prefixing all options with micm_ (#413)

* prefixing all options with micm_

* correcting target compile options

* namespacing compile option

* prefixing gpu arch with micm

.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"
 }

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.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
 

docker/Dockerfile.nvhpc

@@ -45,8 +45,8 @@ RUN mkdir /cuda_build \
       && cd /cuda_build \ 
       && cmake \
         -D CMAKE_BUILD_TYPE=debug \
-        -D ENABLE_CUDA=ON \
-        -D GPU_TYPE="a100" \
+        -D MICM_ENABLE_CUDA=ON \
+        -D MICM_GPU_TYPE="a100" \
         ../micm \
       && make -j 8 install
 

docker/Dockerfile.openmp

@@ -16,9 +16,9 @@ COPY . /micm/
 RUN mkdir /build \
       && cd /build \
       && cmake  \
-        -D ENABLE_CLANG_TIDY:BOOL=FALSE \
-        -D ENABLE_OPENMP:BOOL=TRUE \
-        -D ENABLE_JSON:BOOL=TRUE \
+        -D MICM_ENABLE_CLANG_TIDY:BOOL=FALSE \
+        -D MICM_ENABLE_OPENMP:BOOL=TRUE \
+        -D MICM_ENABLE_JSON:BOOL=TRUE \
         ../micm \
       && make install -j 8
 

docker/Dockerfile.publish

@@ -19,8 +19,8 @@ RUN mkdir /build \
       && cd /build \
       && cmake \
         -D CMAKE_BUILD_TYPE=release \
-        -D ENABLE_LLVM:BOOL=TRUE \
-        -D ENABLE_JSON:BOOL=TRUE \
+        -D MICM_ENABLE_LLVM:BOOL=TRUE \
+        -D MICM_ENABLE_JSON:BOOL=TRUE \
         ../micm \
       && make install -j 8
 

docs/source/contributing/index.rst

@@ -63,7 +63,7 @@ From the root directory of micm:
   cd docs 
   pip install -r requirements.txt
   cd .. && mkdir build && cd build
-  cmake -DBUILD_DOCS=ON ..
+  cmake -DMICM_BUILD_DOCS=ON ..
   make docs
   open docs/sphinx/index.html 
 
@@ -77,7 +77,7 @@ Venv
   cd docs 
   pip install -r requirements.txt
   cd .. && mkdir build && cd build
-  cmake -DBUILD_DOCS=ON ..
+  cmake -DMICM_BUILD_DOCS=ON ..
   make docs
   open docs/sphinx/index.html 
 
@@ -91,6 +91,6 @@ Conda
   cd docs 
   pip install -r requirements.txt
   cd .. && mkdir build && cd build
-  cmake -DBUILD_DOCS=ON ..
+  cmake -DMICM_BUILD_DOCS=ON ..
   make docs
   open docs/sphinx/index.html 

docs/source/getting_started.rst

@@ -29,7 +29,7 @@ step will simply copy the header files into the normal location required by your
     $ make test
 
 CMake will allow for setting options such as the installation directory
-with CMAKE_INSTALL_PREFIX, or various build flags such as BUILD_DOCS, ENABLE_CUDA, etc.
+with CMAKE_INSTALL_PREFIX, or various build flags such as MICM_BUILD_DOCS, MICM_ENABLE_CUDA, etc.
 
 Options
 -------
@@ -43,13 +43,13 @@ Some of these libraries can be included automatically with cmake build options,
 others require that you have libraries installed on your system.
 
 - JSON configuration support
-  - When building micm, you need to enable the JSON option. This will download and configure the `nlohmann/jsoncpp library <https://github.com/nlohmann/json>`_  for you. For example: ``cmake -DENABLE_JSON=ON ..``
+  - When building micm, you need to enable the JSON option. This will download and configure the `nlohmann/jsoncpp library <https://github.com/nlohmann/json>`_  for you. For example: ``cmake -DMICM_ENABLE_JSON=ON ..``
 - JIT-compiled chemistry functions 
   - This requires `LLVM <https://llvm.org/docs/index.html>`_ to be installed with on your system. Once it is, you can include the jit options with ``cmake -DENBABLE_LLVM=ON ..``
 - GPU support
   - Coming soon
 - OpenMP
-  - On macOS, you either need to configure cmake to use gcc which ships with OpenMP (either ``CXX=g++ cmake -DENABLE_OPENMP=ON ..`` or ``cmake -DCMAKE_CXX_COMPILER=g++ -DENABLE_OPENMP=ON ..``)
+  - On macOS, you either need to configure cmake to use gcc which ships with OpenMP (either ``CXX=g++ cmake -DMICM_ENABLE_OPENMP=ON ..`` or ``cmake -DCMAKE_CXX_COMPILER=g++ -DMICM_ENABLE_OPENMP=ON ..``)
 
 For more ways to build and install micm, see :ref:`Installation and usage`. If you would like instructions for building
 the docs, see :ref:`Contributing`.

docs/source/user_guide/index.rst

@@ -30,7 +30,7 @@ If you would like to include the json examples, you must configure micm to build
 
 .. code-block:: console
   
-    $ cmake -DENABLE_JSON=ON ..
+    $ cmake -DMICM_ENABLE_JSON=ON ..
     $ make
     $ ./test_rate_constants_no_user_defined_example_with_config
     $ ./test_rate_constants_user_defined_example_with_config

include/micm/process/jit_process_set.hpp

@@ -15,7 +15,7 @@ namespace micm
 
   /// @brief JIT-compiled solver function calculators for a collection of processes
   ///        The template parameter is the number of grid cells to solve simultaneously
-  template<std::size_t L = DEFAULT_VECTOR_SIZE>
+  template<std::size_t L = MICM_DEFAULT_VECTOR_SIZE>
   class JitProcessSet : public ProcessSet
   {
     std::shared_ptr<JitCompiler> compiler_;

include/micm/solver/jit_lu_decomposition.hpp

@@ -16,7 +16,7 @@ namespace micm
   ///
   /// See LuDecomposition class description for algorithm details
   /// The template parameter is the number of blocks (i.e. grid cells) in the block-diagonal matrix
-  template<std::size_t L = DEFAULT_VECTOR_SIZE>
+  template<std::size_t L = MICM_DEFAULT_VECTOR_SIZE>
   class JitLuDecomposition : public LuDecomposition
   {
     std::shared_ptr<JitCompiler> compiler_;

include/micm/solver/jit_rosenbrock.hpp

@@ -32,8 +32,8 @@ namespace micm
   template<
       template<class> class MatrixPolicy = VectorMatrix,
       template<class> class SparseMatrixPolicy = VectorSparseMatrix,
-      class LinearSolverPolicy = JitLinearSolver<DEFAULT_VECTOR_SIZE, SparseMatrixPolicy>,
-      class ProcessSetPolicy = JitProcessSet<DEFAULT_VECTOR_SIZE>>
+      class LinearSolverPolicy = JitLinearSolver<MICM_DEFAULT_VECTOR_SIZE, SparseMatrixPolicy>,
+      class ProcessSetPolicy = JitProcessSet<MICM_DEFAULT_VECTOR_SIZE>>
   class JitRosenbrockSolver : public RosenbrockSolver<MatrixPolicy, SparseMatrixPolicy, LinearSolverPolicy, ProcessSetPolicy>
   {
     std::shared_ptr<JitCompiler> compiler_;