Yade

YADE-1.20.0 compiled with Intel Compiler

Asked by Feng Chen

Hi, All:

I am now trying to use YADE-1.20.0 on a cluster (Redhat Enterprise 6) compiled with Intel Compiler 15.0.0, I made some attempt yesterday and was successful in compiling YADE with the following cmake configure and make, I compiled loki, boost 1.54 (1.55 has a problem with shard_ptr), eigen and minieigen using the same intel compiler,

#!/bin/bash
export CC=icc
export CXX=icpc
export BSTTARGET=/project/fchen14/yade/boost/boost_1_54_0/install/
cmake -DCMAKE_C_COMPILER="icc" \
    -DCMAKE_CXX_COMPILER="icpc" \
    -DBoost_NO_BOOST_CMAKE=TRUE \
    -DBoost_NO_SYSTEM_PATHS=TRUE \
    -DBOOST_ROOT:PATHNAME=$BSTTARGET \
    -DBoost_LIBRARY_DIRS:FILEPATH=${BSTTARGET}/lib \
    -DBoost_INCLUDE_DIRS=${BSTTARGET}/include \
    -DENABLE_GTS=OFF \
    -DENABLE_GL2PS=OFF -DENABLE_GTS=OFF \
    -DPY_minieigen=/project/fchen14/yade/eigen/minieigen-0.5.3/install/ \
    -DEIGEN3_INCLUDE_DIR=/project/fchen14/yade/eigen/eigen-3.2.8/install/include/eigen3 \
    -DLOKI_INCLUDE_DIR=/project/fchen14/yade/loki/loki-0.1.7/install/include \
    -DLOKI_LIBRARY=/project/fchen14/yade/loki/loki-0.1.7/install/lib \
    -DCMAKE_INSTALL_PREFIX=../install \
    ../trunk-1.20.0/ #/project/fchen14/yade/loki/loki-0.1.7/install/include

the libyade.so was generated successfully, however when I tried to launch yade-1.20.0 with the following command it resulted in a segmentation fault:

[fchen14@host001 bin]$ ./yade-1.20.0
Welcome to Yade 1.20.0
Segmentation fault

further exploring into the script ./yade-1.20.0 I located the segmentation fault happens at the line 129 in ./yade-1.20.0

129 import yade

So I am wondering

1) does anyone have the experience of using YADE with intel compiler?

2) As this will be only using the cluster with batch job so I do not need any GUI and use as few dependencies as possible, I just want to run a very simple case like free fall/collision of a few thousand particles and then benchmark the run, can I run yade without python interface? (If trying to diagnose the segmentation fault with python interface will take a long time?

Thanks for any suggestions!

Feng Chen

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Revision history for this message
Anton Gladky (gladky-anton) said : 		#1

Hi,

you need to compile Yade in debug-mode to get debugging symbols:
-DDEBUG=1 option on the cmake-step.

After that you start Yade and should get a lot of information during
the crash, which can be useful to understand the source the problems.

Regards

Anton

Revision history for this message
Feng Chen (fchen3-gmail) said : 		#2

Hi, Anton, thanks for your quick reply, I attached here the debug info for the run, it seems quite long, do you have any idea which part went wrong?

[fchen14@host003 bin]$ ./yade-1.20.0 >err.log 2>&1
Segmentation fault

below is the err.log:
-----------------------------------------------------------------------------------
Welcome to Yade 1.20.0
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.hpp:108 Omega: Constructing Omega.
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:212 loadPlugins: Loading plugin /project/fchen14/yade/install/lib64/yade-1.20.0/libyade.so
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:136 buildDynlibDatabase: called with 234 plugins.
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Aabb
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin AxialGravityEngine
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin BicyclePedalEngine
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Bo1_Box_Aabb
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Bo1_ChainedCylinder_Aabb
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Bo1_Cylinder_Aabb
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Bo1_Facet_Aabb
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Bo1_GridConnection_Aabb
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Bo1_Sphere_Aabb
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Bo1_Tetra_Aabb
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Bo1_Wall_Aabb
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Body
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Bound
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin BoundDispatcher
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin BoundFunctor
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin BoundaryController
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Box
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin BoxFactory
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin BubbleMat
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin BubblePhys
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin CapillaryPhys
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin CapillaryStressRecorder
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin CapillaryTriaxialTest
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Cell
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin CentralGravityEngine
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin ChCylGeom6D
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin ChainedCylinder
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin ChainedState
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin CircularFactory
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Clump
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin CohFrictMat
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin CohFrictPhys
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin CohesiveFrictionalContactLaw
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin CohesiveTriaxialTest
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Collider
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin CombinedKinematicEngine
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin CpmMat
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin CpmPhys
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin CpmState
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin CpmStateUpdater
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin CylScGeom
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin CylScGeom6D
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Cylinder
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Disp2DPropLoadEngine
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Dispatcher
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin DomainLimiter
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin DragEngine
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin ElastMat
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin ElasticContactLaw
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin EnergyTracker
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Engine
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Facet
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin FacetTopologyAnalyzer
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin FieldApplier
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin FileGenerator
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin FlatGridCollider
DEBUG /project/fchen14/yade/trunk-1.20.0/pkg/dem/FlatGridCollider.cpp:44 initIndices: sphereIdx=1
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin ForceEngine
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin ForceRecorder
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin ForceResetter
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin FrictMat
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin FrictPhys
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin FrictViscoMat
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin FrictViscoPhys
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Functor
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin GeneralIntegratorInsertionSortCollider
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin GenericSpheresContact
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin GlobalEngine
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin GlobalStiffnessTimeStepper
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin GravityEngine
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin GridCoGridCoGeom
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin GridConnection
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin GridNode
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin GridNodeGeom6D
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin HarmonicMotionEngine
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin HarmonicRotationEngine
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin HdapsGravityEngine
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin HelixEngine
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin HydroForceEngine
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin HydrodynamicsLawLBM
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin IGeom
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin IGeomDispatcher
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin IGeomFunctor
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin IPhys
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin IPhysDispatcher
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin IPhysFunctor
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Ig2_Box_Sphere_ScGeom
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Ig2_Box_Sphere_ScGeom6D
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Ig2_ChainedCylinder_ChainedCylinder_ScGeom6D
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Ig2_Facet_Sphere_L3Geom
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Ig2_Facet_Sphere_ScGeom
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Ig2_Facet_Sphere_ScGeom6D
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Ig2_GridConnection_GridConnection_GridCoGridCoGeom
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Ig2_GridNode_GridNode_GridNodeGeom6D
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Ig2_Sphere_ChainedCylinder_CylScGeom
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Ig2_Sphere_ChainedCylinder_CylScGeom6D
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Ig2_Sphere_GridConnection_ScGridCoGeom
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Ig2_Sphere_Sphere_L3Geom
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Ig2_Sphere_Sphere_L6Geom
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Ig2_Sphere_Sphere_ScGeom
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Ig2_Sphere_Sphere_ScGeom6D
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Ig2_Tetra_Tetra_TTetraGeom
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Ig2_Wall_Sphere_L3Geom
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Ig2_Wall_Sphere_ScGeom
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin InelastCohFrictMat
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin InelastCohFrictPhys
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin InsertionSortCollider
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Integrator
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Interaction
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin InteractionLoop
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin InterpolatingDirectedForceEngine
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin InterpolatingHelixEngine
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin IntrCallback
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Ip2_2xInelastCohFrictMat_InelastCohFrictPhys
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Ip2_2xNormalInelasticMat_NormalInelasticityPhys
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Ip2_BubbleMat_BubbleMat_BubblePhys
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Ip2_CohFrictMat_CohFrictMat_CohFrictPhys
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Ip2_CpmMat_CpmMat_CpmPhys
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Ip2_ElastMat_ElastMat_NormPhys
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Ip2_ElastMat_ElastMat_NormShearPhys
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Ip2_FrictMat_CpmMat_FrictPhys
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Ip2_FrictMat_FrictMat_CapillaryPhys
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Ip2_FrictMat_FrictMat_FrictPhys
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Ip2_FrictMat_FrictMat_MindlinCapillaryPhys
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Ip2_FrictMat_FrictMat_MindlinPhys
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Ip2_FrictMat_FrictMat_ViscoFrictPhys
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Ip2_FrictMat_FrictViscoMat_FrictViscoPhys
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Ip2_FrictViscoMat_FrictViscoMat_FrictViscoPhys
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Ip2_JCFpmMat_JCFpmMat_JCFpmPhys
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Ip2_LudingMat_LudingMat_LudingPhys
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Ip2_ViscElCapMat_ViscElCapMat_ViscElCapPhys
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Ip2_ViscElMat_ViscElMat_ViscElPhys
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Ip2_WireMat_WireMat_WirePhys
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin JCFpmMat
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin JCFpmPhys
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin JCFpmState
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin KinemCNDEngine
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin KinemCNLEngine
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin KinemCNSEngine
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin KinemCTDEngine
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin KinemSimpleShearBox
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin KinematicEngine
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin L3Geom
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin L6Geom
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin LBMbody
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin LBMlink
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin LBMnode
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Law2_ChCylGeom6D_CohFrictPhys_CohesionMoment
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Law2_CylScGeom6D_CohFrictPhys_CohesionMoment
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Law2_CylScGeom_FrictPhys_CundallStrack
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Law2_GridCoGridCoGeom_FrictPhys_CundallStrack
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Law2_L3Geom_FrictPhys_ElPerfPl
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Law2_L6Geom_FrictPhys_Linear
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Law2_ScGeom6D_CohFrictPhys_CohesionMoment
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Law2_ScGeom6D_InelastCohFrictPhys_CohesionMoment
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Law2_ScGeom6D_NormalInelasticityPhys_NormalInelasticity
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Law2_ScGeom_BubblePhys_Bubble
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Law2_ScGeom_CapillaryPhys_Capillarity
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Law2_ScGeom_CpmPhys_Cpm
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Law2_ScGeom_FrictPhys_CundallStrack
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Law2_ScGeom_FrictViscoPhys_CundallStrackVisco
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Law2_ScGeom_LudingPhys_Basic
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Law2_ScGeom_MindlinPhys_HertzWithLinearShear
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Law2_ScGeom_MindlinPhys_Mindlin
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Law2_ScGeom_MindlinPhys_MindlinDeresiewitz
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Law2_ScGeom_ViscElCapPhys_Basic
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Law2_ScGeom_ViscElPhys_Basic
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Law2_ScGeom_ViscoFrictPhys_CundallStrack
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Law2_ScGeom_WirePhys_WirePM
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Law2_ScGridCoGeom_CohFrictPhys_CundallStrack
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Law2_ScGridCoGeom_FrictPhys_CundallStrack
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin LawDispatcher
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin LawFunctor
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin LawTester
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin LinearDragEngine
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin LudingMat
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin LudingPhys
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin MatchMaker
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Material
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin MindlinCapillaryPhys
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin MindlinPhys
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin NewtonIntegrator
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin NormPhys
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin NormShearPhys
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin NormalInelasticMat
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin NormalInelasticityPhys
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin ParallelEngine
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin PartialEngine
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Peri3dController
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin PeriIsoCompressor
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin PeriTriaxController
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin PeriodicEngine
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin PyRunner
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin RadialForceEngine
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Recorder
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin ResetRandomPosition
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin RotationEngine
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin RungeKuttaCashKarp54Integrator
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin ScGeom
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin ScGeom6D
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin ScGridCoGeom
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Scene
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin ServoPIDController
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Shape
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin SimpleShear
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin SpatialQuickSortCollider
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Sphere
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin SpheresFactory
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin State
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin StepDisplacer
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin SumIntrForcesCb
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin TTetraGeom
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin TTetraSimpleGeom
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Tetra
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin TetraVolumetricLaw
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin ThreeDTriaxialEngine
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin TimeStepper
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin TorqueEngine
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin TorqueRecorder
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin TranslationEngine
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin TriaxialCompressionEngine
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin TriaxialStateRecorder
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin TriaxialStressController
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin TriaxialTest
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin UniaxialStrainer
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin ViscElCapMat
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin ViscElCapPhys
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin ViscElMat
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin ViscElPhys
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin ViscoFrictPhys
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin Wall
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin WireMat
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin WirePhys
DEBUG /project/fchen14/yade/trunk-1.20.0/core/Omega.cpp:142 buildDynlibDatabase: Factoring plugin WireState
DEBUG /project/fchen14/yade/trunk-1.20.0/pkg/dem/FlatGridCollider.cpp:44 initIndices: sphereIdx=1
DEBUG /project/fchen14/yade/trunk-1.20.0/pkg/dem/FlatGridCollider.cpp:44 initIndices: sphereIdx=1
SIGSEGV/SIGABRT handler called; gdb batch file is `/tmp/yade-fLGwIL/tmp-0'
GNU gdb (GDB) Red Hat Enterprise Linux (7.2-60.el6)
Copyright (C) 2010 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law. Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-redhat-linux-gnu".
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>.
[Thread debugging using libthread_db enabled]
Missing separate debuginfo for /home/packages/python/2.7.7-anaconda/bin/../lib/libm.so.6
Missing separate debuginfo for /usr/local/packages/python/2.7.7-anaconda/lib/python2.7/site-packages/numpy/linalg/../../../../libgfortran.so.1
0x000000354a6ac65e in waitpid () from /lib64/libc.so.6
No symbol "info" in current context.

Thread 1 (Thread 0x2b1a0759fc20 (LWP 66779)):
#0 0x000000354a6ac65e in waitpid () from /lib64/libc.so.6
#1 0x000000354a63e609 in do_system () from /lib64/libc.so.6
#2 0x00002b1a0f3ebc77 in crashHandler (sig=66780) at /project/fchen14/yade/trunk-1.20.0/core/main/pyboot.cpp:13
#3 <signal handler called>
#4 0x00002b1a1136bbdc in boost::python::objects::polymorphic_id_generator<Bo1_Sphere_Aabb>::execute (p_=0x2b1a139ee406) at /project/fchen14/yade/boost/boost_1_54_0/install/include/boost/python/object/inheritance.hpp:43
#5 0x00002b1a13c740a1 in boost::python::objects::find_dynamic_type(void*, boost::python::type_info, boost::python::type_info) () from /project/fchen14/yade/boost/boost_1_54_0/install/lib/libboost_python.so.1.54.0
#6 0x00002b1a13c6f3fb in boost::python::objects::find_instance_impl(_object*, boost::python::type_info, bool) () from /project/fchen14/yade/boost/boost_1_54_0/install/lib/libboost_python.so.1.54.0
#7 0x00002b1a13c68ee5 in boost::python::converter::get_lvalue_from_python(_object*, boost::python::converter::registration const&) () from /project/fchen14/yade/boost/boost_1_54_0/install/lib/libboost_python.so.1.54.0
#8 0x00002b1a13c68fb7 in boost::python::converter::rvalue_from_python_stage1(_object*, boost::python::converter::registration const&) () from /project/fchen14/yade/boost/boost_1_54_0/install/lib/libboost_python.so.1.54.0
#9 0x00002b1a180cf769 in custom_vector_from_seq<boost::shared_ptr<BoundFunctor> >::construct (obj_ptr=0x2348ab0, data=0x2b1a139ee406) at /project/fchen14/yade/boost/boost_1_54_0/install/include/boost/python/extract.hpp:165
#10 0x00002b1a13c69016 in boost::python::converter::rvalue_from_python_stage2(_object*, boost::python::converter::rvalue_from_python_stage1_data&, boost::python::converter::registration const&) () from /project/fchen14/yade/boost/boost_1_54_0/install/lib/libboost_python.so.1.54.0
#11 0x00002b1a1124090e in operator() (this=0x2348ab0, t=..., d=...) at /project/fchen14/yade/boost/boost_1_54_0/install/include/boost/python/extract.hpp:185
#12 Collider::pyHandleCustomCtorArgs (this=0x2348ab0, t=..., d=...) at /project/fchen14/yade/trunk-1.20.0/pkg/common/Collider.cpp:39
#13 0x00002b1a11284b46 in Serializable_ctor_kwAttrs (t=..., d=...) at /project/fchen14/yade/trunk-1.20.0/lib/serialization/Serializable.hpp:309
#14 0x00002b1a1129f02d in boost::python::objects::signature_py_function_impl<boost::python::detail::caller<void (*)(boost::shared_ptr<InsertionSortCollider>*, boost::python::tuple&, boost::python::dict&), boost::python::detail::constructor_policy<boost::python::default_call_policies>, boost::mpl::vector3<boost::shared_ptr<InsertionSortCollider>, boost::python::tuple&, boost::python::dict&> >, boost::python::detail::outer_constructor_signature<boost::mpl::vector3<boost::shared_ptr<InsertionSortCollider>, boost::python::tuple&, boost::python::dict&> >::type>::operator() (this=0x2348ab0, args=0x2b1a139ee406, kw=0x0) at /project/fchen14/yade/boost/boost_1_54_0/install/include/boost/python/detail/invoke.hpp:75
#15 0x00002b1a13c6fc6e in boost::python::objects::function::call(_object*, _object*) const () from /project/fchen14/yade/boost/boost_1_54_0/install/lib/libboost_python.so.1.54.0
#16 0x00002b1a13c6f9a5 in boost::detail::function::void_function_ref_invoker0<boost::python::objects::(anonymous namespace)::bind_return, void>::invoke(boost::detail::function::function_buffer&) () from /project/fchen14/yade/boost/boost_1_54_0/install/lib/libboost_python.so.1.54.0
#17 0x00002b1a13c7b75e in boost::python::handle_exception_impl(boost::function0<void>) () from /project/fchen14/yade/boost/boost_1_54_0/install/lib/libboost_python.so.1.54.0
#18 0x00002b1a13c713fe in function_call () from /project/fchen14/yade/boost/boost_1_54_0/install/lib/libboost_python.so.1.54.0
#19 0x00002b1a071fa318 in PyObject_Call (func=0x1e31390, arg=0x2b1a1c72d320, kw=0x0) at Objects/abstract.c:2529
#20 0x00002b1a0729b996 in PyEval_CallObjectWithKeywords (func=0x1e31390, arg=0x2b1a1c72d320, kw=0x0) at Python/ceval.c:3889
#21 0x00002b1a072c2574 in PyEval_CallFunction (obj=0x1e31390, format=<value optimized out>) at Python/modsupport.c:557
#22 0x00002b1a11295aaf in boost::python::objects::full_py_function_impl<boost::python::detail::raw_constructor_dispatcher<void (*)(boost::shared_ptr<InsertionSortCollider>*, boost::python::tuple&, boost::python::dict&)>, boost::mpl::vector2<void, boost::python::api::object> >::operator() (this=0x2348ab0, args=0x2b1a139ee406, kw=0x0) at /project/fchen14/yade/boost/boost_1_54_0/install/include/boost/python/call.hpp:62
#23 0x00002b1a13c6fc6e in boost::python::objects::function::call(_object*, _object*) const () from /project/fchen14/yade/boost/boost_1_54_0/install/lib/libboost_python.so.1.54.0
#24 0x00002b1a13c6f9a5 in boost::detail::function::void_function_ref_invoker0<boost::python::objects::(anonymous namespace)::bind_return, void>::invoke(boost::detail::function::function_buffer&) () from /project/fchen14/yade/boost/boost_1_54_0/install/lib/libboost_python.so.1.54.0
#25 0x00002b1a13c7b75e in boost::python::handle_exception_impl(boost::function0<void>) () from /project/fchen14/yade/boost/boost_1_54_0/install/lib/libboost_python.so.1.54.0
#26 0x00002b1a13c713fe in function_call () from /project/fchen14/yade/boost/boost_1_54_0/install/lib/libboost_python.so.1.54.0
#27 0x00002b1a071fa318 in PyObject_Call (func=0x1e31400, arg=0x2b1a1c72aa28, kw=0x0) at Objects/abstract.c:2529
#28 0x00002b1a0720a99f in instancemethod_call (func=<value optimized out>, arg=0x2b1a1c72aa28, kw=0x0) at Objects/classobject.c:2602
#29 0x00002b1a071fa318 in PyObject_Call (func=0x2b1a1aeef280, arg=0x2b1a1c724350, kw=0x0) at Objects/abstract.c:2529
#30 0x00002b1a0725d04c in slot_tp_init (self=<value optimized out>, args=0x2b1a1c724350, kwds=0x0) at Objects/typeobject.c:5692
#31 0x00002b1a07256f88 in type_call (type=<value optimized out>, args=0x2b1a1c724350, kwds=0x0) at Objects/typeobject.c:743
#32 0x00002b1a071fa318 in PyObject_Call (func=0x1e347e0, arg=0x2b1a1c724350, kw=0x0) at Objects/abstract.c:2529
#33 0x00002b1a0729d7b2 in call_function (f=0x2b1a0e263988, throwflag=<value optimized out>) at Python/ceval.c:4238
#34 PyEval_EvalFrameEx (f=0x2b1a0e263988, throwflag=<value optimized out>) at Python/ceval.c:2666
#35 0x00002b1a072a4419 in PyEval_EvalCodeEx (co=0x2b1a076f5d30, globals=<value optimized out>, locals=<value optimized out>, args=0x0, argcount=0, kws=0x0, kwcount=0, defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:3252
#36 0x00002b1a072a4492 in PyEval_EvalCode (co=0x2348ab0, globals=0x2b1a139ee406, locals=0x0) at Python/ceval.c:667
#37 0x00002b1a072b7d12 in PyImport_ExecCodeModuleEx (name=0x1d03250 "yade", co=0x2b1a076f5d30, pathname=0x1d06280 "/project/fchen14/yade/install/lib64/yade-1.20.0/py/yade/__init__.pyc") at Python/import.c:709
#38 0x00002b1a072ba2d0 in load_source_module (name=0x1d03250 "yade", pathname=0x1d06280 "/project/fchen14/yade/install/lib64/yade-1.20.0/py/yade/__init__.pyc", fp=<value optimized out>) at Python/import.c:1099
#39 0x00002b1a072bbf52 in load_package (name=0x1d03250 "yade", pathname=<value optimized out>) at Python/import.c:1166
#40 0x00002b1a072baa89 in import_submodule (mod=0x2b1a0754d7d0, subname=0x1d03250 "yade", fullname=0x1d03250 "yade") at Python/import.c:2700
#41 0x00002b1a072baf22 in load_next (mod=0x2b1a0754d7d0, altmod=0x2b1a0754d7d0, p_name=<value optimized out>, buf=0x1d03250 "yade", p_buflen=0x7fffba34e808) at Python/import.c:2515
#42 0x00002b1a072bb257 in import_module_level (name=<value optimized out>, globals=0x2b1a075f6168, locals=<value optimized out>, fromlist=0x2b1a0754d7d0, level=-1) at Python/import.c:2224
#43 PyImport_ImportModuleLevel (name=<value optimized out>, globals=0x2b1a075f6168, locals=<value optimized out>, fromlist=0x2b1a0754d7d0, level=-1) at Python/import.c:2288
#44 0x00002b1a0729b34d in builtin___import__ (self=<value optimized out>, args=<value optimized out>, kwds=<value optimized out>) at Python/bltinmodule.c:49
#45 0x00002b1a071fa318 in PyObject_Call (func=0x2b1a075dc050, arg=0x2b1a076a0a48, kw=0x0) at Objects/abstract.c:2529
#46 0x00002b1a0729b996 in PyEval_CallObjectWithKeywords (func=0x2b1a075dc050, arg=0x2b1a076a0a48, kw=0x0) at Python/ceval.c:3889
#47 0x00002b1a0729ff3c in PyEval_EvalFrameEx (f=0x2b1a076d0450, throwflag=<value optimized out>) at Python/ceval.c:2333
#48 0x00002b1a072a4419 in PyEval_EvalCodeEx (co=0x2b1a076efdb0, globals=<value optimized out>, locals=<value optimized out>, args=0x0, argcount=0, kws=0x0, kwcount=0, defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:3252
#49 0x00002b1a072a4492 in PyEval_EvalCode (co=0x2348ab0, globals=0x2b1a139ee406, locals=0x0) at Python/ceval.c:667
#50 0x00002b1a072c7b61 in run_mod (fp=0x1c02d70, filename=0x7fffba3508e9 "./yade-1.20.0", start=<value optimized out>, globals=0x2b1a075f6168, locals=0x2b1a075f6168, closeit=1, flags=0x7fffba34edb0) at Python/pythonrun.c:1370
#51 PyRun_FileExFlags (fp=0x1c02d70, filename=0x7fffba3508e9 "./yade-1.20.0", start=<value optimized out>, globals=0x2b1a075f6168, locals=0x2b1a075f6168, closeit=1, flags=0x7fffba34edb0) at Python/pythonrun.c:1356
#52 0x00002b1a072c7e07 in PyRun_SimpleFileExFlags (fp=<value optimized out>, filename=0x7fffba3508e9 "./yade-1.20.0", closeit=1, flags=0x7fffba34edb0) at Python/pythonrun.c:948
#53 0x00002b1a072da5e2 in Py_Main (argc=<value optimized out>, argv=0x7fffba34eed8) at Modules/main.c:645
#54 0x000000354a61ed5d in __libc_start_main () from /lib64/libc.so.6
#55 0x0000000000400649 in _start ()

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

Difficult to say. Looks like a problem in Boost. Try to use
another boost-version. Can you try to compile with gcc?

Anton

2016-06-02 22:17 GMT+02:00 Feng Chen <email address hidden>:
> Question #294790 on Yade changed:
> https://answers.launchpad.net/yade/+question/294790
>
> Status: Answered => Open
>
> Feng Chen is still having a problem:
> Hi, Anton, thanks for your quick reply, I attached here the debug info
> for the run, it seems quite long, do you have any idea which part went
> wrong?
>
> [fchen14@host003 bin]$ ./yade-1.20.0 >err.log 2>&1
> Segmentation fault

Revision history for this message
Feng Chen (fchen3-gmail) said : 		#4

Hi, Anton:

The purpose of using the intel compiler is that I intended to use the Xeon Phi co-processor which might be able to have some speedup on openmp (shared memory model) enabled codes (which I think YADE should be a good candidate), in order to use it the first step is to compile with the intel's compiler. Currently gcc does not have support for Knights Corner vector instructions therefore should not be used.

Is it possible to compile part of yade and run some benchmark problems (which was true many years ago^_^) without the python interface (the benchmark/optimization using Xeon Phi will not need python)?

Thanks

Feng

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

The purpose of compiling with gcc is just to check,
whether gcc is able to produce the working binaries
for your platform.

You can theoretically write a simple C++ code, link it
against libyade and use this C++ program without
python bindings. But it can also be not so easy
and bug-free though....

Cheers

Anton

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