diff --git a/HySoP/CMake/FindPythonLibs.cmake b/HySoP/CMake/FindPythonLibs.cmake
new file mode 100755
index 0000000000000000000000000000000000000000..af80e2c7daefe7a8563f3f4b31a78d67f47a8f07
--- /dev/null
+++ b/HySoP/CMake/FindPythonLibs.cmake
@@ -0,0 +1,276 @@
+# - Find python libraries
+# This module finds if Python is installed and determines where the
+# include files and libraries are. It also determines what the name of
+# the library is. This code sets the following variables:
+#
+# PYTHONLIBS_FOUND - have the Python libs been found
+# PYTHON_LIBRARIES - path to the python library
+# PYTHON_INCLUDE_PATH - path to where Python.h is found (deprecated)
+# PYTHON_INCLUDE_DIRS - path to where Python.h is found
+# PYTHON_DEBUG_LIBRARIES - path to the debug library (deprecated)
+# PYTHONLIBS_VERSION_STRING - version of the Python libs found (since CMake 2.8.8)
+#
+# The Python_ADDITIONAL_VERSIONS variable can be used to specify a list of
+# version numbers that should be taken into account when searching for Python.
+# You need to set this variable before calling find_package(PythonLibs).
+#
+# If you'd like to specify the installation of Python to use, you should modify
+# the following cache variables:
+# PYTHON_LIBRARY - path to the python library
+# PYTHON_INCLUDE_DIR - path to where Python.h is found
+
+#=============================================================================
+# Copyright 2001-2009 Kitware, Inc.
+#
+# Distributed under the OSI-approved BSD License (the "License");
+# see accompanying file Copyright.txt for details.
+#
+# This software is distributed WITHOUT ANY WARRANTY; without even the
+# implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the License for more information.
+#=============================================================================
+# (To distribute this file outside of CMake, substitute the full
+# License text for the above reference.)
+
+INCLUDE(CMakeFindFrameworks)
+# Search for the python framework on Apple.
+CMAKE_FIND_FRAMEWORKS(Python)
+
+SET(_PYTHON1_VERSIONS 1.6 1.5)
+SET(_PYTHON2_VERSIONS 2.7 2.6 2.5 2.4 2.3 2.2 2.1 2.0)
+SET(_PYTHON3_VERSIONS 3.3 3.2 3.1 3.0)
+
+IF(PythonLibs_FIND_VERSION)
+ IF(PythonLibs_FIND_VERSION MATCHES "^[0-9]+\\.[0-9]+(\\.[0-9]+.*)?$")
+ STRING(REGEX REPLACE "^([0-9]+\\.[0-9]+).*" "\\1" _PYTHON_FIND_MAJ_MIN "${PythonLibs_FIND_VERSION}")
+ STRING(REGEX REPLACE "^([0-9]+).*" "\\1" _PYTHON_FIND_MAJ "${_PYTHON_FIND_MAJ_MIN}")
+ UNSET(_PYTHON_FIND_OTHER_VERSIONS)
+ IF(PythonLibs_FIND_VERSION_EXACT)
+ IF(_PYTHON_FIND_MAJ_MIN STREQUAL PythonLibs_FIND_VERSION)
+ SET(_PYTHON_FIND_OTHER_VERSIONS "${PythonLibs_FIND_VERSION}")
+ ELSE(_PYTHON_FIND_MAJ_MIN STREQUAL PythonLibs_FIND_VERSION)
+ SET(_PYTHON_FIND_OTHER_VERSIONS "${PythonLibs_FIND_VERSION}" "${_PYTHON_FIND_MAJ_MIN}")
+ ENDIF(_PYTHON_FIND_MAJ_MIN STREQUAL PythonLibs_FIND_VERSION)
+ ELSE(PythonLibs_FIND_VERSION_EXACT)
+ FOREACH(_PYTHON_V ${_PYTHON${_PYTHON_FIND_MAJ}_VERSIONS})
+ IF(NOT _PYTHON_V VERSION_LESS _PYTHON_FIND_MAJ_MIN)
+ LIST(APPEND _PYTHON_FIND_OTHER_VERSIONS ${_PYTHON_V})
+ ENDIF()
+ ENDFOREACH()
+ ENDIF(PythonLibs_FIND_VERSION_EXACT)
+ UNSET(_PYTHON_FIND_MAJ_MIN)
+ UNSET(_PYTHON_FIND_MAJ)
+ ELSE(PythonLibs_FIND_VERSION MATCHES "^[0-9]+\\.[0-9]+(\\.[0-9]+.*)?$")
+ SET(_PYTHON_FIND_OTHER_VERSIONS ${_PYTHON${PythonLibs_FIND_VERSION}_VERSIONS})
+ ENDIF(PythonLibs_FIND_VERSION MATCHES "^[0-9]+\\.[0-9]+(\\.[0-9]+.*)?$")
+ELSE(PythonLibs_FIND_VERSION)
+ SET(_PYTHON_FIND_OTHER_VERSIONS ${_PYTHON3_VERSIONS} ${_PYTHON2_VERSIONS} ${_PYTHON1_VERSIONS})
+ENDIF(PythonLibs_FIND_VERSION)
+
+# Set up the versions we know about, in the order we will search. Always add
+# the user supplied additional versions to the front.
+SET(_Python_VERSIONS
+ ${Python_ADDITIONAL_VERSIONS}
+ ${_PYTHON_FIND_OTHER_VERSIONS}
+ )
+
+UNSET(_PYTHON_FIND_OTHER_VERSIONS)
+UNSET(_PYTHON1_VERSIONS)
+UNSET(_PYTHON2_VERSIONS)
+UNSET(_PYTHON3_VERSIONS)
+
+FOREACH(_CURRENT_VERSION ${_Python_VERSIONS})
+ STRING(REPLACE "." "" _CURRENT_VERSION_NO_DOTS ${_CURRENT_VERSION})
+ IF(WIN32)
+ FIND_LIBRARY(PYTHON_DEBUG_LIBRARY
+ NAMES python${_CURRENT_VERSION_NO_DOTS}_d python
+ PATHS
+ [HKEY_LOCAL_MACHINE\\SOFTWARE\\Python\\PythonCore\\${_CURRENT_VERSION}\\InstallPath]/libs/Debug
+ [HKEY_CURRENT_USER\\SOFTWARE\\Python\\PythonCore\\${_CURRENT_VERSION}\\InstallPath]/libs/Debug
+ [HKEY_LOCAL_MACHINE\\SOFTWARE\\Python\\PythonCore\\${_CURRENT_VERSION}\\InstallPath]/libs
+ [HKEY_CURRENT_USER\\SOFTWARE\\Python\\PythonCore\\${_CURRENT_VERSION}\\InstallPath]/libs
+ )
+ ENDIF(WIN32)
+ FIND_LIBRARY(PYTHON_LIBRARY
+ NAMES
+ python${_CURRENT_VERSION_NO_DOTS}
+ python${_CURRENT_VERSION}mu
+ python${_CURRENT_VERSION}m
+ python${_CURRENT_VERSION}u
+ python${_CURRENT_VERSION}
+ PATHS ENV LD_LIBRARY_PATH ENV DYLD_LIBRARY_PATH
+# PATHS
+# [HKEY_LOCAL_MACHINE\\SOFTWARE\\Python\\PythonCore\\${_CURRENT_VERSION}\\InstallPath]/libs
+# [HKEY_CURRENT_USER\\SOFTWARE\\Python\\PythonCore\\${_CURRENT_VERSION}\\InstallPath]/libs
+ # Avoid finding the .dll in the PATH. We want the .lib.
+ # NO_SYSTEM_ENVIRONMENT_PATH
+ )
+
+ # Look for the static library in the Python config directory
+ FIND_LIBRARY(PYTHON_LIBRARY
+ NAMES python${_CURRENT_VERSION_NO_DOTS} python${_CURRENT_VERSION}
+ # Avoid finding the .dll in the PATH. We want the .lib.
+ NO_SYSTEM_ENVIRONMENT_PATH
+ # This is where the static library is usually located
+ PATH_SUFFIXES python${_CURRENT_VERSION}/config
+ )
+
+ # For backward compatibility, honour value of PYTHON_INCLUDE_PATH, if
+ # PYTHON_INCLUDE_DIR is not set.
+ IF(DEFINED PYTHON_INCLUDE_PATH AND NOT DEFINED PYTHON_INCLUDE_DIR)
+ SET(PYTHON_INCLUDE_DIR "${PYTHON_INCLUDE_PATH}" CACHE PATH
+ "Path to where Python.h is found" FORCE)
+ ENDIF(DEFINED PYTHON_INCLUDE_PATH AND NOT DEFINED PYTHON_INCLUDE_DIR)
+
+ SET(PYTHON_FRAMEWORK_INCLUDES)
+ IF(Python_FRAMEWORKS AND NOT PYTHON_INCLUDE_DIR)
+ FOREACH(dir ${Python_FRAMEWORKS})
+ SET(PYTHON_FRAMEWORK_INCLUDES ${PYTHON_FRAMEWORK_INCLUDES}
+ ${dir}/Versions/${_CURRENT_VERSION}/include/python${_CURRENT_VERSION})
+ ENDFOREACH(dir)
+ ENDIF(Python_FRAMEWORKS AND NOT PYTHON_INCLUDE_DIR)
+
+ FIND_PATH(PYTHON_INCLUDE_DIR
+ NAMES Python.h
+ PATHS
+ ${PYTHON_FRAMEWORK_INCLUDES}
+ [HKEY_LOCAL_MACHINE\\SOFTWARE\\Python\\PythonCore\\${_CURRENT_VERSION}\\InstallPath]/include
+ [HKEY_CURRENT_USER\\SOFTWARE\\Python\\PythonCore\\${_CURRENT_VERSION}\\InstallPath]/include
+ PATH_SUFFIXES
+ python${_CURRENT_VERSION}mu
+ python${_CURRENT_VERSION}m
+ python${_CURRENT_VERSION}u
+ python${_CURRENT_VERSION}
+ )
+
+ # For backward compatibility, set PYTHON_INCLUDE_PATH.
+ SET(PYTHON_INCLUDE_PATH "${PYTHON_INCLUDE_DIR}")
+
+ IF(PYTHON_INCLUDE_DIR AND EXISTS "${PYTHON_INCLUDE_DIR}/patchlevel.h")
+ FILE(STRINGS "${PYTHON_INCLUDE_DIR}/patchlevel.h" python_version_str
+ REGEX "^#define[ \t]+PY_VERSION[ \t]+\"[^\"]+\"")
+ STRING(REGEX REPLACE "^#define[ \t]+PY_VERSION[ \t]+\"([^\"]+)\".*" "\\1"
+ PYTHONLIBS_VERSION_STRING "${python_version_str}")
+ UNSET(python_version_str)
+ ENDIF(PYTHON_INCLUDE_DIR AND EXISTS "${PYTHON_INCLUDE_DIR}/patchlevel.h")
+
+ IF(PYTHON_LIBRARY AND PYTHON_INCLUDE_DIR)
+ BREAK()
+ ENDIF(PYTHON_LIBRARY AND PYTHON_INCLUDE_DIR)
+ENDFOREACH(_CURRENT_VERSION)
+
+MARK_AS_ADVANCED(
+ PYTHON_DEBUG_LIBRARY
+ PYTHON_LIBRARY
+ PYTHON_INCLUDE_DIR
+)
+
+# We use PYTHON_INCLUDE_DIR, PYTHON_LIBRARY and PYTHON_DEBUG_LIBRARY for the
+# cache entries because they are meant to specify the location of a single
+# library. We now set the variables listed by the documentation for this
+# module.
+SET(PYTHON_INCLUDE_DIRS "${PYTHON_INCLUDE_DIR}")
+SET(PYTHON_DEBUG_LIBRARIES "${PYTHON_DEBUG_LIBRARY}")
+
+# These variables have been historically named in this module different from
+# what SELECT_LIBRARY_CONFIGURATIONS() expects.
+SET(PYTHON_LIBRARY_DEBUG "${PYTHON_DEBUG_LIBRARY}")
+SET(PYTHON_LIBRARY_RELEASE "${PYTHON_LIBRARY}")
+INCLUDE(SelectLibraryConfigurations)
+SELECT_LIBRARY_CONFIGURATIONS(PYTHON)
+# SELECT_LIBRARY_CONFIGURATIONS() sets ${PREFIX}_FOUND if it has a library.
+# Unset this, this prefix doesn't match the module prefix, they are different
+# for historical reasons.
+UNSET(PYTHON_FOUND)
+
+INCLUDE(FindPackageHandleStandardArgs)
+FIND_PACKAGE_HANDLE_STANDARD_ARGS(PythonLibs
+ REQUIRED_VARS PYTHON_LIBRARIES PYTHON_INCLUDE_DIRS
+ VERSION_VAR PYTHONLIBS_VERSION_STRING)
+
+# PYTHON_ADD_MODULE(<name> src1 src2 ... srcN) is used to build modules for python.
+# PYTHON_WRITE_MODULES_HEADER(<filename>) writes a header file you can include
+# in your sources to initialize the static python modules
+FUNCTION(PYTHON_ADD_MODULE _NAME )
+ GET_PROPERTY(_TARGET_SUPPORTS_SHARED_LIBS
+ GLOBAL PROPERTY TARGET_SUPPORTS_SHARED_LIBS)
+ OPTION(PYTHON_ENABLE_MODULE_${_NAME} "Add module ${_NAME}" TRUE)
+ OPTION(PYTHON_MODULE_${_NAME}_BUILD_SHARED
+ "Add module ${_NAME} shared" ${_TARGET_SUPPORTS_SHARED_LIBS})
+
+ # Mark these options as advanced
+ MARK_AS_ADVANCED(PYTHON_ENABLE_MODULE_${_NAME}
+ PYTHON_MODULE_${_NAME}_BUILD_SHARED)
+
+ IF(PYTHON_ENABLE_MODULE_${_NAME})
+ IF(PYTHON_MODULE_${_NAME}_BUILD_SHARED)
+ SET(PY_MODULE_TYPE MODULE)
+ ELSE(PYTHON_MODULE_${_NAME}_BUILD_SHARED)
+ SET(PY_MODULE_TYPE STATIC)
+ SET_PROPERTY(GLOBAL APPEND PROPERTY PY_STATIC_MODULES_LIST ${_NAME})
+ ENDIF(PYTHON_MODULE_${_NAME}_BUILD_SHARED)
+
+ SET_PROPERTY(GLOBAL APPEND PROPERTY PY_MODULES_LIST ${_NAME})
+ ADD_LIBRARY(${_NAME} ${PY_MODULE_TYPE} ${ARGN})
+# TARGET_LINK_LIBRARIES(${_NAME} ${PYTHON_LIBRARIES})
+
+ IF(PYTHON_MODULE_${_NAME}_BUILD_SHARED)
+ SET_TARGET_PROPERTIES(${_NAME} PROPERTIES PREFIX "${PYTHON_MODULE_PREFIX}")
+ IF(WIN32 AND NOT CYGWIN)
+ SET_TARGET_PROPERTIES(${_NAME} PROPERTIES SUFFIX ".pyd")
+ ENDIF(WIN32 AND NOT CYGWIN)
+ ENDIF(PYTHON_MODULE_${_NAME}_BUILD_SHARED)
+
+ ENDIF(PYTHON_ENABLE_MODULE_${_NAME})
+ENDFUNCTION(PYTHON_ADD_MODULE)
+
+FUNCTION(PYTHON_WRITE_MODULES_HEADER _filename)
+
+ GET_PROPERTY(PY_STATIC_MODULES_LIST GLOBAL PROPERTY PY_STATIC_MODULES_LIST)
+
+ GET_FILENAME_COMPONENT(_name "${_filename}" NAME)
+ STRING(REPLACE "." "_" _name "${_name}")
+ STRING(TOUPPER ${_name} _nameUpper)
+ SET(_filename ${CMAKE_CURRENT_BINARY_DIR}/${_filename})
+
+ SET(_filenameTmp "${_filename}.in")
+ FILE(WRITE ${_filenameTmp} "/*Created by cmake, do not edit, changes will be lost*/\n")
+ FILE(APPEND ${_filenameTmp}
+"#ifndef ${_nameUpper}
+#define ${_nameUpper}
+
+#include <Python.h>
+
+#ifdef __cplusplus
+extern \"C\" {
+#endif /* __cplusplus */
+
+")
+
+ FOREACH(_currentModule ${PY_STATIC_MODULES_LIST})
+ FILE(APPEND ${_filenameTmp} "extern void init${PYTHON_MODULE_PREFIX}${_currentModule}(void);\n\n")
+ ENDFOREACH(_currentModule ${PY_STATIC_MODULES_LIST})
+
+ FILE(APPEND ${_filenameTmp}
+"#ifdef __cplusplus
+}
+#endif /* __cplusplus */
+
+")
+
+
+ FOREACH(_currentModule ${PY_STATIC_MODULES_LIST})
+ FILE(APPEND ${_filenameTmp} "int ${_name}_${_currentModule}(void) \n{\n static char name[]=\"${PYTHON_MODULE_PREFIX}${_currentModule}\"; return PyImport_AppendInittab(name, init${PYTHON_MODULE_PREFIX}${_currentModule});\n}\n\n")
+ ENDFOREACH(_currentModule ${PY_STATIC_MODULES_LIST})
+
+ FILE(APPEND ${_filenameTmp} "void ${_name}_LoadAllPythonModules(void)\n{\n")
+ FOREACH(_currentModule ${PY_STATIC_MODULES_LIST})
+ FILE(APPEND ${_filenameTmp} " ${_name}_${_currentModule}();\n")
+ ENDFOREACH(_currentModule ${PY_STATIC_MODULES_LIST})
+ FILE(APPEND ${_filenameTmp} "}\n\n")
+ FILE(APPEND ${_filenameTmp} "#ifndef EXCLUDE_LOAD_ALL_FUNCTION\nvoid CMakeLoadAllPythonModules(void)\n{\n ${_name}_LoadAllPythonModules();\n}\n#endif\n\n#endif\n")
+
+# with CONFIGURE_FILE() cmake complains that you may not use a file created using FILE(WRITE) as input file for CONFIGURE_FILE()
+ EXECUTE_PROCESS(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${_filenameTmp}" "${_filename}" OUTPUT_QUIET ERROR_QUIET)
+
+ENDFUNCTION(PYTHON_WRITE_MODULES_HEADER)
diff --git a/HySoP/CMake/FindPythonModule.cmake b/HySoP/CMake/FindPythonModule.cmake
new file mode 100755
index 0000000000000000000000000000000000000000..d16955492361d3688344bcfdde241191ca7d2136
--- /dev/null
+++ b/HySoP/CMake/FindPythonModule.cmake
@@ -0,0 +1,25 @@
+# Search for a particular python module.
+# Sources : see http://www.cmake.org/pipermail/cmake/2011-January/041666.html
+#
+# Usage : find_python_module(mpi4py REQUIRED)
+#
+function(find_python_module module)
+ string(TOUPPER ${module} module_upper)
+ if(ARGC GREATER 1 AND ARGV1 STREQUAL "REQUIRED")
+ set(${module}_FIND_REQUIRED TRUE)
+ endif()
+ # A module's location is usually a directory, but for binary modules
+ # it's a .so file.
+ execute_process(COMMAND ${PYTHON_EXECUTABLE} -c
+ "import re, ${module}; print re.compile('/__init__.py.*').sub('',${module}.__file__)"
+ RESULT_VARIABLE _${module}_status
+ OUTPUT_VARIABLE _${module}_location
+ ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
+
+ if(NOT _${module}_status)
+ set(python_${module_upper} ${_${module}_location} CACHE STRING
+ "Location of Python module ${module}")
+ endif(NOT _${module}_status)
+
+ find_package_handle_standard_args(${module} DEFAULT_MSG _${module}_location)
+endfunction(find_python_module)
diff --git a/HySoP/CMakeLists.txt b/HySoP/CMakeLists.txt
index 3d36c521f9087b3072f4360156c088670cfb44c0..715d373cb1d9b73714073b622934b43f7c241946 100644
--- a/HySoP/CMakeLists.txt
+++ b/HySoP/CMakeLists.txt
@@ -63,18 +63,33 @@ endif(WITH_TESTS)
# We search for libraries Parmes depends on and
# set the compile/link conf (-I and -L opt)
-# --- MPI ---
+set(PARMES_LIBRARY_NAME parmes)
+set(PACKAGE_NAME Parmes)
+
+# --- Python ---
+
+include(FindPythonInterp)
+include(FindPythonLibs)
+include(FindPythonModule)
+if(NOT PYTHONLIBS_VERSION_STRING VERSION_EQUAL PYTHON_VERSION_STRING)
+ display(PYTHONLIBS_VERSION_STRING)
+ display(PYTHON_VERSION_STRING)
+ message(FATAL_ERROR "Python library and executable versions do not match.")
+endif()
+
+find_python_module(numpy REQUIRED)
#Install dir for python (default = --user)
execute_process(
- COMMAND python -c "import site ; print site.USER_SITE"
+ COMMAND ${PYTHON_EXECUTABLE} -c "import site ; print site.USER_SITE"
OUTPUT_VARIABLE ${PROJECT_NAME}_INSTALL_DIR)
string(STRIP ${${PROJECT_NAME}_INSTALL_DIR} ${PROJECT_NAME}_INSTALL_DIR)
set(CMAKE_INSTALL_PREFIX ${${PROJECT_NAME}_INSTALL_DIR}/${PROJECT_NAME})
-set(PARMES_LIBRARY_NAME parmes)
-set(PACKAGE_NAME Parmes)
+# --- MPI ---
+
if(USE_MPI)
+ find_python_module(mpi4py REQUIRED)
# Find MPI for C++ and fortran.
find_package(MPI REQUIRED)
# -I
@@ -104,14 +119,13 @@ if(EXISTS ${CMAKE_SOURCE_DIR}/parmepy/__init__.py.in)
configure_file(parmepy/__init__.py.in ${CMAKE_SOURCE_DIR}/parmepy/__init__.py)
endif()
-set(PYTHON_EXECUTABLE python)
set_directory_properties(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES ${CMAKE_BINARY_DIR}/build)
-ADD_CUSTOM_TARGET(python-build ALL COMMAND python ${CMAKE_CURRENT_BINARY_DIR}/setup.py build config_fc --f90exec=${CMAKE_Fortran_COMPILER}
+ADD_CUSTOM_TARGET(python-build ALL COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/setup.py build config_fc --f90exec=${CMAKE_Fortran_COMPILER}
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} COMMENT "build parmepy package")
# To install python package AND parmes library and modules
-ADD_CUSTOM_TARGET(python-install COMMAND python ${CMAKE_CURRENT_BINARY_DIR}/setup.py install --user config_fc --f90exec=${CMAKE_Fortran_COMPILER}
+ADD_CUSTOM_TARGET(python-install COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/setup.py install --user config_fc --f90exec=${CMAKE_Fortran_COMPILER}
COMMAND make install
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} COMMENT "build/install parmepy package")
@@ -141,6 +155,9 @@ set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
# ============= Summary =============
if(VERBOSE_MODE)
message(STATUS "====================== Summary ======================")
+ message(STATUS " Python version :${PYTHON_VERSION_STRING}")
+ message(STATUS " Python executable : ${PYTHON_EXECUTABLE}"})
+ message(STATUS " Python libraries : ${PYTHON_LIBRARIES}")
message(STATUS " Compiler : ${CMAKE_Fortran_COMPILER}")
message(STATUS " Sources are in : ${CMAKE_SOURCE_DIR}")
message(STATUS " Project uses MPI : ${USE_MPI}")
diff --git a/HySoP/hysop/domain/topology.py b/HySoP/hysop/domain/topology.py
index d99ece672f73396be2c2ef59027de2fc4cef3685..f74b923fe5f2b0f465ab4b925f4fb56e2e5be493 100644
--- a/HySoP/hysop/domain/topology.py
+++ b/HySoP/hysop/domain/topology.py
@@ -15,7 +15,7 @@ class CartesianTopology(object):
- dim : dimension of the topology
- comm : MPI communicator used to create this topology
- periods : periodicity of the topology (in each direction)
- - ghosts : number of poinst in the ghost layer
+ - ghosts : number of points in the ghost layer
"""
def __init__(self, domain, resolution, dim=None, dims=None, comm=MPI.COMM_WORLD, periods=None, ghosts=None):
diff --git a/HySoP/hysop/f2py/fftw2py.f90 b/HySoP/hysop/f2py/fftw2py.f90
new file mode 100755
index 0000000000000000000000000000000000000000..7e59d963dcb25149d1a8eccc92b70a12b5dc073d
--- /dev/null
+++ b/HySoP/hysop/f2py/fftw2py.f90
@@ -0,0 +1,42 @@
+
+!> Interface to mpi-fftw utilities
+module fftw2py
+
+ use poisson
+ use parmesparam
+
+ implicit none
+
+contains
+
+ subroutine initFFTW(resolution,lengths)
+
+ !> GLOBAL resolution
+ integer, dimension(:), intent(in) :: resolution
+ !> Length of the domain
+ real(kind=pk),dimension(:),intent(in) :: lengths
+
+ print *, "Initialize fftw poisson solver ..."
+ call initFFTW2D(resolution,lengths)
+
+ end subroutine initFFTW
+
+ subroutine solve(resolution,fieldIn,res)
+
+ integer, dimension(:), intent(in) :: resolution
+ real(kind=pk),dimension(6,6,1),intent(inout) :: fieldIn
+ real(kind=pk),dimension(6,6,1),intent(out) :: res
+ real(kind=pk),dimension(:,:,:,:),pointer :: dummy
+
+ print *, "Start fftw-based poisson solver ..."
+
+! allocate(fieldIn(resolution(1),resolution(2),1))
+
+
+ call solvePoisson(fieldIn,dummy,resolution)
+ print *, "sol ... ", fieldIn
+ res(:,:,:) = fieldIn(:,:,:)
+
+ end subroutine solve
+
+end module fftw2py
diff --git a/HySoP/hysop/scales2py/scales2py.f90 b/HySoP/hysop/f2py/scales2py.f90
similarity index 77%
rename from HySoP/hysop/scales2py/scales2py.f90
rename to HySoP/hysop/f2py/scales2py.f90
index 74424b08fcca95610d34abc78a28b1c71f347449..d315a2f341f0842e1bdd22a2001e6ff5bc13efcd 100755
--- a/HySoP/hysop/scales2py/scales2py.f90
+++ b/HySoP/hysop/f2py/scales2py.f90
@@ -1,24 +1,23 @@
!> Specific parameters for parmepy interface
!! to deal with the problem explained here:
!! http://projects.scipy.org/numpy/ticket/1835
-module parmepyparameters
-
-implicit none
-
-integer, parameter :: mk = 8
-integer, parameter :: dim3 = 3
-
-end module parmepyparameters
-
+!!$module parmepyparameters
+!!$
+!!$implicit none
+!!$
+!!$integer, parameter :: mk = 8
+!!$integer, parameter :: dim3 = 3
+!!$
+!!$end module parmepyparameters
+!!$
!> Interface to scale code from Legi
module scales2py
use cart_topology, only : cart_create,set_group_size,discretisation_create,N_proc,coord,cart_rank
use advec, only : advec_init,advec_step
!!use precision, only : wp
-use parmepyparameters
use mpi
-
+use parmesparam
implicit none
!! problem dimension
@@ -44,9 +43,9 @@ contains
subroutine discretisationCreate(resolution,domainLengths)
!! global resolution
- integer, dimension(dim3),intent(in) :: resolution
+ integer, dimension(:),intent(in) :: resolution
!! global domain dimensions
- real(mk), dimension(dim3),intent(in) :: domainLengths
+ real(pk), dimension(:),intent(in) :: domainLengths
call discretisation_create(resolution(1),resolution(2),resolution(3),domainLengths(1),domainLengths(2),domainLengths(3))
@@ -54,31 +53,35 @@ contains
subroutine advecInit(order,stab_coeff)
character(len=*), optional, intent(in) :: order
- real(mk), optional, intent(inout) :: stab_coeff
+ real(pk), optional, intent(inout) :: stab_coeff
call advec_init(order,stab_coeff)
end subroutine advecInit
subroutine getLocalResolution(resolution)
+
integer,dimension(dim3),intent(out) :: resolution
resolution = N_proc
+
end subroutine getLocalResolution
subroutine getTopoCoords(topocoords)
+
integer,dimension(dim3),intent(out) :: topocoords
topocoords = coord
end subroutine getTopoCoords
subroutine advecStep(timeStep,Vx,Vy,Vz,scal,dim_split)
- real(mk), intent(in) :: timeStep
- real(mk), dimension(:,:,:), intent(in) :: Vx, Vy, Vz
- real(mk), dimension(:,:,:), intent(inout) :: scal
+
+ real(pk), intent(in) :: timeStep
+ real(pk), dimension(:,:,:), intent(in) :: Vx, Vy, Vz
+ real(pk), dimension(:,:,:), intent(inout) :: scal
character(len=*), optional, intent(in) :: dim_split
- real(mk) :: t0
+ real(pk) :: t0
t0 = MPI_Wtime()
call advec_step(timeStep,Vx,Vy,Vz,scal,dim_split)
diff --git a/HySoP/hysop/fftw2py/fftw2py.f90 b/HySoP/hysop/fftw2py/fftw2py.f90
deleted file mode 100755
index 5d1c1b7b54cb1460e2a9bec0de6e4aa86740099a..0000000000000000000000000000000000000000
--- a/HySoP/hysop/fftw2py/fftw2py.f90
+++ /dev/null
@@ -1,39 +0,0 @@
-!> Interface to mpi-fftw utilities
-module fftw2py
-
-use parmepyparameters
-!use poisson, only : testpoisson
-use poisson
-
-implicit none
-
-contains
-
- subroutine initFFTW(resolution,lengths)
-
- !> GLOBAL resolution
- integer, dimension(3), intent(in) :: resolution
- !> Length of the domain
- real(kind=8),dimension(3),intent(in) :: lengths
- print *, "ahahaha"
-
- call initFFTW2D(resolution,lengths)
-
- print *, "ahahaha"
-
- end subroutine initFFTW
-
-!!$ subroutine initFFTW(resolution,lengths)
-!!$
-!!$ !> GLOBAL resolution
-!!$ integer, dimension(:), intent(in) :: resolution
-!!$ !> Length of the domain
-!!$ real(kind=8),dimension(:),intent(in) :: lengths
-!!$
-!!$ print *, "this is a call to fftw-mpi ..."
-!!$
-!!$ call initfftw2d(resolution,lengths)
-!!$
-!!$ end subroutine initFFTW
-
-end module fftw2py
diff --git a/HySoP/setup.py.in b/HySoP/setup.py.in
index 225d2665e333ad378c7f52d48ee4ea06210d682d..0a5fdf5f595a8a75fd8bb9b2495de1ef91a5e817 100644
--- a/HySoP/setup.py.in
+++ b/HySoP/setup.py.in
@@ -32,37 +32,32 @@ parmes_libdir = ['@CMAKE_BINARY_DIR@/src']
parmeslib = ['@PARMES_LIBRARY_NAME@']
f2py_options = ['--no-lower']
-scales_src = glob.glob('@CMAKE_SOURCE_DIR@/parmepy/scales2py/*.f90')
-scalesModule = Extension(name='parmepy.scales2py',
- f2py_options=f2py_options,
- sources=scales_src,
- include_dirs=inc_dir,
- library_dirs=parmes_libdir,
- libraries=parmeslib,
- define_macros=[('F2PY_REPORT_ON_ARRAY_COPY', '1')])
+## scales_src = glob.glob('@CMAKE_SOURCE_DIR@/parmepy/scales2py/*.f90')
+## scalesModule = Extension(name='parmepy.scales2py',
+## f2py_options=f2py_options,
+## sources=scales_src,
+## include_dirs=inc_dir,
+## library_dirs=parmes_libdir,
+## libraries=parmeslib,
+## define_macros=[('F2PY_REPORT_ON_ARRAY_COPY', '1')])
-ext_modules = [scalesModule]
-
-test_src = glob.glob('@CMAKE_SOURCE_DIR@/parmepy/testf2py/*.f90')
-testf2pyModule = Extension(name='parmepy.testf2py',
- f2py_options=f2py_options,
- sources=test_src,
- include_dirs=inc_dir,
- library_dirs=parmes_libdir,
- libraries=parmeslib,
- define_macros=[('F2PY_REPORT_ON_ARRAY_COPY', '1')])
-
-ext_modules.append(testf2pyModule)
+## ext_modules=[scalesModule]
+ext_modules =[]
withfftw = "@WITH_FFTW@"
if(withfftw is "ON"):
- fortran_src = glob.glob('@CMAKE_SOURCE_DIR@/parmepy/fftw2py/*.f90')
+ #fortran_src = glob.glob('@CMAKE_SOURCE_DIR@/parmepy/f2py/*.f90')
+ fortran_dir = '@CMAKE_SOURCE_DIR@/parmepy/f2py/'
+ fortran_src = [fortran_dir+'parameters.f90',fortran_dir+'fftw2py.f90',fortran_dir+'scales2py.f90']
+
+# rep = '@CMAKE_SOURCE_DIR@/parmepy/f2py/'
+ # fortran_src.insert(0,rep+'/parameters.f90')
fftwdir = '@FFTWLIB@'
fftwdir = os.path.split(fftwdir)[0]
parmeslib.append('fftw3')
parmeslib.append('fftw3_mpi')
parmes_libdir.append(fftwdir)
- parpyModule = Extension(name='parmepy.fftw2py',
+ parpyModule = Extension(name='parmepy.f2py',
f2py_options=f2py_options,
sources=fortran_src,
include_dirs=inc_dir,
diff --git a/HySoP/src/CMakeLists.txt b/HySoP/src/CMakeLists.txt
index 53beaa4519f6e29639ff3faaac81961d0c23e3a2..62487b93c35b5130e3f29191ef21b8b6a2caf595 100644
--- a/HySoP/src/CMakeLists.txt
+++ b/HySoP/src/CMakeLists.txt
@@ -16,8 +16,6 @@ set(EXE_NAME ${PARMES_LIBRARY_NAME}Run)
set(${PARMES_LIBRARY_NAME}_SRCDIRS
.
poisson
- #src/interfaces/Fortran2Cpp
- # src/interfaces/ppm
)
# --- scales ---
if(WITH_SCALES)