Yade

error at installtion with wrong header path detection

Asked by Mathan

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
[ 12%] Building CXX object CMakeFiles/core.dir/core/Cell.cpp.o
[ 13%] Building CXX object CMakeFiles/core.dir/core/Clump.cpp.o
[ 13%] Building CXX object CMakeFiles/core.dir/core/Dispatcher.cpp.o
[ 14%] Building CXX object CMakeFiles/core.dir/core/EnergyTracker.cpp.o
[ 14%] Building CXX object CMakeFiles/core.dir/core/Engine.cpp.o
[ 15%] Building CXX object CMakeFiles/core.dir/core/FileGenerator.cpp.o
[ 16%] Building CXX object CMakeFiles/core.dir/core/FrontEnd.cpp.o
[ 16%] Building CXX object CMakeFiles/core.dir/core/Interaction.cpp.o
[ 17%] Building CXX object CMakeFiles/core.dir/core/InteractionContainer.cpp.o
[ 17%] Building CXX object CMakeFiles/core.dir/core/Material.cpp.o
[ 18%] Building CXX object CMakeFiles/core.dir/core/Omega.cpp.o
[ 18%] Building CXX object CMakeFiles/core.dir/core/PartialEngine.cpp.o
[ 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
[ 22%] Building CXX object CMakeFiles/core.dir/core/ThreadWorker.cpp.o
[ 23%] Building CXX object CMakeFiles/core.dir/core/TimeStepper.cpp.o
[ 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
[ 25%] Building CXX object gui/CMakeFiles/_GLViewer.dir/qt4/_GLViewer.cpp.o
[ 26%] Building CXX object gui/CMakeFiles/_GLViewer.dir/qt4/OpenGLManager.cpp.o
[ 27%] Building CXX object gui/CMakeFiles/_GLViewer.dir/qt4/moc_GLViewer.cxx.o
[ 27%] Building CXX object gui/CMakeFiles/_GLViewer.dir/qt4/moc_OpenGLManager.cxx.o
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
[ 28%] Building CXX object CMakeFiles/plugins.dir/pkg/common/Bo1_Facet_Aabb.cpp.o
[ 29%] Building CXX object CMakeFiles/plugins.dir/pkg/common/Bo1_Sphere_Aabb.cpp.o
[ 30%] Building CXX object CMakeFiles/plugins.dir/pkg/common/BoundaryController.cpp.o
[ 30%] Building CXX object CMakeFiles/plugins.dir/pkg/common/Box.cpp.o
[ 31%] Building CXX object CMakeFiles/plugins.dir/pkg/common/Callbacks.cpp.o
[ 31%] Building CXX object CMakeFiles/plugins.dir/pkg/common/Collider.cpp.o
[ 32%] Building CXX object CMakeFiles/plugins.dir/pkg/common/CylScGeom6D.cpp.o
[ 32%] Building CXX object CMakeFiles/plugins.dir/pkg/common/Cylinder.cpp.o
[ 33%] Building CXX object CMakeFiles/plugins.dir/pkg/common/Dispatching.cpp.o
[ 34%] Building CXX object CMakeFiles/plugins.dir/pkg/common/ElastMat.cpp.o
[ 34%] Building CXX object CMakeFiles/plugins.dir/pkg/common/Facet.cpp.o
[ 35%] Building CXX object CMakeFiles/plugins.dir/pkg/common/FieldApplier.cpp.o
[ 35%] Building CXX object CMakeFiles/plugins.dir/pkg/common/ForceEngine.cpp.o
[ 36%] Building CXX object CMakeFiles/plugins.dir/pkg/common/ForceResetter.cpp.o
[ 36%] Building CXX object CMakeFiles/plugins.dir/pkg/common/GLDrawFunctors.cpp.o
[ 37%] Building CXX object CMakeFiles/plugins.dir/pkg/common/Gl1_Aabb.cpp.o
[ 38%] Building CXX object CMakeFiles/plugins.dir/pkg/common/Gl1_Box.cpp.o
[ 38%] Building CXX object CMakeFiles/plugins.dir/pkg/common/Gl1_Facet.cpp.o
[ 39%] Building CXX object CMakeFiles/plugins.dir/pkg/common/Gl1_NormPhys.cpp.o
[ 39%] Building CXX object CMakeFiles/plugins.dir/pkg/common/Gl1_Sphere.cpp.o
[ 40%] Building CXX object CMakeFiles/plugins.dir/pkg/common/GravityEngines.cpp.o
[ 40%] Building CXX object CMakeFiles/plugins.dir/pkg/common/Grid.cpp.o
[ 41%] Building CXX object CMakeFiles/plugins.dir/pkg/common/InsertionSortCollider.cpp.o
[ 42%] Building CXX object CMakeFiles/plugins.dir/pkg/common/InteractionLoop.cpp.o
[ 42%] Building CXX object CMakeFiles/plugins.dir/pkg/common/KinematicEngines.cpp.o
[ 43%] Building CXX object CMakeFiles/plugins.dir/pkg/common/MatchMaker.cpp.o
[ 43%] Building CXX object CMakeFiles/plugins.dir/pkg/common/NormShearPhys.cpp.o
[ 44%] Building CXX object CMakeFiles/plugins.dir/pkg/common/OpenGLRenderer.cpp.o
[ 44%] Building CXX object CMakeFiles/plugins.dir/pkg/common/ParallelEngine.cpp.o
[ 45%] Building CXX object CMakeFiles/plugins.dir/pkg/common/PeriodicEngines.cpp.o
[ 46%] Building CXX object CMakeFiles/plugins.dir/pkg/common/PersistentTriangulationCollider.cpp.o
[ 46%] Building CXX object CMakeFiles/plugins.dir/pkg/common/PyRunner.cpp.o
[ 47%] Building CXX object CMakeFiles/plugins.dir/pkg/common/Recorder.cpp.o
[ 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
[ 49%] Building CXX object CMakeFiles/plugins.dir/pkg/common/Sphere.cpp.o
[ 49%] Building CXX object CMakeFiles/plugins.dir/pkg/common/StepDisplacer.cpp.o
[ 50%] Building CXX object CMakeFiles/plugins.dir/pkg/common/TorqueEngine.cpp.o
[ 50%] Building CXX object CMakeFiles/plugins.dir/pkg/common/Wall.cpp.o
[ 51%] Building CXX object CMakeFiles/plugins.dir/pkg/common/ZECollider.cpp.o
[ 51%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/CapillaryPhys.cpp.o
[ 52%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/CapillaryStressRecorder.cpp.o
[ 53%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/CapillaryTriaxialTest.cpp.o
[ 53%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/CohFrictMat.cpp.o
[ 54%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/CohFrictPhys.cpp.o
[ 54%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/CohesiveFrictionalContactLaw.cpp.o
[ 55%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/CohesiveFrictionalPM.cpp.o
[ 55%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/CohesiveStateRPMRecorder.cpp.o
[ 56%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/CohesiveTriaxialTest.cpp.o
[ 57%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/ConcretePM.cpp.o
[ 57%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/Dem3DofGeom_FacetSphere.cpp.o
[ 58%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/Dem3DofGeom_SphereSphere.cpp.o
[ 58%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/Dem3DofGeom_WallSphere.cpp.o
[ 59%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/DemXDofGeom.cpp.o
[ 59%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/Disp2DPropLoadEngine.cpp.o
[ 60%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/DomainLimiter.cpp.o
[ 61%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/ElasticContactLaw.cpp.o
[ 61%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/FacetTopologyAnalyzer.cpp.o
[ 62%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/FlatGridCollider.cpp.o
[ 62%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/FlowEngine.cpp.o
[ 63%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/ForceTorqueRecorder.cpp.o
[ 63%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/FrictPhys.cpp.o
[ 64%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/GlobalStiffnessTimeStepper.cpp.o
[ 65%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/HertzMindlin.cpp.o
[ 65%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/Ig2_Box_Sphere_ScGeom.cpp.o
[ 66%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/Ig2_Facet_Sphere_ScGeom.cpp.o
[ 66%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/Ig2_Sphere_Sphere_ScGeom.cpp.o
[ 67%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/Ip2_2xNormalInelasticMat_NormalInelasticityPhys.cpp.o
[ 67%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/Ip2_CohFrictMat_CohFrictMat_CohFrictPhys.cpp.o
[ 68%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/Ip2_FrictMat_FrictMat_CapillaryPhys.cpp.o
[ 69%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/Ip2_FrictMat_FrictMat_FrictPhys.cpp.o
[ 69%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/Ip2_FrictMat_FrictMat_MindlinCapillaryPhys.cpp.o
[ 70%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/KinemCNDEngine.cpp.o
[ 70%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/KinemCNLEngine.cpp.o
[ 71%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/KinemCNSEngine.cpp.o
[ 71%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/KinemCTDEngine.cpp.o
[ 72%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/KinemSimpleShearBox.cpp.o
[ 73%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/L3Geom.cpp.o
[ 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
[ 76%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/NormalInelasticityPhys.cpp.o
[ 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

Question information

Language:
English Edit question
Status:
Answered
For:
Yade Edit question
Assignee:
No assignee Edit question
Last query:
Last reply:
Revision history for this message
Anton Gladky (gladky-anton) said : 		#1

Hi,

try to add -DCMAKE_PREFIX_PATH=/usr/lib/python2.6/site-packages/numpy/core/include/
into configuration options.

HTH,

Anton

Revision history for this message
Mathan (rmsdiscover) said : 		#2

Hi,
Thanks Anton.
But it doest solve the problem, occurs same error.

here is the log..

altix5 113% cmake -DINSTALL_PREFIX=/home2/mkr/source_yade/yade-build -DCMAKE_PREFIX_PATH=/usr/lib/python2.6/site-packages/numpy/core/include/ 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

error part ..

[ 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:

Please give me some other ways to make it out.

Regards
MathanK Raja

Revision history for this message
Bruno Chareyre (bruno-chareyre) said : 		#3

It doesn't matter which hardware you are using (ref. your other question). More important is your linux distribution.
Do you have python-numpy installed? If so, check where numpy/arrayobject.h is located and add this path to the compilers flags.

Revision history for this message
Anton Gladky (gladky-anton) said : 		#4

Please, add -DCMAKE_VERBOSE_MAKEFILE=1 option and show an output of the compilation process.

Revision history for this message
Anton Gladky (gladky-anton) said : 		#5

The freshest yade version should handle numpy
installation. You can download it from github [1] or
just "git clone..." as described in documentation.

Anton

[1] https://github.com/yade/trunk/archive/master.zip

Revision history for this message
Mathan (rmsdiscover) said : 		#6

Thank you Anton and Bruno Chareyre

I have used the freshest version from git (from your link) and tried to compile it,
Numpy path is detected at the configuration part this time and shows like
--
--
-- Using GTS from /usr/local
-- Found GL2PS: /usr/local/lib/libgl2ps.so
-- Found CGAL: /usr/local/include/CGAL, /usr/local/lib/libCGAL.so
-- Found NumPy: version "1.3.0" /usr/lib/python2.6/site-packages/numpy/core/include
-- Boost version: 1.52.0
--
--

but same error occurs again,

[ 82%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/TesselationWrapper.cpp.o
In file included from /home2/mkr/ynew/yade/lib/pyutil/numpy.hpp:3,
                 from /home2/mkr/ynew/trunk-master/pkg/dem/TesselationWrapper.cpp:11:
/home2/mkr/ynew/yade/lib/pyutil/numpy_boost.hpp:44:31: error: numpy/arrayobject.h: No such file or directory
In file included from /home2/mkr/ynew/yade/lib/pyutil/numpy.hpp:3,
                 from /home2/mkr/ynew/trunk-master/pkg/dem/TesselationWrapper.cpp:11:
/home2/mkr/ynew/yade/lib/pyutil/numpy_boost.hpp:58: error: ‘NPY_FLOAT’ was not declared in this scope

As I posted before Numpy installed and available in the detected location.

Please let know if you want more information regarding this.

MathanK Raja

Revision history for this message
Anton Gladky (gladky-anton) said : 		#7

Not sure, but maybe your numpy version is too old.
Try to disable CGAL-feature for a while, add:

-DENABLE_CGAL=0

into compilation options.

Anton

Revision history for this message
Mathan (rmsdiscover) said : 		#8

Hi,
Thanks Anton,
Disabling CGAL solved error message at 82% level but the same occurred at the 99%
Also I got the error with VTK and I have disabled it..
[ 89%] Building CXX object CMakeFiles/plugins.dir/pkg/dem/WirePM.cpp.o

:::::::::::::::::::::::::::::::
/usr/lib/gcc/ia64-suse-linux/4.3/../../../../ia64-suse-linux/bin/ld: /usr/local/lib/vtk-5.10/libvtkFiltering.a(vtkAlgorithm.cxx.o): @gprel relocation against dynamic symbol vtkAlgorithm::DefaultExecutivePrototype
/usr/lib/gcc/ia64-suse-linux/4.3/../../../../ia64-suse-linux/bin/ld: /usr/local/lib/vtk-5.10/libvtkFiltering.a(vtkAlgorithm.cxx.o): @gprel relocation against dynamic symbol vtkAlgorithm::DefaultExecutivePrototype

/usr/lib/gcc/ia64-suse-linux/4.3/../../../../ia64-suse-linux/bin/ld: final link failed: Nonrepresentable section on output
collect2: ld returned 1 exit status

after disabling VTK, these errors are solved
but I stuck with numpy again at 99%,

[ 99%] Building CXX object py/CMakeFiles/_utils.dir/_utils.cpp.o
cd /home2/mkr/ynew/py && /usr/bin/c++ -D_utils_EXPORTS -DYADE_PTR_CAST=static_pointer_cast -DYADE_CAST=static_cast -Wall -fPIC -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -s -DYADE_OPENMP -fopenmp -DYADE_GTS -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/local/include -DQGLVIEWER_FOUND -DYADE_OPENGL -DYADE_GL2PS -O3 -DNDEBUG -fPIC -I/usr/local/include -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/QtDesigner -I/usr/include/QtAssistant -I/usr/include/QtScriptTools -I/usr/include/QtDBus -I/usr/include/QtXml -I/usr/include/QtSql -I/usr/include/QtOpenGL -I/usr/include/QtMultimedia -I/usr/include/QtNetwork -I/usr/include/QtHelp -I/usr/include/QtUiTools -I/usr/include/QtTest -I/usr/include/QtScript -I/usr/include/QtSvg -I/usr/include/Qt3Support -I/usr/include/QtGui -I/usr/include/QtCore -I/usr/share/qt4/mkspecs/default -I/usr/include/python2.6 -I/home2/mkr/ynew/trunk-master/extra/floating_point_utilities_v3 -I/home2/mkr/ynew -o CMakeFiles/_utils.dir/_utils.cpp.o -c /home2/mkr/ynew/trunk-master/py/_utils.cpp

/home2/mkr/ynew/trunk-master/py/_utils.cpp:16:32: error: numpy/ndarrayobject.h: No such file or directory
/home2/mkr/ynew/trunk-master/py/_utils.cpp: In function ‘bool pointInsidePolygon(boost::python::tuple, boost::python::api::object)’:
/home2/mkr/ynew/trunk-master/py/_utils.cpp:293: error: ‘PyArrayObject’ was not declared in this scope
/home2/mkr/ynew/trunk-master/py/_utils.cpp:293: error: ‘vert’ was not declared in this scope
/home2/mkr/ynew/trunk-master/py/_utils.cpp:293: error: expected primary-expression before ‘)’ token
/home2/mkr/ynew/trunk-master/py/_utils.cpp:293: error: expected `;' before ‘vertices’
/home2/mkr/ynew/trunk-master/py/_utils.cpp:294: error: ‘PyArray_DOUBLE’ was not declared in this scope
/home2/mkr/ynew/trunk-master/py/_utils.cpp:294: error: ‘PyArray_As2D’ was not declared in this scope
/home2/mkr/ynew/trunk-master/py/_utils.cpp: In function ‘void init_module__utils()’:
/home2/mkr/ynew/trunk-master/py/_utils.cpp:497: error: ‘import_array’ was not declared in this scope

make[2]: *** [py/CMakeFiles/_utils.dir/_utils.cpp.o] Error 1
make[2]: Leaving directory `/home2/mkr/ynew'
make[1]: *** [py/CMakeFiles/_utils.dir/all] Error 2
make[1]: Leaving directory `/home2/mkr/ynew'
make: *** [all] Error 2

I tried to manually add the installation path of Numpy (using -I/path/to/Numpy/) and compile the /home2/mkr/ynew/trunk-master/py/_utils.cpp
it works !

So I am trying to do this in the following way (compilation is running for last 4 hours)
set CCFLAG "Path/to/numpy"

Is there any other way to do it ?

MathanK Raja

Revision history for this message
Mathan (rmsdiscover) said : 		#9

Sorry for mistake,
This is how I am trying to link,

setenv CPPFLAGS "-I/usr/lib/python2.6/site-packages/numpy/core/include/"

MathanK Raja

Revision history for this message
Anton Gladky (gladky-anton) said : 		#10

Try -DNUMPY_INCLUDE_DIRS="/usr/lib/python2.6/site-packages/numpy/core/include/"
But I think your numpy version is too old.

Anton

Revision history for this message
Mathan (rmsdiscover) said : 		#11

Thanks Anton,

But nor "setenv CPPFLAGS" neither " -DNUMPY_INCLUDE_DIRS" worked.
I even looked around FindNumpy.cmake and tested the Numpy path by importing it through the python, I got the proper path details.
I found the wrong path from the CMakeCache.txt like as follows

-----------------------------------------------------------------------------------------------------------------------------------------------------------
//Details about finding NUMPY
FIND_PACKAGE_MESSAGE_DETAILS_NUMPY:INTERNAL=/usr/lib/python2.6/site-packages/numpy/core/include1.3.0
-----------------------------------------------------------------------------------------------------------------------------------------------------------

In a dirty way, I have included the path of Numpy on the source program itself (#include "path/to/Numpy") and it compiles without an error.
Agian I got the problem with GUI, like as follows,

------------------------------------------------------------------------------------------
CMake Error at gui/cmake_install.cmake:88 (FILE):
 file INSTALL cannot find "/home2/mkr/ynew/img_rc.py".
------------------------------------------------------------------------------------------

after this i disabled the gui feature and it is installed with out an error.
While I try to launch the yade, I am facing error,

----------------------------------------------------------------------------------------------
Altix5 223% ./yade-Unknown
Welcome to Yade Unknown
Traceback (most recent call last):
  File "./yade-Unknown", line 85, in <module>
    import yade
  File "/home2/mkr/ynew/yade-build/lib/yade-Unknown/py/yade/__init__.py", line 65, in <module>
    import boot
ImportError: /home2/mkr/ynew/yade-build/lib/yade-Unknown/libcore.so: undefined symbol: _ZN5boost9iostreams6detail9zlib_base8xdeflateEi
-------------------------------------------------------------------------------------------------

Boost libraries are installed as well as the iostreams is available on the library path.
Please help on this problem.

MathanK Raja

Revision history for this message
Anton Gladky (gladky-anton) said : 		#12

---------------------------------
> //Details about finding NUMPY
> FIND_PACKAGE_MESSAGE_DETAILS_NUMPY:INTERNAL=/usr/lib/python2.6/site-packages/numpy/core/include1.3.0
> -----------------------------------------------------------------------------------------------------------------------------------------------------------

Did you execute "cmake-command" in a clean folder, free from previous
fiiles?

> after this i disabled the gui feature and it is installed with out an error.
> While I try to launch the yade, I am facing error,
>
> ----------------------------------------------------------------------------------------------
> Altix5 223% ./yade-Unknown
> Welcome to Yade Unknown
> Traceback (most recent call last):
> File "./yade-Unknown", line 85, in <module>
> import yade
> File "/home2/mkr/ynew/yade-build/lib/yade-Unknown/py/yade/__init__.py", line 65, in <module>
> import boot
> ImportError: /home2/mkr/ynew/yade-build/lib/yade-Unknown/libcore.so: undefined symbol: _ZN5boost9iostreams6detail9zlib_base8xdeflateEi
> -------------------------------------------------------------------------------------------------
>
> Boost libraries are installed as well as the iostreams is available on the library path.
> Please help on this problem.

It seems, libcore.so is not linked against one of boost libraries. No idea why.
Do you install yade in the same folder, where it was built? If so, try to set
-DINSTALL_PREFIX=/home/install/path out of build-directory.

Most of us are using Debian and Debian-based distros. So yade works
and compiles on such systems usually well.

Anton

Revision history for this message
Mathan (rmsdiscover) said : 		#13

Anton,
I am trying to build it on the same folder which is clean and as you said I used the following syntax,

 cmake -DINSTALL_PREFIX=/home2/mkr/ynew/yade-build -DENABLE_CGAL=0 -DENABLE_VTK=0 -DCMAKE_VERBOSE_MAKEFILE=1 -DENABLE_GUI=0 trunk-master/

Yes, Yade is working well on Debian based distros, even we are running jobs on our local machines (Ubuntu based 4-12 CPU machines and simple jobs takes 7 days to finish )

If we can able to install Yade on our Clusters, multiple number of people can use Yade nationwide and they can submit their multiple jobs through PBS.

Thank you

MathanK Raja

Revision history for this message
Anton Gladky (gladky-anton) said : 		#14

Try the latest trunk-version (on github). At least it compiles and
works good on OpenSuse 12.

Cheers,

Anton

Revision history for this message
Mathan (rmsdiscover) said : 		#15

Thanks Anton,
Latest trunk-version, smoothly installed (without Numpy issue) but at the launch it is giving same sort of error,

altix5 257% ./yade-Unknown
Welcome to Yade Unknown
Traceback (most recent call last):
  File "./yade-Unknown", line 85, in <module>
    import yade
  File "/home2/mkr/yade-build/lib/yade-Unknown/py/yade/__init__.py", line 65, in <module>
    import boot
ImportError: /home2/mkr/yade-build/lib/yade-Unknown/libcore.so: undefined symbol: _ZN5boost9iostreams6detail9zlib_base8xdeflateEi

I am planning to reinstall boost libraries and planning to test it again.

Get back to you soon

MathanK Raja

Revision history for this message
Klaus Thoeni (klaus.thoeni) said : 		#16

Hi Mathan,

I think I had a similar problem on our Redhat server. It was a problem of
linking boost correctly. Have a look if this helps you:

https://lists.launchpad.net/yade-dev/msg08345.html

And I added the option of defining a local installed boost in cmake, e.g. -
DLocalBoost=1.46.1

HTH Klaus

On Thu, 31 Jan 2013 04:26:00 PM Mathan wrote:
> Question #220027 on Yade changed:
> https://answers.launchpad.net/yade/+question/220027
>
> Mathan posted a new comment:
> Thanks Anton,
> Latest trunk-version, smoothly installed (without Numpy issue) but at the
> launch it is giving same sort of error,
>
> altix5 257% ./yade-Unknown
> Welcome to Yade Unknown
> Traceback (most recent call last):
> File "./yade-Unknown", line 85, in <module>
> import yade
> File "/home2/mkr/yade-build/lib/yade-Unknown/py/yade/__init__.py", line
> 65, in <module> import boot
> ImportError: /home2/mkr/yade-build/lib/yade-Unknown/libcore.so: undefined
> symbol: _ZN5boost9iostreams6detail9zlib_base8xdeflateEi
>
> I am planning to reinstall boost libraries and planning to test it again.
>
> Get back to you soon
>
> MathanK Raja

Revision history for this message
Mathan (rmsdiscover) said : 		#17

Thanks Klaus Thoeni but it doest not solve the problem and I even found same sort of problem from the previous bug list

https://bugs.launchpad.net/yade/+bug/707966

 here is the ldd libcore.so,

 linux-gate.so.1 => (0xa000000000000000)
 libsupport.so => /home2/mkr/yade-build/lib/yade-Unknown/libsupport.so (0x2000000800990000)
 libboost_python.so.1.52.0 => /usr/local/lib/libboost_python.so.1.52.0 (0x2000000800a50000)
 libboost_thread.so.1.52.0 => /usr/local/lib/libboost_thread.so.1.52.0 (0x2000000800b10000)
 libboost_date_time.so.1.52.0 => /usr/local/lib/libboost_date_time.so.1.52.0 (0x2000000800b60000)
 libboost_filesystem.so.1.52.0 => /usr/local/lib/libboost_filesystem.so.1.52.0 (0x2000000800b90000)
 libboost_iostreams.so.1.36.0 => /usr/local/lib/libboost_iostreams.so.1.36.0 (0x2000000800bd0000)
 libboost_regex.so.1.52.0 => /usr/local/lib/libboost_regex.so.1.52.0 (0x2000000800bf0000)
 libboost_serialization.so.1.52.0 => /usr/local/lib/libboost_serialization.so.1.52.0 (0x2000000800de0000)
 libpython2.6.so.1.0 => /usr/lib/libpython2.6.so.1.0 (0x2000000800ee0000)
 libgl2ps.so.1 => /usr/local/lib/libgl2ps.so.1 (0x2000000801210000)
 librt.so.1 => /lib/librt.so.1 (0x2000000801270000)
 libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x2000000801290000)
 libm.so.6.1 => /lib/libm.so.6.1 (0x2000000801470000)
 libgomp.so.1 => /usr/lib/libgomp.so.1 (0x2000000801540000)
 libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x2000000801560000)
 libunwind.so.7 => /lib/libunwind.so.7 (0x2000000801590000)
 libpthread.so.0 => /lib/libpthread.so.0 (0x20000008015e0000)
 libc.so.6.1 => /lib/libc.so.6.1 (0x2000000801620000)
 libutil.so.1 => /lib/libutil.so.1 (0x20000008018b0000)
 libdl.so.2 => /lib/libdl.so.2 (0x20000008018d0000)
 libboost_system.so.1.52.0 => /usr/local/lib/libboost_system.so.1.52.0 (0x20000008018f0000)
 libbz2.so.1 => /lib/libbz2.so.1 (0x2000000801910000)
 libz.so.1 => /lib/libz.so.1 (0x2000000801940000)
 libGLU.so.1 => /usr/lib/libGLU.so.1 (0x2000000801980000)
 libGL.so.1 => /usr/lib/libGL.so.1 (0x2000000801a80000)
 libSM.so.6 => /usr/lib/libSM.so.6 (0x2000000801c00000)
 libICE.so.6 => /usr/lib/libICE.so.6 (0x2000000801c20000)
 libX11.so.6 => /usr/lib/libX11.so.6 (0x2000000801c70000)
 libXext.so.6 => /usr/lib/libXext.so.6 (0x2000000801ea0000)
 libglut.so.3 => /usr/lib/libglut.so.3 (0x2000000801ee0000)
 libXmu.so.6 => /usr/lib/libXmu.so.6 (0x2000000801f60000)
 libXi.so.6 => /usr/lib/libXi.so.6 (0x2000000801fa0000)
 libpng12.so.0 => /usr/lib/libpng12.so.0 (0x2000000801fd0000)
 /lib/ld-linux-ia64.so.2 (0x2000000800000000)
 libXxf86vm.so.1 => /usr/lib/libXxf86vm.so.1 (0x2000000802040000)
 libXdamage.so.1 => /usr/lib/libXdamage.so.1 (0x2000000802060000)
 libXfixes.so.3 => /usr/lib/libXfixes.so.3 (0x2000000802080000)
 libdrm.so.2 => /usr/lib/libdrm.so.2 (0x20000008020a0000)
 libuuid.so.1 => /lib/libuuid.so.1 (0x20000008020d0000)
 libxcb-xlib.so.0 => /usr/lib/libxcb-xlib.so.0 (0x20000008020f0000)
 libxcb.so.1 => /usr/lib/libxcb.so.1 (0x2000000802110000)
 libXau.so.6 => /usr/lib/libXau.so.6 (0x2000000802150000)
 libXt.so.6 => /usr/lib/libXt.so.6 (0x2000000802170000)

Looking for the possible solution

MathanK Raja

Revision history for this message
Anton Gladky (gladky-anton) said : 		#18

You have mess in boost versions. From your output:

libboost_filesystem.so.1.52.0 =>
/usr/local/lib/libboost_filesystem.so.1.52.0 (0x2000000800b90000)
libboost_iostreams.so.1.36.0 =>
/usr/local/lib/libboost_iostreams.so.1.36.0 (0x2000000800bd0000)

libcore is linked against different versions of boost and it causes problems.
What do you type in cmake-configuration string?

Anton

2013/2/6 Mathan <email address hidden>:
> Question #220027 on Yade changed:
> https://answers.launchpad.net/yade/+question/220027
>
> Status: Answered => Open
>
> Mathan is still having a problem:
> Thanks Klaus Thoeni but it doest not solve the problem and I even found
> same sort of problem from the previous bug list
>
> https://bugs.launchpad.net/yade/+bug/707966
>
> here is the ldd libcore.so,
>
> linux-gate.so.1 => (0xa000000000000000)
> libsupport.so => /home2/mkr/yade-build/lib/yade-Unknown/libsupport.so (0x2000000800990000)
> libboost_python.so.1.52.0 => /usr/local/lib/libboost_python.so.1.52.0 (0x2000000800a50000)
> libboost_thread.so.1.52.0 => /usr/local/lib/libboost_thread.so.1.52.0 (0x2000000800b10000)
> libboost_date_time.so.1.52.0 => /usr/local/lib/libboost_date_time.so.1.52.0 (0x2000000800b60000)
> libboost_filesystem.so.1.52.0 => /usr/local/lib/libboost_filesystem.so.1.52.0 (0x2000000800b90000)
> libboost_iostreams.so.1.36.0 => /usr/local/lib/libboost_iostreams.so.1.36.0 (0x2000000800bd0000)
> libboost_regex.so.1.52.0 => /usr/local/lib/libboost_regex.so.1.52.0 (0x2000000800bf0000)
> libboost_serialization.so.1.52.0 => /usr/local/lib/libboost_serialization.so.1.52.0 (0x2000000800de0000)
> libpython2.6.so.1.0 => /usr/lib/libpython2.6.so.1.0 (0x2000000800ee0000)
> libgl2ps.so.1 => /usr/local/lib/libgl2ps.so.1 (0x2000000801210000)
> librt.so.1 => /lib/librt.so.1 (0x2000000801270000)
> libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x2000000801290000)
> libm.so.6.1 => /lib/libm.so.6.1 (0x2000000801470000)
> libgomp.so.1 => /usr/lib/libgomp.so.1 (0x2000000801540000)
> libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x2000000801560000)
> libunwind.so.7 => /lib/libunwind.so.7 (0x2000000801590000)
> libpthread.so.0 => /lib/libpthread.so.0 (0x20000008015e0000)
> libc.so.6.1 => /lib/libc.so.6.1 (0x2000000801620000)
> libutil.so.1 => /lib/libutil.so.1 (0x20000008018b0000)
> libdl.so.2 => /lib/libdl.so.2 (0x20000008018d0000)
> libboost_system.so.1.52.0 => /usr/local/lib/libboost_system.so.1.52.0 (0x20000008018f0000)
> libbz2.so.1 => /lib/libbz2.so.1 (0x2000000801910000)
> libz.so.1 => /lib/libz.so.1 (0x2000000801940000)
> libGLU.so.1 => /usr/lib/libGLU.so.1 (0x2000000801980000)
> libGL.so.1 => /usr/lib/libGL.so.1 (0x2000000801a80000)
> libSM.so.6 => /usr/lib/libSM.so.6 (0x2000000801c00000)
> libICE.so.6 => /usr/lib/libICE.so.6 (0x2000000801c20000)
> libX11.so.6 => /usr/lib/libX11.so.6 (0x2000000801c70000)
> libXext.so.6 => /usr/lib/libXext.so.6 (0x2000000801ea0000)
> libglut.so.3 => /usr/lib/libglut.so.3 (0x2000000801ee0000)
> libXmu.so.6 => /usr/lib/libXmu.so.6 (0x2000000801f60000)
> libXi.so.6 => /usr/lib/libXi.so.6 (0x2000000801fa0000)
> libpng12.so.0 => /usr/lib/libpng12.so.0 (0x2000000801fd0000)
> /lib/ld-linux-ia64.so.2 (0x2000000800000000)
> libXxf86vm.so.1 => /usr/lib/libXxf86vm.so.1 (0x2000000802040000)
> libXdamage.so.1 => /usr/lib/libXdamage.so.1 (0x2000000802060000)
> libXfixes.so.3 => /usr/lib/libXfixes.so.3 (0x2000000802080000)
> libdrm.so.2 => /usr/lib/libdrm.so.2 (0x20000008020a0000)
> libuuid.so.1 => /lib/libuuid.so.1 (0x20000008020d0000)
> libxcb-xlib.so.0 => /usr/lib/libxcb-xlib.so.0 (0x20000008020f0000)
> libxcb.so.1 => /usr/lib/libxcb.so.1 (0x2000000802110000)
> libXau.so.6 => /usr/lib/libXau.so.6 (0x2000000802150000)
> libXt.so.6 => /usr/lib/libXt.so.6 (0x2000000802170000)
>
> Looking for the possible solution
>
> MathanK Raja
>
> --
> You received this question notification because you are a member of
> yade-users, which is an answer contact for Yade.
>
> _______________________________________________
> Mailing list: https://launchpad.net/~yade-users
> Post to : <email address hidden>
> Unsubscribe : https://launchpad.net/~yade-users
> More help : https://help.launchpad.net/ListHelp

Revision history for this message
Mathan (rmsdiscover) said : 		#19

Hi,
I have reinstalled the boost libraries and even faced some problem with Ipython packages.
After successful corrections of above errors, Yade compiled and installed successfully.
When I trying to run sample script, it is showing the following fatal error,

FATAL /home2/mkr/YADE/trunk-master/pkg/common/Facet.cpp:26 postLoad: Facet has coincident vertices 0 (0 -2.68156e+152 -4.02234e+152) and 1 (0 -2.68156e+152 -4.02234e+152)!

I looked into your bug list and learned, it is because of import error of geometry.
Please advice me further.

Another test yielded this:

Welcome to Yade Unknown
###################################
running: checkGravity.py
Status: success
___________________________________
###################################
running: checkTestDummy.py
checkTestDummy.py failure
###################################
running: checkTestNormalInelasticity.py
Status: success
___________________________________
###################################
running: checkTestTriax.py
checkTestTriax.py failure
###################################
running: checkWeight.py
Precalculated weight 4536.560323
Obtained weight -0.000000
checkWeight.py failure

MathanK Raja

Revision history for this message
Anton Gladky (gladky-anton) said : 		#20

Is at your locale-settings the divider between integer and fractional
part of the number not a point?

Anton

Revision history for this message
Mathan (rmsdiscover) said : 		#21

Dear Anton,

I checked the locale settings and I posted it below. Is this the detail you wanted. Please clarify me further.
Do i have to set LC_NUMERIC ?

----------------------------------------------------------------------------
altix5 102% locale
LANG=en_IN
LC_CTYPE="en_IN"
LC_NUMERIC="en_IN"
LC_TIME="en_IN"
LC_COLLATE="en_IN"
LC_MONETARY="en_IN"
LC_MESSAGES="en_IN"
LC_PAPER="en_IN"
LC_NAME="en_IN"
LC_ADDRESS="en_IN"
LC_TELEPHONE="en_IN"
LC_MEASUREMENT="en_IN"
LC_IDENTIFICATION="en_IN"
LC_ALL=

MathanK Raja

Revision history for this message
Anton Gladky (gladky-anton) said : 		#22

I have tried your locale-settings and yade works fine in this case. I
remember we had similar problems with that. The problem was in ipython.
Try to find corresponding bug.

Actually, I have successfully compiled and installed Yade on OpenSuse
(the latest one). Don't know, how it differs from your installation.

Cheers,

Anton

On 02/14/2013 08:45 AM, Mathan wrote:
> Question #220027 on Yade changed:
> https://answers.launchpad.net/yade/+question/220027
>
> Status: Answered => Open
>
> Mathan is still having a problem:
> Dear Anton,
>
> I checked the locale settings and I posted it below. Is this the detail you wanted. Please clarify me further.
> Do i have to set LC_NUMERIC ?
>
> ----------------------------------------------------------------------------
> altix5 102% locale
> LANG=en_IN
> LC_CTYPE="en_IN"
> LC_NUMERIC="en_IN"
> LC_TIME="en_IN"
> LC_COLLATE="en_IN"
> LC_MONETARY="en_IN"
> LC_MESSAGES="en_IN"
> LC_PAPER="en_IN"
> LC_NAME="en_IN"
> LC_ADDRESS="en_IN"
> LC_TELEPHONE="en_IN"
> LC_MEASUREMENT="en_IN"
> LC_IDENTIFICATION="en_IN"
> LC_ALL=
>
>
> MathanK Raja
>

Can you help with this problem?

Provide an answer of your own, or ask Mathan for more information if necessary.

To post a message you must log in.