fix dynamic loading bug + reorg

HySoP/CMake

-../CMake
\ No newline at end of file

HySoP/CMakeLists.txt

@@ -63,6 +63,13 @@ endif(WITH_TESTS)
 # We search for libraries Parmes depends on and 
 # set the compile/link conf (-I and -L opt)
 
+#Install dir for python (default = --user)
+execute_process(
+  COMMAND python -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)
 add_subdirectory(src)
@@ -74,13 +81,6 @@ if(EXISTS ${CMAKE_SOURCE_DIR}/setup.py.in)
   configure_file(setup.py.in setup.py)
 endif()
 
-
-#Install dir for python (default = --user)
-execute_process(
-  COMMAND python -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})
 # The file __init__.py will be generated from __init__.py.in.
 if(EXISTS ${CMAKE_SOURCE_DIR}/parmepy/__init__.py.in)
   message(STATUS "Generate __init__.py file ...")
@@ -94,8 +94,10 @@ set_directory_properties(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES ${CMAKE_BINARY_D
 ADD_CUSTOM_TARGET(python-build ALL COMMAND python ${CMAKE_CURRENT_BINARY_DIR}/setup.py build config_fc --f90exec=${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}
-   WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} COMMENT "build/install parmepy package")
+  COMMAND make install
+  WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} COMMENT "build/install parmepy package")
 
 ADD_CUSTOM_TARGET(python-cleaninstall COMMAND rm -rf ${${PROJECT_NAME}_INSTALL_DIR}/${PROJECT_NAME}*
   COMMENT "remove parmepy package and its dependencies")
@@ -103,6 +105,7 @@ ADD_CUSTOM_TARGET(python-cleaninstall COMMAND rm -rf ${${PROJECT_NAME}_INSTALL_D
 add_dependencies(python-build ${PARMES_LIBRARY_NAME})
 add_dependencies(python-install ${PARMES_LIBRARY_NAME})
 
+
 # ============= RPATH =============
 # Concerning rpath see for example http://www.itk.org/Wiki/CMake_RPATH_handling
 
@@ -111,7 +114,7 @@ add_dependencies(python-install ${PARMES_LIBRARY_NAME})
 set(CMAKE_SKIP_BUILD_RPATH FALSE)
 # when building, don't use the install RPATH already
 # (but later on when installing)
-set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE) 
+set(CMAKE_BUILD_WITH_INSTALL_RPATH TRUE) 
 # the RPATH to be used when installing
 set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
 # add the automatically determined parts of the RPATH

HySoP/hysop/__init__.py.in

@@ -4,26 +4,21 @@
 Python package dedicated to flow simulation using particular methods on hybrid architectures (MPI-GPU)
 
 """
-__version__ = 1.00
-__all__ = ['Box', 'CartesianTopology', 'ScalarField']
+__version__=1.00
+__all__=['Box','CartesianTopology','ScalarField']
 
 import os
 import site
 import mpi4py.MPI as MPI
 
-if 'LD_LIBRARY_PATH' in os.environ:
-    os.environ['LD_LIBRARY_PATH'] = os.environ['LD_LIBRARY_PATH'] + ':' + "@CMAKE_INSTALL_PREFIX@"
-else:
-    os.environ['LD_LIBRARY_PATH'] = "@CMAKE_INSTALL_PREFIX@"
-
 rank_world = MPI.COMM_WORLD.Get_rank()
 if(rank_world == 0):
-    print "Starting @PACKAGE_NAME@ version " + str(__version__) + ".\n"
+    print "Starting @PACKAGE_NAME@ version "+str(__version__)+".\n"
 
 import constants
 
 import domain.box
-## Box-type physical domain
+## Box-type physical domain 
 Box = domain.box.Box
 
 ## Cartesian grid
@@ -35,23 +30,5 @@ CartesianTopology = fields.topology.CartesianTopology
 ## Fields
 import fields.discrete
 import fields.continuous
-import fields.analytical
 ScalarField = fields.discrete.ScalarField
 ContinuousField = fields.continuous.ContinuousField
-AnalyticalField = fields.analytical.AnalyticalField
-
-## Operators
-import operator.Transport
-Transport = operator.Transport.Transport
-
-## Problem
-import problem.problem
-Problem = problem.problem.Problem
-
-## Solver
-import ParticularSolvers.basic
-ParticularSolver = ParticularSolvers.basic.ParticularSolver
-
-## Tools
-import tools.printer
-Printer = tools.printer.Printer

HySoP/hysop/domain/grid.py

@@ -13,15 +13,14 @@ class CartesianGrid(DiscreteDomain):
     def __init__(self, resolution, domain):
         DiscreteDomain.__init__(self, domain)
         assert(self.dimension == len(resolution))
+        ## lowest point of the grid
         self.origin = domain.origin
+        ## size of the grid in each direction
         self.length = domain.length
+        ## number of points in each direction
         self.resolution = resolution
-        self.size = self.length / self.resolution
-
-        ## self.elementNumber = spec
-        ## self.elementSize = box.length / self.elementNumber
-        ## ##  Grid length.
-        ## self.length = box.length
+        ## space step size
+        self.step = self.length/(self.resolution-1)
         ## self.axes = [np.asarray(np.arange(self.min[i], self.max[i], self.elementSize[i]), dtype=dtype_real, order=order) for i in xrange(self.dimension)]
 
     def update(start):
@@ -46,7 +45,7 @@ class CartesianGrid(DiscreteDomain):
         @param index list : index to get
         @return point with given index
         """
-        return self.__coords.__getitem__(i)
+        return self.__coords.__getitem__(index)
 
     def __str__(self):
         """