Yade

Collision detection and dense sphere packing problem with compiled yade-daily

Asked by Ehsan Izadi

Hi,

I already had yade-daily installed on my linux mint 15 and it worked very well.
I compiled yade-daily package on my Ubuntu 13.10 (since I intended to use coupled analysis using PFV method, and yade-daily installable was not prepared due to some reasons).
I wrote a code (something like PFV-oedometer.py example but using randomDensePack command) it worked good on my former version of yade-daily, but when I try to run it on my compiled version of yade-daily, i got strange errors! which I had not faced them before with the same code!:

1) Sometimes the "randomDensePack" works, and sometimes it does not work (no spheres will be generated!) with the same code.
2) In the cases that the "randomDensePack" worked, when I run the code, the collision detection between facets and sphere does not work (see the attached snapshots).

Another thing that makes me even more surprised is that when I try to run the oedometer code example code, it works very well and there is no problem about generating spheres and collision detection!!

What do you think about the source of problem? any thing I missed when compiling?
FYI I've appended below the warnings I got after running my code (In the case of generation of spheres):

       (1) WARN /home/ehsan/yade-daily/trunk/pkg/dem/SpherePack.cpp:107 makeCloud: porosity must be >0, changing it for you. It will be ineffective if rMean>0.
      (2) /home/ehsan/yade-daily/build/lib/x86_64-linux-gnu/yade-2013-11-21.git-6927b03/py/yade/pack.py:294: FutureWarning: The default behavior will change; specify returnSpherePack=True for the new behavior, and False to get rid of this warning (your code will break in the future, however). The returned SpherePack object can be added to the simulation using SpherePack.toSimulation()
        (3) warnings.warn('The default behavior will change; specify returnSpherePack=True for the new behavior, and False to get rid of this warning (your code will break in the future, however). The returned SpherePack object can be added to the simulation using SpherePack.toSimulation()',category=FutureWarning

The I used to get the first warning in the yade-daily I had before, but I got also 2 and 3, for the yade I compiled myself.

Thank you in advance

Question information

Language:
English Edit question
Status:
Solved
For:
Yade Edit question
Assignee:
No assignee Edit question
Solved by:
Anton Gladky
Solved:
Last query:
Last reply:
Revision history for this message
Jérôme Duriez (jduriez) said : 		#1

Hi,

For 1) I also faced the situation some times. randomDensePack() uses some different operations to generate your packing : generate a cloud of spheres not in contact, then perform an isotropic compression to obtain an dense sample... It may happen that the cloud generation is not successfull (e.g. because you tried to put too many non overlapping spheres in a given volume or something like that) => no packing...

 Nothing really bad in itself, retest a second time : you observed yourself that sometimes it works ! If you want however to get rid of this feature, consider save a sucessfully generated sample that you could import (with ymport.text) each time you launch your script

For the warnings, they are all related to the way you generate your packing, and are also not really bad from my point of view (once you get your packing, you can consider that all is ok). You will understand 1) if you dive into the details of randomDensePack().
2) and 3) are in fact apparently the same, it is more or less self-explanatory, and, again it depends on the commands you typed to get a packing.

Your problem 2) is more annoying. Maybe you define wrong "contact laws" so that sphere-facets interactions could be handled. We would need your script to give you more info.

Jerome

Revision history for this message
Ehsan Izadi (ehsan-izadi) said : 		#2

I guess running same code in two different versions and getting different feedback, is a strange and there should be a problem with my compiled yade-daily.

I compiled yade-daily again on my Ubuntu 13.10 and reported all the responses I got below (sorry if it is too long!):

----------------------------------------------------------------------------------------------------------------------------------------------------------------------
ehsan@ehsan-ugent:~/yade-daily/build$ cmake -DINSTALL_PREFIX=~/yade-daily/build/ ~/yade-daily/trunk/
-- The C compiler identification is GNU 4.8.1
-- The CXX compiler identification is GNU 4.8.1
-- 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/x86_64-linux-gnu/libpython2.7.so (found version "2.7.5+")
-- Found PythonInterp: /usr/bin/python (found version "2.7.5")
-- 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 "4.8.4")
-- The imported target "vtkParseJava" references the file
   "/usr/bin/vtkParseJava"
but this file does not exist. Possible reasons include:
* The file was deleted, renamed, or moved to another location.
* An install or uninstall procedure did not complete successfully.
* The installation package was faulty and contained
   "/usr/lib/vtk-5.8/VTKTargets.cmake"
but not all the files it references.

-- The imported target "vtkWrapJava" references the file
   "/usr/bin/vtkWrapJava"
but this file does not exist. Possible reasons include:
* The file was deleted, renamed, or moved to another location.
* An install or uninstall procedure did not complete successfully.
* The installation package was faulty and contained
   "/usr/lib/vtk-5.8/VTKTargets.cmake"
but not all the files it references.

-- The imported target "vtkCommonJava" references the file
   "/usr/lib/jni/libvtkCommonJava.so.5.8.0"
but this file does not exist. Possible reasons include:
* The file was deleted, renamed, or moved to another location.
* An install or uninstall procedure did not complete successfully.
* The installation package was faulty and contained
   "/usr/lib/vtk-5.8/VTKTargets.cmake"
but not all the files it references.

-- The imported target "vtkFilteringJava" references the file
   "/usr/lib/jni/libvtkFilteringJava.so.5.8.0"
but this file does not exist. Possible reasons include:
* The file was deleted, renamed, or moved to another location.
* An install or uninstall procedure did not complete successfully.
* The installation package was faulty and contained
   "/usr/lib/vtk-5.8/VTKTargets.cmake"
but not all the files it references.

-- The imported target "vtkImagingJava" references the file
   "/usr/lib/jni/libvtkImagingJava.so.5.8.0"
but this file does not exist. Possible reasons include:
* The file was deleted, renamed, or moved to another location.
* An install or uninstall procedure did not complete successfully.
* The installation package was faulty and contained
   "/usr/lib/vtk-5.8/VTKTargets.cmake"
but not all the files it references.

-- The imported target "vtkGraphicsJava" references the file
   "/usr/lib/jni/libvtkGraphicsJava.so.5.8.0"
but this file does not exist. Possible reasons include:
* The file was deleted, renamed, or moved to another location.
* An install or uninstall procedure did not complete successfully.
* The installation package was faulty and contained
   "/usr/lib/vtk-5.8/VTKTargets.cmake"
but not all the files it references.

-- The imported target "vtkGenericFilteringJava" references the file
   "/usr/lib/jni/libvtkGenericFilteringJava.so.5.8.0"
but this file does not exist. Possible reasons include:
* The file was deleted, renamed, or moved to another location.
* An install or uninstall procedure did not complete successfully.
* The installation package was faulty and contained
   "/usr/lib/vtk-5.8/VTKTargets.cmake"
but not all the files it references.

-- The imported target "vtkIOJava" references the file
   "/usr/lib/jni/libvtkIOJava.so.5.8.0"
but this file does not exist. Possible reasons include:
* The file was deleted, renamed, or moved to another location.
* An install or uninstall procedure did not complete successfully.
* The installation package was faulty and contained
   "/usr/lib/vtk-5.8/VTKTargets.cmake"
but not all the files it references.

-- The imported target "vtkRenderingJava" references the file
   "/usr/lib/jni/libvtkRenderingJava.so.5.8.0"
but this file does not exist. Possible reasons include:
* The file was deleted, renamed, or moved to another location.
* An install or uninstall procedure did not complete successfully.
* The installation package was faulty and contained
   "/usr/lib/vtk-5.8/VTKTargets.cmake"
but not all the files it references.

-- The imported target "vtkVolumeRenderingJava" references the file
   "/usr/lib/jni/libvtkVolumeRenderingJava.so.5.8.0"
but this file does not exist. Possible reasons include:
* The file was deleted, renamed, or moved to another location.
* An install or uninstall procedure did not complete successfully.
* The installation package was faulty and contained
   "/usr/lib/vtk-5.8/VTKTargets.cmake"
but not all the files it references.

-- The imported target "vtkHybridJava" references the file
   "/usr/lib/jni/libvtkHybridJava.so.5.8.0"
but this file does not exist. Possible reasons include:
* The file was deleted, renamed, or moved to another location.
* An install or uninstall procedure did not complete successfully.
* The installation package was faulty and contained
   "/usr/lib/vtk-5.8/VTKTargets.cmake"
but not all the files it references.

-- The imported target "vtkWidgetsJava" references the file
   "/usr/lib/jni/libvtkWidgetsJava.so.5.8.0"
but this file does not exist. Possible reasons include:
* The file was deleted, renamed, or moved to another location.
* An install or uninstall procedure did not complete successfully.
* The installation package was faulty and contained
   "/usr/lib/vtk-5.8/VTKTargets.cmake"
but not all the files it references.

-- The imported target "vtkParallelJava" references the file
   "/usr/lib/jni/libvtkParallelJava.so.5.8.0"
but this file does not exist. Possible reasons include:
* The file was deleted, renamed, or moved to another location.
* An install or uninstall procedure did not complete successfully.
* The installation package was faulty and contained
   "/usr/lib/vtk-5.8/VTKTargets.cmake"
but not all the files it references.

-- The imported target "vtkInfovisJava" references the file
   "/usr/lib/jni/libvtkInfovisJava.so.5.8.0"
but this file does not exist. Possible reasons include:
* The file was deleted, renamed, or moved to another location.
* An install or uninstall procedure did not complete successfully.
* The installation package was faulty and contained
   "/usr/lib/vtk-5.8/VTKTargets.cmake"
but not all the files it references.

-- The imported target "vtkGeovisJava" references the file
   "/usr/lib/jni/libvtkGeovisJava.so.5.8.0"
but this file does not exist. Possible reasons include:
* The file was deleted, renamed, or moved to another location.
* An install or uninstall procedure did not complete successfully.
* The installation package was faulty and contained
   "/usr/lib/vtk-5.8/VTKTargets.cmake"
but not all the files it references.

-- The imported target "vtkViewsJava" references the file
   "/usr/lib/jni/libvtkViewsJava.so.5.8.0"
but this file does not exist. Possible reasons include:
* The file was deleted, renamed, or moved to another location.
* An install or uninstall procedure did not complete successfully.
* The installation package was faulty and contained
   "/usr/lib/vtk-5.8/VTKTargets.cmake"
but not all the files it references.

-- The imported target "vtkQtChart" references the file
   "/usr/lib/libvtkQtChart.so.5.8.0"
but this file does not exist. Possible reasons include:
* The file was deleted, renamed, or moved to another location.
* An install or uninstall procedure did not complete successfully.
* The installation package was faulty and contained
   "/usr/lib/vtk-5.8/VTKTargets.cmake"
but not all the files it references.

-- The imported target "QVTK" references the file
   "/usr/lib/libQVTK.so.5.8.0"
but this file does not exist. Possible reasons include:
* The file was deleted, renamed, or moved to another location.
* An install or uninstall procedure did not complete successfully.
* The installation package was faulty and contained
   "/usr/lib/vtk-5.8/VTKTargets.cmake"
but not all the files it references.

-- The imported target "vtkChartsJava" references the file
   "/usr/lib/jni/libvtkChartsJava.so.5.8.0"
but this file does not exist. Possible reasons include:
* The file was deleted, renamed, or moved to another location.
* An install or uninstall procedure did not complete successfully.
* The installation package was faulty and contained
   "/usr/lib/vtk-5.8/VTKTargets.cmake"
but not all the files it references.

-- Found PkgConfig: /usr/bin/pkg-config (found version "0.26")
-- Version is set to 2013-12-10.git-2e0c7cd
-- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so;/usr/lib/x86_64-linux-gnu/libXext.so
-- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so;/usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/libX11.so
-- Found OpenGL: /usr/lib/x86_64-linux-gnu/libGL.so
-- GTS using gts-config /usr/bin/gts-config
-- Using GTS from /usr
-- Found GL2PS: /usr/lib/libgl2ps.so
-- Found CGAL: /usr/include/CGAL, /usr/lib/libCGAL.so
-- Found NumPy: version "1.7.1" /usr/lib/python2.7/dist-packages/numpy/core/include
-- Found Loki: /usr/include
-- GCC Version >= 4.8. Adding -ftrack-macro-expansion=0 and -save-temps
-- Boost version: 1.53.0
-- Found the following Boost libraries:
-- python
-- thread
-- date_time
-- filesystem
-- iostreams
-- regex
-- serialization
-- system
-- Boost_VERSION: 105300
-- Boost_LIB_VERSION: 1_53
-- Boost_INCLUDE_DIRS: /usr/include
-- Boost_LIBRARIES: /usr/lib/x86_64-linux-gnu/libboost_python.so/usr/lib/x86_64-linux-gnu/libboost_thread.so/usr/lib/x86_64-linux-gnu/libboost_date_time.so/usr/lib/x86_64-linux-gnu/libboost_filesystem.so/usr/lib/x86_64-linux-gnu/libboost_iostreams.so/usr/lib/x86_64-linux-gnu/libboost_regex.so/usr/lib/x86_64-linux-gnu/libboost_serialization.so/usr/lib/x86_64-linux-gnu/libboost_system.so/usr/lib/x86_64-linux-gnu/libpthread.so
-- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0")
-- Found BZip2: /usr/lib/x86_64-linux-gnu/libbz2.so (found version "1.0.6")
-- Looking for BZ2_bzCompressInit in /usr/lib/x86_64-linux-gnu/libbz2.so
-- Looking for BZ2_bzCompressInit in /usr/lib/x86_64-linux-gnu/libbz2.so - found
-- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.8")
-- Found Eigen3
-- Found VTK
-- Found OpenMP
-- GTS using gts-config /usr/bin/gts-config
-- Using GTS from /usr
-- checking for one of the modules 'glib-2.0'
-- Found GLib2: glib-2.0 /usr/include/glib-2.0;/usr/lib/x86_64-linux-gnu/glib-2.0/include
-- Looking for include file glib/gregex.h
-- Looking for include file glib/gregex.h - not found
-- Found GTS
-- Found Qt4: /usr/bin/qmake (found version "4.8.4")
-- Found GLUT: /usr/lib/x86_64-linux-gnu/libglut.so
-- Found QGLViewer: /usr/lib/x86_64-linux-gnu/libQGLViewer.so
-- Found GUI-LIBS
-- GMP libs: /usr/lib/x86_64-linux-gnu/libgmp.so /usr/lib/x86_64-linux-gnu/libgmpxx.so
-- Found GMP: /usr/include/x86_64-linux-gnu
-- GMP libs: /usr/lib/x86_64-linux-gnu/libgmp.so /usr/lib/x86_64-linux-gnu/libgmpxx.so
-- Found CGAL
-- Found Cholmod: /usr/lib/libcholmod.so
-- Found OpenBlas: /usr/lib/openblas-base/libopenblas.so
-- Found Metis: /usr/include
-- Found Cholmod
-- Found OpenBlas
-- Found Metis
-- Found GL2PS
Yade will be installed to /home/ehsan/yade-daily/build
-- Suffix is set to -2013-12-10.git-2e0c7cd
-- LIBRARY_OUTPUT_PATH is set to lib/x86_64-linux-gnu
-- runtimePREFIX is set to /home/ehsan/yade-daily/build
-- Found gts: /usr/lib/python2.7/dist-packages/gts
-- Use system gts version
-- Found minieigen: /usr/lib/python2.7/dist-packages/minieigen.so
-- Use system minieigen version
-- Found Tkinter: /usr/lib/python2.7/lib-tk/Tkinter.py
-- ===========================================================
-- Yade configured with following features: Eigen3 VTK OpenMP GTS GUI CGAL PFVflow LinSolv GL2PS
-- Disabled features:
-- Optimized build
-- ===========================================================
-- Configuring done
-- Generating done
-- Build files have been written to: /home/ehsan/yade-daily/build

ehsan@ehsan-ugent:~/yade-daily/build$ make
[ 0%] Generating qt4/moc_OpenGLManager.cxx
[ 1%] Generating qt4/moc_GLViewer.cxx
Scanning dependencies of target _GLViewer
[ 2%] Building CXX object gui/CMakeFiles/_GLViewer.dir/qt4/GLViewer.cpp.o
[ 2%] Building CXX object gui/CMakeFiles/_GLViewer.dir/qt4/_GLViewer.cpp.o
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[ 4%] Building CXX object gui/CMakeFiles/_GLViewer.dir/qt4/GLViewerDisplay.cpp.o
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[ 5%] Building CXX object gui/CMakeFiles/_GLViewer.dir/qt4/moc_GLViewer.cxx.o
[ 5%] Building CXX object gui/CMakeFiles/_GLViewer.dir/qt4/moc_OpenGLManager.cxx.o
Linking CXX shared library lib/x86_64-linux-gnu/_GLViewer.so
[ 5%] Built target _GLViewer
Scanning dependencies of target yade
[ 5%] Building CXX object CMakeFiles/yade.dir/core/ThreadWorker.cpp.o
[ 6%] Building CXX object CMakeFiles/yade.dir/core/BodyContainer.cpp.o
[ 7%] Building CXX object CMakeFiles/yade.dir/core/Interaction.cpp.o
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[ 8%] Building CXX object CMakeFiles/yade.dir/core/FileGenerator.cpp.o
[ 8%] Building CXX object CMakeFiles/yade.dir/core/TimeStepper.cpp.o
[ 9%] Building CXX object CMakeFiles/yade.dir/core/Shape.cpp.o
[ 10%] Building CXX object CMakeFiles/yade.dir/core/Cell.cpp.o
[ 10%] Building CXX object CMakeFiles/yade.dir/core/ThreadRunner.cpp.o
[ 11%] Building CXX object CMakeFiles/yade.dir/core/Bound.cpp.o
[ 11%] Building CXX object CMakeFiles/yade.dir/core/Body.cpp.o
[ 12%] Building CXX object CMakeFiles/yade.dir/core/Clump.cpp.o
[ 12%] Building CXX object CMakeFiles/yade.dir/core/Scene.cpp.o
[ 13%] Building CXX object CMakeFiles/yade.dir/core/InteractionContainer.cpp.o
[ 14%] Building CXX object CMakeFiles/yade.dir/core/Dispatcher.cpp.o
[ 14%] Building CXX object CMakeFiles/yade.dir/core/Engine.cpp.o
[ 15%] Building CXX object CMakeFiles/yade.dir/core/PartialEngine.cpp.o
[ 15%] Building CXX object CMakeFiles/yade.dir/core/corePlugins.cpp.o
[ 16%] Building CXX object CMakeFiles/yade.dir/core/Material.cpp.o
[ 16%] Building CXX object CMakeFiles/yade.dir/core/EnergyTracker.cpp.o
[ 17%] Building CXX object CMakeFiles/yade.dir/core/Omega.cpp.o
[ 18%] Building CXX object CMakeFiles/yade.dir/core/FrontEnd.cpp.o
[ 18%] Building CXX object CMakeFiles/yade.dir/core/SimulationFlow.cpp.o
[ 19%] Building CXX object CMakeFiles/yade.dir/pkg/dem/KinemCTDEngine.cpp.o
[ 19%] Building CXX object CMakeFiles/yade.dir/pkg/dem/CapillaryStressRecorder.cpp.o
[ 20%] Building CXX object CMakeFiles/yade.dir/pkg/dem/DemXDofGeom.cpp.o
[ 21%] Building CXX object CMakeFiles/yade.dir/pkg/dem/Law2_ScGeom_CapillaryPhys_Capillarity.cpp.o
[ 21%] Building CXX object CMakeFiles/yade.dir/pkg/dem/SnapshotEngine.cpp.o
[ 22%] Building CXX object CMakeFiles/yade.dir/pkg/dem/Polyhedra_splitter.cpp.o
[ 22%] Building CXX object CMakeFiles/yade.dir/pkg/dem/FacetTopologyAnalyzer.cpp.o
[ 23%] Building CXX object CMakeFiles/yade.dir/pkg/dem/L3Geom.cpp.o
[ 23%] Building CXX object CMakeFiles/yade.dir/pkg/dem/SampleCapillaryPressureEngine.cpp.o
[ 24%] Building CXX object CMakeFiles/yade.dir/pkg/dem/InelastCohFrictPhys.cpp.o
[ 25%] Building CXX object CMakeFiles/yade.dir/pkg/dem/CapillaryPhys.cpp.o
[ 25%] Building CXX object CMakeFiles/yade.dir/pkg/dem/FrictPhys.cpp.o
[ 26%] Building CXX object CMakeFiles/yade.dir/pkg/dem/TriaxialStateRecorder.cpp.o
[ 26%] Building CXX object CMakeFiles/yade.dir/pkg/dem/ConcretePM.cpp.o
^[O1;5R[ 27%] Building CXX object CMakeFiles/yade.dir/pkg/dem/TesselationWrapper.cpp.o
In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1728:0,
                 from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:17,
                 from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:15,
                 from /home/ehsan/yade-daily/build/yade/lib/pyutil/numpy_boost.hpp:40,
                 from /home/ehsan/yade-daily/build/yade/lib/pyutil/numpy.hpp:3,
                 from /home/ehsan/yade-daily/trunk/pkg/dem/TesselationWrapper.cpp:11:
/usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION"
  ^
[ 27%] Building CXX object CMakeFiles/yade.dir/pkg/dem/Ig2_Sphere_Sphere_ScGeom.cpp.o
[ 28%] Building CXX object CMakeFiles/yade.dir/pkg/dem/HertzMindlin.cpp.o
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[ 39%] Building CXX object CMakeFiles/yade.dir/pkg/dem/Law2_ScGeom6D_InelastCohFrictPhys_CohesionMoment.cpp.o
[ 40%] Building CXX object CMakeFiles/yade.dir/pkg/dem/NormalInelasticMat.cpp.o
[ 40%] Building CXX object CMakeFiles/yade.dir/pkg/dem/KinemCNDEngine.cpp.o
[ 41%] Building CXX object CMakeFiles/yade.dir/pkg/dem/DomainLimiter.cpp.o
[ 41%] Building CXX object CMakeFiles/yade.dir/pkg/dem/GlobalStiffnessTimeStepper.cpp.o
[ 42%] Building CXX object CMakeFiles/yade.dir/pkg/dem/Ip2_ElastMat.cpp.o
[ 42%] Building CXX object CMakeFiles/yade.dir/pkg/dem/VTKRecorder.cpp.o
In file included from /usr/include/c++/4.8/backward/strstream:51:0,
                 from /usr/include/vtk-5.8/vtkIOStream.h:112,
                 from /usr/include/vtk-5.8/vtkSystemIncludes.h:40,
                 from /usr/include/vtk-5.8/vtkIndent.h:24,
                 from /usr/include/vtk-5.8/vtkObjectBase.h:43,
                 from /usr/include/vtk-5.8/vtkObject.h:41,
                 from /usr/include/vtk-5.8/vtkCell.h:40,
                 from /usr/include/vtk-5.8/vtkQuad.h:25,
                 from /home/ehsan/yade-daily/trunk/pkg/dem/VTKRecorder.hpp:3,
                 from /home/ehsan/yade-daily/trunk/pkg/dem/VTKRecorder.cpp:3:
/usr/include/c++/4.8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
 #warning \
  ^
[ 43%] Building CXX object CMakeFiles/yade.dir/pkg/dem/Ip2_2xNormalInelasticMat_NormalInelasticityPhys.cpp.o
[ 44%] Building CXX object CMakeFiles/yade.dir/pkg/dem/UniaxialStrainer.cpp.o
[ 44%] Building CXX object CMakeFiles/yade.dir/pkg/dem/JointedCohesiveFrictionalPM.cpp.o
[ 45%] Building CXX object CMakeFiles/yade.dir/pkg/dem/CohesiveTriaxialTest.cpp.o
[ 45%] Building CXX object CMakeFiles/yade.dir/pkg/dem/FlowEngine.cpp.o
In file included from /home/ehsan/yade-daily/trunk/pkg/dem/FlowEngine.cpp:28:0:
/home/ehsan/yade-daily/trunk/pkg/dem/FlowEngine.hpp: In member function ‘void FlowEngine::cholmodStats()’:
/home/ehsan/yade-daily/trunk/pkg/dem/FlowEngine.hpp:199:91: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
      cerr << cholmod_print_common("PFV Cholmod factorization",&(solver->eSolver.cholmod()))<<endl;
                                                                                           ^
[ 46%] Building CXX object CMakeFiles/yade.dir/pkg/dem/Polyhedra_support.cpp.o
[ 47%] Building CXX object CMakeFiles/yade.dir/pkg/dem/FlatGridCollider.cpp.o
[ 47%] Building CXX object CMakeFiles/yade.dir/pkg/dem/MicroMacroAnalyser.cpp.o
[ 48%] Building CXX object CMakeFiles/yade.dir/pkg/dem/TriaxialStressController.cpp.o
[ 48%] Building CXX object CMakeFiles/yade.dir/pkg/dem/SpherePack.cpp.o
[ 49%] Building CXX object CMakeFiles/yade.dir/pkg/dem/Shop_01.cpp.o
[ 49%] Building CXX object CMakeFiles/yade.dir/pkg/dem/BubbleMat.cpp.o
[ 50%] Building CXX object CMakeFiles/yade.dir/pkg/dem/Shop_02.cpp.o
[ 51%] Building CXX object CMakeFiles/yade.dir/pkg/dem/CohFrictMat.cpp.o
[ 51%] Building CXX object CMakeFiles/yade.dir/pkg/dem/Polyhedra_Ig2.cpp.o
[ 52%] Building CXX object CMakeFiles/yade.dir/pkg/dem/PeriIsoCompressor.cpp.o
[ 52%] Building CXX object CMakeFiles/yade.dir/pkg/dem/UnbalancedForceCallbacks.cpp.o
[ 53%] Building CXX object CMakeFiles/yade.dir/pkg/dem/Disp2DPropLoadEngine.cpp.o
[ 53%] Building CXX object CMakeFiles/yade.dir/pkg/dem/STLImporter.cpp.o
In file included from /home/ehsan/yade-daily/trunk/pkg/dem/STLImporter.cpp:10:0:
/home/ehsan/yade-daily/build/yade/lib/import/STLReader.hpp: In member function ‘bool STLReader::open_ascii(const char*, OutV, OutE, OutF, OutN) [with OutV = std::back_insert_iterator<std::vector<double> >; OutE = std::back_insert_iterator<std::vector<int> >; OutF = std::back_insert_iterator<std::vector<int> >; OutN = std::back_insert_iterator<std::vector<double> >]’:
/home/ehsan/yade-daily/build/yade/lib/import/STLReader.hpp:120:2: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
  fscanf(fp, "%*s %*s %f %f %f\n", &n[0], &n[1], &n[2]);
  ^
/home/ehsan/yade-daily/build/yade/lib/import/STLReader.hpp:121:2: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
  fscanf(fp, "%*s %*s");
  ^
/home/ehsan/yade-daily/build/yade/lib/import/STLReader.hpp:122:2: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
  fscanf(fp, "%*s %f %f %f\n", &v[0][0], &v[0][1], &v[0][2]);
  ^
/home/ehsan/yade-daily/build/yade/lib/import/STLReader.hpp:123:2: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
  fscanf(fp, "%*s %f %f %f\n", &v[1][0], &v[1][1], &v[1][2]);
  ^
/home/ehsan/yade-daily/build/yade/lib/import/STLReader.hpp:124:2: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
  fscanf(fp, "%*s %f %f %f\n", &v[2][0], &v[2][1], &v[2][2]);
  ^
/home/ehsan/yade-daily/build/yade/lib/import/STLReader.hpp:125:2: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
  fscanf(fp, "%*s"); // end loop
  ^
/home/ehsan/yade-daily/build/yade/lib/import/STLReader.hpp:126:2: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
  fscanf(fp, "%*s"); // end facet
  ^
[ 54%] Building CXX object CMakeFiles/yade.dir/pkg/dem/SpheresFactory.cpp.o
[ 55%] Building CXX object CMakeFiles/yade.dir/pkg/dem/ViscoelasticPM.cpp.o
[ 55%] Building CXX object CMakeFiles/yade.dir/pkg/dem/ThreeDTriaxialEngine.cpp.o
[ 56%] Building CXX object CMakeFiles/yade.dir/pkg/dem/CohesiveFrictionalContactLaw.cpp.o
[ 56%] Building CXX object CMakeFiles/yade.dir/pkg/dem/Ip2_FrictMat_FrictMat_CapillaryPhys.cpp.o
[ 57%] Building CXX object CMakeFiles/yade.dir/pkg/dem/ElasticContactLaw.cpp.o
[ 58%] Building CXX object CMakeFiles/yade.dir/pkg/dem/CapillaryTriaxialTest.cpp.o
[ 58%] Building CXX object CMakeFiles/yade.dir/pkg/dem/NormalInelasticityPhys.cpp.o
[ 59%] Building CXX object CMakeFiles/yade.dir/pkg/dem/ForceTorqueRecorder.cpp.o
[ 59%] Building CXX object CMakeFiles/yade.dir/pkg/dem/WirePM.cpp.o
[ 60%] Building CXX object CMakeFiles/yade.dir/pkg/dem/KinemCNSEngine.cpp.o
[ 60%] Building CXX object CMakeFiles/yade.dir/pkg/dem/Ip2_2xInelastCohFrictMat_InelastCohFrictPhys.cpp.o
[ 61%] Building CXX object CMakeFiles/yade.dir/pkg/dem/LudingPM.cpp.o
[ 62%] Building CXX object CMakeFiles/yade.dir/pkg/common/CylScGeom6D.cpp.o
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[ 73%] Building CXX object CMakeFiles/yade.dir/pkg/common/Sphere.cpp.o
[ 73%] Building CXX object CMakeFiles/yade.dir/pkg/common/Gl1_Sphere.cpp.o
[ 74%] Building CXX object CMakeFiles/yade.dir/pkg/common/GLDrawFunctors.cpp.o
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[ 75%] Building CXX object CMakeFiles/yade.dir/pkg/common/BoundaryController.cpp.o
[ 76%] Building CXX object CMakeFiles/yade.dir/pkg/common/Cylinder.cpp.o
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[ 77%] Building CXX object CMakeFiles/yade.dir/pkg/common/GravityEngines.cpp.o
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[ 81%] Building CXX object CMakeFiles/yade.dir/pkg/common/ForceResetter.cpp.o
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[ 82%] Building CXX object CMakeFiles/yade.dir/pkg/common/Aabb.cpp.o
[ 83%] Building CXX object CMakeFiles/yade.dir/pkg/common/Grid_GUI.cpp.o
[ 84%] Building CXX object CMakeFiles/yade.dir/pkg/common/ElastMat.cpp.o
[ 84%] Building CXX object CMakeFiles/yade.dir/pkg/common/TorqueEngine.cpp.o
[ 85%] Building CXX object CMakeFiles/yade.dir/pkg/common/OpenGLRenderer.cpp.o
[ 85%] Building CXX object CMakeFiles/yade.dir/pkg/common/NormShearPhys.cpp.o
[ 86%] Building CXX object CMakeFiles/yade.dir/pkg/common/SpatialQuickSortCollider.cpp.o
[ 86%] Building CXX object CMakeFiles/yade.dir/lib/base/Math.cpp.o
[ 87%] Building CXX object CMakeFiles/yade.dir/lib/factory/ClassFactory.cpp.o
[ 88%] Building CXX object CMakeFiles/yade.dir/lib/factory/DynLibManager.cpp.o
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[ 89%] Building CXX object CMakeFiles/yade.dir/lib/pyutil/gil.cpp.o
[ 90%] Building CXX object CMakeFiles/yade.dir/core/main/pyboot.cpp.o
[ 90%] Building CXX object CMakeFiles/yade.dir/lib/opengl/GLUtils.cpp.o
[ 91%] Building CXX object CMakeFiles/yade.dir/lib/triangulation/TriaxialState.cpp.o
[ 92%] Building CXX object CMakeFiles/yade.dir/lib/triangulation/basicVTKwritter.cpp.o
[ 92%] Building CXX object CMakeFiles/yade.dir/lib/triangulation/KinematicLocalisationAnalyser.cpp.o
[ 93%] Building CXX object CMakeFiles/yade.dir/lib/triangulation/FlowBoundingSphere.cpp.o
[ 93%] Building CXX object CMakeFiles/yade.dir/lib/triangulation/PeriodicFlow.cpp.o
[ 94%] Building CXX object CMakeFiles/yade.dir/lib/triangulation/Tenseur3.cpp.o
[ 95%] Building CXX object CMakeFiles/yade.dir/lib/triangulation/Timer.cpp.o
Linking CXX shared library lib/x86_64-linux-gnu/libyade.so
[ 95%] Built target yade
Scanning dependencies of target boot
[ 95%] Building CXX object CMakeFiles/boot.dir/core/main/pyboot.cpp.o
Linking CXX shared library lib/x86_64-linux-gnu/boot.so
[ 95%] Built target boot
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[ 95%] Building CXX object py/CMakeFiles/WeightedAverage2d.dir/WeightedAverage2d.cpp.o
Linking CXX shared library lib/x86_64-linux-gnu/WeightedAverage2d.so
[ 95%] Built target WeightedAverage2d
Scanning dependencies of target _customConverters
[ 96%] Building CXX object py/CMakeFiles/_customConverters.dir/wrapper/customConverters.cpp.o
Linking CXX shared library lib/x86_64-linux-gnu/_customConverters.so
[ 96%] Built target _customConverters
Scanning dependencies of target _packObb
[ 96%] Building CXX object py/CMakeFiles/_packObb.dir/pack/_packObb.cpp.o
Linking CXX shared library lib/x86_64-linux-gnu/_packObb.so
[ 96%] Built target _packObb
Scanning dependencies of target _packPredicates
[ 97%] Building CXX object py/CMakeFiles/_packPredicates.dir/pack/_packPredicates.cpp.o
Linking CXX shared library lib/x86_64-linux-gnu/_packPredicates.so
[ 97%] Built target _packPredicates
Scanning dependencies of target _packSpheres
[ 98%] Building CXX object py/CMakeFiles/_packSpheres.dir/pack/_packSpheres.cpp.o
Linking CXX shared library lib/x86_64-linux-gnu/_packSpheres.so
[ 98%] Built target _packSpheres
Scanning dependencies of target _polyhedra_utils
[ 98%] Building CXX object py/CMakeFiles/_polyhedra_utils.dir/_polyhedra_utils.cpp.o
In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1728:0,
                 from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:17,
                 from /home/ehsan/yade-daily/trunk/py/_polyhedra_utils.cpp:17:
/usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION"
  ^
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[ 99%] Building CXX object py/CMakeFiles/_utils.dir/_utils.cpp.o
In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1728:0,
                 from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:17,
                 from /home/ehsan/yade-daily/trunk/py/_utils.cpp:18:
/usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION"
  ^
Linking CXX shared library lib/x86_64-linux-gnu/_utils.so
[ 99%] Built target _utils
Scanning dependencies of target wrapper
[100%] Building CXX object py/CMakeFiles/wrapper.dir/wrapper/yadeWrapper.cpp.o
Linking CXX shared library lib/x86_64-linux-gnu/wrapper.so
[100%] Built target wrapper
--------------------------------------------------------------------------------------------------------------------------------------

Since I am new to linux and yade, I don't understand some warnings. but it seems to be some issues with that.
What can I do to solve my problem? any ideas?

Ehsan

Revision history for this message
Best Anton Gladky (gladky-anton) said : 		#3

Warnings are nor critical here. PFV-module should work.
Try to uninstall yade-daily from PPA, is it can cause some problem with the compiled
version. See [1].

[1] https://bugs.launchpad.net/yade/+bug/1254708

Anton

Revision history for this message
Ehsan Izadi (ehsan-izadi) said : 		#4

Thanks Anton Gladky, that solved my question.