Merge branch 'main' into release

.devcontainer/devcontainer.json

@@ -6,5 +6,5 @@
   ],
   "settings": {
   },
-  "postCreateCommand": "cd /workspaces/micm && mkdir build && cd build && cmake -D CMAKE_BUILD_TYPE=release -D ENABLE_CLANG_TIDY:BOOL=FALSE -D ENABLE_LLVM:BOOL=TRUE -D ENABLE_MEMCHECK:BOOL=TRUE .. && make install -j 2"
+  "postCreateCommand": "cd /workspaces/micm && mkdir build && cd build && cmake -D CMAKE_BUILD_TYPE=release -D MICM_ENABLE_LLVM:BOOL=TRUE -D MICM_ENABLE_MEMCHECK:BOOL=TRUE .. && make install -j 2"
 }

.github/workflows/docker_and_coverage.yml

@@ -23,19 +23,23 @@ jobs:
           - Dockerfile.no_json
           - Dockerfile.nvhpc
           - Dockerfile.openmp
-          # - Dockerfile.intel # intel image is too large for GH action
+          - Dockerfile.intel
           # - Dockerfile.mpi
     steps:
       - name: Checkout code
         uses: actions/checkout@v3
         with:
           submodules: recursive
+
+      - name: Delete huge unnecessary tools folder
+        run: rm -rf /opt/hostedtoolcache
 
       - name: Build Docker image
         run: docker build -t micm -f docker/${{ matrix.dockerfile }} .
 
       - name: Run tests in container
-        if: matrix.dockerfile != 'Dockerfile.coverage'
+        # only run this if we are not running coverage tests or have built the cuda files
+        if: matrix.dockerfile != 'Dockerfile.coverage' && matrix.dockerfile != 'Dockerfile.nvhpc'
         run: docker run --name test-container -t micm bash -c 'make test ARGS="--rerun-failed --output-on-failure -j8"'
 
       - name: Run coverage tests in container

.github/workflows/windows.yml

@@ -45,12 +45,7 @@ jobs:
     - uses: actions/checkout@v3
 
     - name: Run CMake
-      run: cmake -S . -B build -G "Visual Studio 16 2019" -A ${{ matrix.architecture }}
-      if: matrix.build_type == 'Release'
-
-    - name: Run CMake
-      run: cmake -S . -B build -G "Visual Studio 16 2019" -A ${{ matrix.architecture }}
-      if: matrix.build_type == 'Debug'
+      run: cmake -S . -B build -G "Visual Studio 16 2019" -A ${{ matrix.architecture }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }}
 
     - name: Build
       run: cmake --build build --config ${{ matrix.build_type }} --parallel 10
@@ -82,11 +77,7 @@ jobs:
     steps:
     - uses: actions/checkout@v3
     - name: Run CMake
-      run: cmake -S . -B build -G "Visual Studio 17 2022" -A ${{ matrix.architecture }}
-      if: matrix.build_type == 'Release'
-    - name: Run CMake
-      run: cmake -S . -B build -G "Visual Studio 17 2022" -A ${{ matrix.architecture }}
-      if: matrix.build_type == 'Debug'
+      run: cmake -S . -B build -G "Visual Studio 17 2022" -A ${{ matrix.architecture }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }}
     - name: Build
       run: cmake --build build --config ${{ matrix.build_type }} --parallel 10
     - name: Test

CITATION.cff

@@ -0,0 +1,30 @@
+cff-version: 1.2.0
+message: If you use this software, please cite it as below.
+title: Model Independent Chemistry Model (MICM)
+version: v3.3.1
+doi: "10.5281/zenodo.10472189"
+authors:
+  - family-names: Dawson
+    given-names: Matthew
+  - family-names: Sun
+    given-names: Jian
+  - family-names: Shores
+    given-names: Kyle
+  - family-names: Fillmore
+    given-names: David
+  - family-names: Tan
+    given-names: Qina
+  - family-names: Craig
+    given-names: Cheryl
+  - family-names: Gim
+    given-names: Jiwon
+  - family-names: Waxmonsky
+    given-names: Michael
+  - family-names: Vitt
+    given-names: Francis
+  - family-names: Conley
+    given-names: Andrew
+  - family-names: Karsenti
+    given-names: Aharon
+license: Apache-2.0
+url: "https://github.com/NCAR/micm"

CMakeLists.txt

@@ -27,31 +27,29 @@ set(CMAKE_MODULE_PATH "${CMAKE_MODULE_PATH};${PROJECT_SOURCE_DIR}/cmake")
 # Set up include and lib directories
 set(MICM_LIB_DIR "${PROJECT_BINARY_DIR}/lib")
 
-option(ENABLE_CLANG_TIDY "Enable clang-tiday to format source code" OFF)
-option(ENABLE_MPI "Enable MPI parallel support" OFF)
-option(ENABLE_OPENMP "Enable OpenMP support" OFF)
-option(ENABLE_COVERAGE "Enable code coverage output" OFF)
-option(ENABLE_MEMCHECK "Enable memory checking in tests" OFF)
-option(ENABLE_JSON "Enable json configureation file reading" ON)
-option(BUILD_DOCS "Build the documentation" OFF)
-option(ENABLE_CUDA "Build with Cuda support" OFF)
-option(ENABLE_OPENACC "Build with OpenACC Support" OFF)
-option(ENABLE_LLVM "Build with LLVM support for JIT-compiling" OFF)
-option(ENABLE_TESTS "Build the tests" ON)
-option(ENABLE_EXAMPLES "Build the examples" ON)
-set(DEFAULT_VECTOR_MATRIX_SIZE "4" CACHE STRING "Default size for vectorizable matrix types")
+option(MICM_ENABLE_CLANG_TIDY "Enable clang-tiday to format source code" OFF)
+option(MICM_ENABLE_MPI "Enable MPI parallel support" OFF)
+option(MICM_ENABLE_OPENMP "Enable OpenMP support" OFF)
+option(MICM_ENABLE_COVERAGE "Enable code coverage output" OFF)
+option(MICM_ENABLE_MEMCHECK "Enable memory checking in tests" OFF)
+option(MICM_ENABLE_JSON "Enable json configureation file reading" ON)
+option(MICM_BUILD_DOCS "Build the documentation" OFF)
+option(MICM_ENABLE_CUDA "Build with Cuda support" OFF)
+option(MICM_ENABLE_OPENACC "Build with OpenACC Support" OFF)
+option(MICM_ENABLE_LLVM "Build with LLVM support for JIT-compiling" OFF)
+option(MICM_ENABLE_TESTS "Build the tests" ON)
+option(MICM_ENABLE_EXAMPLES "Build the examples" ON)
+set(MICM_DEFAULT_VECTOR_MATRIX_SIZE "4" CACHE STRING "Default size for vectorizable matrix types")
 
 include(CMakeDependentOption)
 # Option to collect custom OpenACC flags
-cmake_dependent_option(ENABLE_GPU_TYPE "Enable custom CUDA flags" OFF
-  "ENABLE_OPENACC OR ENABLE_CUDA" ON)
+cmake_dependent_option(MICM_ENABLE_GPU_TYPE "Enable custom CUDA flags" OFF
+  "MICM_ENABLE_OPENACC OR MICM_ENABLE_CUDA" ON)
 
-if(ENABLE_GPU_TYPE)
-  set(GPU_TYPE "" CACHE STRING "The GPU type being targeted")
+if(MICM_ENABLE_GPU_TYPE)
+  set(MICM_GPU_TYPE "" CACHE STRING "The GPU type being targeted")
 endif()
 
-add_compile_definitions(DEFAULT_VECTOR_SIZE=${DEFAULT_VECTOR_MATRIX_SIZE})
-
 # on ubuntu with clang, an incorrect version of the c++ standard library was being linked
 if (${CMAKE_HOST_SYSTEM_NAME} MATCHES "Linux" AND "${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
     # If the compiler is Clang, use libc++
@@ -68,16 +66,16 @@ include(cmake/dependencies.cmake)
 
 add_subdirectory(src)
 
-if(BUILD_DOCS)
+if(MICM_BUILD_DOCS)
   add_subdirectory(docs)
 endif()
 
 ################################################################################
 # Tests
 
-if(PROJECT_IS_TOP_LEVEL AND ENABLE_TESTS)
+if(PROJECT_IS_TOP_LEVEL AND MICM_ENABLE_TESTS)
   # Test code coverage
-  if(ENABLE_COVERAGE)
+  if(MICM_ENABLE_COVERAGE)
     include(CodeCoverage)
     append_coverage_compiler_flags()
     setup_target_for_coverage_lcov(
@@ -111,14 +109,14 @@ endif()
 ################################################################################
 # Command-line driver examples
 
-if(PROJECT_IS_TOP_LEVEL AND ENABLE_EXAMPLES AND ENABLE_JSON)
+if(PROJECT_IS_TOP_LEVEL AND MICM_ENABLE_EXAMPLES AND MICM_ENABLE_JSON)
   add_subdirectory(examples)
 endif()
 
 ################################################################################
 # Copy configuration data
 
-if(PROJECT_IS_TOP_LEVEL AND (ENABLE_TESTS OR ENABLE_EXAMPLES))
+if(PROJECT_IS_TOP_LEVEL AND (MICM_ENABLE_TESTS OR MICM_ENABLE_EXAMPLES))
   add_custom_target(copy_example_configs ALL ${CMAKE_COMMAND} -E copy_directory
     ${CMAKE_SOURCE_DIR}/examples/configs ${CMAKE_BINARY_DIR}/examples/configs)
 endif()

cmake/StaticAnalyzers.cmake

@@ -1,6 +1,6 @@
 # modified from https://github.com/filipdutescu/modern-cpp-template/blob/master/cmake/StaticAnalyzers.cmake
 
-if(ENABLE_CLANG_TIDY)
+if(MICM_ENABLE_CLANG_TIDY)
   find_program(CLANGTIDY clang-tidy)
   if(CLANGTIDY)
     set(CMAKE_CXX_CLANG_TIDY ${CLANGTIDY} -extra-arg=-Wno-unknown-warning-option)

cmake/dependencies.cmake

@@ -3,7 +3,7 @@ include(FetchContent)
 ################################################################################
 # Memory check
 
-if(ENABLE_MEMCHECK)
+if(MICM_ENABLE_MEMCHECK)
   find_file(MEMCHECK_SUPPRESS_FILE
     DOC "Suppression file for memory checking"
     NAMES openmpi-valgrind.supp
@@ -22,7 +22,7 @@ endif()
 ################################################################################
 # OpenMP
 
-if(ENABLE_OPENMP)
+if(MICM_ENABLE_OPENMP)
   if(APPLE)
     # Apple clang by default doesn't include support for openmp
     # but if omp was installed with `brew install libomp`, support can be configured
@@ -65,7 +65,7 @@ endif()
 ################################################################################
 # MPI
 
-if(ENABLE_MPI)
+if(MICM_ENABLE_MPI)
   find_package(MPI REQUIRED)
   message(STATUS "Compiling with MPI support")
 endif()
@@ -94,7 +94,7 @@ endif()
 ################################################################################
 # nlohmann::json
 
-if(ENABLE_JSON)
+if(MICM_ENABLE_JSON)
   FetchContent_Declare(json
       GIT_REPOSITORY https://github.com/nlohmann/json.git
       GIT_TAG v3.11.2
@@ -105,20 +105,20 @@ endif()
 ################################################################################
 # Docs
 
-if(BUILD_DOCS)
+if(MICM_BUILD_DOCS)
   find_package(Doxygen REQUIRED)
   find_package(Sphinx REQUIRED)
 endif()
 
 ################################################################################
 # GPU Support
 
-if(ENABLE_CUDA)
+if(MICM_ENABLE_CUDA)
   find_package(CUDA REQUIRED)
   enable_language(CUDA)
 endif()
 
-if(ENABLE_OPENACC)
+if(MICM_ENABLE_OPENACC)
   find_package(OpenACC REQUIRED)
 endif()
 
@@ -127,7 +127,7 @@ endif()
 #
 # TODO: Try to use fetch content for LLVM libraries
 
-if(ENABLE_LLVM)
+if(MICM_ENABLE_LLVM)
   find_package(LLVM REQUIRED CONFIG)
   if(LLVM_FOUND)
     message(STATUS "Found LLVM ${LLVM_PACKAGE_VERSION}")

cmake/test_util.cmake

@@ -1,7 +1,7 @@
 ################################################################################
 # Utility functions for creating tests
 
-if(ENABLE_MEMCHECK)
+if(MICM_ENABLE_MEMCHECK)
   find_program(MEMORYCHECK_COMMAND "valgrind")
 endif()
 
@@ -37,7 +37,7 @@ endfunction(create_standard_test)
 # Add a test
 
 function(add_micm_test test_name test_binary test_args working_dir test_skip_memcheck)
-  if(ENABLE_MPI)
+  if(MICM_ENABLE_MPI)
     add_test(NAME ${test_name}
       COMMAND mpirun -v -np 2 ${CMAKE_BINARY_DIR}/${test_binary} ${test_args}
              WORKING_DIRECTORY ${working_dir})
@@ -49,11 +49,11 @@ function(add_micm_test test_name test_binary test_args working_dir test_skip_mem
   set(MEMORYCHECK_COMMAND_OPTIONS "--error-exitcode=1 --trace-children=yes --leak-check=full --gen-suppressions=all ${MEMCHECK_SUPPRESS}")
   set(memcheck "${MEMORYCHECK_COMMAND} ${MEMORYCHECK_COMMAND_OPTIONS}")
   separate_arguments(memcheck)
-  if(ENABLE_MPI AND MEMORYCHECK_COMMAND AND ENABLE_MEMCHECK AND NOT test_skip_memcheck)
+  if(MICM_ENABLE_MPI AND MEMORYCHECK_COMMAND AND MICM_ENABLE_MEMCHECK AND NOT test_skip_memcheck)
     add_test(NAME memcheck_${test_name}
       COMMAND mpirun -v -np 2 ${memcheck} ${CMAKE_BINARY_DIR}/${test_binary} ${test_args}
              WORKING_DIRECTORY ${working_dir})
-  elseif(MEMORYCHECK_COMMAND AND ENABLE_MEMCHECK AND NOT test_skip_memcheck)
+  elseif(MEMORYCHECK_COMMAND AND MICM_ENABLE_MEMCHECK AND NOT test_skip_memcheck)
     add_test(NAME memcheck_${test_name}
              COMMAND ${memcheck} ${CMAKE_BINARY_DIR}/${test_binary} ${test_args}
              WORKING_DIRECTORY ${working_dir})

docker/Dockerfile

@@ -18,7 +18,7 @@ RUN mkdir /build \
       && cd /build \
       && cmake \
         -D CMAKE_BUILD_TYPE=release \
-        -D ENABLE_CLANG_TIDY:BOOL=FALSE \
+        -D MICM_ENABLE_CLANG_TIDY:BOOL=FALSE \
         ../micm \
       && make install -j 8
 

docker/Dockerfile.coverage

@@ -24,11 +24,11 @@ RUN mkdir /build \
       && cd /build \
       && cmake \
         -D CMAKE_BUILD_TYPE=debug \
-        -D ENABLE_CLANG_TIDY:BOOL=FALSE \
-        -D ENABLE_COVERAGE:BOOL=TRUE \
-        -D ENABLE_LLVM:BOOL=TRUE \
-        # -D ENABLE_MPI:BOOL=TRUE \
-        # -D ENABLE_OPENMP:BOOL=TRUE \
+        -D MICM_ENABLE_CLANG_TIDY:BOOL=FALSE \
+        -D MICM_ENABLE_COVERAGE:BOOL=TRUE \
+        -D MICM_ENABLE_LLVM:BOOL=TRUE \
+        # -D MICM_ENABLE_MPI:BOOL=TRUE \
+        # -D MICM_ENABLE_OPENMP:BOOL=TRUE \
         ../micm \
       && make install -j 8
 

docker/Dockerfile.docs

@@ -26,7 +26,7 @@ RUN echo "The suffix is '$SWITCHER_SUFFIX'"
 
 RUN mkdir /build \
       && cd /build \
-      && cmake -D BUILD_DOCS=ON \
+      && cmake -D MICM_BUILD_DOCS=ON \
                /micm \
       && make docs
 

docker/Dockerfile.intel

@@ -28,7 +28,6 @@ RUN mkdir /build \
       && cd /build \ 
       && cmake \
         -D CMAKE_BUILD_TYPE=release \
-        # -D CMAKE_CXX_FLAGS_DEBUG="-g -Rno-debug-disables-optimization" \
         ../micm \
       && make -j 8 install
 

docker/Dockerfile.llvm

@@ -21,9 +21,9 @@ RUN mkdir /build \
       && cd /build \
       && cmake \
         -D CMAKE_BUILD_TYPE=release \
-        -D ENABLE_CLANG_TIDY:BOOL=FALSE \
-        -D ENABLE_LLVM:BOOL=TRUE \
-        -D ENABLE_MEMCHECK:BOOL=TRUE \
+        -D MICM_ENABLE_CLANG_TIDY:BOOL=FALSE \
+        -D MICM_ENABLE_LLVM:BOOL=TRUE \
+        -D MICM_ENABLE_MEMCHECK:BOOL=TRUE \
         ../micm \
       && make install -j 8
 

docker/Dockerfile.memcheck

@@ -17,8 +17,8 @@ RUN mkdir /build \
       && cd /build \
       && cmake \
         -D CMAKE_BUILD_TYPE=release \
-        -D ENABLE_CLANG_TIDY:BOOL=FALSE \
-        -D ENABLE_MEMCHECK:BOOL=TRUE \
+        -D MICM_ENABLE_CLANG_TIDY:BOOL=FALSE \
+        -D MICM_ENABLE_MEMCHECK:BOOL=TRUE \
         ../micm \
       && make install -j 8
 

docker/Dockerfile.mpi

@@ -20,8 +20,8 @@ ENV OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 RUN mkdir /build \
       && cd /build \
       && cmake \
-        -D ENABLE_CLANG_TIDY:BOOL=FALSE \
-        -D ENABLE_MPI:BOOL=TRUE \
+        -D MICM_ENABLE_CLANG_TIDY:BOOL=FALSE \
+        -D MICM_ENABLE_MPI:BOOL=TRUE \
         ../micm \
       && make install -j 8