so
+          make
+          
+          # Run serial and parallel tests
+          make check
+          # Run serial tests only
+          make check_serial
+          
+      - name: Build h5bench SYNC
+        run: |
+          mkdir build_sync
+          cd build_sync
+          cmake .. -DCMAKE_C_COMPILER=/usr/bin/h5pcc
+          make
+
+      - name: Build h5bench ASYNC
+        run: |  
+          mydir="$PWD"
+          mkdir build_async
+          cd build_async
+          cmake .. -DWITH_ASYNC_VOL:BOOL=ON -DCMAKE_C_FLAGS="-I/$mydir/vol-async/src -L/$mydir/vol-async/src" -DCMAKE_C_COMPILER=$mydir/hdf5/install/bin/h5pcc
+          make
+          
+      - name: Test h5bench SYNC Read & Write (NON)
+        run: |
+          cd build_sync
+          ./h5bench_write /home/runner/work/h5bench/h5bench/h5bench_patterns/sample_config/sample_write_cc1d_small.cfg testwrite.h5
+          ./h5bench_read /home/runner/work/h5bench/h5bench/h5bench_patterns/sample_config/sample_read_cc1d_small.cfg testwrite.h5
+          
+      - name: Test h5bench ASYNC Read & Write (NON)
+        run: |
+          cd build_async
+          ./h5bench_write /home/runner/work/h5bench/h5bench/h5bench_patterns/sample_config/sample_write_cc1d_small.cfg testwrite.h5
+          ./h5bench_read /home/runner/work/h5bench/h5bench/h5bench_patterns/sample_config/sample_read_cc1d_small.cfg testwrite.h5
+          
+      - name: Test h5bench ASYNC Read & Write (IMP)
+        run: |
+          cd build_async
+          ./h5bench_write /home/runner/work/h5bench/h5bench/h5bench_patterns/sample_config/sample_write_cc1d_small_IMP.cfg testwrite_IMP.h5
+          ./h5bench_read /home/runner/work/h5bench/h5bench/h5bench_patterns/sample_config/sample_read_cc1d_small_IMP.cfg testwrite_IMP.h5
+          
+      - name: Test h5bench ASYNC Read & Write (EXP)
+        run: |
+          cd build_async
+          ./h5bench_write /home/runner/work/h5bench/h5bench/h5bench_patterns/sample_config/sample_write_cc1d_small_EXP.cfg testwrite_EXP.h5
+          ./h5bench_read /home/runner/work/h5bench/h5bench/h5bench_patterns/sample_config/sample_read_cc1d_small_EXP.cfg testwrite_EXP.h5

.gitlab-ci.yml

@@ -0,0 +1,45 @@
+variables:
+    HDF5_DIR: "/global/cfs/cdirs/m2621/h5bench/hdf5/install"
+    H5BENCH_BUILD_PATH: "${CI_PROJECT_DIR}/build"
+    H5BENCH_INSTALL_PATH: "${CI_PROJECT_DIR}/install"
+
+stages:
+    - build
+    - test
+
+build:
+    stage: build
+    tags:
+      - cori
+    variables:
+        SCHEDULER_PARAMETERS: "-C haswell --qos=debug -N 1 -t 00:30:00 --gres=craynetwork:3"
+    script:
+      - echo "Build h5bench"
+      - module swap PrgEnv-intel PrgEnv-gnu 
+      - module list
+      - mkdir ${H5BENCH_BUILD_PATH}
+      - cd ${H5BENCH_BUILD_PATH}
+      - cmake .. -DCMAKE_C_COMPILER=$HDF5_DIR/bin/h5pcc -DCMAKE_CXX_COMPILER=$HDF5_DIR/bin/h5pcc -DCMAKE_INSTALL_PREFIX=${H5BENCH_INSTALL_PATH}
+      - make
+      - make install
+    artifacts:
+        paths:
+            - ${H5BENCH_BUILD_PATH}
+            - ${H5BENCH_INSTALL_PATH}
+
+test:
+    stage: test
+    tags:
+        - cori
+    variables:
+        SCHEDULER_PARAMETERS: "-C haswell --qos=debug -N 1 -t 00:30:00 --gres=craynetwork:3"
+    script:
+      - echo "Test h5bench SYNC"
+      - cd ${H5BENCH_BUILD_PATH}
+      - export LD_LIBRARY_PATH=$HDF5_DIR/lib:$LD_LIBRARY_PATH
+      - export MPICH_MAX_THREAD_SAFETY=multiple
+      - echo "Test h5bench SYNC write"
+      - srun -n 2 ./h5bench_write ../h5bench_patterns/sample_config/sample_write_cc1d_small.cfg file.h5
+      - echo "Test h5bench SYNC read"
+      - srun -n 2 ./h5bench_read ../h5bench_patterns/sample_config/sample_read_cc1d_small.cfg file.h5
+      - ls -larth file.h5

CMakeLists.txt

@@ -15,7 +15,7 @@ message("Detected hdf5 version: ${HDF5_VERSION}")
 include_directories(${HDF5_HOME}/include)
 link_directories(${HDF5_HOME}/lib)
 
-#Dependency: Async
+# Dependency: VOL Async
 set(ASYNC_HOME $ENV{ASYNC_HOME})
 option(WITH_ASYNC_VOL "" OFF)
 if(WITH_ASYNC_VOL)