yade-users team mailing list archive

[Mathan <question220027@xxxxxxxxxxxxxxxxxxxxx>]

New question #220027 on Yade:
https://answers.launchpad.net/yade/+question/220027

Hi,
I am trying to insatll Yade on the SLES11 based SGI ALTIX 4700 HPC .
I have build all the dependencies and configuarion part went smoothly.

============================================================
altix5 157% cmake -DINSTALL_PREFIX=/home2/mkr/source_yade/yade-build trunk-0.90.3/
-- The C compiler identification is GNU 4.3.4
-- The CXX compiler identification is GNU 4.3.4
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Found PythonLibs: /usr/lib/libpython2.6.so (found version "2.6") 
-- Found PythonInterp: /usr/bin/python (found version "2.6") 
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp  
-- Looking for Q_WS_X11
-- Looking for Q_WS_X11 - found
-- Looking for Q_WS_WIN
-- Looking for Q_WS_WIN - not found
-- Looking for Q_WS_QWS
-- Looking for Q_WS_QWS - not found
-- Looking for Q_WS_MAC
-- Looking for Q_WS_MAC - not found
-- Found Qt4: /usr/bin/qmake (found version "4.6.2") 
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.23") 
-- Version is set to 0.90.3
-- Looking for XOpenDisplay in /usr/lib/libX11.so;/usr/lib/libXext.so
-- Looking for XOpenDisplay in /usr/lib/libX11.so;/usr/lib/libXext.so - found
-- Looking for gethostbyname
-- Looking for gethostbyname - found
-- Looking for connect
-- Looking for connect - found
-- Looking for remove
-- Looking for remove - found
-- Looking for shmat
-- Looking for shmat - found
-- Looking for IceConnectionNumber in ICE
-- Looking for IceConnectionNumber in ICE - found
-- Found X11: /usr/lib/libX11.so
-- Found OpenGL: /usr/lib/libGL.so  
-- GTS using gts-config /usr/local/bin/gts-config
-- Using GTS from /usr/local
-- Found GL2PS: /usr/local/lib/libgl2ps.so  
-- Found CGAL: /usr/local/include/CGAL, /usr/local/lib/libCGAL.so
-- Boost version: 1.52.0
-- Found the following Boost libraries:
--   python
--   thread
--   date_time
--   filesystem
--   iostreams
--   regex
--   serialization
--   Boost_VERSION: 105200
--   Boost_LIB_VERSION: 1_52
--   Boost_INCLUDE_DIRS: /usr/local/include
--   Boost_LIBRARIES: /usr/local/lib/libboost_python.so/usr/local/lib/libboost_thread.so/usr/local/lib/libboost_date_time.so/usr/local/lib/libboost_filesystem.so/usr/local/lib/libboost_iostreams.so/usr/local/lib/libboost_regex.so/usr/local/lib/libboost_serialization.so
-- Found Eigen3: /usr/local/include (Required is at least version "2.91.0") 
-- Found Eigen3
-- Found VTK
-- Found OpenMP
-- GTS using gts-config /usr/local/bin/gts-config
-- Using GTS from /usr/local
-- checking for one of the modules 'glib-2.0'
-- Found GLib2: glib-2.0 /usr/include/glib-2.0;/usr/lib/glib-2.0/include
-- Looking for include file glib/gregex.h
-- Looking for include file glib/gregex.h - found
-- Found GTS
-- Found Qt4: /usr/bin/qmake (found version "4.6.2") 
-- Found GLUT: /usr/lib/libglut.so  
-- Found QGLViewer: /usr/lib/libQGLViewer.so
-- Found GUI-LIBS
-- GMP libs: /usr/lib/libgmp.so /usr/lib/libgmpxx.so
-- Found GMP: /usr/include  
-- GMP libs: /usr/lib/libgmp.so /usr/lib/libgmpxx.so
-- Found CGAL
-- Found GL2PS
Yade will be installed to /home2/mkr/source_yade/yade-build
-- Suffix is set to -0.90.3
-- LIBRARY_OUTPUT_PATH is set to lib
-- runtimePREFIX is set to /home2/mkr/source_yade/yade-build
-- ===========================================================
-- Yade configured with following features: Eigen3 VTK OpenMP GTS GUI CGAL GL2PS
-- Disabled features:
-- Optimized build
-- ===========================================================
-- Configuring done
-- Generating done
-- Build files have been written to: /home2/mkr/source_yade

=================================================================

In the compilation part, It is showing " error: numpy/arrayobject.h: No such file or directory" 

=================================================================
make install
Scanning dependencies of target miniEigen
[  1%] Building CXX object CMakeFiles/miniEigen.dir/py/mathWrap/miniEigen.cpp.o
Linking CXX shared library lib/miniEigen.so
[  1%] Built target miniEigen
Scanning dependencies of target support
[  2%] Building CXX object CMakeFiles/support.dir/lib/base/Math.cpp.o
[  2%] Building CXX object CMakeFiles/support.dir/lib/factory/ClassFactory.cpp.o
[  3%] Building CXX object CMakeFiles/support.dir/lib/factory/DynLibManager.cpp.o
[  4%] Building CXX object CMakeFiles/support.dir/lib/multimethods/Indexable.cpp.o
[  4%] Building CXX object CMakeFiles/support.dir/lib/serialization/Serializable.cpp.o
[  5%] Building CXX object CMakeFiles/support.dir/lib/pyutil/gil.cpp.o
[  5%] Building CXX object CMakeFiles/support.dir/core/main/pyboot.cpp.o
[  6%] Building CXX object CMakeFiles/support.dir/lib/opengl/GLUtils.cpp.o
[  6%] Building CXX object CMakeFiles/support.dir/lib/triangulation/FlowBoundingSphere.cpp.o
[  7%] Building CXX object CMakeFiles/support.dir/lib/triangulation/KinematicLocalisationAnalyser.cpp.o
[  8%] Building CXX object CMakeFiles/support.dir/lib/triangulation/PeriodicFlow.cpp.o
[  8%] Building CXX object CMakeFiles/support.dir/lib/triangulation/Tenseur3.cpp.o
[  9%] Building CXX object CMakeFiles/support.dir/lib/triangulation/Timer.cpp.o
[  9%] Building CXX object CMakeFiles/support.dir/lib/triangulation/TriaxialState.cpp.o
[ 10%] Building CXX object CMakeFiles/support.dir/lib/triangulation/basicVTKwritter.cpp.o
Linking CXX shared library lib/libsupport.so
[ 10%] Built target support
Scanning dependencies of target core
[ 10%] Building CXX object CMakeFiles/core.dir/core/Body.cpp.o
[ 11%] Building CXX object CMakeFiles/core.dir/core/BodyContainer.cpp.o
[ 12%] Building CXX object CMakeFiles/core.dir/core/Bound.cpp.o
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[ 18%] Building CXX object CMakeFiles/core.dir/core/Omega.cpp.o
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[ 19%] Building CXX object CMakeFiles/core.dir/core/Scene.cpp.o
[ 20%] Building CXX object CMakeFiles/core.dir/core/Shape.cpp.o
[ 20%] Building CXX object CMakeFiles/core.dir/core/SimulationFlow.cpp.o
[ 21%] Building CXX object CMakeFiles/core.dir/core/State.cpp.o
[ 21%] Building CXX object CMakeFiles/core.dir/core/ThreadRunner.cpp.o
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[ 23%] Building CXX object CMakeFiles/core.dir/core/corePlugins.cpp.o
Linking CXX shared library lib/libcore.so
[ 23%] Built target core
[ 23%] Generating qt4/moc_OpenGLManager.cxx
[ 24%] Generating qt4/moc_GLViewer.cxx
Scanning dependencies of target _GLViewer
[ 25%] Building CXX object gui/CMakeFiles/_GLViewer.dir/qt4/GLViewer.cpp.o
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Linking CXX shared library lib/_GLViewer.so
[ 27%] Built target _GLViewer
Scanning dependencies of target plugins
[ 27%] Building CXX object CMakeFiles/plugins.dir/pkg/common/Aabb.cpp.o
[ 28%] Building CXX object CMakeFiles/plugins.dir/pkg/common/Bo1_Box_Aabb.cpp.o
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[ 30%] Building CXX object CMakeFiles/plugins.dir/pkg/common/BoundaryController.cpp.o
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[ 34%] Building CXX object CMakeFiles/plugins.dir/pkg/common/ElastMat.cpp.o
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[ 36%] Building CXX object CMakeFiles/plugins.dir/pkg/common/GLDrawFunctors.cpp.o
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[ 47%] Building CXX object CMakeFiles/plugins.dir/pkg/common/ResetRandomPosition.cpp.o
/home2/mkr/source_yade/trunk-0.90.3/pkg/common/ResetRandomPosition.cpp: In member function ‘virtual void ResetRandomPosition::action()’:
/home2/mkr/source_yade/trunk-0.90.3/pkg/common/ResetRandomPosition.cpp:77: warning: ‘is_overlap’ may be used uninitialized in this function
[ 48%] Building CXX object CMakeFiles/plugins.dir/pkg/common/SpatialQuickSortCollider.cpp.o
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[ 63%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/ForceTorqueRecorder.cpp.o
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[ 67%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/Ip2_2xNormalInelasticMat_NormalInelasticityPhys.cpp.o
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[ 69%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/Ip2_FrictMat_FrictMat_FrictPhys.cpp.o
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[ 73%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/Law2_ScGeom_CapillaryPhys_Capillarity.cpp.o
[ 74%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/MicroMacroAnalyser.cpp.o
[ 74%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/NewtonIntegrator.cpp.o
[ 75%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/NormalInelasticMat.cpp.o
[ 76%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/NormalInelasticityLaw.cpp.o
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[ 77%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/ParticleSizeDistrbutionRPMRecorder.cpp.o
[ 77%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/PeriIsoCompressor.cpp.o
[ 78%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/RockPM.cpp.o
[ 78%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/STLImporter.cpp.o
[ 79%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/SampleCapillaryPressureEngine.cpp.o
[ 80%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/ScGeom.cpp.o
[ 80%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/Shop.cpp.o
[ 81%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/SimpleShear.cpp.o
[ 81%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/SnapshotEngine.cpp.o
[ 82%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/SpherePack.cpp.o
[ 82%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/SpheresFactory.cpp.o
[ 83%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/TesselationWrapper.cpp.o
In file included from /home2/mkr/source_yade/yade/lib/pyutil/numpy.hpp:3,
                 from /home2/mkr/source_yade/trunk-0.90.3/pkg/dem/TesselationWrapper.cpp:11:
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:44:31: error: numpy/arrayobject.h: No such file or directory
In file included from /home2/mkr/source_yade/yade/lib/pyutil/numpy.hpp:3,
                 from /home2/mkr/source_yade/trunk-0.90.3/pkg/dem/TesselationWrapper.cpp:11:
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:58: error: ‘NPY_FLOAT’ was not declared in this scope
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:61: error: ‘NPY_CFLOAT’ was not declared in this scope
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:64: error: ‘NPY_DOUBLE’ was not declared in this scope
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:67: error: ‘NPY_CDOUBLE’ was not declared in this scope
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:70: error: ‘NPY_LONGDOUBLE’ was not declared in this scope
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:73: error: ‘NPY_CLONGDOUBLE’ was not declared in this scope
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:76: error: ‘NPY_INT8’ was not declared in this scope
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:79: error: ‘NPY_UINT8’ was not declared in this scope
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:82: error: ‘NPY_INT16’ was not declared in this scope
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:85: error: ‘NPY_UINT16’ was not declared in this scope
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:88: error: ‘NPY_INT32’ was not declared in this scope
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:91: error: ‘NPY_UINT32’ was not declared in this scope
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:94: error: ‘NPY_INT64’ was not declared in this scope
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:97: error: ‘NPY_INT64’ was not declared in this scope
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:114: error: ISO C++ forbids declaration of ‘PyArrayObject’ with no type
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:114: error: expected ‘;’ before ‘*’ token
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:116: error: ‘PyArrayObject’ has not been declared
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp: In member function ‘void numpy_boost<T, NDims>::init_from_array(int*)’:
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:117: error: ‘array’ was not declared in this scope
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:118: error: there are no arguments to ‘PyArray_DATA’ that depend on a template parameter, so a declaration of ‘PyArray_DATA’ must be available
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:118: error: (if you use ‘-fpermissive’, G++ will accept your code, but allowing the use of an undeclared name is deprecated)
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:126: error: there are no arguments to ‘PyArray_DIMS’ that depend on a template parameter, so a declaration of ‘PyArray_DIMS’ must be available
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:128: error: there are no arguments to ‘PyArray_STRIDE’ that depend on a template parameter, so a declaration of ‘PyArray_STRIDE’ must be available
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp: In constructor ‘numpy_boost<T, NDims>::numpy_boost(PyObject*)’:
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:142: error: class ‘numpy_boost<T, NDims>’ does not have any field named ‘array’
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:144: error: ‘PyArrayObject’ was not declared in this scope
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:144: error: ‘a’ was not declared in this scope
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:146: error: expected primary-expression before ‘)’ token
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:146: error: expected `;' before ‘PyArray_FromObject’
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp: In copy constructor ‘numpy_boost<T, NDims>::numpy_boost(const numpy_boost<T, NDims>&)’:
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:157: error: class ‘numpy_boost<T, NDims>’ does not have any field named ‘array’
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp: In constructor ‘numpy_boost<T, NDims>::numpy_boost(const ExtentsList&)’:
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:166: error: class ‘numpy_boost<T, NDims>’ does not have any field named ‘array’
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:168: error: ‘npy_intp’ was not declared in this scope
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:168: error: expected `;' before ‘shape’
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:169: error: ‘PyArrayObject’ was not declared in this scope
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:169: error: ‘a’ was not declared in this scope
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:171: error: ‘shape’ was not declared in this scope
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:173: error: expected primary-expression before ‘)’ token
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:173: error: expected `;' before ‘PyArray_SimpleNew’
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp: In destructor ‘numpy_boost<T, NDims>::~numpy_boost()’:
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:183: error: ‘array’ was not declared in this scope
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp: In member function ‘void numpy_boost<T, NDims>::operator=(const numpy_boost<T, NDims>&)’:
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:187: error: ‘array’ was not declared in this scope
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp: In member function ‘PyObject* numpy_boost<T, NDims>::py_ptr()’:
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:194: error: ‘array’ was not declared in this scope
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp: In member function ‘void numpy_boost<T, NDims>::init_from_array(int*) [with T = double, int NDims = 1]’:
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:179:   instantiated from ‘numpy_boost<T, NDims>::numpy_boost(const ExtentsList&) [with ExtentsList = int [1], T = double, int NDims = 1]’
/home2/mkr/source_yade/trunk-0.90.3/pkg/dem/TesselationWrapper.cpp:367:   instantiated from here
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:118: error: ‘PyArray_DATA’ was not declared in this scope
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:179:   instantiated from ‘numpy_boost<T, NDims>::numpy_boost(const ExtentsList&) [with ExtentsList = int [1], T = double, int NDims = 1]’
/home2/mkr/source_yade/trunk-0.90.3/pkg/dem/TesselationWrapper.cpp:367:   instantiated from here
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:126: error: ‘PyArray_DIMS’ was not declared in this scope
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:179:   instantiated from ‘numpy_boost<T, NDims>::numpy_boost(const ExtentsList&) [with ExtentsList = int [1], T = double, int NDims = 1]’
/home2/mkr/source_yade/trunk-0.90.3/pkg/dem/TesselationWrapper.cpp:367:   instantiated from here
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:128: error: ‘PyArray_STRIDE’ was not declared in this scope
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp: In member function ‘void numpy_boost<T, NDims>::init_from_array(int*) [with T = double, int NDims = 2]’:
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:179:   instantiated from ‘numpy_boost<T, NDims>::numpy_boost(const ExtentsList&) [with ExtentsList = int [2], T = double, int NDims = 2]’
/home2/mkr/source_yade/trunk-0.90.3/pkg/dem/TesselationWrapper.cpp:369:   instantiated from here
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:118: error: ‘PyArray_DATA’ was not declared in this scope
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:179:   instantiated from ‘numpy_boost<T, NDims>::numpy_boost(const ExtentsList&) [with ExtentsList = int [2], T = double, int NDims = 2]’
/home2/mkr/source_yade/trunk-0.90.3/pkg/dem/TesselationWrapper.cpp:369:   instantiated from here
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:126: error: ‘PyArray_DIMS’ was not declared in this scope
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:179:   instantiated from ‘numpy_boost<T, NDims>::numpy_boost(const ExtentsList&) [with ExtentsList = int [2], T = double, int NDims = 2]’
/home2/mkr/source_yade/trunk-0.90.3/pkg/dem/TesselationWrapper.cpp:369:   instantiated from here
/home2/mkr/source_yade/yade/lib/pyutil/numpy_boost.hpp:128: error: ‘PyArray_STRIDE’ was not declared in this scope
make[2]: *** [CMakeFiles/plugins.dir/pkg/dem/TesselationWrapper.cpp.o] Error 1
make[1]: *** [CMakeFiles/plugins.dir/all] Error 2
make: *** [all] Error 2
altix5 159% 


But numpy/arrayobject.h is found under the following folder 

/usr/lib/python2.6/site-packages/numpy/core/include/numpy/arrayobject.h

Please help me resolve this error
Thank you in advance

Mathan


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