Another major restructuring to place the python code more central to …

…the project. More inclusion of scikit-build stuff in the cmake files, though not complete

CMakeLists.txt

@@ -7,65 +7,58 @@
 # You should have received a copy of the GNU General Public License along with Swiftest. 
 # If not, see: https://www.gnu.org/licenses. 
 
-# CMake project file for SWIFTEST
-
+# CMake project file for Swiftest
 ##################################################
 # Define the project and the depencies that it has
 ##################################################
 
 CMAKE_MINIMUM_REQUIRED(VERSION 3.20.1)
 # Get version stored in text file
 FILE(READ "version.txt" VERSION)
-PROJECT(swiftest VERSION ${VERSION} LANGUAGES Fortran)
+PROJECT(swiftest VERSION ${VERSION} LANGUAGES C Fortran)
+
+# The following section is modified from Numpy f2py documentation
+IF(PROJECT_SOURCE_DIR STREQUAL PROJECT_BINARY_DIR)
+  MESSAGE(FATAL_ERROR "In-source builds not allowed. Please make a new directory (called a build directory) and run CMake from there.\n")
+ENDIF()
+
+# Ensure scikit-build modules
+IF (NOT SKBUILD)
+  FIND_PACKAGE(Python3 COMPONENTS Interpreter Development REQUIRED)
+  EXECUTE_PROCESS(
+    COMMAND "${Python3_EXECUTABLE}"
+    -c "import os, skbuild; print(os.path.dirname(skbuild.__file__))"
+    OUTPUT_VARIABLE SKBLD_DIR
+    OUTPUT_STRIP_TRAILING_WHITESPACE
+  )
+  LIST(APPEND CMAKE_MODULE_PATH "${SKBLD_DIR}/resources/cmake")
+  MESSAGE(STATUS "Looking in ${SKBLD_DIR}/resources/cmake for CMake modules")
+ENDIF()
+
+# scikit-build style includes
+FIND_PACKAGE(Cython REQUIRED)
+SET(PYTHON_EXTENSION_MODULE_SUFFIX "${Python3_SOABI}" CACHE STRING "Suffix for python extension modules")
+
+# Communicate version number and other CMake build variables to the source code
+SET(SETUP_PY_IN "${PROJECT_SOURCE_DIR}/setup.py.in")
+SET(SETUP_PY_OUT "${PROJECT_SOURCE_DIR}/setup.py")
+CONFIGURE_FILE(${SETUP_PY_IN} ${SETUP_PY_OUT})
 
 INCLUDE(CTest)
 
-# Add our local modlues to the module path
-SET(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake/Modules/")
-
-# Uncomment if it is required that Fortran 90 is supported
-IF(NOT CMAKE_Fortran_COMPILER_SUPPORTS_F90)
-    MESSAGE(FATAL_ERROR "Fortran compiler does not support F90")
-ENDIF(NOT CMAKE_Fortran_COMPILER_SUPPORTS_F90)
-
-
-IF (CMAKE_Fortran_COMPILER_ID MATCHES "^Intel")
-    SET(COMPILER_OPTIONS "Intel" CACHE STRING "Compiler identified as Intel")
-ELSEIF (CMAKE_Fortran_COMPILER_ID STREQUAL "GNU")
-    SET(COMPILER_OPTIONS "GNU" CACHE STRING "Compiler identified as gfortran")
-ELSE ()
-    MESSAGE(FATAL_ERROR "Compiler not recognized!") 
-ENDIF ()
+# Add our local modules to the module path
+LIST(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake/Modules/")
 
-# Set some options the user may choose
-OPTION(USE_COARRAY "Use Coarray Fortran for parallelization of test particles" OFF)
-OPTION(USE_OPENMP "Use OpenMP for parallelization" ON)
-OPTION(USE_SIMD "Use SIMD vectorization" ON)
-OPTION(BUILD_SHARED_LIBS "Build using shared libraries" ON)
-
-INCLUDE(${CMAKE_MODULE_PATH}/SetParallelizationLibrary.cmake)
-INCLUDE(${CMAKE_MODULE_PATH}/SetUpNetCDF.cmake)
-IF (COMPILER_OPTIONS STREQUAL "Intel")
-    INCLUDE(${CMAKE_MODULE_PATH}/SetMKL.cmake)
-ENDIF ()
-
-# This INCLUDE statement executes code that sets the compile flags for DEBUG,
-# RELEASE, PROFILING, and TESTING.  
-INCLUDE(${CMAKE_MODULE_PATH}/SetFortranFlags.cmake) 
-
-INCLUDE_DIRECTORIES($ENV{NETCDF_FORTRAN_HOME}/include;$ENV{NETCDF_HOME}/include)
 ############################################################
 # Define the actual files and folders that make up the build
 ############################################################
 
-
 # Define some directories
 SET(SRC ${CMAKE_SOURCE_DIR}/src)
 SET(LIB ${CMAKE_SOURCE_DIR}/lib)
 SET(BIN ${CMAKE_SOURCE_DIR}/bin)
 SET(MOD ${CMAKE_SOURCE_DIR}/include)
-#SET(TEST ${CMAKE_SOURCE_DIR}/test)
-SET(PY ${CMAKE_SOURCE_DIR}/python)
+#SET(TEST ${CMAKE_SOURCE_DIR}/tests)
 
 set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${LIB})
 set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${LIB})
@@ -76,7 +69,6 @@ SET(CMAKE_Fortran_MODULE_DIRECTORY ${MOD})
 
 # The source for the SWIFTEST binary and have it placed in the bin folder
 ADD_SUBDIRECTORY(${SRC} ${BIN})
-ADD_SUBDIRECTORY(${PY})
 
 # # Set up test directory
 # ENABLE_TESTING()

Dockerfile

@@ -16,10 +16,11 @@
 FROM intel/oneapi-hpckit:2023.1.0-devel-ubuntu20.04 as build_deps
 
 ENV INSTALL_DIR="/usr/local"
-ENV CC="${ONEAPI_ROOT}/compiler/latest/linux/bin/icx"
-ENV FC="${ONEAPI_ROOT}/compiler/latest/linux/bin/ifx"
-ENV CXX="${ONEAPI_ROOT}/compiler/latest/linux/bin/icpx"
+ENV FC="${ONEAPI_ROOT}/mpi/latest/bin/mpiifort"
+ENV CC="${ONEAPI_ROOT}/mpi/latest/bin/mpicc -cc=icx"
+ENV CXX="${ONEAPI_ROOT}/mpi/latest/bin/mpicc -cc=icpx"
 ENV F77="${FC}"
+ENV CFLAGS="-fPIC"
 
 # Get the HDF5, NetCDF-C, and NetCDF-Fortran libraries
 RUN wget -qO- https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.14/hdf5-1.14.1/src/hdf5-1.14.1-2.tar.gz | tar xvz && \
@@ -65,7 +66,6 @@ ENV HDF5_INCLUDE_DIR="${HDF5_ROOT}/include"
 ENV HDF5_PLUGIN_PATH="${HDF5_LIBDIR}/plugin"
 
 # NetCDF-Fortran library
-ENV CFLAGS="-fPIC"
 ENV FCFLAGS="${CFLAGS} -standard-semantics"
 ENV FFLAGS=${CFLAGS}
 ENV CPPFLAGS="-I${INSTALL_DIR}/include"
@@ -77,7 +77,8 @@ RUN cd netcdf-fortran-4.6.1 && \
 
 FROM intel/oneapi-hpckit:2023.1.0-devel-ubuntu20.04 as build_driver
 SHELL ["/bin/bash", "-c"]
-COPY --from=build_deps /usr/local/. /usr/local/
+ENV INSTALL_DIR="/usr/local"
+COPY --from=build_deps ${INSTALL_DIR}/. ${INSTALL_DIR}/
 ENV PATH /root/miniconda3/bin:$PATH
 
 RUN wget https://repo.anaconda.com/miniconda/Miniconda3-py311_23.5.2-0-Linux-x86_64.sh  && \
@@ -89,12 +90,6 @@ RUN wget https://repo.anaconda.com/miniconda/Miniconda3-py311_23.5.2-0-Linux-x86
   conda install -c conda-forge scikit-build -y&& \ 
   conda install -c anaconda cython -y
 
-ENV INSTALL_DIR="/usr/local"
-ENV CC="${ONEAPI_ROOT}/compiler/latest/linux/bin/icx"
-ENV FC="${ONEAPI_ROOT}/compiler/latest/linux/bin/ifx"
-ENV CXX="${ONEAPI_ROOT}/compiler/latest/linux/bin/icpx"
-ENV F77="${FC}"
-
 # The MACHINE_CODE_VALUE argument is a string that is used when compiling the swiftest_driver. It is appended to the "-x" compiler 
 # option: (-x${MACHINE_CODE_VALUE}). The default value is set to "sse2" which allows for certain SIMD instructions to be used while 
 # remaining # compatible with a wide range of CPUs. To get the highest performance, you can pass "host" as an argument, but the 
@@ -119,7 +114,7 @@ ENV FC="${ONEAPI_ROOT}/mpi/latest/bin/mpiifort"
 ENV CC="${ONEAPI_ROOT}/mpi/latest/bin/mpicc -cc=icx"
 ENV CXX="${ONEAPI_ROOT}/mpi/latest/bin/mpicc -cc=icpx"
 ENV FFLAGS="-fPIC -standard-semantics"
-ENV LDFLAGS="-L/usr/local/lib"
+ENV LDFLAGS="-L${INSTALL_DIR}/lib"
 ENV LIBS="-lhdf5_hl -lhdf5 -lz"
 
 COPY ./cmake/ /swiftest/cmake/
@@ -138,8 +133,8 @@ RUN cd swiftest && \
   cmake --build build && \
   cmake --install build 
 
-RUN cd swiftest/python && \
-  python setup.py build_ext --inplace 
+# RUN cd swiftest/python && \
+#   python setup.py build_ext --inplace 
 
 
 # This build target creates a container that executes just the driver program
@@ -159,19 +154,20 @@ COPY --from=build_driver /usr/local/lib/libswiftest.a /
 FROM scratch as export_module
 COPY --from=build_driver /swiftest/include/ /swiftest/
 
-
 # This build target creates a container with a conda environment with all dependencies needed to run the Python front end and 
 # analysis tools
 FROM continuumio/miniconda3 as python
 SHELL ["/bin/bash", "--login", "-c"]
+ENV INSTALL_DIR="/usr/local"
+ENV CONDA_DIR="/opt/conda"
 ENV SHELL="/bin/bash"
-ENV PATH="/opt/conda/bin:${PATH}"
-ENV LD_LIBRARY_PATH="/usr/local/lib"
+ENV PATH="${CONDA_DIR}/bin:${PATH}"
+ENV LD_LIBRARY_PATH="${INSTALL_DIR}/lib"
 
-COPY --from=build_driver /usr/local/bin/swiftest_driver /opt/conda/bin/swiftest_driver
-COPY --from=build_driver /usr/local/lib/libswiftest.a  /opt/conda/lib/libswiftest.a
-COPY --from=build_driver /swiftest/include/ /opt/conda/include/swiftest/
-COPY ./python/. /opt/conda/pkgs/swiftest/
+COPY --from=build_driver ${INSTALL_DIR}/bin/swiftest_driver ${CONDA_DIR}/bin/swiftest_driver
+COPY --from=build_driver ${INSTALL_DIR}/lib/libswiftest.a  ${CONDA_DIR}/conda/lib/libswiftest.a
+COPY --from=build_driver /swiftest/include/ ${CONDA_DIR}/include/swiftest/
+COPY ./python/. ${CONDA_DIR}/pkgs/swiftest/
 COPY environment.yml .
 
 RUN conda update --all -y && \

cmake/Modules/FindCoarray_Fortran.cmake

@@ -23,7 +23,7 @@
 
 #=============================================================================
 
-INCLUDE (${CMAKE_ROOT}/Modules/FindPackageHandleStandardArgs.cmake)
+INCLUDE (FindPackageHandleStandardArgs)
 
 STRING(TOUPPER "${CMAKE_BUILD_TYPE}" BT)
 IF(BT STREQUAL "DEBUG")

cmake/Modules/FindOpenMP_Fortran.cmake

@@ -23,7 +23,7 @@
 
 #=============================================================================
 
-INCLUDE (${CMAKE_ROOT}/Modules/FindPackageHandleStandardArgs.cmake)
+INCLUDE (FindPackageHandleStandardArgs)
 
 IF (COMPILER_OPTIONS STREQUAL "Intel")
     IF (USE_SIMD)

cmake/Modules/SetFortranFlags.cmake

@@ -14,7 +14,7 @@
 ####################################################################
 # Make sure that the default build type is RELEASE if not specified.
 ####################################################################
-INCLUDE(${CMAKE_MODULE_PATH}/SetCompileFlag.cmake)
+INCLUDE(SetCompileFlag)
 
 # Make sure the build type is uppercase
 STRING(TOUPPER "${CMAKE_BUILD_TYPE}" BT)

python/setup.py.in → setup.py

@@ -10,18 +10,17 @@
  If not, see: https://www.gnu.org/licenses. 
 """
 
-#from skbuild import setup
-from setuptools import setup
+from skbuild import setup
 from setuptools import find_packages, Extension
 from Cython.Build import cythonize
 import os
 
 # Build the pybindings extension that allows us to run the Fortran driver as a Python module. 
 root_dir = 'pybindings'
-include_dirs = "${SWIFTEST_INCLUDE_DIR}"
+include_dirs = ""
 include_dirs = include_dirs.split()
 include_dirs.append(root_dir)
-link_flags = "${SWIFTEST_LINK_FLAGS}"
+link_flags = ""
 link_flags = link_flags.split()
 
 pybindings_extension = [Extension('swiftest.bindings',
@@ -32,7 +31,7 @@
                          )]
 
 setup(name='swiftest',
-      version='${CMAKE_PROJECT_VERSION}',
+      version='2023.8.0',
       author='David A. Minton',
       author_email='daminton@purdue.edu',
       url='https://github.itap.purdue.edu/MintonGroup/swiftest',

src/CMakeLists.txt

@@ -12,6 +12,37 @@ set(GLOBAL_MODULE_IN ${SRC}/globals/globals_module.f90.in)
 set(GLOBAL_MODULE_OUT ${SRC}/globals/globals_module.f90)
 CONFIGURE_FILE(${GLOBAL_MODULE_IN} ${GLOBAL_MODULE_OUT})
 
+IF(NOT CMAKE_Fortran_COMPILER_SUPPORTS_F90)
+    MESSAGE(FATAL_ERROR "Fortran compiler does not support F90")
+ENDIF(NOT CMAKE_Fortran_COMPILER_SUPPORTS_F90)
+
+IF (CMAKE_Fortran_COMPILER_ID MATCHES "^Intel")
+    SET(COMPILER_OPTIONS "Intel" CACHE STRING "Compiler identified as Intel")
+ELSEIF (CMAKE_Fortran_COMPILER_ID STREQUAL "GNU")
+    SET(COMPILER_OPTIONS "GNU" CACHE STRING "Compiler identified as gfortran")
+ELSE ()
+    MESSAGE(FATAL_ERROR "Compiler not recognized!") 
+ENDIF ()
+
+# Set some options the user may choose
+OPTION(USE_COARRAY "Use Coarray Fortran for parallelization of test particles" OFF)
+OPTION(USE_OPENMP "Use OpenMP for parallelization" ON)
+OPTION(USE_SIMD "Use SIMD vectorization" ON)
+OPTION(BUILD_SHARED_LIBS "Build using shared libraries" ON)
+
+INCLUDE(SetParallelizationLibrary)
+INCLUDE(SetUpNetCDF)
+IF (COMPILER_OPTIONS STREQUAL "Intel")
+    INCLUDE(SetMKL)
+ENDIF ()
+
+# This INCLUDE statement executes code that sets the compile flags for DEBUG,
+# RELEASE, PROFILING, and TESTING.  
+INCLUDE(SetFortranFlags) 
+
+INCLUDE_DIRECTORIES($ENV{NETCDF_FORTRAN_HOME}/include;$ENV{NETCDF_HOME}/include)
+
+
 # Add the source files
 SET(STRICT_MATH_FILES
             ${SRC}/collision/collision_generate.f90

src/globals/globals_module.f90

@@ -44,7 +44,7 @@ module globals
    integer(I4B), parameter :: UPPERCASE_OFFSET = iachar('A') - iachar('a') !! ASCII character set parameter for lower to upper 
                                                                            !! conversion - offset between upper and lower
 
-   character(*), parameter :: VERSION = "2023.08.00" !! Swiftest version
+   character(*), parameter :: VERSION = "2023.8.0" !! Swiftest version
 
    !> Symbolic name for integrator types
    character(*), parameter :: UNKNOWN_INTEGRATOR = "UKNOWN INTEGRATOR"