From d6b48db112ef6d3840d1b695b3c3652fe047437d Mon Sep 17 00:00:00 2001
From: Jonathan Lambrechts <jonathan.lambrechts@uclouvain.be>
Date: Sat, 19 Nov 2011 07:02:10 +0000
Subject: [PATCH] Solver/function : add numpy function, combined with blitz
those function are >5 times faster than previous "functionPython"
---
CMakeLists.txt | 21 +++++++++++
Common/GmshConfig.h.in | 1 +
Solver/functionNumpy.h | 80 ++++++++++++++++++++++++++++++++++++++++++
gmshpy/CMakeLists.txt | 52 ++++++++++++---------------
gmshpy/gmshSolver.i | 2 ++
5 files changed, 126 insertions(+), 30 deletions(-)
create mode 100644 Solver/functionNumpy.h
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 2bb0932573..2a88e89592 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -41,6 +41,7 @@ option(ENABLE_MPEG_ENCODE "Enable built-in MPEG encoder" ON)
option(ENABLE_MPI "Enable MPI parallelization" OFF)
option(ENABLE_MSVC_STATIC_RUNTIME "Use static Visual C++ runtime" OFF)
option(ENABLE_NATIVE_FILE_CHOOSER "Enable native file chooser in GUI" ON)
+option(ENABLE_NUMPY "Enable Numpy function in solvers (requires SWIG)" ON)
option(ENABLE_NETGEN "Enable Netgen mesh generator" ON)
option(ENABLE_OCC "Enable Open CASCADE geometrical models" ON)
option(ENABLE_OSMESA "Use OSMesa for offscreen rendering" OFF)
@@ -799,6 +800,26 @@ if(ENABLE_OSMESA)
endif(OSMESA_LIB)
endif(ENABLE_OSMESA)
+if(ENABLE_SWIG)
+ find_package(SWIG)
+ find_package(PythonLibs)
+ if(SWIG_FOUND AND PYTHONLIBS_FOUND)
+ message(STATUS "Found SWIG version " ${SWIG_VERSION})
+ string(SUBSTRING ${SWIG_VERSION} 0 1 SWIG_MAJOR_VERSION)
+ if(SWIG_MAJOR_VERSION EQUAL 1)
+ message("WARNING: Python bindings require SWIG >= 2: disabling Python")
+ else(SWIG_MAJOR_VERSION EQUAL 1)
+ set_config_option(HAVE_SWIG "Swig")
+ if(ENABLE_NUMPY)
+ find_path(NUMPY_INC "numpyconfig.h" PATH_SUFFIXES include/numpy)
+ if(NUMPY_INC)
+ set_config_option(HAVE_NUMPY "Numpy")
+ endif(NUMPY_INC)
+ endif(ENABLE_NUMPY)
+ endif(SWIG_MAJOR_VERSION EQUAL 1)
+ endif(SWIG_FOUND AND PYTHONLIBS_FOUND)
+endif(ENABLE_SWIG)
+
check_function_exists(vsnprintf HAVE_VSNPRINTF)
if(NOT HAVE_VSNPRINTF)
set_config_option(HAVE_NO_VSNPRINTF "NoVsnprintf")
diff --git a/Common/GmshConfig.h.in b/Common/GmshConfig.h.in
index 30771075fb..edc5de2f8e 100644
--- a/Common/GmshConfig.h.in
+++ b/Common/GmshConfig.h.in
@@ -38,6 +38,7 @@
#cmakedefine HAVE_NETGEN
#cmakedefine HAVE_NO_SOCKLEN_T
#cmakedefine HAVE_NO_VSNPRINTF
+#cmakedefine HAVE_NUMPY
#cmakedefine HAVE_OCC
#cmakedefine HAVE_OPENGL
#cmakedefine HAVE_OSMESA
diff --git a/Solver/functionNumpy.h b/Solver/functionNumpy.h
new file mode 100644
index 0000000000..bfce74bc37
--- /dev/null
+++ b/Solver/functionNumpy.h
@@ -0,0 +1,80 @@
+#ifndef _FUNCTION_NUMPY_H_
+#define _FUNCTION_NUMPY_H_
+#include "GmshConfig.h"
+#ifdef HAVE_NUMPY
+#include "Python.h"
+#include "numpy/arrayobject.h"
+
+class functionNumpy : public function {
+ PyObject *_pycallback;
+ std::vector<fullMatrix<double> > args;
+public:
+ static PyObject *pyArrayFromFullMatrix(fullMatrix<double> &m) {
+ long int n[2] = {m.size1(), m.size2()};
+ return PyArray_New(&PyArray_Type, 2, n, NPY_DOUBLE, NULL, &m(0, 0), 0, NPY_FARRAY, NULL);
+ }
+ void call (dataCacheMap *m, fullMatrix<double> &res)
+ {
+ PyObject *swigR;
+ PyObject *pyargs;
+ std::vector<PyObject*> swigA(args.size());
+ swigR = pyArrayFromFullMatrix(res);
+ for (int i = 0; i < args.size(); i++) {
+ swigA[i] = pyArrayFromFullMatrix(args[i]);
+ }
+ switch(args.size()) {
+ case 0 : pyargs = Py_BuildValue("(N)", swigR); break;
+ case 1 : pyargs = Py_BuildValue("(NN)", swigR, swigA[0]); break;
+ case 2 : pyargs = Py_BuildValue("(NNN)", swigR, swigA[0], swigA[1]); break;
+ case 3 : pyargs = Py_BuildValue("(NNNN)", swigR, swigA[0], swigA[1], swigA[2]); break;
+ case 4 : pyargs = Py_BuildValue("(NNNNN)", swigR, swigA[0], swigA[1], swigA[2], swigA[3]); break;
+ case 5 : pyargs = Py_BuildValue("(NNNNNN)", swigR, swigA[0], swigA[1], swigA[2], swigA[3], swigA[4]); break;
+ case 6 : pyargs = Py_BuildValue("(NNNNNNN)", swigR, swigA[0], swigA[1], swigA[2], swigA[3], swigA[4], swigA[5]); break;
+ case 7 : pyargs = Py_BuildValue("(NNNNNNNN)", swigR, swigA[0], swigA[1], swigA[2], swigA[3], swigA[4], swigA[5], swigA[6]); break;
+ case 8 : pyargs = Py_BuildValue("(NNNNNNNNN)", swigR, swigA[0], swigA[1], swigA[2], swigA[3], swigA[4], swigA[5], swigA[6], swigA[7]); break;
+ default:Msg::Error("python function not implemented for more than 8 arguments");
+ }
+ PyObject *result = PyEval_CallObject(_pycallback, pyargs);
+ if (result) {
+ Py_DECREF(result);
+ }
+ else {
+ PyErr_Print();
+ Msg::Fatal("An error occurs in the python function.");
+ }
+/* for (int i = 0; i < args.size(); i++) {
+ Py_DECREF(swigA[i]);
+ }
+ Py_DECREF(swigR);*/
+ }
+ functionNumpy (int nbCol, PyObject *callback, std::vector<const function*> dependencies)
+ : function(nbCol), _pycallback(callback)
+ {
+ args.resize(dependencies.size());
+ for (int i = 0; i < dependencies.size(); i++) {
+ setArgument(args[i], dependencies[i]);
+ }
+ static bool _arrayImported = false;
+ if (! _arrayImported){
+ _import_array();
+ _arrayImported = true;
+ }
+ }
+ functionNumpy (int nbCol, PyObject *callback, std::vector<std::pair<const function*, int> > dependencies)
+ : function(nbCol), _pycallback(callback)
+ {
+ args.resize(dependencies.size());
+ for (int i = 0; i < dependencies.size(); i++) {
+ setArgument(args[i], dependencies[i].first, dependencies[i].second);
+ }
+ printf("import array !!!\n");
+ static bool _arrayImported = false;
+ if (! _arrayImported) {
+ printf("import array !!!\n");
+ _import_array();
+ _arrayImported = true;
+ }
+ }
+};
+#endif
+#endif
diff --git a/gmshpy/CMakeLists.txt b/gmshpy/CMakeLists.txt
index 9521b8628b..4933e7db41 100644
--- a/gmshpy/CMakeLists.txt
+++ b/gmshpy/CMakeLists.txt
@@ -56,37 +56,29 @@ MACRO(SWIG_GET_WRAPPER_DEPENDENCIES swigFile genWrapper language DEST_VARIABLE)
ENDIF(NOT ${swig_getdeps_error} EQUAL 0)
ENDMACRO(SWIG_GET_WRAPPER_DEPENDENCIES)
-if(ENABLE_SWIG)
- find_package(SWIG)
- if(SWIG_FOUND)
- message(STATUS "Found SWIG version " ${SWIG_VERSION})
- string(SUBSTRING ${SWIG_VERSION} 0 1 SWIG_MAJOR_VERSION)
- if(SWIG_MAJOR_VERSION EQUAL 1)
- message("WARNING: Python bindings require SWIG >= 2: disabling Python")
- else(SWIG_MAJOR_VERSION EQUAL 1)
- include(${SWIG_USE_FILE})
- find_package(PythonLibs)
- include_directories(${PYTHON_INCLUDE_DIR})
+if(HAVE_SWIG)
+ include(${SWIG_USE_FILE})
+ include_directories(${PYTHON_INCLUDE_DIR})
+ if(HAVE_NUMPY)
+ include_directories(${NUMPY_INC})
+ add_definitions(-DHAVE_NUMPY)
+ endif(HAVE_NUMPY)
- foreach(module ${SWIG_MODULES})
- set_source_files_properties(${module}.i PROPERTIES CPLUSPLUS ON)
+ foreach(module ${SWIG_MODULES})
+ set_source_files_properties(${module}.i PROPERTIES CPLUSPLUS ON)
- # code backported from CMake git version, see CMake bug 4147
- SWIG_GET_WRAPPER_DEPENDENCIES(${CMAKE_CURRENT_SOURCE_DIR}/\${module}.i ${CMAKE_CURRENT_BINARY_DIR}/${module}PYTHON_wrap.cxx python swig_extra_dependencies)
- LIST(APPEND SWIG_MODULE_${module}_EXTRA_DEPS ${swig_extra_dependencies})
+ # code backported from CMake git version, see CMake bug 4147
+ SWIG_GET_WRAPPER_DEPENDENCIES(${CMAKE_CURRENT_SOURCE_DIR}/\${module}.i ${CMAKE_CURRENT_BINARY_DIR}/${module}PYTHON_wrap.cxx python swig_extra_dependencies)
+ LIST(APPEND SWIG_MODULE_${module}_EXTRA_DEPS ${swig_extra_dependencies})
- swig_add_module(${module} python ${module}.i)
- swig_link_libraries(${module} ${PYTHON_LIBRARIES} shared)
- SET(GMSH_PYTHON_MODULES_INCLUDE_CODE
- "${GMSH_PYTHON_MODULES_INCLUDE_CODE}from ${module} import *\n")
- list(APPEND GMSHPY_DEPENDS "_${module}")
- endforeach(module)
- add_custom_target("_gmshpy" DEPENDS ${GMSHPY_DEPENDS})
+ swig_add_module(${module} python ${module}.i)
+ swig_link_libraries(${module} ${PYTHON_LIBRARIES} shared)
+ SET(GMSH_PYTHON_MODULES_INCLUDE_CODE
+ "${GMSH_PYTHON_MODULES_INCLUDE_CODE}from ${module} import *\n")
+ list(APPEND GMSHPY_DEPENDS "_${module}")
+ endforeach(module)
+ add_custom_target("_gmshpy" DEPENDS ${GMSHPY_DEPENDS})
- configure_file(${CMAKE_CURRENT_SOURCE_DIR}/__init__.py.in
- ${CMAKE_CURRENT_BINARY_DIR}/__init__.py)
-
-
- endif(SWIG_MAJOR_VERSION EQUAL 1)
- endif(SWIG_FOUND)
-endif(ENABLE_SWIG)
+ configure_file(${CMAKE_CURRENT_SOURCE_DIR}/__init__.py.in
+ ${CMAKE_CURRENT_BINARY_DIR}/__init__.py)
+endif(HAVE_SWIG)
diff --git a/gmshpy/gmshSolver.i b/gmshpy/gmshSolver.i
index 1d350c8b66..97832aa66a 100644
--- a/gmshpy/gmshSolver.i
+++ b/gmshpy/gmshSolver.i
@@ -13,6 +13,7 @@
#include "function.h"
#include "functionDerivator.h"
#include "functionPython.h"
+ #include "functionNumpy.h"
#include "linearSystem.h"
#include "linearSystemCSR.h"
#include "linearSystemFull.h"
@@ -31,6 +32,7 @@ namespace std {
%include "function.h"
%include "functionDerivator.h"
%include "functionPython.h"
+%include "functionNumpy.h"
%include "linearSystem.h"
%template(linearSystemDouble) linearSystem<double>;
%template(linearSystemFullMatrixDouble) linearSystem<fullMatrix<double> >;
--
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