Feature/initial bulk reactions

.github/workflows/continuousIntegration.yml

@@ -0,0 +1,287 @@
+name: hpcReactCI
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+  workflow_dispatch:
+
+concurrency:
+   group: ${{ github.workflow }}-${{ github.ref }}
+   cancel-in-progress: true
+
+jobs:
+
+  get_docker_image_tag_hash:
+    runs-on: ubuntu-22.04
+    outputs:
+      DOCKER_IMAGE_TAG_HASH: ${{ steps.extract_docker_image_tag_hash.outputs.DOCKER_IMAGE_TAG_HASH }}
+    steps:
+      - name: Extract docker image tag hash
+        id: extract_docker_image_tag_hash
+        run: |
+          echo "DOCKER_IMAGE_TAG_HASH=310f70ba6065b94858af2cafeba828ea76c02a1d" >> "$GITHUB_OUTPUT"
+
+  # code_style:
+  #   needs: [check_pull_request_is_not_a_draft]
+  #   runs-on: ubuntu-22.04
+  #   steps:
+  #   - name: Checkout Repository
+  #     uses: actions/checkout@v4.1.6
+  #     with:
+  #       submodules: true
+  #       lfs: false
+  #   - name: Check style
+  #     env:
+  #       DOCKER_REPOSITORY: geosx/ubuntu20.04-gcc9
+  #       CMAKE_BUILD_TYPE: Release
+  #       BUILD_AND_TEST_ARGS: --test-code-style
+  #     run: ./scripts/ci_build_and_test.sh
+
+  doxygen_check:
+    runs-on: ubuntu-22.04
+    needs:
+      - get_docker_image_tag_hash
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v4.1.6
+        with:
+          submodules: true
+          lfs: false
+      - name: Check doxygen
+        env:
+          DOCKER_REPOSITORY: geosx/ubuntu:22.04-${{ needs.get_docker_image_tag_hash.outputs.DOCKER_IMAGE_TAG_HASH }}
+          HOST_CONFIG: hostconfigs/environment.cmake
+          CMAKE_CXX_COMPILER: /usr/bin/clang++
+          CMAKE_C_COMPILER: /usr/bin/clang
+          CMAKE_BUILD_TYPE: Release
+          BUILD_AND_TEST_ARGS: --test-doxygen
+        run: ./scripts/ci_build_and_test.sh
+
+
+  code_checks:
+    runs-on: ubuntu-22.04
+    needs:
+      - get_docker_image_tag_hash
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v4.1.6
+        with:
+          submodules: true
+          lfs: false
+      - name: code_checks
+        env:
+          DOCKER_REPOSITORY: geosx/ubuntu:22.04-${{ needs.get_docker_image_tag_hash.outputs.DOCKER_IMAGE_TAG_HASH }}
+          HOST_CONFIG: hostconfigs/environment.cmake
+          CMAKE_CXX_COMPILER: /usr/bin/clang++
+          CMAKE_C_COMPILER: /usr/bin/clang
+          CMAKE_BUILD_TYPE: Release
+          BUILD_AND_TEST_ARGS: --code-checks
+        run: ./scripts/ci_build_and_test.sh
+
+  linux_builds:
+    name: ${{matrix.name}}
+    runs-on: ${{matrix.RUNS_ON}}
+    needs:
+      - get_docker_image_tag_hash
+    strategy:
+      # Set fail-fast to false to ensure that feedback is delivered for all matrix combinations. Consider changing this to true when your workflow is stable.
+      fail-fast: false
+      matrix:
+        include:
+          # - name: RHEL8.10-clang17-dbg (ubi8.10, clang-17.0.6, Debug)
+          #   DOCKER_REPOSITORY: geosx/ubi:8.10
+          #   RUNS_ON: ubuntu-22.04
+          #   CMAKE_CXX_COMPILER: clang++
+          #   CMAKE_C_COMPILER: clang
+          #   CMAKE_BUILD_TYPE: Debug
+
+          # - name: RHEL8.10-clang17-rel (ubi8.10, clang-17.0.6, Release)
+          #   DOCKER_REPOSITORY: geosx/ubi:8.10
+          #   RUNS_ON: ubuntu-22.04
+          #   CMAKE_CXX_COMPILER: clang++
+          #   CMAKE_C_COMPILER: clang
+          #   CMAKE_BUILD_TYPE: Release
+
+          # - name: RHEL8.10-gcc13-dbg (ubi8.10, gcc 13.2.1, Debug)
+          #   DOCKER_REPOSITORY: geosx/ubi:8.10
+          #   RUNS_ON: ubuntu-22.04
+          #   CMAKE_CXX_COMPILER: /opt/rh/gcc-toolset-13/root/bin/g++
+          #   CMAKE_C_COMPILER: /opt/rh/gcc-toolset-13/root/bin/gcc
+          #   CMAKE_BUILD_TYPE: Debug
+
+          # - name: RHEL8.10-gcc13-rel (ubi8.10, gcc 13.2.1, Release)
+          #   DOCKER_REPOSITORY: geosx/ubi:8.10
+          #   RUNS_ON: ubuntu-22.04
+          #   CMAKE_CXX_COMPILER: /opt/rh/gcc-toolset-13/root/bin/g++
+          #   CMAKE_C_COMPILER: /opt/rh/gcc-toolset-13/root/bin/gcc
+          #   CMAKE_BUILD_TYPE: Release
+
+          - name: ubuntu22-gcc11-dbg (ubuntu-22, gcc 11.4.0, Release)
+            DOCKER_REPOSITORY: geosx/ubuntu:22.04
+            RUNS_ON: ubuntu-22.04
+            CMAKE_CXX_COMPILER: /usr/bin/g++
+            CMAKE_C_COMPILER: /usr/bin/gcc
+            CMAKE_BUILD_TYPE: Debug
+
+          - name: ubuntu22-gcc11-rel (ubuntu-22, gcc 11.4.0, Release)
+            DOCKER_REPOSITORY: geosx/ubuntu:22.04
+            RUNS_ON: ubuntu-22.04
+            CMAKE_CXX_COMPILER: /usr/bin/g++
+            CMAKE_C_COMPILER: /usr/bin/gcc
+            CMAKE_BUILD_TYPE: Release
+
+          - name: ubuntu22-clang14-dbg (ubuntu-22, clang-14.0.0, Debug)
+            DOCKER_REPOSITORY: geosx/ubuntu:22.04
+            RUNS_ON: ubuntu-22.04
+            CMAKE_CXX_COMPILER: /usr/bin/clang++
+            CMAKE_C_COMPILER: /usr/bin/clang
+            CMAKE_BUILD_TYPE: Debug
+
+          - name: ubuntu22-clang14-rel (ubuntu-22, clang-14.0.0, Release)
+            DOCKER_REPOSITORY: geosx/ubuntu:22.04
+            RUNS_ON: ubuntu-22.04
+            CMAKE_CXX_COMPILER: /usr/bin/clang++
+            CMAKE_C_COMPILER: /usr/bin/clang
+            CMAKE_BUILD_TYPE: Release
+
+          # - name: ubuntu22-gcc11-cuda11-rel (ubuntu-22, gcc 11.4.0, cuda-11.8.0, Release)
+          #   DOCKER_REPOSITORY: geosx/ubuntu:22.04-cuda11.8
+          #   RUNS_ON: streak2
+          #   CMAKE_CXX_COMPILER: /usr/bin/g++
+          #   CMAKE_C_COMPILER: /usr/bin/gcc
+          #   CMAKE_BUILD_TYPE: Release
+          #   ENABLE_CUDA: ON
+          #   CMAKE_CUDA_ARCHITECTURES: "86"
+          #   NPROC: 4
+          #   DOCKER_RUN_ARGS: "--cpus=4 --memory=64g --runtime=nvidia --gpus all"
+
+          # - name: ubuntu22-gcc11-cuda11-dbg (ubuntu-22, gcc 11.4.0, cuda-11.8.0, Debug)
+          #   DOCKER_REPOSITORY: geosx/ubuntu:22.04-cuda11.8
+          #   RUNS_ON: streak2
+          #   CMAKE_CXX_COMPILER: /usr/bin/g++
+          #   CMAKE_C_COMPILER: /usr/bin/gcc
+          #   CMAKE_BUILD_TYPE: Debug
+          #   ENABLE_CUDA: ON
+          #   CMAKE_CUDA_ARCHITECTURES: "86"
+          #   NPROC: 4
+          #   DOCKER_RUN_ARGS: "--cpus=4 --memory=64g --runtime=nvidia --gpus all"
+
+          # - name: ubuntu22-clang14-cuda11-rel (ubuntu-22, clang-14.0.0, cuda-11.8.0, Release)
+          #   DOCKER_REPOSITORY: geosx/ubuntu:22.04-cuda11.8
+          #   RUNS_ON: streak2
+          #   CMAKE_CXX_COMPILER: /usr/bin/clang++
+          #   CMAKE_C_COMPILER: /usr/bin/clang
+          #   CMAKE_BUILD_TYPE: Release
+          #   ENABLE_CUDA: ON
+          #   CMAKE_CUDA_ARCHITECTURES: "86"
+          #   NPROC: 4
+          #   DOCKER_RUN_ARGS: "--cpus=4 --memory=64g --runtime=nvidia --gpus all"
+
+          # - name: ubuntu22-clang14-cuda11-dbg (ubuntu-22, clang-14.0.0, cuda-11.8.0, Debug)
+          #   DOCKER_REPOSITORY: geosx/ubuntu:22.04-cuda11.8
+          #   RUNS_ON: streak2
+          #   CMAKE_CXX_COMPILER: /usr/bin/clang++
+          #   CMAKE_C_COMPILER: /usr/bin/clang
+          #   CMAKE_BUILD_TYPE: Debug
+          #   ENABLE_CUDA: ON
+          #   CMAKE_CUDA_ARCHITECTURES: "86"
+          #   NPROC: 4
+          #   DOCKER_RUN_ARGS: "--cpus=4 --memory=64g --runtime=nvidia --gpus all"
+
+          # - name: RHEL8.10-clang17-cuda12-rel (ubi8.10, clang-17.0.6, cuda-12.4.1, Release)
+          #   DOCKER_REPOSITORY: geosx/ubi:8.10-cuda12.8
+          #   RUNS_ON: streak2
+          #   CMAKE_CXX_COMPILER: clang++
+          #   CMAKE_C_COMPILER: clang
+          #   CMAKE_BUILD_TYPE: Release
+          #   ENABLE_CUDA: ON
+          #   CMAKE_CUDA_ARCHITECTURES: "86"
+          #   NPROC: 4
+          #   DOCKER_RUN_ARGS: "--cpus=4 --memory=64g --runtime=nvidia --gpus all"
+
+          # - name: RHEL8.10-gcc13-cuda12-rel (ubi8.10, gcc 13.2.1, cuda-12.4.1, Release)
+          #   DOCKER_REPOSITORY: geosx/ubi:8.10-cuda12.8
+          #   RUNS_ON: streak2
+          #   CMAKE_CXX_COMPILER: /opt/rh/gcc-toolset-13/root/bin/g++
+          #   CMAKE_C_COMPILER: /opt/rh/gcc-toolset-13/root/bin/gcc
+          #   CMAKE_BUILD_TYPE: Release
+          #   ENABLE_CUDA: ON
+          #   CMAKE_CUDA_ARCHITECTURES: "86"
+          #   NPROC: 4
+          #   DOCKER_RUN_ARGS: "--cpus=4 --memory=64g --runtime=nvidia --gpus all"
+
+    steps:
+    - name: Checkout Repository
+      uses: actions/checkout@v4.1.6
+      with:
+        submodules: true
+        lfs: false
+
+    - name: Print environment
+      run: printenv
+
+    - name: Build and test
+      env:
+        DOCKER_REPOSITORY: ${{ matrix.DOCKER_REPOSITORY }}-${{ needs.get_docker_image_tag_hash.outputs.DOCKER_IMAGE_TAG_HASH }}
+        CMAKE_CXX_COMPILER: ${{ matrix.CMAKE_CXX_COMPILER }}
+        CMAKE_C_COMPILER: ${{ matrix.CMAKE_C_COMPILER }}
+        CMAKE_BUILD_TYPE: ${{ matrix.CMAKE_BUILD_TYPE }}
+        ENABLE_CUDA: ${{ matrix.ENABLE_CUDA }}
+        CMAKE_CUDA_ARCHITECTURES: ${{ matrix.CMAKE_CUDA_ARCHITECTURES }}
+        NPROC: ${{ matrix.NPROC }}
+        BUILD_AND_TEST_ARGS: ${{ matrix.BUILD_AND_TEST_ARGS }} --build-exe
+        DOCKER_RUN_ARGS: ${{ matrix.DOCKER_RUN_ARGS }}
+        HOST_CONFIG: hostconfigs/environment.cmake
+      run: ./scripts/ci_build_and_test.sh
+
+  code_coverage:
+    runs-on: ubuntu-22.04
+    needs:
+      - get_docker_image_tag_hash
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v4.1.6
+        with:
+          submodules: true
+          lfs: false
+      - name: run code coverage
+        env:
+          DOCKER_REPOSITORY: geosx/ubuntu:22.04-${{ needs.get_docker_image_tag_hash.outputs.DOCKER_IMAGE_TAG_HASH }}
+          HOST_CONFIG: hostconfigs/environment.cmake
+          CMAKE_CXX_COMPILER: /usr/bin/g++
+          CMAKE_C_COMPILER: /usr/bin/gcc
+          CMAKE_BUILD_TYPE: Debug
+          BUILD_AND_TEST_ARGS: "--build-exe --code-coverage"
+        run: ./scripts/ci_build_and_test.sh
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v3
+        with:
+          files: hpcReact_coverage.info.cleaned
+          fail_ci_if_error: true
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
+
+  check_that_all_jobs_succeeded:
+    runs-on: ubuntu-22.04
+    needs:
+      - get_docker_image_tag_hash
+      - linux_builds
+      - doxygen_check
+      - code_checks
+    if: ${{ always() }}
+    env:
+      RETURN_VAL: |
+        ${{
+        needs.linux_builds.result == 'success' &&
+        needs.doxygen_check.result == 'success' &&
+        needs.code_checks.result == 'success'
+        }}
+    steps:
+    - name: PR Success
+      if: ${{ contains(env.RETURN_VAL, 'true') }}
+      run: "true"
+    - name: PR Failure
+      if: ${{ contains(env.RETURN_VAL, 'false') }}
+      run: "false"

.gitignore

@@ -0,0 +1,2 @@
+build*
+cmake/blt*

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "cmake/blt"]
+	path = cmake/blt
+	url = git@github.com:LLNL/blt.git

CMakeLists.txt

@@ -0,0 +1,44 @@
+cmake_minimum_required( VERSION 3.23.1 )
+
+# Set version number
+set( HPCREACT_VERSION_MAJOR 0 )
+set( HPCREACT_VERSION_MINOR 1 )
+set( HPCREACT_VERSION_PATCHLEVEL 0 )
+
+# check if this is build as a submodule or a separate project
+get_directory_property( parent_dir PARENT_DIRECTORY )
+if(parent_dir)
+    set( is_submodule ON )
+else()
+    set( is_submodule OFF )
+endif()
+
+if( NOT is_submodule )
+    message( "not a submodule")
+    project( hpcReact LANGUAGES CXX C )
+
+    set( BLT_SOURCE_DIR ${PROJECT_SOURCE_DIR}/cmake/blt CACHE PATH "" )
+    set( BLT_CXX_STD "c++17" CACHE STRING "Version of C++ standard" FORCE )
+    set( ENABLE_WARNINGS_AS_ERRORS "ON" CACHE PATH "" )
+
+    option( HPCREACT_ENABLE_UNIT_TESTS "Builds tests" ON )
+
+    option( ENABLE_CUDA "Build with CUDA" OFF )
+    option( ENABLE_HIP "Build with HIP" OFF )
+
+endif()
+
+include( ${BLT_SOURCE_DIR}/SetupBLT.cmake )
+
+include( cmake/CMakeBasics.cmake )
+include( cmake/Macros.cmake )
+#include( cmake/Config.cmake )
+
+
+add_subdirectory( src )
+
+# if( HPCREACT_ENABLE_DOCS )
+#     add_subdirectory( docs )
+# endif()
+
+

README.md

@@ -1,2 +1,2 @@
-# HPCReact
+# hpcReact
 Package for modeling of chemical reactions on High Performance Computing Systems

cmake/CMakeBasics.cmake

@@ -0,0 +1,29 @@
+set(CMAKE_ENABLE_EXPORTS ON)
+
+if( CMAKE_BUILD_TYPE MATCHES "Debug" )
+
+else()
+
+endif()
+
+option( ENABLE_COVERAGE "Enable coverage" OFF )
+#set( SHIVA_BUILD_OBJ_LIBS OFF CACHE BOOL "" )
+
+
+# if( CMAKE_CXX_STANDARD IN_LIST "98; 11; 14" )
+#     MESSAGE(FATAL_ERROR "Shiva requires at least c++17")
+# endif()
+
+
+blt_append_custom_compiler_flag( FLAGS_VAR CMAKE_CXX_FLAGS DEFAULT "${OpenMP_CXX_FLAGS}")
+blt_append_custom_compiler_flag( FLAGS_VAR CMAKE_CXX_FLAGS
+                                 GNU   "-Wpedantic -pedantic-errors -Wshadow -Wfloat-equal -Wcast-align -Wcast-qual"
+                                 CLANG "-Wpedantic -pedantic-errors -Wshadow -Wfloat-equal -Wcast-align -Wcast-qual -Wabsolute-value"
+                               )
+
+blt_append_custom_compiler_flag( FLAGS_VAR CMAKE_CXX_FLAGS_DEBUG
+                                 GNU ""
+                                 CLANG "-fstandalone-debug"
+                                )
+
+set( CAMP_ENABLE_TESTS OFF CACHE BOOL "")