diff --git a/CMake/FindFFTW.cmake b/CMake/FindFFTW.cmake
index 08ece4c55fcdbc1b5305b1d5770a97d333496f84..cfef1dff0a491254d77d9f48736b46ab73e635bd 100644
--- a/CMake/FindFFTW.cmake
+++ b/CMake/FindFFTW.cmake
@@ -50,7 +50,7 @@
# Examples: fFtW3Q => FFTW3Q, fftw3f-mpi => FFTW3F_MPI
#
# == Using a specific FFTW ==
-# Set the variable ${fftw_DIR} to you desired search paths if it's not in a "classic" place or if you want a specific version.
+# Set the variable ${FFTW_DIR} to your desired search paths if it's not in a standard place or if you want a specific version.
#
# == Checking against a specific version or the library ==
# Not supported yet.
@@ -160,7 +160,7 @@ foreach(fftw_comp ${FFTW_FIND_COMPONENTS})
set(LIBRARY_DIR_FOUND FALSE)
else()
get_filename_component(${COMPONENT}_LIBRARY_DIR "${${COMPONENT}_LIBRARY}" DIRECTORY)
- set(${COMPONENT}_LIBRARY "${library}")
+ #set(${COMPONENT}_LIBRARY "${library}")
set(LIBRARY_DIR_FOUND TRUE)
endif()
@@ -169,12 +169,18 @@ foreach(fftw_comp ${FFTW_FIND_COMPONENTS})
if(FFTWQ_POS EQUAL 0)
if(NOT "${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
set(DEPENDENCIES_FOUND FALSE) # -- only gcc supports quadmaths
- else()
- list(APPEND ${COMPONENT}_LIBRARIES "quadmath")
- list(APPEND ${COMPONENT}_DEFINES "-DHAS_QUADMATHS")
- list(APPEND FFTW_COMPILE_FLAGS "-fext-numeric-literals")
- set(DEPENDENCIES_FOUND TRUE)
- endif()
+ else()
+ find_library(QUADMATHLIB
+ NAMES quadmath
+ )
+ if(QUADMATHLIB_FOUND)
+ list(APPEND ${COMPONENT}_LIBRARIES ${QUADMATHLIB})
+ #list(APPEND ${COMPONENT}_LIBRARIES "quadmath")
+ list(APPEND ${COMPONENT}_DEFINES "-DHAS_QUADMATHS")
+ list(APPEND FFTW_COMPILE_FLAGS "-fext-numeric-literals")
+ set(DEPENDENCIES_FOUND TRUE)
+ endif()
+ endif()
else()
set(DEPENDENCIES_FOUND TRUE)
endif()
@@ -217,7 +223,6 @@ foreach(fftw_comp ${FFTW_FIND_COMPONENTS})
unset(component)
unset(COMPONENT)
endforeach()
-
list(REMOVE_DUPLICATES FFTW_INCLUDE_DIRS)
list(REMOVE_DUPLICATES FFTW_LIBRARY_DIRS)
list(REMOVE_DUPLICATES FFTW_LIBRARIES)
diff --git a/CMake/HySoPInstallSetup.cmake b/CMake/HySoPInstallSetup.cmake
old mode 100644
new mode 100755
index ee14dcb52e25c91fcd9fbeb045cec30e954194d1..e977a87a7b10f190f8d0950d755f08b45c8bfff0
--- a/CMake/HySoPInstallSetup.cmake
+++ b/CMake/HySoPInstallSetup.cmake
@@ -27,95 +27,31 @@
#
#
-# Function to compute the install path/options
-#
-# Usage :
-# set_install_options()
-#
-# Resutl :
-# - set CMAKE_INSTALL_PREFIX (directory where lib and packages
-# will be installed)
-# - set install-opt : list of options given to 'python setup.py install' command.
-#
-function(set_install_options)
- # CMAKE_INSTALL_PREFIX given in cmake options :
- if(NOT restart)
- if(NOT CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
- set(restart 1 CACHE INTERNAL "True if this is not the first cmake run.")
- # if 'CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT' is false, it means
- # that -DCMAKE_INSTALL_PREFIX=something has been given to cmake.
- # A prefix is given by user. installation in PREFIX
- # (as python --prefix=<PREFIX>).
- set(install-opt "--prefix=${CMAKE_INSTALL_PREFIX}" CACHE INTERNAL
- "options for python installer")
- # Need to set the CMAKE_INSTALL_PREFIX to the proper site
- # (subdirectory of PREFIX)
- # Get python install suffix (~> lib/pythonX.X/site-packages) from numpy package
- set(PYTHON_COMMAND_GET_INSTALL_DIR
- "import os, re, numpy; print os.path.join(os.path.join(\"${CMAKE_INSTALL_PREFIX}\",*re.compile('/numpy/__init__.py.*').sub('',numpy.__file__).split('/')[-3:]), \"${PROJECT_NAME}\")")
- else()
- # Default case, check virtualenv
- set(restart 1 CACHE INTERNAL "True if this is not the first cmake run.")
- # First, we need to check if '--user' option works in the current environment.
- execute_process(COMMAND ${PYTHON_EXECUTABLE} -c
- "import site; print site.ENABLE_USER_SITE" OUTPUT_VARIABLE ENABLE_USER)
- string(STRIP ${ENABLE_USER} ENABLE_USER)
- if(ENABLE_USER)
- # Default prefix (as python --user) -> installation in site.USER_SITE
- execute_process(COMMAND ${PYTHON_EXECUTABLE} -c
- "import site; print site.USER_BASE" OUTPUT_VARIABLE USER_BASE)
- set(install-opt "--prefix=${USER_BASE}" CACHE INTERNAL "")
- # Need to set the CMAKE_INSTALL_PREFIX to site.USER_SITE
- # Get python user site and install path = USER_SITE + project_name
- set(PYTHON_COMMAND_GET_INSTALL_DIR
- "import site, os, sys ; print os.path.join(site.USER_BASE, os.path.join(\"lib\", os.path.join(\"python\" + str(sys.version_info.major) + '.' + str(sys.version_info.minor), os.path.join(\"site-packages\", \"${PROJECT_NAME}\"))))")
- else()
- # user site not included in the path,
- # which probably means that python is run using virtualenv
- # Command to find 'global' site-packages
- set(GET_SITE_PACKAGE
- "from distutils.sysconfig import get_python_lib; print(get_python_lib())")
- execute_process(COMMAND ${PYTHON_EXECUTABLE} -c
- "${GET_SITE_PACKAGE}" OUTPUT_VARIABLE GLOBAL_SITE_PACKAGE)
- string(STRIP ${GLOBAL_SITE_PACKAGE} GLOBAL_SITE_PACKAGE)
- set(PYTHON_COMMAND_GET_INSTALL_DIR ${GET_SITE_PACKAGE})
- set(install-opt "" CACHE INTERNAL "")
- endif()
- endif()
- # Set the CMAKE_INSTALL_DIR to the proper path
- execute_process(
- COMMAND ${PYTHON_EXECUTABLE} -c "${PYTHON_COMMAND_GET_INSTALL_DIR}"
- OUTPUT_VARIABLE ${PROJECT_NAME}_INSTALL_DIR)
- string(STRIP ${${PROJECT_NAME}_INSTALL_DIR} ${PROJECT_NAME}_INSTALL_DIR)
-
- set(CMAKE_INSTALL_PREFIX ${${PROJECT_NAME}_INSTALL_DIR}
- CACHE PATH "default install path" FORCE)
-
- endif()
-
-endfunction()
-
+include(PythonInstallSetup)
-### Start the configuration for installation ###
-
-set_install_options()
+# =========== Find python install prefix, determined by HYSOP_INSTALL value ===========
+set_python_install_path()
+# ---> set HYSOP_PYTHON_INSTALL_DIR and python_install_options
+# =========== install target ===========
+add_custom_target(python-install
+ COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/setup.py install ${python_install_options}
+ VERBATIM
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} COMMENT "build/install hysop package")
+install(CODE "execute_process(COMMAND ${CMAKE_BUILD_TOOL} python-install WORKING_DIRECTORY \"${CMAKE_CURRENT_BINARY_DIR}\")")
-# Target to remove hysop from install-path.
-if(CMAKE_PATCH_VERSION LESS 12)
- set(${PROJECT_NAME}_PYTHONPATH ${CMAKE_INSTALL_PREFIX}/..)
- get_filename_component(${PROJECT_NAME}_PYTHONPATH ${${PROJECT_NAME}_PYTHONPATH} REALPATH)
-else()
- set(${PROJECT_NAME}_PYTHONPATH ${CMAKE_INSTALL_PREFIX})
- get_filename_component(${PROJECT_NAME}_PYTHONPATH ${${PROJECT_NAME}_PYTHONPATH} DIRECTORY)
+if(USE_FORTRAN)
+ add_dependencies(python-install ${HYSOP_LIBRARY_NAME})
endif()
-set(${PROJECT_NAME}_PYTHONPATH ${${PROJECT_NAME}_PYTHONPATH} CACHE PATH "PYTHONPATH for hysop")
-add_custom_target(uninstall COMMAND rm -rf ${${PROJECT_NAME}_PYTHONPATH}/${PYPACKAGE_NAME}*
- COMMENT "Remove ${${PROJECT_NAME}_PYTHONPATH}/${PYPACKAGE_NAME} directory (hysop package and its dependencies)")
-# To install python package AND hysop library and modules
-add_custom_target(python-install COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/setup.py install ${install-opt} config_fc --f90exec=${CMAKE_Fortran_COMPILER}
- #COMMAND make install
- WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} COMMENT "build/install hysop package")
-install(CODE "execute_process(COMMAND ${CMAKE_BUILD_TOOL} python-install WORKING_DIRECTORY \"${CMAKE_CURRENT_BINARY_DIR}\")")
+# =========== uninstall target ===========
+configure_file(
+ "${CMAKE_CURRENT_SOURCE_DIR}/CMake/cmake_uninstall.cmake.in"
+ "${CMAKE_CURRENT_BINARY_DIR}/cmake_uninstall.cmake"
+ IMMEDIATE @ONLY)
+
+add_custom_target(uninstall
+ echo >> ${CMAKE_CURRENT_BINARY_DIR}/install_manifest.txt
+ COMMAND cat ${CMAKE_CURRENT_BINARY_DIR}/python_install_manifest.txt >> ${CMAKE_CURRENT_BINARY_DIR}/install_manifest.txt
+ COMMAND ${CMAKE_COMMAND} -P ${CMAKE_CURRENT_BINARY_DIR}/cmake_uninstall.cmake)
diff --git a/CMake/HySoPTests.cmake b/CMake/HySoPTests.cmake
old mode 100644
new mode 100755
index f4df2ffc010bc298eb8c3665d7e32f2a3706112b..e9daf953bef516ed2074b891f98e39b3d2bc1d30
--- a/CMake/HySoPTests.cmake
+++ b/CMake/HySoPTests.cmake
@@ -3,25 +3,53 @@
# --> collect test directories/files
# --> create tests (ctest)
#
+# For each function 'test_something' in all files of directories
+# 'tests' a new test is created.
+#
# Those tests will be run after a call to 'make test'
# or a call to ctest.
enable_testing()
find_python_module(pytest REQUIRED)
-# Choose python build dir as directory where tests will be run.
-# --> get build dir for python
-execute_process(
- COMMAND ${PYTHON_EXECUTABLE} -c "import distutils.util as ut ; import distutils.sysconfig as sy; print 'lib.'+ut.get_platform()+'-'+sy.get_python_version()"
- OUTPUT_VARIABLE ${PROJECT_NAME}_PYTHON_BUILD_DIR)
-string(STRIP ${${PROJECT_NAME}_PYTHON_BUILD_DIR} ${PROJECT_NAME}_PYTHON_BUILD_DIR)
+# Declaration of python test
+# Usage:
+# add_python_test(name file)
+# with 'name' is the name of the test and file the source
+# file for the test.
+macro(add_python_test test_name test_file)
+ add_test(${test_name} py.test "${pytest_opt}" ${test_file})
+ set_tests_properties(${test_name} PROPERTIES FAIL_REGULAR_EXPRESSION "FAILURE;Exception;[^x]failed;ERROR;Assertion")
+ set_tests_properties(${test_name} PROPERTIES WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/dataForTests)
+ set_tests_properties(${test_name} PROPERTIES ENVIRONMENT "PYTHONPATH=$ENV{PYTHONPATH}:${HYSOP_BUILD_PYTHONPATH}")
+ set_tests_properties(${test_name} PROPERTIES ENVIRONMENT "PYTHONPATH=$ENV{PYTHONPATH}:${HYSOP_BUILD_PYTHONPATH},LD_LIBRARY_PATH=$ENV{LD_LIBRARY_PATH}:${HYSOP_BUILD_PYTHONPATH}")
+ if(WITH_MPI_TESTS)
+ # Run the same test using mpi multi process run.
+ # The number of processes used is set with NBPROCS_FOR_TESTS variable (user option for cmake, default=8)
+ add_test(${test_name}_mpi ${MPIEXEC} -np ${NBPROCS_FOR_TESTS} ${PYTHON_EXECUTABLE} -m pytest "${pytest_opt}" ${test_file})
+
+ #mpirun -np 1 python -m pytest -v
+
+ set_tests_properties(${test_name}_mpi PROPERTIES FAIL_REGULAR_EXPRESSION "FAILURE;Exception;[^x]failed;ERROR;Assertion")
+ set_tests_properties(${test_name}_mpi PROPERTIES WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/dataForTests)
+ set_tests_properties(${test_name}_mpi PROPERTIES ENVIRONMENT "PYTHONPATH=$ENV{PYTHONPATH}:${HYSOP_BUILD_PYTHONPATH},LD_LIBRARY_PATH=$ENV{LD_LIBRARY_PATH}:${HYSOP_BUILD_PYTHONPATH}")
+ endif()
+
+endmacro()
+# Choose python build dir as directory where tests will be run.
# --> set test dir
-set(testDir ${CMAKE_BINARY_DIR}/build/${${PROJECT_NAME}_PYTHON_BUILD_DIR})
-# 1 - Collect files for Python unitary tests (user-defined) -----
+set(testDir ${HYSOP_BUILD_PYTHONPATH})
+
+# === Tests options ===
+if(FULL_TEST)
+ set(pytest_opt "-s -v -pep8" CACHE INTERNAL "extra options for py.test")
+else()
+ set(pytest_opt "-v" CACHE INTERNAL "extra options for py.test")
+endif()
-# We create a new test for each test_XXX.py found in each directory (i.e. module) of hysop listed below
+# === Set the list of all directories which may contain tests ===
set(py_src_dirs
fields
domain
@@ -29,18 +57,12 @@ set(py_src_dirs
numerics
problem
tools
+ mpi
)
-# If mpi is on, we add test_XXX.py files of hysop/mpi directory
-if(USE_MPI)
- set(py_src_dirs
- ${py_src_dirs} mpi)
-endif()
-
# If GPU is on, we add test_XXX.py files of hysop/gpu directory
if(WITH_GPU)
- set(py_src_dirs
- ${py_src_dirs} gpu)
+ list(APPEND py_src_dirs gpu)
endif()
# Copy the OpenCL sources files to build dir (required since only python files are copied by setup.py)
@@ -57,24 +79,19 @@ foreach(_F ${clfiles})
configure_file(${_F} ${testDir}/${_F} COPYONLY)
endforeach()
+# === Create the files list from all directories in py_src_dirs ===
+
# Build a list of test_*.py files for each directory of hysop/${py_src_dirs}
set(py_test_files)
foreach(testdir ${py_src_dirs})
file(GLOB testfiles RELATIVE ${CMAKE_SOURCE_DIR} hysop/${testdir}/tests/test_*.py)
set(py_test_files ${py_test_files} ${testfiles})
# copy data files
- file(GLOB datfiles hysop/${testdir}/tests/*.dat)
- file(GLOB mapfiles hysop/${testdir}/tests/*.map)
file(GLOB reffiles hysop/${testdir}/tests/ref_files/*)
- set(datafiles ${mapfiles} ${datfiles})
file(COPY ${reffiles} DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/dataForTests)
- foreach(_F ${datafiles})
- get_filename_component(fname ${_F} NAME)
- configure_file(${_F} ${CMAKE_CURRENT_BINARY_DIR}/dataForTests/${fname} COPYONLY)
- endforeach()
endforeach()
-# 2 - Collect files for Python doctest -----
+# Build doctests
# Handling doctest in *.py files recursively for each directory of hysop/${py_src_dirs}
# excluding __init__ or test_ files.
# Doctest are run for every line which contains '>>>'
@@ -89,38 +106,17 @@ foreach(testdir ${py_src_dirs})
endforeach()
endforeach()
-# 3 - Create tests for all collected files -----
-message(STATUS "=== TESTS === ")
+# === Create tests from py_test_files ===
foreach(testfile ${py_test_files})
get_filename_component(testName ${testfile} NAME_WE)
- set(testExe ${testDir}/${testfile})
- message(STATUS "Add test ${testfile} ...")
- if(FULL_TEST)
- add_test(NAME ${testName} WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/dataForTests
- COMMAND py.test -v --pep8 ${testExe})
- else()
- add_test(NAME ${testName} WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/dataForTests
- COMMAND py.test -v ${testExe})
- endif()
-
- # Run the same test using mpi multi process run.
- # The number of processes used is set with NBPROCS_FOR_TESTS variable (user option for cmake, default=8)
- if(WITH_MPI_TESTS)
- message(STATUS "Add test mpi_${testName}.")
- add_test(
- NAME mpi_${testName}
- WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/dataForTests
- COMMAND mpirun -np ${NBPROCS_FOR_TESTS} ${PYTHON_EXECUTABLE} ${testExe}
- )
- set_tests_properties(mpi_${testName}
- PROPERTIES ENVIRONMENT "PYTHONPATH=${testDir}")
- endif()
+ set(exename ${testDir}/${testfile})
+ message(STATUS "Add test ${exename} ...")
+ add_python_test(${testName} ${exename})
endforeach()
# Add files containing doctests
foreach(testfile ${py_doctest_files})
get_filename_component(testName ${testfile} NAME_WE)
- message(STATUS "Add test from doc doctest_${testName} ...")
add_test("doctest_${testName}" py.test -v --doctest-modules ${testfile})
endforeach()
-message(STATUS "===")
+
diff --git a/CMake/HysopVersion.cmake b/CMake/HysopVersion.cmake
new file mode 100644
index 0000000000000000000000000000000000000000..dc6db0275703022bc6bd5c213743d69b693ade6e
--- /dev/null
+++ b/CMake/HysopVersion.cmake
@@ -0,0 +1,5 @@
+# --- set hysop current version ---
+set(MAJOR_VERSION 2)
+set(MINOR_VERSION 0)
+set(PATCH_VERSION 0)
+set(HYSOP_VERSION "${MAJOR_VERSION}.${MINOR_VERSION}.${PATCH_VERSION}")
diff --git a/CMake/MyTools.cmake b/CMake/MyTools.cmake
index 018c8d5ba2315f44bd8a4d25bffeb746501acbfa..bfe3fde4ad943c8b287cb978061ba1df5ce28d50 100644
--- a/CMake/MyTools.cmake
+++ b/CMake/MyTools.cmake
@@ -1,4 +1,7 @@
-include(LibFindMacros)
+#
+# Some convenience macros
+#
+include(CMakeParseArguments)
# -- Basic list manipulation --
# Get first element of list var
@@ -12,23 +15,23 @@ macro(CDR var junk)
endmacro(CDR)
# LIST(APPEND ...) is not correct on <COMPILER>_FLAGS
-macro(APPEND_FLAGS)
+macro(append_flags)
CAR(_V ${ARGV})
CDR(_F ${ARGV})
set(${_V} "${${_V}} ${_F}")
-endmacro(APPEND_FLAGS)
+endmacro(append_flags)
# The use of ADD_DEFINITION results in a warning with Fortran compiler
macro(APPEND_C_FLAGS)
- APPEND_FLAGS(CMAKE_C_FLAGS ${ARGV})
+ append_flags(CMAKE_C_FLAGS ${ARGV})
endmacro(APPEND_C_FLAGS)
macro(APPEND_CXX_FLAGS)
- APPEND_FLAGS(CMAKE_CXX_FLAGS ${ARGV})
+ append_flags(CMAKE_CXX_FLAGS ${ARGV})
endmacro(APPEND_CXX_FLAGS)
macro(APPEND_Fortran_FLAGS)
- APPEND_FLAGS(CMAKE_Fortran_FLAGS ${ARGV})
+ append_flags(CMAKE_Fortran_FLAGS ${ARGV})
endmacro(APPEND_Fortran_FLAGS)
# Scans DIRS (list of directories) and returns a list of all files in those dirs
@@ -109,6 +112,12 @@ macro(display V)
message(STATUS "${V} = ${${V}}")
endmacro(display V)
+macro(ASSERT VAR)
+ if (NOT DEFINED ${VAR})
+ message( FATAL_ERROR "ASSERTION ERROR : ${VAR} UNSET" )
+ endif()
+endmacro()
+
# =======================================
# For a given package name, try to find
# corresponding headers and libraries and
@@ -127,23 +136,54 @@ endmacro(display V)
# with the same 'options' as find_package
# (see http://www.cmake.org/cmake/help/v3.0/command/find_package.html?highlight=find_package)
macro(COMPILE_WITH)
+
+ set(options REQUIRED)
+ set(oneValueArgs ONLY)
+ set(multiValueArgs COMPONENTS)
+
+ cmake_parse_arguments(COMPILE_WITH "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN} )
+
+ set(_NAME)
+ set(_NAME_VERSION)
+
# Get package name and extra args ...
- CAR(_NAME ${ARGV})
- CDR(_REST ${ARGV})
- CAR(_REQ ${_REST})
- if(_REST)
- CDR(_RREST ${_REST})
- CAR(_COMP ${_RREST})
- endif(_REST)
- string(TOUPPER ${_NAME} _UNAME)
+ CAR(_NAME ${COMPILE_WITH_UNPARSED_ARGUMENTS})
+ CDR(_NAME_VERSION ${COMPILE_WITH_UNPARSED_ARGUMENTS})
+
+ set(_NAMES)
+ STRING(TOUPPER ${_NAME} _UNAME)
list(APPEND _NAMES ${_NAME})
list(APPEND _NAMES ${_UNAME})
set(_FOUND)
- find_package(${ARGV})
-
- foreach(_N ${_NAMES})
+
+ if(COMPILE_WITH_COMPONENTS)
+ set(_COMPONENTS COMPONENTS ${COMPILE_WITH_COMPONENTS})
+ set(_COMPONENTS_STR "components ${COMPILE_WITH_COMPONENTS} of the package")
+ else()
+ set(_COMPONENTS)
+ set(_COMPONENTS_STR "package")
+ endif()
+
+ if(${COMPILE_WITH_REQUIRED})
+ set(_REQUIRED REQUIRED)
+ set(_REQUIRED_STR "required")
+ else()
+ set(_REQUIRED)
+ set(_REQUIRED_STR "optional")
+ endif()
+
+ if(_NAME_VERSION)
+ set(_NAME_VERSION_STR "version ${_NAME_VERSION}")
+ else()
+ set(_NAME_VERSION_STR "")
+ endif()
+
+ FIND_PACKAGE(${_NAME} ${_NAME_VERSION} ${_COMPONENTS} ${_REQUIRED})
+ set(_LINK_LIBRARIES)
+ FOREACH(_N ${_NAMES})
if(${_N}_FOUND)
set(_FOUND TRUE)
+ set(_NAME_VERSION_STR "version ${${_N}_VERSION}")
# add headers dirs into 'include' path
# INCLUDE_DIR var name depends on FindNAME
# We try to check the standard var names.
@@ -158,8 +198,7 @@ macro(COMPILE_WITH)
endif()
# Now we set list of libs that must be linked with.
if(DEFINED ${_N}_LIBRARIES)
- set(HYSOP_LINK_LIBRARIES ${HYSOP_LINK_LIBRARIES}
- ${${_N}_LIBRARIES})
+ list(APPEND _LINK_LIBRARIES ${${_N}_LIBRARIES})
endif()
# And the compiler flags
if(DEFINED ${_N}_DEFINITIONS)
@@ -170,13 +209,59 @@ macro(COMPILE_WITH)
endif()
endif()
endforeach()
- list(REMOVE_DUPLICATES HYSOP_LINK_LIBRARIES)
- set(HYSOP_LINK_LIBRARIES ${HYSOP_LINK_LIBRARIES}
- ${${_N}_LIBRARIES} CACHE INTERNAL "List of external libraries.")
+ if(_LINK_LIBRARIES)
+ list(REMOVE_DUPLICATES _LINK_LIBRARIES)
+ foreach(_lib ${_LINK_LIBRARIES})
+ get_filename_component(libpath ${_lib} DIRECTORY)
+ list(FIND CMAKE_C_IMPLICIT_LINK_DIRECTORIES "${libpath}" isSystemDir)
+ if(${isSystemDir} GREATER -1)
+ list(GET CMAKE_C_IMPLICIT_LINK_DIRECTORIES ${isSystemDir} result)
+ if("${libpath}" STRGREATER "${result}")
+ message("oiaoazoazioazioza ${_lib}")
+ list(APPEND CMAKE_INSTALL_RPATH "${libpath}")
+ list(APPEND CMAKE_BUILD_RPATH "${libpath}")
+ endif()
+ else()#"${isSystemDir}" STREQUAL "-1")
+ #get_property(libpath SOURCE ${_lib} PROPERTY LOCATION)
+ list(APPEND CMAKE_INSTALL_RPATH "${libpath}")
+ list(APPEND CMAKE_BUILD_RPATH "${libpath}")
+ endif()
+ endforeach()
+ if(CMAKE_INSTALL_RPATH)
+ list(REMOVE_DUPLICATES CMAKE_INSTALL_RPATH)
+ endif()
+ if(CMAKE_BUILD_RPATH)
+ list(REMOVE_DUPLICATES CMAKE_BUILD_RPATH)
+ endif()
+ endif()
+ if(COMPILE_WITH_ONLY)
+ set(_sico_component ${COMPILE_WITH_ONLY})
+ set(${_sico_component}_LINK_LIBRARIES ${${_sico_component}_LINK_LIBRARIES}
+ ${_LINK_LIBRARIES} CACHE INTERNAL "List of external libraries for ${_sico_component}.")
+ else()
+ set(HYSOP_LINK_LIBRARIES ${HYSOP_LINK_LIBRARIES}
+ ${_LINK_LIBRARIES} CACHE INTERNAL "List of external libraries.")
+ endif()
+
+ IF (_FOUND)
+ message(STATUS "Compilation with ${_REQUIRED_STR} ${_COMPONENTS_STR} ${_NAME} ${_NAME_VERSION_STR}")
+ else()
+ message(STATUS "Compilation without ${_REQUIRED_STR} ${_COMPONENTS_STR} ${_NAME} ${_NAME_VERSION_STR}")
+ endif()
+
set(_N)
set(_NAME)
+ set(_NAME_VERSION)
+ set(_NAME_VERSION_STR)
set(_UNAME)
set(_NAMES)
+ set(_FOUND)
+ set(_REQUIRED)
+ set(_REQUIRED_STR)
+ set(_COMPONENTS)
+ set(_COMPONENTS_STR)
+ set(_VERSION_STR)
+
endmacro(COMPILE_WITH)
# ==== Save directories required for include_directory ===
diff --git a/CMake/PythonInstallSetup.cmake b/CMake/PythonInstallSetup.cmake
new file mode 100755
index 0000000000000000000000000000000000000000..4a49efe24eb61b4a3afa697a3f583644801b623b
--- /dev/null
+++ b/CMake/PythonInstallSetup.cmake
@@ -0,0 +1,112 @@
+# --- Function to compute the install path/options ---
+#
+# Usage :
+# set_install_options()
+#
+# Read HYSOP_INSTALL option (from user input)
+# and set python install dir according to its value.
+#
+# Summary :
+# cmake path-to-your-sources -Dpython_install_dir=standard
+# make install
+#
+# ---> install in 'system' python site-package
+#
+# cmake path-to-your-sources -Dpython_install_dir=user
+# make install
+#
+# ---> install in USER_SITE (no virtualenv case)
+# ---> install in site-packages of your virtualenv
+#
+# cmake path-to-your-sources -Dpython_install_dir=prefix -DCMAKE_INSTALL_PREFIX=/some/install/path
+# make install
+#
+# ---> install in CMAKE_INSTALL_PREFIX
+#
+# If /some/install/path is not a standard path of your system,
+# you'll probably need something like :
+# export PYTHONPATH=${PYTHONPATH}:/some/install/path
+#
+#
+function(set_python_install_path)
+ set(python_install_options "--record;${CMAKE_BINARY_DIR}/python_install_manifest.txt")
+
+ if(HYSOP_INSTALL STREQUAL "user")
+ # --- Case 1 : HYSOP_INSTALL=user ---
+ # In that case, we need to find the user path. It depends on the operating system
+ # and on which python is used (virtualenv or not)
+ # First, we need to check if '--user' option works in the current environment.
+ execute_process(COMMAND ${PYTHON_EXECUTABLE} -c
+ "import site; print site.ENABLE_USER_SITE" OUTPUT_VARIABLE ENABLE_USER)
+ string(STRIP ${ENABLE_USER} ENABLE_USER)
+
+ if(ENABLE_USER) # --user works ...
+ # Find install path for --user (site.USER_SITE)
+ execute_process(COMMAND ${PYTHON_EXECUTABLE} -c
+ "import site; print site.USER_BASE" OUTPUT_VARIABLE USER_BASE)
+ string(STRIP ${USER_BASE} USER_BASE)
+ list(APPEND python_install_options --prefix=${USER_BASE})
+ # Get python user site and install path = USER_SITE + project_name
+ set(PYTHON_COMMAND_GET_INSTALL_DIR
+ "import site, os, sys ; print os.path.join(site.USER_BASE, os.path.join(\"lib\", os.path.join(\"python\" + str(sys.version_info.major) + '.' + str(sys.version_info.minor),
+ \"site-packages\")))")
+ execute_process(
+ COMMAND ${PYTHON_EXECUTABLE} -c "${PYTHON_COMMAND_GET_INSTALL_DIR}"
+ OUTPUT_VARIABLE PY_INSTALL_DIR)
+
+ else()
+ # user site not included in the path,
+ # which probably means that python is run using virtualenv
+ # Command to find 'global' site-packages
+ # default path will probably be ok --> no options
+ set(GET_SITE_PACKAGE
+ "from distutils.sysconfig import get_python_lib; print(get_python_lib())")
+ execute_process(COMMAND ${PYTHON_EXECUTABLE} -c
+ "${GET_SITE_PACKAGE}" OUTPUT_VARIABLE GLOBAL_SITE_PACKAGE)
+ string(STRIP ${GLOBAL_SITE_PACKAGE} GLOBAL_SITE_PACKAGE)
+ set(PYTHON_COMMAND_GET_INSTALL_DIR ${GET_SITE_PACKAGE})
+ execute_process(
+ COMMAND ${PYTHON_EXECUTABLE} -c "${PYTHON_COMMAND_GET_INSTALL_DIR}"
+ OUTPUT_VARIABLE PY_INSTALL_DIR)
+ endif()
+
+ elseif(HYSOP_INSTALL STREQUAL standard)
+ # install in python standard installation location
+ # (may need to be root)
+ # Depends on OS/platform type, check for example https://docs.python.org/2/install/.
+ #set(PYTHON_COMMAND_GET_INSTALL_DIR
+ # "import site; print(site.getsitepackages()[0])")
+ # --> this does not work properly: the order in resulting
+ # list depends on the OS, the python version ...
+ configure_file(CMake/fake/setup.py tmp/setup.py)
+ configure_file(CMake/fake/__init__.py tmp/fake/__init__.py)
+ configure_file(CMake/find_python_install.py tmp/find_python_install.py)
+ execute_process(
+ COMMAND ${PYTHON_EXECUTABLE} find_python_install.py
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/tmp/
+ OUTPUT_VARIABLE PY_INSTALL_DIR)
+
+ else()#HYSOP_INSTALL STREQUAL prefix)
+ # Last case : HYSOP_INSTALL=prefix, user-defined prefix
+ # we use CMAKE_INSTALL_PREFIX as the path for python install
+ list(APPEND python_install_options --prefix=${HYSOP_INSTALL})
+ set(PY_INSTALL_DIR ${HYSOP_INSTALL})
+ endif()
+
+ string(STRIP ${PY_INSTALL_DIR} PY_INSTALL_DIR)
+ if(NOT CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
+ if(NOT CMAKE_INSTALL_PREFIX STREQUAL PY_INSTALL_DIR)
+ message(STATUS "!!! Warning !!! Use HYSOP_INSTALL option rather than CMAKE_INSTALL_PREFIX that will be overwritten if not complient with HYSOP_INSTALL value.")
+ endif()
+ endif()
+
+ # Set the HYSOP_PYTHON_INSTALL_DIR to the proper path
+ set(HYSOP_PYTHON_INSTALL_DIR ${PY_INSTALL_DIR}
+ CACHE PATH "Install directory for hysop python package" FORCE)
+ set(CMAKE_INSTALL_PREFIX ${PY_INSTALL_DIR}
+ CACHE PATH "Install directory for hysop python package" FORCE)
+ list(APPEND python_install_options config_fc)
+ list(APPEND python_install_options --f90exec=${CMAKE_Fortran_COMPILER})
+ set(python_install_options ${python_install_options} CACHE INTERNAL "")
+endfunction()
+
diff --git a/CMake/cmake_uninstall.cmake.in b/CMake/cmake_uninstall.cmake.in
new file mode 100644
index 0000000000000000000000000000000000000000..d48e08426bf4ab0ad080f83187f2c971ab64fd3e
--- /dev/null
+++ b/CMake/cmake_uninstall.cmake.in
@@ -0,0 +1,28 @@
+# ----------------------------------
+# Setup for make uninstall target
+# See:
+# http://www.cmake.org/Wiki/CMake_FAQ#Can_I_do_.22make_uninstall.22_with_CMake.3F
+# ----------------------------------
+
+if(NOT EXISTS "@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt")
+ message(FATAL_ERROR "Cannot find install manifest: @CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt")
+endif(NOT EXISTS "@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt")
+
+file(READ "@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt" files)
+string(REGEX REPLACE "\n" ";" files "${files}")
+foreach(file ${files})
+ message(STATUS "Uninstalling $ENV{DESTDIR}${file}")
+ if(IS_SYMLINK "$ENV{DESTDIR}${file}" OR EXISTS "$ENV{DESTDIR}${file}")
+ exec_program(
+ "@CMAKE_COMMAND@" ARGS "-E remove \"$ENV{DESTDIR}${file}\""
+ OUTPUT_VARIABLE rm_out
+ RETURN_VALUE rm_retval
+ )
+ if(NOT "${rm_retval}" STREQUAL 0)
+ message(FATAL_ERROR "Problem when removing $ENV{DESTDIR}${file}")
+ endif(NOT "${rm_retval}" STREQUAL 0)
+ else(IS_SYMLINK "$ENV{DESTDIR}${file}" OR EXISTS "$ENV{DESTDIR}${file}")
+ message(STATUS "File $ENV{DESTDIR}${file} does not exist.")
+ endif(IS_SYMLINK "$ENV{DESTDIR}${file}" OR EXISTS "$ENV{DESTDIR}${file}")
+endforeach(file)
+
diff --git a/CMake/fake/__init__.py b/CMake/fake/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/CMake/fake/setup.py b/CMake/fake/setup.py
new file mode 100644
index 0000000000000000000000000000000000000000..2bff192037c8273b5b32f39996c10a71dea0c76c
--- /dev/null
+++ b/CMake/fake/setup.py
@@ -0,0 +1,20 @@
+"""False setup.py used to find where packages installed with
+'python setup.py install'
+will be installed.
+This is the only portable and systematic way we found.
+
+site.getsitepackages() or distutils.sysconfig.get_python_lib() do not
+behave equally on every platforms.
+"""
+from numpy.distutils.core import setup
+from numpy.distutils.misc_util import Configuration
+# List of python modules (directories) to be included
+packages = ['fake',
+ ]
+config = Configuration(
+ name='fake',
+ version='',
+ packages=packages,
+)
+
+setup(**config.todict())
diff --git a/CMake/find_python_install.py b/CMake/find_python_install.py
new file mode 100644
index 0000000000000000000000000000000000000000..4e0a2146a77dbb36cb00e3c5df745b871f73449c
--- /dev/null
+++ b/CMake/find_python_install.py
@@ -0,0 +1,26 @@
+"""Find where python will install things when setup.py is called.
+"""
+import subprocess
+import locale
+
+encoding = locale.getdefaultlocale()[1]
+
+output = subprocess.Popen(["python", "setup.py", "--dry-run", "install"],
+ stdout=subprocess.PIPE).communicate()[0]
+
+if encoding:
+ output = output.decode(encoding).split('\n')
+else: # let's cross fingers here ...
+ output = output.split('\n')
+
+for line in output:
+ if line.count('egg') and line.count('fake'):
+ result = line
+ break
+result = result.split(' ')
+for line in result:
+ if line.count('egg'):
+ result = line
+ break
+result = result.split('fake')[0]
+print(result)
diff --git a/CMake/fortran_utils.cmake b/CMake/fortran_utils.cmake
new file mode 100644
index 0000000000000000000000000000000000000000..8f56794452975c5e23ad0aed1de74d937fb21be4
--- /dev/null
+++ b/CMake/fortran_utils.cmake
@@ -0,0 +1,52 @@
+# --- CMake utilities, to deal with f2py interface ---
+
+
+# Create a pyf file that include
+# all 'fortran' signature files (sub-pyf files)
+# required by f2py.
+#
+# Usage:
+# write_main_pyf_file(fname)
+# where fname must be the name of the generated module
+#
+# For example to create hysop.f2hysop python module,
+# call (in CMakeLists.txt)
+# write_main_pyf_file(f2hysop)
+# --> create f2hysop.pyf that will be used to generate hysop.f2hysop module.
+#
+function(write_main_pyf_file filename)
+ set(_file ${CMAKE_SOURCE_DIR}/${PACKAGE_NAME}/${filename}.pyf.in)
+ file(WRITE ${_file}
+"! -*- f90 -*-\n
+! Generated file - Do not edit.\n
+! Note: the context of this file is case sensitive.\n
+python module f2hysop ! in\n
+ interface\n")
+ file(APPEND ${_file}
+ " ! Example
+ include '@CMAKE_SOURCE_DIR@/hysop/fortran/template.pyf'\n")
+ file(APPEND ${_file}
+ " ! precision
+ include '@CMAKE_SOURCE_DIR@/hysop/f2py/parameters.pyf'\n")
+ if(WITH_FFTW)
+ file(APPEND ${_file}
+ " ! fftw
+ include '@CMAKE_SOURCE_DIR@/hysop/f2py/fftw2py.pyf'\n")
+ endif()
+ if(WITH_SCALES)
+ file(APPEND ${_file}
+ " ! scales
+ include '@CMAKE_SOURCE_DIR@/hysop/f2py/scales2py.pyf'\n")
+ endif()
+ if(WITH_EXTRAS)
+ file(APPEND ${_file}
+ " ! arnoldi
+ include '@CMAKE_SOURCE_DIR@/hysop/fortran/arnoldi2py.pyf'\n")
+ endif()
+ file(APPEND ${_file} " end interface\n
+end python module f2hysop")
+
+message(STATUS "Generate pyf file ...")
+configure_file(${_file} ${CMAKE_SOURCE_DIR}/${PACKAGE_NAME}/${filename}.pyf @ONLY)
+
+endfunction()
diff --git a/HySoP/CMakeLists.txt b/HySoP/CMakeLists.txt
old mode 100644
new mode 100755
index b98a6d94ffa9d6185502694eaca00b22b959e5c9..17397c31f865acadb4217fc77d71bd64083f93a5
--- a/HySoP/CMakeLists.txt
+++ b/HySoP/CMakeLists.txt
@@ -14,10 +14,12 @@
#===============================================================================
# ============= Global cmake Settings =============
# Set minimum version for cmake
-cmake_minimum_required(VERSION 2.8.7)
-if(POLICY CMP0042)
- cmake_policy(SET CMP0042 OLD)
+cmake_minimum_required(VERSION 3.0.2)
+
+if(POLICY CMP0053)
+ cmake_policy(SET CMP0053 NEW)
endif()
+
# Set cmake modules directory (i.e. the one which contains all user-defined FindXXX.cmake files among other things)
set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/CMake")
# Force out-of-source build
@@ -31,10 +33,10 @@ option(DOUBLEPREC "set precision for real numbers to double precision when this
option(USE_MPI "compile and link HySoP with mpi when this mode is enable. Default = on." ON)
option(WITH_TESTS "Enable testing. Default = off" ON)
option(BUILD_SHARED_LIBS "Enable dynamic library build, default = ON." ON)
-option(WITH_LIB_FORTRAN "Generate libhysop from fortran files in src, wrapped into hysop.f2py module. Default = ON." ON)
option(WITH_LIB_CXX "Generate libhysop from fortran files in src, wrapped into hysop.cpp2hysop module. Default = ON." ON)
option(WITH_SCALES "compile/create scales lib and link it with HySoP. Default = ON." ON)
option(WITH_FFTW "Link with fftw library (required for some HySoP solvers), default = ON" ON)
+option(WITH_EXTRAS "Link with some extra fortran libraries (like arnoldi solver), default = OFF" OFF)
option(WITH_GPU "Use of GPU (required for some HySoP solvers), default = ON" ON)
option(WITH_MAIN_FORTRAN "Create an executable (test purpose) from fortran sources in src/main, linked with libhysop, default = ON" ON)
option(WITH_MAIN_CXX "Create an executable (test purpose) from cxx sources in src/hysop++/main, linked with libhysop, default = ON" ON)
@@ -51,32 +53,44 @@ option(WITH_DOCUMENTATION "Build Documentation. Default = OFF" ON)
# - user --> behave as 'python setup.py install --user'
# - standard --> install in python site-package (ie behave as python setup.py install)
# - prefix --> install in python CMAKE_INSTALL_PREFIX (ie behave as python setup.py install --prefix=CMAKE_INSTALL_PREFIX)
-set(hysop_python_install "user" CACHE STRING "Install mode for hysop python package")
+set(HYSOP_INSTALL "user" CACHE STRING "Install mode for hysop python package")
+
+# Install lib directory 32, 64 etc. on Fedora, Debian
+# http://public.kitware.com/Bug/view.php?id=11964
+# See also http://www.cmake.org/cmake/help/v3.0/module/GNUInstallDirs.html?highlight=gnuinstalldirs
+include(GNUInstallDirs)
+# Set prefix path for libraries installation
+# --> means that any library target will be installed
+# in CMAKE_INSTALL_PREFIX/_install_lib
+if(${PROJECT_NAME}_INSTALL_LIB_DIR)
+ set(_install_lib ${${PROJECT_NAME}_INSTALL_LIB_DIR})
+else()
+ ASSERT(CMAKE_INSTALL_LIBDIR)
+ set(_install_lib ${CMAKE_INSTALL_LIBDIR})
+ set(${PROJECT_NAME}_INSTALL_LIB_DIR ${_install_lib})
+endif()
-if(NOT WITH_LIB_FORTRAN)
- message(WARNING "You deactivate libhysop (fortran) generation. This will disable the fortran interface, including fftw and scales fonctionnalities.")
- set(WITH_SCALES "OFF")
- set(WITH_MAIN_FORTRAN "OFF")
+if(NOT USE_MPI)
+ message(FATAL_ERROR "No-mpi version of hysop is broken, please enable mpi.")
+endif()
+
+if(WITH_FFTW OR WITH_SCALES OR WITH_EXTRAS)
+ set(USE_FORTRAN "ON")
endif()
if(NOT WITH_LIB_CXX)
- message(WARNING "You deactivate libhysop (cxx) generation. This will disable the Aitken-Schwarz Poisson solver.")
set(WITH_MAIN_CXX "OFF")
set(WITH_GOOGLE_TESTS "OFF")
endif()
# true if hysop used Fortran and/or c++ sources
-if(${WITH_LIB_FORTRAN} OR ${WITH_LIB_CXX})
+# We can not run scales or fftw without mpi ...
+if(USE_FORTRAN OR WITH_LIB_CXX)
set(WITH_COMPILED_LIB "ON")
- set(WITH_FFTW "ON")
+ #set(WITH_FFTW "ON")
else()
set(WITH_COMPILED_LIB "OFF")
- set(WITH_FFTW "OFF")
-endif()
-
-# We can not run scales without mpi ...
-if(WITH_FFTW OR WITH_SCALES)
- set(USE_MPI "ON")
+ #set(WITH_FFTW "OFF")
endif()
# Force a default build type if not provided by user
@@ -91,10 +105,7 @@ endif()
set(PROJECT_NAME hysop)
# --- Name for the package ---
# This name will be used as the Python Package name
-set(PYPACKAGE_NAME "hysop")
-# --- Set a version number for the package ---
-set(PACKAGE_VERSION 1.0.0)
-set(${PYPACKAGE_NAME}_version ${PACKAGE_VERSION})
+set(PACKAGE_NAME "hysop")
# --- The name (without extension) of the lib to be created ---
set(PROJECT_LIBRARY_NAME ${PROJECT_NAME})
# ============= The project =============
@@ -108,20 +119,21 @@ set(LANGLIST)
if(WITH_LIB_CXX)
set(LANGLIST ${LANGLIST} C CXX)
endif()
-if(WITH_LIB_FORTRAN)
+if(USE_FORTRAN)
set(LANGLIST ${LANGLIST} Fortran)
endif()
-
+include(HysopVersion)
project(${PROJECT_NAME} ${LANGLIST})
set(HYSOP_LIBRARY_NAME hysop)
-set(PACKAGE_NAME HySoP)
+set(HYSOP_INCLUDE_DIRECTORIES
+ CACHE INTERNAL "Include directories for external dependencies.")
+set(HYSOP_LINK_LIBRARIES CACHE INTERNAL "List of external libraries.")
# ============= Python and its packages =============
# - Global setup (interp and lib) -
find_package(PythonFull REQUIRED)
include(FindPythonModule)
-
# - python packages -
find_python_module(numpy REQUIRED)
find_python_module(scipy)
@@ -136,9 +148,20 @@ find_python_module(sympy)
find_python_module(pyopencl REQUIRED)
# --- MPI ---
if(USE_MPI)
+ find_package(MPI REQUIRED)
find_python_module(mpi4py REQUIRED)
endif()
+if(WITH_LIB_CXX)
+ find_package(SWIG 3.0.2 REQUIRED)
+ # WARNING FP : for cmake < 3.0 UseSWIG.cmake
+ # does not work properly (bug for swig outdir)
+ if(CMAKE_VERSION VERSION_LESS 3.0.0)
+ set(SWIG_USE_FILE ${CMAKE_SOURCE_DIR}/cmake/UseSWIG.cmake)
+ endif()
+ include(${SWIG_USE_FILE})
+endif()
+
# Find python build dir name --> needed for tests and doc
if(WITH_COMPILED_LIB)
execute_process(
@@ -152,23 +175,30 @@ endif()
# ============= Other dependencies =============
-# -- Swig --
-if(WITH_LIB_CXX)
- find_package(SWIG 3.0.8 REQUIRED)
- if(CMAKE_VERSION VERSION_LESS 3.0.0)
- set(SWIG_USE_FILE ${CMAKE_SOURCE_DIR}/CMake/UseSWIG.cmake)
- endif()
- include(${SWIG_USE_FILE})
-endif()
-
+# --- FFTW ---
if(WITH_FFTW)
set(FIND_FFTW_VERBOSE OFF)
set(FIND_FFTW_DEBUG OFF)
- find_package(FFTW
- REQUIRED COMPONENTS Fftw3d Fftw3f Fftw3d-mpi Fftw3f-mpi
- OPTIONAL_COMPONENTS Fftw3l Fftw3q)
+ compile_with(FFTW
+ REQUIRED COMPONENTS Fftw3d Fftw3f Fftw3d-mpi Fftw3f-mpi
+ OPTIONAL_COMPONENTS Fftw3l)# Fftw3q)
+ set(dirlist)
+
+ foreach(_file ${FFTW_LIBRARIES})
+ get_filename_component(_name ${_file} DIRECTORY)
+ list(FIND dirlist ${_name} isin)
+ if(isin EQUAL -1)
+ list(APPEND dirlist ${_name})
+ endif()
+ endforeach()
+ set(FFTWLIB ${dirlist} CACHE PATH "fftw libraries dir")
+ add_definitions(${FFTW_DEFINES})
endif()
+if(WITH_EXTRAS)
+ # Arnoldi solver needs zgeev, which means lapack
+ compile_with(LAPACK)
+endif()
# ========= Check which opencl devices are available on the system =========
if(WITH_GPU)
@@ -190,6 +220,33 @@ list(GET MY_LIST 0 OPENCL_DEFAULT_OPENCL_PLATFORM_ID)
list(GET MY_LIST 1 OPENCL_DEFAULT_OPENCL_DEVICE_ID)
display(OPENCL_DEFAULT_OPENCL_PLATFORM_ID)
display(OPENCL_DEFAULT_OPENCL_DEVICE_ID)
+# =========== RPATH stuff ===========
+# Doc :
+# - https://cmake.org/Wiki/CMake_RPATH_handling
+# - https://cmake.org/cmake/help/git-master/manual/cmake-packages.7.html#creating-packages
+# - http://matthew-brett.github.io/docosx/mac_runtime_link.html
+
+# Force MACOSX_RPATH, whatever the cmake version is.
+# RPATH management on macosx with cmake is quite a mess, so please
+# think hard before changing the following lines ...
+set(CMAKE_MACOSX_RPATH 1)
+
+# don't skip the full RPATH for the build tree
+# except if explicitely asked by user
+if(FORCE_SKIP_RPATH)
+ set(CMAKE_SKIP_BUILD_RPATH TRUE)
+else()
+ set(CMAKE_SKIP_BUILD_RPATH FALSE)
+endif()
+
+# when building, don't use the install RPATH already
+# (but later on when installing)
+set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
+set(CMAKE_INSTALL_RPATH "${HYSOP_PYTHON_INSTALL_DIR}/${PACKAGE_NAME}")
+
+# add the automatically determined parts of the RPATH
+# which point to directories outside the build tree to the install RPATH
+set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
# ====== Create (and setup) install/uninstall targets ======
#
@@ -200,19 +257,18 @@ include(HySoPInstallSetup)
# Remark : this must be done before add_subdir below, since install process in src needs CMAKE_INSTALL_PREFIX
# to be properly set.
-if(EXISTS ${CMAKE_SOURCE_DIR}/${PYPACKAGE_NAME}/.f2py_f2cmap)
- message(STATUS "Generate f2py map file ...")
- configure_file(${CMAKE_SOURCE_DIR}/${PYPACKAGE_NAME}/.f2py_f2cmap
- ${CMAKE_BINARY_DIR}/.f2py_f2cmap)
-endif()
-if(EXISTS ${CMAKE_SOURCE_DIR}/${PYPACKAGE_NAME}/f2hysop.pyf.in)
- message(STATUS "Generate f2hysop.pyf (f2py main signature file) ...")
- configure_file(${CMAKE_SOURCE_DIR}/${PYPACKAGE_NAME}/f2hysop.pyf.in
- ${CMAKE_SOURCE_DIR}/${PYPACKAGE_NAME}/f2hysop.pyf)
-endif()
+if(USE_FORTRAN)
+ if(EXISTS ${CMAKE_SOURCE_DIR}/${PACKAGE_NAME}/.f2py_f2cmap)
+ message(STATUS "Generate f2py map file ...")
+ configure_file(${CMAKE_SOURCE_DIR}/${PACKAGE_NAME}/.f2py_f2cmap
+ ${CMAKE_BINARY_DIR}/.f2py_f2cmap)
+ endif()
+ include(fortran_utils)
+ # Create f2hysop.pyf file
+ write_main_pyf_file(f2hysop)
+
+ # ====== Create non-python (fortran) libraries (fftw and scales interfaces), if required =====
-# ====== Create non-python (fortran) libraries (fftw and scales interfaces), if required =====
-if(WITH_LIB_FORTRAN)
# Set module files directory (i.e. where .mod will be created)
set(CMAKE_Fortran_MODULE_DIRECTORY ${CMAKE_BINARY_DIR}/Modules)
# Add compilation flags:
@@ -220,19 +276,17 @@ if(WITH_LIB_FORTRAN)
append_Fortran_FLAGS("-Wall -fPIC -ffree-line-length-none -cpp")
if(USE_MPI)
- # Find MPI for fortran.
- find_package(MPI REQUIRED)
# -I
include_directories(${MPI_Fortran_INCLUDE_PATH})
# Add compilation/link flags
- set(${HYSOP_LIBRARY_NAME}_LINK_FLAGS ${${HYSOP_LIBRARY_NAME}_LINK_FLAGS} ${MPI_Fortran_LINK_FLAGS})
+ list(APPEND ${HYSOP_LIBRARY_NAME}_LINK_FLAGS ${MPI_Fortran_LINK_FLAGS})
append_Fortran_flags(${MPI_Fortran_COMPILE_FLAGS})
# Append mpi libraries to the list of libraries linked with libhysop.
- set(LIBS ${LIBS} ${MPI_Fortran_LIBRARIES} )
+ list(APPEND HYSOP_LINK_LIBRARIES ${MPI_Fortran_LIBRARIES} )
endif(USE_MPI)
- set(Fortran_FLAGS ${CMAKE_Fortran_FLAGS})
- append_flags(Fortran_FLAGS ${CMAKE_Fortran_FLAGS_${CMAKE_BUILD_TYPE}})
+ #set(Fortran_FLAGS ${CMAKE_Fortran_FLAGS})
+ #append_flags(Fortran_FLAGS ${CMAKE_Fortran_FLAGS_${CMAKE_BUILD_TYPE}})
endif()
if(WITH_COMPILED_LIB)
@@ -278,7 +332,7 @@ endif()
set_directory_properties(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES ${CMAKE_BINARY_DIR}/build)
set(PYTHON_SETUP "${CMAKE_CURRENT_BINARY_DIR}/setup.py")
-if(WITH_LIB_FORTRAN)
+if(USE_FORTRAN)
add_custom_target(python-build ALL
COMMAND ${PYTHON_EXECUTABLE} ${PYTHON_SETUP} build config_fc --f90exec=${CMAKE_Fortran_COMPILER}
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} COMMENT "build hysop package"
@@ -342,6 +396,39 @@ if(WITH_LIB_CXX)
endif()
endif()
+# =========== RPATH stuff ===========
+# Doc :
+# - https://cmake.org/Wiki/CMake_RPATH_handling
+# - https://cmake.org/cmake/help/git-master/manual/cmake-packages.7.html#creating-packages
+# - http://matthew-brett.github.io/docosx/mac_runtime_link.html
+
+# Force MACOSX_RPATH, whatever the cmake version is.
+# RPATH management on macosx with cmake is quite a mess, so please
+# think hard before changing the following lines ...
+set(CMAKE_MACOSX_RPATH 1)
+
+# don't skip the full RPATH for the build tree
+# except if explicitely asked by user
+if(FORCE_SKIP_RPATH)
+ set(CMAKE_SKIP_BUILD_RPATH TRUE)
+else()
+ set(CMAKE_SKIP_BUILD_RPATH FALSE)
+endif()
+
+# when building, don't use the install RPATH already
+# (but later on when installing)
+set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
+set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/${PACKAGE_NAME}")
+
+# add the automatically determined parts of the RPATH
+# which point to directories outside the build tree to the install RPATH
+set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
+
+# the RPATH to be used when installing, but only if it's not a system directory
+list(FIND CMAKE_PLATFORM_IMPLICIT_LINK_DIRECTORIES "${CMAKE_INSTALL_PREFIX}/${PACKAGE_NAME}" isSystemDir)
+if("${isSystemDir}" STREQUAL "-1")
+ set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/${PACKAGE_NAME}")
+endif()
# ====== Create a Target to clean sources (remove .pyc files) and build dir ======
@@ -372,7 +459,8 @@ endif()
if(WITH_TESTS)
include(CTest)
# Number of mpi processes used to run tests.
- set(NBPROCS_FOR_TESTS 8)
+ set(NBPROCS_FOR_TESTS "8" CACHE STRING "Number of mpi processes used to run tests")
+ # set(NBPROCS_FOR_TESTS 8)
if(NOT USE_MPI)
set(WITH_MPI_TESTS "OFF")
endif()
@@ -382,19 +470,23 @@ endif(WITH_TESTS)
# ============= Summary =============
if(VERBOSE_MODE)
- message(STATUS "====================== Summary ======================")
+ message("\n====================== End of configuration process ======================")
+ message("\n Summary: ")
message(STATUS " Python libraries : ${PYTHON_LIBRARIES}")
message(STATUS " Python include : ${PYTHON_INCLUDE_DIRS}")
message(STATUS " Python version : ${PYTHON_VERSION_STRING}")
message(STATUS " Python executable : ${PYTHON_EXECUTABLE}")
- message(STATUS " Python user lib : ${PYTHON_LIBRARY}")
- message(STATUS " ${PACKAGE_NAME} will be installed in : ${HYSOP_PYTHON_INSTALL_DIR}")
+ message(STATUS " Install mode is `${HYSOP_INSTALL}` and ${PACKAGE_NAME} will be installed in : ${HYSOP_PYTHON_INSTALL_DIR}")
message(STATUS " ${PACKAGE_NAME} will be built in ${HYSOP_BUILD_PYTHONPATH}")
- if(WITH_LIB_FORTRAN)
+ if(USE_FORTRAN)
message(STATUS " Fortran compiler : ${CMAKE_Fortran_COMPILER}")
+ else()
+ message(WARNING "You deactivate libhysop (fortran) generation. This will disable the fortran interface, including fftw and scales fonctionnalities.")
endif()
if(WITH_LIB_CXX)
message(STATUS " CXX compiler : ${CMAKE_CXX_COMPILER}")
+ else()
+ message(WARNING "You deactivate libhysop (cxx) generation. This will disable the Aitken-Schwarz Poisson solver.")
endif()
message(STATUS " Sources are in : ${CMAKE_SOURCE_DIR}")
message(STATUS " Project uses MPI : ${USE_MPI}")
@@ -416,4 +508,3 @@ if(VERBOSE_MODE)
message("Try to run python -c 'import hysop'. If it fails, add ${HYSOP_PYTHON_INSTALL_DIR} to PYTHONPATH environment variable.")
message("Example : \n export PYTHONPATH=${HYSOP_PYTHON_INSTALL_DIR}:\${PYTHONPATH}\n")
endif()
-
diff --git a/HySoP/hysop/__init__.py.in b/HySoP/hysop/__init__.py.in
index 134f6a8d48e8d1f8ba7975f8c3ed119e7d06864c..e97188c9404012573229c41bbbc0f1a2c9d389a2 100755
--- a/HySoP/hysop/__init__.py.in
+++ b/HySoP/hysop/__init__.py.in
@@ -3,9 +3,6 @@ on hybrid architectures (MPI-GPU)
"""
-__version__ = 1.00
-__all__ = ['Box', 'Field']
-
# Compilation flags
__MPI_ENABLED__ = "@USE_MPI@" is "ON"
__GPU_ENABLED__ = "@WITH_GPU@" is "ON"
@@ -16,18 +13,49 @@ __DEBUG__ = "@DEBUG@" in ["2", "3"]
__PROFILE__ = "@PROFILE@" in ["0", "1"]
__OPTIMIZE__ = "@OPTIM@" is "ON"
-## import hysop.tools.io_utils as io
-default_path = 'toto' #io.IO.default_path()
-msg_start = '\nStarting @PACKAGE_NAME@ (no mpi) version '
-msg_start += str(__version__)
+from hysop.tools.sys_utils import SysUtils
+# Box-type physical domain
+from hysop.domain.box import Box
+# Fields
+from hysop.fields.continuous import Field
+# Variable parameters
+from hysop.fields.variable_parameter import VariableParameter
+# Simulation parameters
+from hysop.problem.simulation import Simulation
+# Tools (io, mpi ...)
+from hysop.tools.io_utils import IO
+from hysop.tools.parameters import IOParams, MPIParams, Discretization
+import hysop.mpi
+# Problem
+from hysop.problem.problem import Problem
+# Solver
+# import particular_solvers.basic
+# ## #import particular_solvers.gpu
+# ParticleSolver = particular_solvers.basic.ParticleSolver
+# ## #GPUParticleSolver = particular_solvers.gpu.GPUParticleSolver
+## from tools.explore_hardware import explore
+
+
+__all__ = ['Box', 'Field', 'Discretization',
+ 'IOParams', 'Simulation', 'MPIParams', 'Problem', 'IO']
+
+if SysUtils.is_interactive():
+ # Set i/o default path to current directory
+ # for interactive sessions
+ # i.e. python interactive session or any call of ipython.
+ defpath = os.path.join(os.getcwd(), 'interactive')
+ IO.set_default_path(defpath)
+
+default_path = IO.default_path()
+msg_start = '\nStarting @PACKAGE_NAME@ version '
+msg_start += str("@HYSOP_VERSION@")
msg_io = '\nWarning : default path for all i/o is ' + default_path + '.\n'
msg_io += 'If you want to change this, use io.set_default_path function.\n'
# MPI
if __MPI_ENABLED__:
- import hysop.mpi as mpi
if mpi.main_rank == 0:
- msg_start += ' on ' + str(mpi.main_size) + ' mpi process(es).'
+ msg_start += ' with ' + str(mpi.main_size) + ' mpi process(es).'
print msg_start
print msg_io
@@ -41,39 +69,3 @@ __DEFAULT_DEVICE_ID__ = @OPENCL_DEFAULT_OPENCL_DEVICE_ID@
version = "1.0.0"
-# Box-type physical domain
-import hysop.domain.box
-Box = hysop.domain.box.Box
-
-# Fields
-import hysop.fields.continuous
-Field = hysop.fields.continuous.Field
-
-# Variable parameters
-import hysop.fields.variable_parameter
-VariableParameter = hysop.fields.variable_parameter.VariableParameter
-
-# Simulation parameters
-import hysop.problem.simulation
-Simulation = hysop.problem.simulation.Simulation
-
-# Tools (io, mpi ...)
-import hysop.tools.parameters
-IOParams = hysop.tools.parameters.IOParams
-MPIParams = hysop.tools.parameters.MPIParams
-Discretization = hysop.tools.parameters.Discretization
-
-# ## ## Problem
-# import problem.problem
-# Problem = problem.problem.Problem
-
-
-# ## ## Solver
-# import particular_solvers.basic
-# ## #import particular_solvers.gpu
-# ParticleSolver = particular_solvers.basic.ParticleSolver
-# ## #GPUParticleSolver = particular_solvers.gpu.GPUParticleSolver
-
-
-## from tools.explore_hardware import explore
-
diff --git a/HySoP/hysop/domain/tests/test_box.py b/HySoP/hysop/domain/tests/test_box.py
old mode 100644
new mode 100755
index f23e357d3558f4ffb5e6abce6164fe5ef25b3dde..d9ab03cd0075118da370971ed1b1b04e54a78d9f
--- a/HySoP/hysop/domain/tests/test_box.py
+++ b/HySoP/hysop/domain/tests/test_box.py
@@ -141,15 +141,3 @@ def test_topo_from_mesh():
assert (topo.shape == [1, 1, comm_s.Get_size()]).all()
elif dom.is_on_task(GPU):
assert topo.size == 1
-
-
-# This may be useful to run mpi tests
-if __name__ == "__main__":
- test_create_box1()
- test_create_box2()
- test_create_box3()
- test_create_box4()
- test_topo_standard()
- test_topo_multi_tasks()
- test_topo_plane()
- test_topo_from_mesh()
diff --git a/HySoP/hysop/domain/tests/test_control_box.py b/HySoP/hysop/domain/tests/test_control_box.py
old mode 100644
new mode 100755
index 19eac3b1d8b2b46418eba1947c06a46bd3364b03..8feb3b925b4f7e00266eebc15ddd4e44403908f4
--- a/HySoP/hysop/domain/tests/test_control_box.py
+++ b/HySoP/hysop/domain/tests/test_control_box.py
@@ -203,13 +203,3 @@ def test_cb_3d_fulldomain():
except:
res = True
assert res
-
-# This may be useful to run mpi tests
-if __name__ == "__main__":
- test_cb_3d()
- test_cb_3d_2()
- test_cb_3d_3()
- test_cb_2d()
- test_cb_2d_2()
- test_cb_2d_3()
- test_cb_3d_fulldomain()
diff --git a/HySoP/hysop/domain/tests/test_mesh.py b/HySoP/hysop/domain/tests/test_mesh.py
old mode 100644
new mode 100755
index d93cf7362ea5bada82f9b01a39937a97045a9ce0..0ae2b4868b213a6358f65b93656c441287e3b0dd
--- a/HySoP/hysop/domain/tests/test_mesh.py
+++ b/HySoP/hysop/domain/tests/test_mesh.py
@@ -172,13 +172,3 @@ def test_integ_3d():
vol = np.prod(dom.length)
if main_rank == 0:
assert np.abs(il - vol) < tol
-
-if __name__ == '__main__':
- test_mesh3d()
- test_mesh3d_ghost()
- test_mesh2d()
- test_mesh2d_ghost()
- test_convert_local()
- test_convert_global()
- test_integ_2d()
- test_integ_3d()
diff --git a/HySoP/hysop/domain/tests/test_porous.py b/HySoP/hysop/domain/tests/test_porous.py
old mode 100644
new mode 100755
index b813c1d7b5a8140b50692eac9faa6e018da5bc37..3ae7c79c9d72dc47bc3d661176c46ee86523b03f
--- a/HySoP/hysop/domain/tests/test_porous.py
+++ b/HySoP/hysop/domain/tests/test_porous.py
@@ -212,28 +212,3 @@ def test_ringpole_sphere_2d():
def test_ringpole_hemisphere_2d():
assert_ringpole(d2d, HemiSphere, 'ringpole_hemisphere_2d')
-
-# This may be useful to run mpi tests
-if __name__ == "__main__":
- test_porous_sphere_3d()
- test_porous_hemisphere_3d()
- test_porous_cylinder_3d()
- test_porous_hemicylinder_3d()
- test_porous_sphere_2d()
- test_porous_hemisphere_2d()
- test_bipole_sphere_3d()
- test_bipole_hemisphere_3d()
- test_bipole_cylinder_3d()
- test_bipole_hemicylinder_3d()
- test_bipole_sphere_2d()
- test_bipole_hemisphere_2d()
- test_quadripole_sphere_3d()
- test_quadripole_hemisphere_3d()
- test_ring_sphere_3d()
- test_ring_hemisphere_3d()
- test_ring_sphere_2d()
- test_ring_hemisphere_2d()
- test_ringpole_sphere_3d()
- test_ringpole_hemisphere_3d()
- test_ringpole_sphere_2d()
- test_ringpole_hemisphere_2d()
diff --git a/HySoP/hysop/domain/tests/test_regular_subset.py b/HySoP/hysop/domain/tests/test_regular_subset.py
old mode 100644
new mode 100755
index da1b44652d5184dca3bb496bc68251a094d431b5..f20de501d21ede246456ed100600a1b7ca40857a
--- a/HySoP/hysop/domain/tests/test_regular_subset.py
+++ b/HySoP/hysop/domain/tests/test_regular_subset.py
@@ -216,16 +216,3 @@ def test_full2d_in3d():
assert (np.abs(i1 - vref) < 1e-6).all()
print topo
print cub.mesh[topo].iCompute
-
-# This may be useful to run mpi tests
-if __name__ == "__main__":
- test_subbox()
- test_integ()
- test_integ_2()
- test_integ_3()
- test_subbox_2d()
- test_line()
- test_2d_subbox()
- test_2d_line()
- test_integ_fulldom()
- test_integ_fulldom_2d()
diff --git a/HySoP/hysop/domain/tests/test_submesh.py b/HySoP/hysop/domain/tests/test_submesh.py
old mode 100644
new mode 100755
index 86ac5284d54b4b67c3c8dee7288823bf7c90209c..5df5aeb85977417cb2f1e1c2645d6378521af08d
--- a/HySoP/hysop/domain/tests/test_submesh.py
+++ b/HySoP/hysop/domain/tests/test_submesh.py
@@ -139,9 +139,3 @@ def test_integ_3d():
vol = np.prod(subm.global_length)
if main_rank == 0:
assert np.abs(il - vol) < tol
-
-if __name__ == '__main__':
- test_submesh_3d()
- test_submesh_2d()
- test_integ_2d()
- test_integ_3d()
diff --git a/HySoP/hysop/domain/tests/test_subset.py b/HySoP/hysop/domain/tests/test_subset.py
old mode 100644
new mode 100755
index 0b11f5288725e28b070e7f4049f5615a4462738e..5faf5e19ec3d871219e0088b643d1dbf380594a4
--- a/HySoP/hysop/domain/tests/test_subset.py
+++ b/HySoP/hysop/domain/tests/test_subset.py
@@ -189,18 +189,3 @@ def test_subtract_list_3d():
def test_subtract_list_2d():
assert init_subtract_lists(discr2D, 'multi_obst_subslist_2d')
-
-# This may be useful to run mpi tests
-if __name__ == "__main__":
- test_sphere_3d()
- test_hemisphere_3d()
- test_cylinder_3d()
- test_hemicylinder_3d()
- test_sphere_2d()
- test_hemisphere_2d()
- test_union_2d()
- test_union_3d()
- test_subtract_3d()
- test_subtract_2d()
- test_subtract_list_3d()
- test_subtract_list_2d()
diff --git a/HySoP/hysop/f2hysop.pyf.in b/HySoP/hysop/f2hysop.pyf.in
old mode 100644
new mode 100755
index 02ea4c3f685efa9780dcf76cef09a6b55d9a3fb5..a11194e7df7e5f7f02bb55b202ff01bf3faa85e9
--- a/HySoP/hysop/f2hysop.pyf.in
+++ b/HySoP/hysop/f2hysop.pyf.in
@@ -1,18 +1,20 @@
- ! -*- f90 -*-
- ! Note: the context of this file is case sensitive.
-
- python module f2hysop ! in
- interface
- ! Example
- include '@CMAKE_SOURCE_DIR@/hysop/fortran/template.pyf'
- ! precision
- include '@CMAKE_SOURCE_DIR@/hysop/f2py/parameters.pyf'
- ! fftw
- include '@CMAKE_SOURCE_DIR@/hysop/f2py/fftw2py.pyf'
- ! scales
- include '@CMAKE_SOURCE_DIR@/hysop/f2py/scales2py.pyf'
- ! Arnoldi
- include '@CMAKE_SOURCE_DIR@/hysop/fortran/arnoldi2py.pyf'
+! -*- f90 -*-
+
+! Generated file - Do not edit.
+
+! Note: the context of this file is case sensitive.
+python module f2hysop ! in
+
+ interface
+ ! Example
+ include '@CMAKE_SOURCE_DIR@/hysop/fortran/template.pyf'
+ ! precision
+ include '@CMAKE_SOURCE_DIR@/hysop/f2py/parameters.pyf'
+ ! fftw
+ include '@CMAKE_SOURCE_DIR@/hysop/f2py/fftw2py.pyf'
+ ! scales
+ include '@CMAKE_SOURCE_DIR@/hysop/f2py/scales2py.pyf'
end interface
-end python module f2hysop
+
+end python module f2hysop
\ No newline at end of file
diff --git a/HySoP/hysop/f2py/fftw2py.pyf b/HySoP/hysop/f2py/fftw2py.pyf
index 3153e51b9c80f7ba98960bebb9378050867e2e50..a9a833e88b45bf33d735acac589a49ce3fa8f314 100644
--- a/HySoP/hysop/f2py/fftw2py.pyf
+++ b/HySoP/hysop/f2py/fftw2py.pyf
@@ -3,7 +3,7 @@
module fftw2py ! in fftw2py.f90
use fft3d
- use mpi
+ !use mpi
use client_data
use hysopparam
use fft2d
diff --git a/HySoP/hysop/fields/tests/test_field.py b/HySoP/hysop/fields/tests/test_field.py
old mode 100644
new mode 100755
index 1817cfedb2df94e2c2f66a3093c80000b9ac649a..b5181bbd26db39de1929e14bf3630b9da6ccef93
--- a/HySoP/hysop/fields/tests/test_field.py
+++ b/HySoP/hysop/fields/tests/test_field.py
@@ -341,19 +341,3 @@ def test_analytical_field_10():
assert allclose(cafd2[i], refd2.data[i])
assert allclose(cafd[i], refd.data[i])
assert id(cafd2.data[i]) == ids[i]
-
-
-# This may be useful to run mpi tests
-if __name__ == "__main__":
- test_continuous()
- test_analytical()
- test_analytical_reset()
- test_discretization()
- test_analytical_field_1()
- test_analytical_field_2()
- test_analytical_field_3()
- test_analytical_field_4()
- test_analytical_field_5()
- test_analytical_field_6()
- test_analytical_field_7()
- test_analytical_field_8()
diff --git a/HySoP/hysop/fields/tests/test_variable.py b/HySoP/hysop/fields/tests/test_variable.py
old mode 100644
new mode 100755
index 61294b96002f81af98a8212a9874b1b688257260..40e66eafd3a29a9c27e35f6899e662151e0f978e
--- a/HySoP/hysop/fields/tests/test_variable.py
+++ b/HySoP/hysop/fields/tests/test_variable.py
@@ -47,10 +47,3 @@ def test_time_var2():
simu.advance()
var.update(simu)
assert np.allclose(var['alpha'], [sin(0.1), cos(0.1)])
-
-
-# This may be useful to run mpi tests
-if __name__ == "__main__":
- test_constant_var()
- test_time_var()
- test_time_var2()
diff --git a/HySoP/hysop/fortran/arnoldi2py.f90 b/HySoP/hysop/fortran/arnoldi2py.f90
deleted file mode 100644
index 0b2ef50382a783576ada31b2c591c7e4f8c8c285..0000000000000000000000000000000000000000
--- a/HySoP/hysop/fortran/arnoldi2py.f90
+++ /dev/null
@@ -1,29 +0,0 @@
-!> @file arnoldi2py.f90
-!! Fortran to python interface file.
-
-!> Interface to Arnoldi algorithm
-module arnoldi2py
-
-! use client_data
- use hysopparam
- use arnoldi
- use mpi
- implicit none
-
-contains
-
- !> Arnoldi algorithm: solve eigen-problems for global linear stability analysis
- !! @param[in] number of snapshots (i.e. dimension of the Krylov basis)
- !! @param[in] solutions (snapshots as input and eigen-functions as output)
- !! @param[inout] work array. Input: empty array
- subroutine execute_arnoldi(solutions,ncli,ntot,nfp,nmodes,Tps)
-
- integer, intent(in) :: ncli, ntot, nfp, nmodes
- real(pk), intent(in) :: Tps
- real(pk), dimension(:,:), intent(inout) :: solutions
-
- call arnoldi3d(solutions,ncli,ntot,nfp,nmodes,Tps)
-
- end subroutine execute_arnoldi
-
-end module arnoldi2py
diff --git a/HySoP/hysop/fortran/arnoldi2py.pyf b/HySoP/hysop/fortran/arnoldi2py.pyf
index e82d95b29f89b134d6d5ddbf6ba0e3c37d89f3c8..6de3250e8665d2c260478dcd69baabd939ca45e4 100644
--- a/HySoP/hysop/fortran/arnoldi2py.pyf
+++ b/HySoP/hysop/fortran/arnoldi2py.pyf
@@ -5,15 +5,12 @@ module arnoldi2py ! in arnoldi2py.f90
use arnoldi
use hysopparam
use mpi
- subroutine execute_arnoldi(solutions,ncli,ntot,nfp,nmodes,tps) ! in arnoldi2py.f90:arnoldi2py
+ subroutine arnoldi3d(solutions,ncli,ntot,nfp,nmodes,tps) ! in arnoldi2py.f90:arnoldi2py
real(kind=pk) dimension(:,:),intent(inout) :: solutions
integer intent(in) :: ncli
integer intent(in) :: ntot
integer intent(in) :: nfp
integer intent(in) :: nmodes
real(kind=pk) intent(in) :: tps
- end subroutine execute_arnoldi
+ end subroutine arnoldi3d
end module arnoldi2py
-
-! This file was auto-generated with f2py (version:2).
-! See http://cens.ioc.ee/projects/f2py2e/
diff --git a/HySoP/hysop/gpu/tests/test_gpu_multiresolution_filter.py b/HySoP/hysop/gpu/tests/test_gpu_multiresolution_filter.py
old mode 100644
new mode 100755
index 2405503763076604628a99ccd5dcc331d1cfb4f1..4c87351fb8440d1a13bf9cdc9b56bf46be9e26ab
--- a/HySoP/hysop/gpu/tests/test_gpu_multiresolution_filter.py
+++ b/HySoP/hysop/gpu/tests/test_gpu_multiresolution_filter.py
@@ -126,7 +126,3 @@ def test_filter_L2_1():
f_out[0][topo_coarse.mesh.iCompute]), \
np.max(np.abs(valid[0][topo_coarse.mesh.iCompute] -
f_out[0][topo_coarse.mesh.iCompute]))
-
-if __name__ == '__main__':
- test_filter_linear()
- test_filter_L2_1()
diff --git a/HySoP/hysop/gpu/tests/test_multiphase_baroclinic.py b/HySoP/hysop/gpu/tests/test_multiphase_baroclinic.py
old mode 100644
new mode 100755
index aa75f8614728f087e5c58a3eda42df7f648367bc..fbfd41963c69b5dc16748dbf2fbf4adaa2fa7569
--- a/HySoP/hysop/gpu/tests/test_multiphase_baroclinic.py
+++ b/HySoP/hysop/gpu/tests/test_multiphase_baroclinic.py
@@ -131,7 +131,3 @@ def call_operator(func, grad_func, vfunc):
assert np.allclose(d_rhs[2] / max_val[2], d_true_rhs[2] / max_val[2],
atol=1e-8 if HYSOP_REAL != np.float32 else 5e-4)
-
-if __name__ == '__main__':
- test_baroclinic_rhs()
- test_baroclinic_rhs_nonperiodic()
diff --git a/HySoP/hysop/mpi/tests/test_bridge.py b/HySoP/hysop/mpi/tests/test_bridge.py
old mode 100644
new mode 100755
index 0621466c23680c0181c82c2c6a445d8aebbb20b0..ac28390f78740971e8d358a21221fe7596e7fdbd
--- a/HySoP/hysop/mpi/tests/test_bridge.py
+++ b/HySoP/hysop/mpi/tests/test_bridge.py
@@ -120,10 +120,3 @@ def test_bridgeInter3D():
bridge2 = BridgeInter(topo1, main_comm, source_id=GPU, target_id=CPU)
assert bridge2 is not None
-
-if __name__ == '__main__':
- test_bridge2D()
- test_bridge3D()
- test_bridge_overlap()
- test_bridgeInter2D()
- test_bridgeInter3D()
diff --git a/HySoP/hysop/mpi/tests/test_topology.py b/HySoP/hysop/mpi/tests/test_topology.py
old mode 100644
new mode 100755
index 23e6fcb0095075e99cbee9ae29a5123900e21afb..2b22daa48d909d40f3b286063d198637ffdd6677
--- a/HySoP/hysop/mpi/tests/test_topology.py
+++ b/HySoP/hysop/mpi/tests/test_topology.py
@@ -250,18 +250,3 @@ def test_operator_equal():
# test not equal ...
assert topo2 != topo3
-
-if __name__ == "__main__":
- test_create_default_topology_2d()
- test_create_default_topology2_2d()
- test_create_topologyFromDim_2d()
- test_create_topologyFromShape_2d()
- test_create_topologyFromCutdir_2d()
- test_create_planetopology_2d()
- test_create_default_topology()
- test_create_default_topology2()
- test_create_topologyFromDim()
- test_create_topologyFromShape()
- test_create_topologyFromCutdir()
- test_create_planetopology()
- test_operator_equal()
diff --git a/HySoP/hysop/numerics/tests/test_diffOp.py b/HySoP/hysop/numerics/tests/test_diffOp.py
index 50c1e59b251a5aa4b196fc460c72ea8b4744e30a..529542e012b024bd7dd0f7144a96affa79c4f156 100755
--- a/HySoP/hysop/numerics/tests/test_diffOp.py
+++ b/HySoP/hysop/numerics/tests/test_diffOp.py
@@ -220,13 +220,3 @@ def test_div_advection():
errx = (topo3.domain.length[0] / (Nx - 1)) ** 4
assert np.allclose(rd[0][ic3], result[0][ic3], rtol=errx)
-
-if __name__ == "__main__":
- test_curl()
- test_curl_2d()
- test_div_rho_v_2d()
- test_div_rho_v()
- test_laplacian()
- test_divwv()
- test_grad_vxw()
- test_div_advection()
diff --git a/HySoP/hysop/numerics/tests/test_update_ghosts.py b/HySoP/hysop/numerics/tests/test_update_ghosts.py
old mode 100644
new mode 100755
index 694b27c0c931d7d67f67c65e779eeb359effebb3..e1970b2f39c3904a984f5e760d2b9e07dcab6654
--- a/HySoP/hysop/numerics/tests/test_update_ghosts.py
+++ b/HySoP/hysop/numerics/tests/test_update_ghosts.py
@@ -152,18 +152,3 @@ def test_update_ghosts_full_3D():
update(df.data)
verify_full(df, gh)
-
-if __name__ == '__main__':
- for f in (test_update_ghosts_simple_1D,
- test_update_ghosts_simple_2D,
- test_update_ghosts_simple_3D,
- test_update_ghosts_1D,
- test_update_ghosts_2D,
- test_update_ghosts_3D,
- test_update_ghosts_full_simple_1D,
- test_update_ghosts_full_simple_2D,
- test_update_ghosts_full_simple_3D,
- test_update_ghosts_full_1D,
- test_update_ghosts_full_2D,
- test_update_ghosts_full_3D):
- f()
diff --git a/HySoP/hysop/operator/adapt_timestep.py b/HySoP/hysop/operator/adapt_timestep.py
index 0079aa1eb6c29f4f82846e05cfcef484cf790c23..6a60e1ef2b52071ae28dbe2b6e410d56b7f3a5b6 100755
--- a/HySoP/hysop/operator/adapt_timestep.py
+++ b/HySoP/hysop/operator/adapt_timestep.py
@@ -64,7 +64,7 @@ class AdaptTimeStep(Computational):
#assert 'dt' in self.dt_adapt.data
self.input = self.variables
- self.output = [self.vorticity]
+ self.output = []
self.time_range = time_range
self.lcfl, self.cfl, self.maxdt = lcfl, cfl, maxdt
self._intercomms = {}
diff --git a/HySoP/hysop/operator/discrete/adapt_timestep.py b/HySoP/hysop/operator/discrete/adapt_timestep.py
index 90bc6e15d347f36e897b09cdb387a2f67433cbe5..ccbc65d7ebdd5d83ded8df108d3d1a27181745ed 100755
--- a/HySoP/hysop/operator/discrete/adapt_timestep.py
+++ b/HySoP/hysop/operator/discrete/adapt_timestep.py
@@ -1,7 +1,5 @@
# -*- coding: utf-8 -*-
"""
-@file operator/discrete/adapt_timestep.py
-
Evaluation of the adaptative time step according to the flow fields.
"""
@@ -53,7 +51,7 @@ class AdaptTimeStep_D(DiscreteOperator):
**kwds)
self.input = self.variables
- self.output = [self.vorticity]
+ self.output = []
## Courant Fredrich Levy coefficient
self.cfl = cfl
## Lagrangian CFL coefficient
diff --git a/HySoP/hysop/operator/discrete/drag_and_lift.py b/HySoP/hysop/operator/discrete/drag_and_lift.py
index a95d72bde2a003a7969e08a1c169e34e358f2e87..21f3fb77e23572376f05156704be4c3ddfa4c49f 100644
--- a/HySoP/hysop/operator/discrete/drag_and_lift.py
+++ b/HySoP/hysop/operator/discrete/drag_and_lift.py
@@ -307,10 +307,7 @@ class NocaForces(Forces):
# So if you need computation in x and z directions,
# surfdir = [0, 1, 4, 5]
self._surfdir = surfdir
- # buffer used to compute d/dt velocity
- # see integrate_gamma_mom
- self._previous_sum_u = npw.zeros(2 * self._dim)
-
+ # buffers used to compute d/dt velocity
self._previous_velo = [None] * self._dim * 2 * self._dim
self._surf_buffer = None
self._init_surf_buffers()
@@ -355,32 +352,6 @@ class NocaForces(Forces):
"""
pass
- def _allocate_rwork(self, rwork=None):
- """Set or check rwork.
-
- rwork will be required only in formulations where
- an integral over the volume of the control box is computed,
- Noca I and Noca II.
- """
- # !!! Velocity must be set before a call to this function
- # and so before base class initialization !!!
-
- # The only required buffer if for integral on the volume
- # of control.
- toporef = self.velocity.topology
- v_ind = self._voc.mesh[toporef].ind4integ
- shape_v = self.velocity.data[0][v_ind].shape
- # setup for rwork, iwork is useless.
- if rwork is None:
- # --- Local allocation ---
- self._rwork = [npw.zeros(shape_v)]
- else:
- assert isinstance(rwork, list), 'rwork must be a list.'
- # --- External rwork ---
- self._rwork = rwork
- assert len(self._rwork) == 1
- assert self._rwork[0].shape == shape_v
-
def _init_surf_buffers(self):
"""Allocate memory for local buffers (used to compute
time derivative of the velocity on the surfaces of
@@ -524,7 +495,30 @@ class NocaI(NocaForces):
"""Noca, "Impulse Equation" from Noca99
"""
def _set_work_arrays(self, rwork=None, iwork=None):
- self._allocate_rwork(rwork)
+ """Set or check rwork.
+
+ rwork will be required only in formulations where
+ an integral over the volume of the control box is computed,
+ Noca I and Noca II.
+ """
+ # !!! Velocity must be set before a call to this function
+ # and so before base class initialization !!!
+
+ # The only required buffer if for integral on the volume
+ # of control.
+ toporef = self.velocity.topology
+ v_ind = self._voc.mesh[toporef].ind4integ
+ shape_v = self.velocity.data[0][v_ind].shape
+ # setup for rwork, iwork is useless.
+ if rwork is None:
+ # --- Local allocation ---
+ self._rwork = [npw.zeros(shape_v)]
+ else:
+ assert isinstance(rwork, list), 'rwork must be a list.'
+ # --- External rwork ---
+ self._rwork = rwork
+ assert len(self._rwork) == 1
+ assert self._rwork[0].shape == shape_v
def _noca(self, dt):
"""
@@ -574,9 +568,6 @@ class NocaI(NocaForces):
class NocaII(NocaForces):
- def _set_work_arrays(self, rwork=None, iwork=None):
- self._allocate_rwork(rwork)
-
def _init_surf_buffers(self):
"""Allocate memory for local buffers (used to compute
time derivative of the velocity on the surfaces of
diff --git a/HySoP/hysop/operator/penalization.py b/HySoP/hysop/operator/penalization.py
index 81b451ef8960972617c235ec49c7fa85c8f0b55d..2cabff25dfc17f6885c3aa148dd4b6bce23052f4 100644
--- a/HySoP/hysop/operator/penalization.py
+++ b/HySoP/hysop/operator/penalization.py
@@ -134,6 +134,8 @@ class PenalizeVorticity(Penalization):
self.method = default.DIFFERENTIAL
# operator to compute buffer = curl(penalised velocity)
self._curl = None
+ self.input = self.variables
+ self.output = self.vorticity
def discretize(self):
diff --git a/HySoP/hysop/operator/tests/test_Stretching.py b/HySoP/hysop/operator/tests/test_Stretching.py
index deef2a0222519d7e1ff5038c5f06eafd43725f1d..4b6baa5b095789b8abdf684075ffb7e6f816602e 100755
--- a/HySoP/hysop/operator/tests/test_Stretching.py
+++ b/HySoP/hysop/operator/tests/test_Stretching.py
@@ -215,8 +215,3 @@ def test_stretching_external_work():
stretch.setup(rwork=rwork)
simulation = Simulation(tinit=0, tend=1., timeStep=timeStep)
stretch.apply(simulation)
-
-if __name__ == "__main__":
-# test_stretching()
-# test_stretching_external_work()
- test_stretchingLinearized()
diff --git a/HySoP/hysop/operator/tests/test_adaptive_time_step.py b/HySoP/hysop/operator/tests/test_adaptive_time_step.py
old mode 100644
new mode 100755
index 6792f4b3a49fa79a2010890c5b90b4f106306896..f1a7eef4000dbd2ac064721d44bdba0dce5ef244
--- a/HySoP/hysop/operator/tests/test_adaptive_time_step.py
+++ b/HySoP/hysop/operator/tests/test_adaptive_time_step.py
@@ -134,9 +134,3 @@ def test_adapt_4():
refval = simu.timeStep
refval = main_comm.bcast(refval, root=0)
assert refval == simu.timeStep
-
-if __name__ == "__main__":
- #test_adapt()
- #test_adapt_2()
- #test_adapt_3()
- test_adapt_4()
diff --git a/HySoP/hysop/operator/tests/test_advec_scales.py b/HySoP/hysop/operator/tests/test_advec_scales.py
index a4d881a538ddc5cb9a00a2fc6cb49c75ce1ace7e..c5e1c5213ada9107853ad1c80e8fb066f6ec10fa 100755
--- a/HySoP/hysop/operator/tests/test_advec_scales.py
+++ b/HySoP/hysop/operator/tests/test_advec_scales.py
@@ -470,15 +470,3 @@ def test_randomVelocity_vec_m8():
assert np.allclose(scal_ref_d.data[0], scal_d.data[0], atol=1e-07)
assert np.allclose(scal_ref_d.data[1], scal_d.data[1], atol=1e-07)
assert np.allclose(scal_ref_d.data[2], scal_d.data[2], atol=1e-07)
-
-if __name__ == "__main__":
- test_nullVelocity_m4()
- test_nullVelocity_vec_m4()
- test_nullVelocity_m6()
- test_nullVelocity_vec_m6()
- test_nullVelocity_m8()
- test_nullVelocity_vec_m8()
- test_randomVelocity_m6()
- test_randomVelocity_vec_m6()
- test_randomVelocity_m8()
- test_randomVelocity_vec_m8()
diff --git a/HySoP/hysop/operator/tests/test_analytic.py b/HySoP/hysop/operator/tests/test_analytic.py
old mode 100644
new mode 100755
index 38315854f7b52f40eac990eed121591eac19f090..3e2878ff9df036410c3aaa5133b153498feffa20
--- a/HySoP/hysop/operator/tests/test_analytic.py
+++ b/HySoP/hysop/operator/tests/test_analytic.py
@@ -160,10 +160,3 @@ def test_analytical_op_6():
assert allclose(cafd[i], refd.data[i])
assert id(cafd.data[i]) == ids[i]
-
-if __name__ == "__main__":
- test_analytical_op_1()
- test_analytical_op_3()
- test_analytical_op_4()
- test_analytical_op_5()
- test_analytical_op_6()
diff --git a/HySoP/hysop/operator/tests/test_density.py b/HySoP/hysop/operator/tests/test_density.py
old mode 100644
new mode 100755
index be2e412371e9d5c8e4ce5006f6a2fe854a0df5cf..0016e6eedd6796b427483ac17ca796640f4fd5b5
--- a/HySoP/hysop/operator/tests/test_density.py
+++ b/HySoP/hysop/operator/tests/test_density.py
@@ -28,6 +28,3 @@ def test_density():
viscosity.initialize(topo=topo)
# simu = Simulation(nbIter=2)
# op.apply(simu) ## --> need to be reviewed
-
-if __name__ == "__main__":
- test_density()
diff --git a/HySoP/hysop/operator/tests/test_diff_poisson_3D.py b/HySoP/hysop/operator/tests/test_diff_poisson_3D.py
index 1142d2ab764036946f1b2f0e34dd2b9483cbf1a3..d4c9186d1714eda051035d9b0341b24d2112b170 100755
--- a/HySoP/hysop/operator/tests/test_diff_poisson_3D.py
+++ b/HySoP/hysop/operator/tests/test_diff_poisson_3D.py
@@ -67,6 +67,3 @@ def test_Diff_Poisson():
iterMax=1000000)
diffusion.apply(simu)
poisson.apply(simu)
-
-if __name__ == "__main__":
- test_Diff_Poisson()
diff --git a/HySoP/hysop/operator/tests/test_differential.py b/HySoP/hysop/operator/tests/test_differential.py
old mode 100644
new mode 100755
index 5e8c65b66e056a8e3f37f252f147bfe72e50bc4d..7a217638b23f2335873563e391bdc67dc301f9ff
--- a/HySoP/hysop/operator/tests/test_differential.py
+++ b/HySoP/hysop/operator/tests/test_differential.py
@@ -248,21 +248,3 @@ def divadvection_func(res, x, y, z, t):
def test_div_advection():
method = {SpaceDiscretisation: FD_C_4}
call_op(DivAdvection, divadvection_func, topo3_3d, op_dim=1, method=method)
-
-# This may be useful to run mpi tests
-if __name__ == "__main__":
- test_curl_fd_1()
- test_curl_fd_2()
- test_curl_fd_1_2d()
- test_curl_fd_3()
- test_curl_fd_3_2d()
- test_curl_fft_1()
- #test_curl_fft_1_2d()
- #test_curl_fft_2()
- #test_curl_fft_2_2d()
- test_grad_1()
- test_grad_2()
- test_grad_3()
- test_grad_3_2d()
- test_curl_fd_work()
- test_div_advection()
diff --git a/HySoP/hysop/operator/tests/test_diffusion.py b/HySoP/hysop/operator/tests/test_diffusion.py
index 8aa9cd45522ad61cbc5da0b9ae3353cd9656bf97..9a493a7b497c4417d89c1aed59b152b0081fd099 100755
--- a/HySoP/hysop/operator/tests/test_diffusion.py
+++ b/HySoP/hysop/operator/tests/test_diffusion.py
@@ -84,9 +84,3 @@ def test_Diffusion2D():
diff.apply(simu)
diff.finalize()
-
-# This may be useful to run mpi tests
-if __name__ == "__main__":
- test_Diffusion3D()
- test_Diffusion3D_2()
- test_Diffusion2D()
diff --git a/HySoP/hysop/operator/tests/test_drag_and_lift.py b/HySoP/hysop/operator/tests/test_drag_and_lift.py
old mode 100644
new mode 100755
index dfbdb7ba890d6df9972d279bfda2a4209d93c72d..ddda768fcaf51f82aab818df3db66755956c07a1
--- a/HySoP/hysop/operator/tests/test_drag_and_lift.py
+++ b/HySoP/hysop/operator/tests/test_drag_and_lift.py
@@ -189,12 +189,3 @@ def test_all_drags():
op.apply(simu)
simu.advance()
#assert False
-
-# This may be useful to run mpi tests
-if __name__ == "__main__":
- test_momentum_forces_3d()
- test_noca1()
- test_noca2()
- test_noca3()
- test_all_drags()
-# test_noca_1_vol()
diff --git a/HySoP/hysop/operator/tests/test_energy_enstrophy.py b/HySoP/hysop/operator/tests/test_energy_enstrophy.py
old mode 100644
new mode 100755
index 124466d2694b8c8980e758352d7d991872552859..87505acb65773f87b55818fc9c8c5e0cb25f0f29
--- a/HySoP/hysop/operator/tests/test_energy_enstrophy.py
+++ b/HySoP/hysop/operator/tests/test_energy_enstrophy.py
@@ -82,6 +82,3 @@ def test_energy_enstrophy():
tol = (topo.mesh.space_step).max() ** 2
assert (op.energy() - eref * 0.5) < tol
assert (op.enstrophy() - eref) < tol
-
-if __name__ == "__main__":
- test_energy_enstrophy()
diff --git a/HySoP/hysop/operator/tests/test_hdf5_io.py b/HySoP/hysop/operator/tests/test_hdf5_io.py
old mode 100644
new mode 100755
index c1c0f5ab7bd4ecc68e4bdbd30da19e570288ccbd..0dee976d0007880c4532e38a1b9ac9f1921e1072
--- a/HySoP/hysop/operator/tests/test_hdf5_io.py
+++ b/HySoP/hysop/operator/tests/test_hdf5_io.py
@@ -387,15 +387,3 @@ def test_write_read_subset_2():
assert not np.allclose(b1.data[d][ind], v3d.data[d][ind])
assert np.allclose(b1.data[d][indsubset], v3d.data[d][indsubset])
-
-# This may be useful to run mpi tests
-if __name__ == "__main__":
- test_write_read_scalar_3D()
- test_write_read_scalar_3D_defaults()
- test_write_read_vectors_3D_defaults()
- test_write_read_vectors_3D()
- test_write_read_subset_1()
- test_write_read_subset_2()
- if main_rank == 0:
- shutil.rmtree(IO.default_path())
- purgeFiles()
diff --git a/HySoP/hysop/operator/tests/test_multiphase_gradp.py b/HySoP/hysop/operator/tests/test_multiphase_gradp.py
old mode 100644
new mode 100755
index 8b4bdf11d2c8c13020c5f38121184a2158feac2a..43aac523e8a34c2008b39e39cb45d688a1096a15
--- a/HySoP/hysop/operator/tests/test_multiphase_gradp.py
+++ b/HySoP/hysop/operator/tests/test_multiphase_gradp.py
@@ -70,8 +70,3 @@ def test_gradp():
assert np.allclose(d_res[0][iCompute], d_true_res[0][iCompute], atol=8e-3)
assert np.allclose(d_res[1][iCompute], d_true_res[1][iCompute], atol=8e-3)
assert np.allclose(d_res[2][iCompute], d_true_res[2][iCompute])
-
-
-if __name__ == '__main__':
- #compute_true_res_formula()
- test_gradp()
diff --git a/HySoP/hysop/operator/tests/test_multiresolution_filter.py b/HySoP/hysop/operator/tests/test_multiresolution_filter.py
old mode 100644
new mode 100755
index de4d72cc17cfa8fb13e3f39b2b04d8c175d1244b..6d66f25139a707a4eeb56f71c08dc217da4510c4
--- a/HySoP/hysop/operator/tests/test_multiresolution_filter.py
+++ b/HySoP/hysop/operator/tests/test_multiresolution_filter.py
@@ -216,19 +216,3 @@ def test_filter_l2_1():
np.max(np.abs(valid[0][topo_coarse.mesh.iCompute] -
f_out[0][topo_coarse.mesh.iCompute]))
-
-if __name__ == '__main__':
- if main_size == 1:
- # These tests are too small to run un parrallel
- test_linear_X()
- test_linear_Y()
- test_linear_Z()
- test_linear_XY()
- #order_linear()
- test_L21_X()
- test_L21_Y()
- test_L21_Z()
- test_L21_XY()
- #order_L21()
- test_filter_linear()
- test_filter_l2_1()
diff --git a/HySoP/hysop/operator/tests/test_particle_advection.py b/HySoP/hysop/operator/tests/test_particle_advection.py
old mode 100644
new mode 100755
index e8c0de92618c3fcac96ccd357815311bafdba348..7ca871bea643158b25ffd0d323d2be0b1712ee20
--- a/HySoP/hysop/operator/tests/test_particle_advection.py
+++ b/HySoP/hysop/operator/tests/test_particle_advection.py
@@ -211,10 +211,3 @@ def test_nullVelocity_dict_3D():
advec = Advection(velocity=velo, variables=scal, discretization=d3d)
assert assertion_list(scal.keys(), advec)
-
-#if __name__ == '__main__':
- #test_nullVelocity_2D()
- #test_nullVelocity_vector_2D()
- #test_nullVelocity_list_2D()
- #test_nullVelocity_3D()
- #test_nullVelocity_vector_3D()
diff --git a/HySoP/hysop/operator/tests/test_penalization.py b/HySoP/hysop/operator/tests/test_penalization.py
old mode 100644
new mode 100755
index 4a55ca752d880f0dc14ba806abc1a97571bfa2bc..d26e3b36b168387bb4ebfab20cb0f702a1043ac5
--- a/HySoP/hysop/operator/tests/test_penalization.py
+++ b/HySoP/hysop/operator/tests/test_penalization.py
@@ -367,16 +367,3 @@ def test_penal_vort_multi_3d():
obstacles={hsphere: [1, 10, 1e8]})
check_penal_vort(penal, wref, vref, vorti, velo)
-
-if __name__ == "__main__":
- test_penal_2d()
- test_penal_3d()
- test_penal_2d_multi()
- test_penal_3d_multi()
- test_penal_2d_porous()
- test_penal_3d_porous()
- test_penal_3d_porous_cyl()
- test_penal_vort_3d()
- test_penal_vort_2d()
- test_penal_vort_multi_2d()
- test_penal_vort_multi_3d()
diff --git a/HySoP/hysop/operator/tests/test_poisson.py b/HySoP/hysop/operator/tests/test_poisson.py
index 30bc1106e39a49b4014d08e90d5a07b7b041f4ee..57de254e06728c022fcb340b5b16e97d870e3b05 100755
--- a/HySoP/hysop/operator/tests/test_poisson.py
+++ b/HySoP/hysop/operator/tests/test_poisson.py
@@ -298,12 +298,3 @@ def test_Poisson3D_projection_2():
for i in range(dom.dimension):
assert np.allclose(vd[i], refD[i])
poisson.finalize()
-
-# This may be useful to run mpi tests
-if __name__ == "__main__":
- test_Poisson_Pressure_3D()
- test_Poisson3D()
- test_Poisson2D()
- test_Poisson3D_correction()
- test_Poisson3D_projection_1()
- test_Poisson3D_projection_2()
diff --git a/HySoP/hysop/operator/tests/test_redistribute.py b/HySoP/hysop/operator/tests/test_redistribute.py
old mode 100644
new mode 100755
index 9aa4f730bbf0e86f15857a6d18a35619a80a8254..a8bae9037aa321bed99017c317f03e9cfc706cdc
--- a/HySoP/hysop/operator/tests/test_redistribute.py
+++ b/HySoP/hysop/operator/tests/test_redistribute.py
@@ -3,11 +3,10 @@ from hysop.operator.redistribute_inter import RedistributeInter
from hysop.operator.redistribute_overlap import RedistributeOverlap
#from hysop.mpi.main_var import main_size, main_rank, main_comm
from hysop.tools.parameters import Discretization, MPIParams
+from hysop import testsenv
import hysop as pp
import numpy as np
-sin = np.sin
import math
-pi = math.pi
from hysop import Simulation
from hysop.operator.analytic import Analytic
from hysop.mpi.main_var import main_comm, main_size
@@ -15,6 +14,9 @@ from hysop.mpi.tests.utils import create_inter_topos, CPU, GPU, OTHER,\
create_multitask_context
from hysop.fields.tests.func_for_tests import v3d, v2d, v3dbis
from hysop.operator.poisson import Poisson
+from hysop.mpi.tests.test_bridge import create_subtopos
+sin = np.sin
+pi = math.pi
dim3 = 3
@@ -79,7 +81,8 @@ def test_distribute_intra_1():
assert np.allclose(vd_2.data[d][ind_ng], wd.data[d][ind_ng])
-def test_distribute_intra_failed_1():
+@testsenv.hysop_failed
+def test_distribute_intra_fail_1():
"""
redistribute data, intra comm, from one
topology to another, no variables -> must fail
@@ -91,12 +94,7 @@ def test_distribute_intra_failed_1():
# 3D topo, ghosts
default_topo = dom.create_topology(discretization=r_wg)
# Redistribute operator
- res = False
- try:
- RedistributeIntra(source=plane_topo, target=default_topo)
- except:
- res = True
- assert res
+ RedistributeIntra(source=plane_topo, target=default_topo)
def test_distribute_intra_2():
@@ -293,7 +291,8 @@ def test_distribute_intra_5():
assert np.allclose(wd.data[d][ind_ng], rd.data[d][ind_ng])
-def test_distribute_intra_failed_4():
+@testsenv.hysop_failed
+def test_distribute_intra_fail_4():
"""
redistribute data, intra comm, between two operators.
"""
@@ -321,17 +320,11 @@ def test_distribute_intra_failed_4():
red = RedistributeIntra(source=source, target=target,
variables=[velocity])
- res = False
- try:
- red.setup()
- except:
- res = True
- assert res
-
-from hysop.mpi.tests.test_bridge import create_subtopos
+ red.setup()
-def test_distribute_failed_5():
+@testsenv.hysop_failed
+def test_distribute_fail_5():
"""
Try the pathologic case where source and target do not apply on
the same group of process but when groups overlap.
@@ -349,13 +342,7 @@ def test_distribute_failed_5():
mpi_ref = MPIParams(comm=main_comm)
red = RedistributeIntra(source=source_topo, target=target_topo,
mpi_params=mpi_ref, variables=[velocity])
- res = False
- try:
- red.setup()
- except:
- res = True
-
- assert res
+ red.setup()
def test_distribute_overlap():
@@ -686,21 +673,3 @@ def test_distribute_inter_2d():
for d in xrange(2):
assert np.allclose(wd.data[d], vd.data[d])
-
-# This may be useful to run mpi tests
-if __name__ == "__main__":
- test_distribute_intra_1()
- test_distribute_intra_failed_1()
- test_distribute_intra_2()
- test_distribute_intra_3()
- test_distribute_intra_4()
- test_distribute_intra_failed_4()
- test_distribute_intra_5()
- test_distribute_failed_5()
- test_distribute_overlap()
- test_distribute_inter()
- test_distribute_inter_2()
- test_distribute_inter_3()
- test_distribute_inter_4()
- test_distribute_inter_5()
- test_distribute_inter_2d()
diff --git a/HySoP/hysop/operator/tests/test_velocity_correction.py b/HySoP/hysop/operator/tests/test_velocity_correction.py
index e0f2a0905ec33cda080531dfd8d9320d9fe69aa7..34f9629296e17bf8ce4bf90707d993d46c7b95a6 100755
--- a/HySoP/hysop/operator/tests/test_velocity_correction.py
+++ b/HySoP/hysop/operator/tests/test_velocity_correction.py
@@ -112,8 +112,3 @@ def test_velocity_correction_2D():
sref = op.cb.surf[0]
flowrate = sref.integrate_field_allc(velo, topo)
assert (np.abs(flowrate - ref_rate) < tol).all()
-
-# This may be useful to run mpi tests
-if __name__ == "__main__":
- test_velocity_correction_2D()
- test_velocity_correction_3D()
diff --git a/HySoP/hysop/tools/sys_utils.py b/HySoP/hysop/tools/sys_utils.py
old mode 100644
new mode 100755
index 82cd50c30690c742cd303863448ebc0e2aedd49f..0767cf2bb2e2c5972f03f46111599acfd428021f
--- a/HySoP/hysop/tools/sys_utils.py
+++ b/HySoP/hysop/tools/sys_utils.py
@@ -1,5 +1,6 @@
"""Tools related to global config.
"""
+import sys
class SysUtils(object):
@@ -8,9 +9,19 @@ class SysUtils(object):
"""
@staticmethod
def in_ipython():
+ """True if current session is run under ipython
+ """
try:
__IPYTHON__
except NameError:
return False
else:
return True
+
+ @staticmethod
+ def is_interactive():
+ """True if run under interactive session, else
+ False. Warning : return true in any case if ipython is
+ used.
+ """
+ return hasattr(sys, 'ps1') or hasattr(sys, 'ipcompleter')
diff --git a/HySoP/hysop/tools/tests/test_parameters.py b/HySoP/hysop/tools/tests/test_parameters.py
old mode 100644
new mode 100755
index b67f3e03efa61fa25e7808231bc7d1492ef8908f..f13a18f3b199ebd9809610c5be7145e7a1cecc13
--- a/HySoP/hysop/tools/tests/test_parameters.py
+++ b/HySoP/hysop/tools/tests/test_parameters.py
@@ -60,7 +60,3 @@ def test_io_params_6():
assert iop.filename == filename
assert iop.filepath == os.path.dirname(filename)
-
-if __name__ == "__main__":
- # test 1 is enough ...
- test_io_params_1()
diff --git a/HySoP/hysop/tools/tests/test_profiler.py b/HySoP/hysop/tools/tests/test_profiler.py
old mode 100644
new mode 100755
index 0c324b3eeb90768a8b760f58d924f739cca421cf..5823d1ec20d81e5a6bc4d4853906d023280ce8a8
--- a/HySoP/hysop/tools/tests/test_profiler.py
+++ b/HySoP/hysop/tools/tests/test_profiler.py
@@ -46,6 +46,3 @@ def test_profilers():
assert a.profiler['call'].n == 2
assert a.profiler['call_other'].n == 1
assert a.profiler['manual'].n == 1
-
-if __name__ == '__main__':
- test_profilers()
diff --git a/HySoP/setup.py.in b/HySoP/setup.py.in
index c5ce7c57465a4944d8ea6623189353108bba0d72..dddbc81f6a24f1946806101939510c24056e6de1 100644
--- a/HySoP/setup.py.in
+++ b/HySoP/setup.py.in
@@ -4,8 +4,10 @@
setup.py file for @PYPACKAGE_NAME@
"""
+from setuptools import find_packages
from numpy.distutils.core import setup, Extension
from numpy.distutils.misc_util import Configuration
+from distutils.spawn import find_executable
import os
import re
@@ -17,6 +19,11 @@ import sys
sys.path.append('@CMAKE_SOURCE_DIR@/')
import sort_f90
+enable_cpp = "@WITH_LIB_CXX@"
+if enable_cpp:
+ swig_executable = find_executable("@SWIG_EXECUTABLE@")
+
+
def parseCMakeVar(var):
if var != "":
return var.split(';')
@@ -41,6 +48,18 @@ def parseCMakeDefines(var):
return res
+hysop_link_libraries = parseCMakeVar("@HYSOP_LINK_LIBRARIES@")
+hysop_link_libraries_names = set([])
+hysop_link_libraries_dirs = set([])
+# use set to avoid dupl.
+link_list = ""
+for lib in hysop_link_libraries:
+ hysop_link_libraries_names.add(os.path.basename(lib))
+ hysop_link_libraries_dirs.add(os.path.dirname(lib))
+ link_list += lib + " "
+hysop_link_libraries_names = list(hysop_link_libraries_names)
+hysop_link_libraries_dirs = list(hysop_link_libraries_dirs)
+
def create_fortran_extension(name, pyf_file=None, src_dirs=None, sources=None,
libdir=None, libs=None, debug_mode=0):
"""Create a new f2py module from fortran files
@@ -60,6 +79,7 @@ def create_fortran_extension(name, pyf_file=None, src_dirs=None, sources=None,
if pyf_file is not None:
sources.append(pyf_file)
sources = sort_f90.sort(sources)
+ print "FORTRAN SOURCES : ", sources
if debug_mode == 0:
options.append(('F2PY_REPORT_ON_ARRAY_COPY', '1'))
if os.uname()[0] == 'Linux':
@@ -75,7 +95,13 @@ def create_fortran_extension(name, pyf_file=None, src_dirs=None, sources=None,
#if(includes != None):
#for exti in includes:
#inc_dir.append(exti)
-
+ #libs += hysop_link_libraries_names
+ #libdir += hysop_link_libraries_dirs
+ print libs
+ print libdir
+ # we trust cmake for external libraries and
+ # add them to linker, without using libraries option
+ extra_link_args = hysop_link_libraries
ext_fort = Extension(name=name,
sources=sources,
f2py_options=f2py_options,
@@ -83,7 +109,8 @@ def create_fortran_extension(name, pyf_file=None, src_dirs=None, sources=None,
define_macros=options,
library_dirs=libdir,
libraries=libs,
- extra_f90_compile_args=fortran_flags
+ extra_f90_compile_args=fortran_flags,
+ extra_link_args=extra_link_args
)
return ext_fort
@@ -155,39 +182,41 @@ def create_swig_extension(name, inc_dirs, src_dirs=None, sources=None):
# ------------ Set list of packages required to build the module -------------
-# Full package name
-name = '@PYPACKAGE_NAME@'
# List of modules (directories) to be included
-packages = ['hysop',
- 'hysop.domain',
- 'hysop.fields',
- 'hysop.operator',
- 'hysop.operator.discrete',
- 'hysop.problem',
- 'hysop.tools',
- 'hysop.numerics',
- 'hysop.numerics.integrators',
- ]
-
-packages_for_tests = ['hysop.domain.tests',
- 'hysop.fields.tests',
- 'hysop.operator.tests',
- 'hysop.numerics.tests',
- 'hysop.tools.tests',
- 'hysop.problem.tests',
- 'hysop.numerics.tests',
- ]
-
-if "@USE_MPI@" is "ON":
- packages.append('hysop.mpi')
- packages_for_tests.append('hysop.mpi.tests')
+with_test = "@WITH_TESTS@" is "ON"
+if with_test:
+ packages = find_packages(exclude=["*fakef2py*", "*gpu*"],where="@CMAKE_SOURCE_DIR@")
+else:
+ packages = find_packages(exclude=["*tests*","*fakef2py*", "*gpu*"],where="@CMAKE_SOURCE_DIR@")
+
+# packages = ['hysop',
+# 'hysop.domain',
+# 'hysop.fields',
+# 'hysop.operator',
+# 'hysop.operator.discrete',
+# 'hysop.problem',
+# 'hysop.tools',
+# 'hysop.numerics',
+# 'hysop.numerics.integrators',
+# ]
+
+# packages_for_tests = ['hysop.domain.tests',
+# 'hysop.fields.tests',
+# 'hysop.operator.tests',
+# 'hysop.numerics.tests',
+# 'hysop.tools.tests',
+# 'hysop.problem.tests',
+# 'hysop.numerics.tests',
+# ]
+
+# if "@USE_MPI@" is "ON":
+# packages.append('hysop.mpi')
+# packages_for_tests.append('hysop.mpi.tests')
if "@WITH_GPU@" is "ON":
packages.append('hysop.gpu')
- packages_for_tests.append('hysop.gpu.tests')
-
-if "@WITH_TESTS@" is "ON":
- packages = packages + packages_for_tests
+ if with_test:
+ packages.append('hysop.gpu.tests')
# Enable this to get debug info
DISTUTILS_DEBUG = 1
@@ -197,7 +226,7 @@ DISTUTILS_DEBUG = 1
ext_modules = []
# Check if fortran interface is enabled
-enable_fortran = "@WITH_LIB_FORTRAN@"
+enable_fortran = "@USE_FORTRAN@"
ext = {}
if enable_fortran is "ON":
@@ -207,14 +236,14 @@ if enable_fortran is "ON":
hysoplib = ['@HYSOP_LIBRARY_NAME@']
f2py_options = ['--no-lower']
fortran_src = set([])
+ fortran_src.add('f2py/parameters.f90')
# -- fftw fortran sources --
withfftw = "@WITH_FFTW@"
if withfftw is "ON":
- fortran_src.add('f2py/parameters.f90')
fortran_src.add('f2py/fftw2py.f90')
fftwdir = '@FFTWLIB@'
- hysoplib.append('fftw3')
- hysoplib.append('fftw3_mpi')
+ #hysoplib.append('fftw3')
+ #hysoplib.append('fftw3_mpi')
hysop_libdir.append(fftwdir)
else:
packages.append('hysop.fakef2py')
@@ -222,7 +251,6 @@ if enable_fortran is "ON":
# -- scales sources --
withscales = '@WITH_SCALES@'
if withscales is "ON":
- fortran_src.add('f2py/parameters.f90')
fortran_src.add('f2py/scales2py.f90')
else:
packages.append('hysop.fakef2py')
@@ -237,8 +265,7 @@ if enable_fortran is "ON":
pyf_file = os.path.join(fortran_root, 'f2hysop.pyf')
# -- list of directories which contains fortran sources --
# those dirs must be in hysop package directory
- subdirs = ['fortran',
- ]
+ subdirs = ['fortran',]
num_dirs = []
for sd in subdirs:
num_dirs.append(os.path.join(fortran_root, sd))
@@ -265,7 +292,7 @@ else:
# --- C++ files and swig interface --
-enable_cpp = "@WITH_LIB_CXX@"
+
if enable_cpp is "ON":
# path to .i files
swig_include_dirs = [os.path.join('@CMAKE_SOURCE_DIR@','swig')]
@@ -297,8 +324,8 @@ descr = 'Hybrid Computation with Particles.'
authors = 'G.H Cottet, J.M Etancelin, J.B Keck, C.Mimeau, F.Pérignon, C. Picard'
# authors = 'HySoP development team'
config = Configuration(
- name=name,
- version='@PYPACKAGE_VERSION@',
+ name='@PACKAGE_NAME@',
+ version='@HYSOP_VERSION@',
description=descr,
author=authors,
author_email='hysop-members@lists.forge.imag.fr',
diff --git a/HySoP/src/CMakeLists.txt b/HySoP/src/CMakeLists.txt
index 3fb7e14f8e3738c51f3380d49a9aba54be61158d..5eea76945fb822e3da511063aaf27f35d84576f3 100644
--- a/HySoP/src/CMakeLists.txt
+++ b/HySoP/src/CMakeLists.txt
@@ -8,89 +8,48 @@
# The list of all dirs containing sources to be compiled for the HySoP lib
# Any file in those dirs will be used to create libhysop
set(${HYSOP_LIBRARY_NAME}_SRCDIRS
- ${CMAKE_CURRENT_SOURCE_DIR}
- )
+ .)
# --- fftw interface ---
if(WITH_FFTW)
- set(${HYSOP_LIBRARY_NAME}_SRCDIRS
- ${${HYSOP_LIBRARY_NAME}_SRCDIRS} ${CMAKE_CURRENT_SOURCE_DIR}/fftw
- )
+ list(APPEND ${HYSOP_LIBRARY_NAME}_SRCDIRS fftw)
endif()
+
if(WITH_LIB_CXX)
- set(${HYSOP_LIBRARY_NAME}_SRCDIRS
- ${${HYSOP_LIBRARY_NAME}_SRCDIRS} ${CMAKE_CURRENT_SOURCE_DIR}/hysop++/src
- )
+ list(APPEND ${HYSOP_LIBRARY_NAME}_SRCDIRS hysop++/src)
endif()
-#set(SCALES_DIR scalesReduced)
-set(SCALES_DIR ${CMAKE_CURRENT_SOURCE_DIR}/scalesInterface)
+# --- Choose scales sources location ---
+# --> cache var to allow user input
+set(SCALES_DIR scalesInterface CACHE FILEPATH "Scales sources location, default=src/scalesInterface")
# --- scales ---
if(WITH_SCALES)
set(${HYSOP_LIBRARY_NAME}_SRCDIRS
${${HYSOP_LIBRARY_NAME}_SRCDIRS}
- ${SCALES_DIR}/
+ ${SCALES_DIR}/.
${SCALES_DIR}/layout
${SCALES_DIR}/particles
${SCALES_DIR}/particles/advec_line
)
endif()
-list(APPEND FORTRAN_INCLUDE_DIRS ${${HYSOP_LIBRARY_NAME}_SRCDIRS})
-
-# Matching expr for files to be compiled.
-set(EXTS *.f90 *.f95 *F90)
-# Matching expr for headers (install purpose)
-set(EXTS_HDRS *.hpp *.h)
-# Note FP : we can also use cmake vars ${CMAKE_Fortran_SOURCE_FILE_EXTENSIONS} ${CMAKE_C_SOURCE_FILE_EXTENSIONS} ${CMAKE_CXX_SOURCE_FILE_EXTENSIONS}
-
-# ============= The project =============
-# Set project name and project languages
-# => this automatically defines:
-# - ${HYSOP_LIBRARY_NAME}_BINARY_DIR : where you have run cmake, i.e. the place for compilation
-# - ${HYSOP_LIBRARY_NAME}_SOURCE_DIR : where sources (.f and .h and this CMakeLists.txt) are located
-# Note that because of OutOfSourceBuild, binary_dir and source_dir must be different.
-project(${HYSOP_LIBRARY_NAME} Fortran CXX)
-
-# ============= Search for libraries =============
-# We search for libraries HySoP depends on and
-# set the compile/link conf (-I and -L opt)
-
-# ============= Prepare compilation =============
-
-# Force a default build type if not provided by user
-# CMAKE_BUILD_TYPE = empty, Debug, Release, RelWithDebInfo or MinSizeRel.
-if (NOT CMAKE_BUILD_TYPE)
- set (CMAKE_BUILD_TYPE RELEASE CACHE STRING "Choose the type of build, options are: None, Debug, Release, RelWithDebInfo or MinSizeRel." FORCE)
-endif (NOT CMAKE_BUILD_TYPE)
-
-# Set module files directory (i.e. where .mod will be created)
-set(CMAKE_Fortran_MODULE_DIRECTORY ${CMAKE_BINARY_DIR}/Modules)
-# Add compilation flags:
-#append_Fortran_FLAGS("-Wall -fPIC -ffree-line-length-none -DBLOCKING_SEND_PLUS -DBLOCKING_SEND")
-append_Fortran_FLAGS("-Wall -fPIC -ffree-line-length-none")
-
-# --- MPI ---
-if(USE_MPI)
- # Find MPI for fortran.
- find_package(MPI REQUIRED)
- # -I
- include_directories(${MPI_Fortran_INCLUDE_PATH})
- # Add compilation/link flags
- set(${HYSOP_LIBRARY_NAME}_LINK_FLAGS ${${HYSOP_LIBRARY_NAME}_LINK_FLAGS} ${MPI_Fortran_LINK_FLAGS})
- append_Fortran_flags(${MPI_Fortran_COMPILE_FLAGS})
- # Append mpi libraries to the list of libraries linked with libhysop.
- set(LIBS ${LIBS} ${MPI_Fortran_LIBRARIES} )
-endif(USE_MPI)
-
-# --- FFTW ---
-if(WITH_FFTW)
- include_directories(SYSTEM ${FFTW_INCLUDE_DIRS})
- link_directories(${FFTW_LIBRARY_DIRS})
- add_definitions(${FFTW_DEFINES})
- set(LIBS ${LIBS} ${FFTW_LIBRARIES})
+if(WITH_EXTRAS)
+ list(APPEND ${HYSOP_LIBRARY_NAME}_SRCDIRS} extras)
endif()
+# extensions of source files that must be taken into account
+get_standard_ext()
+set(SRC_EXTS ${ALL_EXTS})
+set(HDR_EXTS *.hpp *.h)
+#============= Collect source and header files and create the library =============
+
+get_sources("${${HYSOP_LIBRARY_NAME}_SRCDIRS}")
+set(${HYSOP_LIBRARY_NAME}_SRCS ${SOURCES_FILES})
+# --- Collect headers ---
+# --> set HYSOP_HDRS (for installation)
+set(HDRS_DIRS ${${HYSOP_LIBRARY_NAME}_SRCDIRS})
+get_headers("${HDRS_DIRS}")
+set(${HYSOP_LIBRARY_NAME}_HDRS ${HDRS_FILES})
# ============= Generates HySoPConfig.hpp =============
# The file HYSOP_LIBRARY_NAME_defines.hpp will be generated from config.hpp.cmake;
@@ -99,92 +58,48 @@ if(EXISTS ${CMAKE_SOURCE_DIR}/config.hpp.cmake)
include_directories(${CMAKE_BINARY_DIR})
endif()
-# ============= Collect source and header files and create the library =============
-
-# 1 - We scan all files with matching extension in directories containing sources.
-foreach(_DIR ${${HYSOP_LIBRARY_NAME}_SRCDIRS})
- set(_DIR_FILES)
- foreach(_EXT ${EXTS}) # Source files
- file(GLOB _DIR_FILES_EXT ${_DIR}/${_EXT})
- if(_DIR_FILES_EXT)
- list(APPEND ${HYSOP_LIBRARY_NAME}_SRC ${_DIR_FILES_EXT})
- endif()
- endforeach()
- foreach(_EXT ${EXTS_HDRS}) # Headers
- file(GLOB _DIR_FILES_EXT ${_DIR}/${_EXT})
- if(_DIR_FILES_EXT)
- list(APPEND ${HYSOP_LIBRARY_NAME}_HDRS ${_DIR_FILES_EXT})
- endif()
- endforeach()
-endforeach()
list(APPEND ${HYSOP_LIBRARY_NAME}_HDRS "hysop_defines.hpp")
# We add headers to source files list
-list(APPEND ${HYSOP_LIBRARY_NAME}_SRC ${${HYSOP_LIBRARY_NAME}_HDRS})
+list(APPEND ${HYSOP_LIBRARY_NAME}_SRCS ${${HYSOP_LIBRARY_NAME}_HDRS})
-include_directories(${${HYSOP_LIBRARY_NAME}_SRCDIRS})
+# --- include dirs for library ---
+# for local headers ...
+include_directories(${HDRS_DIRS})
include_directories(${CMAKE_Fortran_MODULE_DIRECTORY})
+# and for headers of external libraries
+include_directories(${HYSOP_INCLUDE_DIRECTORIES})
+
+add_library(${HYSOP_LIBRARY_NAME} STATIC ${${HYSOP_LIBRARY_NAME}_SRCS})
+target_link_libraries(${HYSOP_LIBRARY_NAME} PRIVATE ${HYSOP_LINK_LIBRARIES})
-# Cmake tools to handle fortran-c interface. It will generate F2CMangle.hpp, a file
-# that will contain some useful macros to deal with fortran-C name mangling.
-# See cmake doc for this module.
-#include(FortranCInterface)
-#FortranCInterface_HEADER(${CMAKE_Fortran_MODULE_DIRECTORY}/F2CMangle.hpp
-# MACRO_NAMESPACE "F2C_"
-# SYMBOL_NAMESPACE "F2C_")
-message("AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA")
-# static library
-display(${HYSOP_LIBRARY_NAME}_SRC)
-add_library(${HYSOP_LIBRARY_NAME} STATIC ${${HYSOP_LIBRARY_NAME}_SRC})
-target_link_libraries(${HYSOP_LIBRARY_NAME} ${LIBS})
+#install(TARGETS ${HYSOP_LIBRARY_NAME}
+# LIBRARY DESTINATION ${HYSOP_PYTHON_INSTALL_DIR}/${PACKAGE_NAME})
# ============= Create an executable linked with libhysop =============
# This part is optional and only useful to test libhysop in a
# way that does not depends on python.
# At the time it only includes fftw tests.
-
-if(WITH_FFTW)
- # Set the name of a executable file that will be linked with libHYSOP_LIBRARY_NAME.
- # Useful to test libhysop in a way that does not depend on python.
- set(EXE_NAME ${HYSOP_LIBRARY_NAME}Run)
- # A main file to create an executable (test purpose)
- # Any files in these dirs will be used to create HySoP exec (linked with libhysop)
- set(${EXE_NAME}_SRCDIRS main)
- # Source and header files list, to generate a working executable based on libhysop.
- foreach(_DIR ${${EXE_NAME}_SRCDIRS})
- set(_DIR_FILES)
- foreach(_EXT ${EXTS})
- file(GLOB _DIR_FILES_EXT ${_DIR}/${_EXT})
- if(_DIR_FILES_EXT)
- list(APPEND ${EXE_NAME}_SRC ${_DIR_FILES_EXT})
- endif()
- endforeach()
- foreach(_EXT ${EXTS_HDRS})
- file(GLOB _DIR_FILES_EXT ${_DIR}/${_EXT})
- if(_DIR_FILES_EXT)
- list(APPEND ${EXE_NAME}_HDRS ${_DIR_FILES_EXT})
- endif()
- endforeach()
- endforeach()
- list(APPEND ${EXE_NAME}_SRC ${${EXE_NAME}_HDRS})
- include_directories(${${EXE_NAME}_HDRS})
- add_executable(${EXE_NAME} ${${EXE_NAME}_SRC})
- add_dependencies(${EXE_NAME} ${HYSOP_LIBRARY_NAME})
-
- # libs to link with EXE_NAME
- target_link_libraries(${EXE_NAME} ${HYSOP_LIBRARY_NAME})
- target_link_libraries(${EXE_NAME} ${LIBS})
-endif()
-
-# ============== Add tests ==============
-if(WITH_TESTS)
-# message(STATUS "Enable testing ...")
-# begin_test(src/tests/F2003)
-# new_test(testAllocatedPtr userMod.f90 wrapper.f90 testAllocatedPtr.cxx)
-# new_test(testNullPtr userMod.f90 wrapper.f90 testNullPtr.cxx)
-# end_test()
-# begin_test(src/tests/Particles)
-# new_test(testCreate3D testCreate3D.f90)
-# new_test(testCreate2D testCreate2D.f90)
-# end_test()
-endif(WITH_TESTS)
+if(WITH_FORTRAN_TESTS)
+ if(WITH_FFTW)
+ # Set the name of a executable file that will be linked with libHYSOP_LIBRARY_NAME.
+ # Useful to test libhysop in a way that does not depend on python.
+ set(EXE_NAME ${HYSOP_LIBRARY_NAME}Run)
+ # A main file to create an executable (test purpose)
+ # Any files in these dirs will be used to create HySoP exec (linked with libhysop)
+ set(${EXE_NAME}_SRCDIRS main)
+ # Source and header files list, to generate a working executable based on libhysop.
+ get_sources("${${EXE_NAME}_SRCDIRS}")
+ get_headers("${${EXE_NAME}_SRCDIRS}")
+ set(${EXE_NAME}_SRCS ${SOURCES_FILES})
+ set(${EXE_NAME}_HDRS ${HDRS_FILES})
+ list(APPEND ${EXE_NAME}_SRC ${${EXE_NAME}_HDRS})
+ include_directories(${${EXE_NAME}_HDRS})
+ add_executable(${EXE_NAME} ${${EXE_NAME}_SRCS})
+ add_dependencies(${EXE_NAME} ${HYSOP_LIBRARY_NAME})
+
+ # libs to link with EXE_NAME
+ target_link_libraries(${EXE_NAME} ${HYSOP_LIBRARY_NAME})
+ target_link_libraries(${EXE_NAME} ${HYSOP_LINK_LIBRARIES})
+ endif()
+endif()
\ No newline at end of file
diff --git a/HySoP/src/arnoldi.f90 b/HySoP/src/extras/arnoldi.f90
similarity index 100%
rename from HySoP/src/arnoldi.f90
rename to HySoP/src/extras/arnoldi.f90