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[Bug 1732210] Re: getNeighbors_Segmentation fault (core dumped)

To: yade-dev@xxxxxxxxxxxxxxxxxxx
From: Son Pham Thai <pham_thai_son_987@xxxxxxxxx>
Date: Wed, 15 Nov 2017 11:04:12 -0000
Reply-to: Bug 1732210 <1732210@xxxxxxxxxxxxxxxxxx>
Sender: bounces@xxxxxxxxxxxxx
-----------------------------------------------------------------------------------------
num_spheres=50
-----------------------------------------------------------------------------------------


Yade [1]: execfile('Error_getNeighbors.py') ####
DEBUG /home/son/Desktop/myYade/trunk/pkg/dem/SpherePack.cpp:129 makeCloud: 0. 0.2995, cdf=0, cdf2=0
DEBUG /home/son/Desktop/myYade/trunk/pkg/dem/SpherePack.cpp:129 makeCloud: 1. 0.3, cdf=0.35, cdf2=1085,8516816647427
DEBUG /home/son/Desktop/myYade/trunk/pkg/dem/SpherePack.cpp:129 makeCloud: 2. 0.4245, cdf=0.35, cdf2=1085,8516816647427
DEBUG /home/son/Desktop/myYade/trunk/pkg/dem/SpherePack.cpp:129 makeCloud: 3. 0.425, cdf=0.7, cdf2=1467,4861723291381
DEBUG /home/son/Desktop/myYade/trunk/pkg/dem/SpherePack.cpp:129 makeCloud: 4. 0.5, cdf=0.7, cdf2=1467,4861723291381
DEBUG /home/son/Desktop/myYade/trunk/pkg/dem/SpherePack.cpp:129 makeCloud: 5. 0.7, cdf=1, cdf2=1590,2628427143145
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641DEBUG  wait: WAIT!
/home/son/Desktop/myYade/trunk/pkg/common/InsertionSortCollider.cpp:207 action: Resize bounds containers from 0 to 112, will std::sort.
DEBUG /home/son/Desktop/myYade/trunk/core/ForceContainerParallel.cpp:224 resize: Resize ForceContainer from the size 0 to the size 212
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
INFO  /home/son/Desktop/myYade/trunk/core/Omega.cpp:265 saveSimulation: Saving file 1kPacking.yade
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
/home/son/Desktop/myYade/install/bin/yade-Unknown in <module>()
----> 1 execfile('Error_getNeighbors.py') ####

/home/son/Desktop/myYade/install/bin/yade-Unknown in <module>()
    137 
    138 for i in range(unsat.nCells()):
--> 139         unsat.getNeighbors(i)
    140 ## Segmentation fault (core dumped)
    141 

RuntimeError: CGAL ERROR: precondition violation!
Expr: dimension() == 3
File: /usr/include/CGAL/Triangulation_3.h
Line: 799


-----------------------------------------------------------------------------------------
num_spheres=100
-----------------------------------------------------------------------------------------

Yade [1]: execfile('Error_getNeighbors.py') ####
DEBUG /home/son/Desktop/myYade/trunk/pkg/dem/SpherePack.cpp:129 makeCloud: 0. 0.2995, cdf=0, cdf2=0
DEBUG /home/son/Desktop/myYade/trunk/pkg/dem/SpherePack.cpp:129 makeCloud: 1. 0.3, cdf=0.35, cdf2=1085,8516816647427
DEBUG /home/son/Desktop/myYade/trunk/pkg/dem/SpherePack.cpp:129 makeCloud: 2. 0.4245, cdf=0.35, cdf2=1085,8516816647427
DEBUG /home/son/Desktop/myYade/trunk/pkg/dem/SpherePack.cpp:129 makeCloud: 3. 0.425, cdf=0.7, cdf2=1467,4861723291381
DEBUG /home/son/Desktop/myYade/trunk/pkg/dem/SpherePack.cpp:129 makeCloud: 4. 0.5, cdf=0.7, cdf2=1467,4861723291381
DEBUG /home/son/Desktop/myYade/trunk/pkg/dem/SpherePack.cpp:129 makeCloud: 5. 0.7, cdf=1, cdf2=1590,2628427143145
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/pkg/common/InsertionSortCollider.cpp:207 action: Resize bounds containers from 0 to 212, will std::sort.
DEBUG /home/son/Desktop/myYade/trunk/core/ForceContainerParallel.cpp:224 resize: Resize ForceContainer from the size 0 to the size 312
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
INFO  /home/son/Desktop/myYade/trunk/core/Omega.cpp:265 saveSimulation: Saving file 1kPacking.yade
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!


------------------------------------------------------------------------------------------
num_spheres=150

Yade [1]: execfile('Error_getNeighbors.py') ####
DEBUG /home/son/Desktop/myYade/trunk/pkg/dem/SpherePack.cpp:129 makeCloud: 0. 0.2995, cdf=0, cdf2=0
DEBUG /home/son/Desktop/myYade/trunk/pkg/dem/SpherePack.cpp:129 makeCloud: 1. 0.3, cdf=0.35, cdf2=1085,8516816647427
DEBUG /home/son/Desktop/myYade/trunk/pkg/dem/SpherePack.cpp:129 makeCloud: 2. 0.4245, cdf=0.35, cdf2=1085,8516816647427
DEBUG /home/son/Desktop/myYade/trunk/pkg/dem/SpherePack.cpp:129 makeCloud: 3. 0.425, cdf=0.7, cdf2=1467,4861723291381
DEBUG /home/son/Desktop/myYade/trunk/pkg/dem/SpherePack.cpp:129 makeCloud: 4. 0.5, cdf=0.7, cdf2=1467,4861723291381
DEBUG /home/son/Desktop/myYade/trunk/pkg/dem/SpherePack.cpp:129 makeCloud: 5. 0.7, cdf=1, cdf2=1590,2628427143145
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
/home/son/Desktop/myYade/trunk/pkg/common/InsertionSortCollider.cpp:207 action: Resize bounds containers from 0 to 312, will std::sort.
DEBUG /home/son/Desktop/myYade/trunk/core/ForceContainerParallel.cpp:224 resize: Resize ForceContainer from the size 0 to the size 412
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
INFO  /home/son/Desktop/myYade/trunk/core/Omega.cpp:265 saveSimulation: Saving file 1kPacking.yade
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!


------------------------------------------------------------------------------------------
num_spheres=200
-----------------------------------------------------------------------------------------

Yade [1]: execfile('Error_getNeighbors.py') ####
DEBUG /home/son/Desktop/myYade/trunk/pkg/dem/SpherePack.cpp:129 makeCloud: 0. 0.2995, cdf=0, cdf2=0
DEBUG /home/son/Desktop/myYade/trunk/pkg/dem/SpherePack.cpp:129 makeCloud: 1. 0.3, cdf=0.35, cdf2=1085,8516816647427
DEBUG /home/son/Desktop/myYade/trunk/pkg/dem/SpherePack.cpp:129 makeCloud: 2. 0.4245, cdf=0.35, cdf2=1085,8516816647427
DEBUG /home/son/Desktop/myYade/trunk/pkg/dem/SpherePack.cpp:129 makeCloud: 3. 0.425, cdf=0.7, cdf2=1467,4861723291381
DEBUG /home/son/Desktop/myYade/trunk/pkg/dem/SpherePack.cpp:129 makeCloud: 4. 0.5, cdf=0.7, cdf2=1467,4861723291381
DEBUG /home/son/Desktop/myYade/trunk/pkg/dem/SpherePack.cpp:129 makeCloud: 5. 0.7, cdf=1, cdf2=1590,2628427143145
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 runDEBUG : RUN/home/son/Desktop/myYade/trunk/pkg/common/InsertionSortCollider.cpp:207 action: Resize bounds containers from 0 to 412, will std::sort. (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:
641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/core/ForceContainerParallel.cpp:224 resize: Resize ForceContainer from the size 0 to the size 512
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
INFO  /home/son/Desktop/myYade/trunk/core/Omega.cpp:265 saveSimulation: Saving file 1kPacking.yade
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
SIGSEGV/SIGABRT handler called; gdb batch file is `/tmp/yade-obqZZX/tmp-0'
GNU gdb (Ubuntu 7.7.1-0ubuntu5~14.04.3) 7.7.1
Copyright (C) 2014 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-linux-gnu".
Type "show configuration" for configuration details.
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>.
Find the GDB manual and other documentation resources online at:
<http://www.gnu.org/software/gdb/documentation/>.
For help, type "help".
Type "apropos word" to search for commands related to "word".
Could not attach to process.  If your uid matches the uid of the target
process, check the setting of /proc/sys/kernel/yama/ptrace_scope, or try
again as the root user.  For more details, see /etc/sysctl.d/10-ptrace.conf
/tmp/yade-obqZZX/tmp-0:1: Error in sourced command file:
ptrace: Operation not permitted.
(gdb) quit
Segmentation fault (core dumped)



------------------------------------------------------------------------------------------
num_spheres=250
-----------------------------------------------------------------------------------------

Yade [1]: execfile('Error_getNeighbors.py') ####
DEBUG /home/son/Desktop/myYade/trunk/pkg/dem/SpherePack.cpp:129 makeCloud: 0. 0.2995, cdf=0, cdf2=0
DEBUG /home/son/Desktop/myYade/trunk/pkg/dem/SpherePack.cpp:129 makeCloud: 1. 0.3, cdf=0.35, cdf2=1085,8516816647427
DEBUG /home/son/Desktop/myYade/trunk/pkg/dem/SpherePack.cpp:129 makeCloud: 2. 0.4245, cdf=0.35, cdf2=1085,8516816647427
DEBUG /home/son/Desktop/myYade/trunk/pkg/dem/SpherePack.cpp:129 makeCloud: 3. 0.425, cdf=0.7, cdf2=1467,4861723291381
DEBUG /home/son/Desktop/myYade/trunk/pkg/dem/SpherePack.cpp:129 makeCloud: 4. 0.5, cdf=0.7, cdf2=1467,4861723291381
DEBUG /home/son/Desktop/myYade/trunk/pkg/dem/SpherePack.cpp:129 makeCloud: 5. 0.7, cdf=1, cdf2=1590,2628427143145
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)DEBUG !
/home/son/Desktop/myYade/trunk/pkg/common/InsertionSortCollider.cpp:DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
207 action: Resize bounds containers from 0 to 512, will std::sort.
DEBUG /home/son/Desktop/myYade/trunk/core/ForceContainerParallel.cpp:224 resize: Resize ForceContainer from the size 0 to the size 612
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
INFO  /home/son/Desktop/myYade/trunk/core/Omega.cpp:265 saveSimulation: Saving file 1kPacking.yade
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
/home/son/Desktop/myYade/install/bin/yade-Unknown in <module>()
----> 1 execfile('Error_getNeighbors.py') ####

/home/son/Desktop/myYade/install/bin/yade-Unknown in <module>()
    137 
    138 for i in range(unsat.nCells()):
--> 139         unsat.getNeighbors(i)
    140 ## Segmentation fault (core dumped)
    141 

RuntimeError: CGAL ERROR: precondition violation!
Expr: dimension() == 3
File: /usr/include/CGAL/Triangulation_3.h
Line: 799


------------------------------------------------------------------------------------------
num_spheres=300
-----------------------------------------------------------------------------------------

Yade [1]: execfile('Error_getNeighbors.py') ####
DEBUG /home/son/Desktop/myYade/trunk/pkg/dem/SpherePack.cpp:129 makeCloud: 0. 0.2995, cdf=0, cdf2=0
DEBUG /home/son/Desktop/myYade/trunk/pkg/dem/SpherePack.cpp:129 makeCloud: 1. 0.3, cdf=0.35, cdf2=1085,8516816647427
DEBUG /home/son/Desktop/myYade/trunk/pkg/dem/SpherePack.cpp:129 makeCloud: 2. 0.4245, cdf=0.35, cdf2=1085,8516816647427
DEBUG /home/son/Desktop/myYade/trunk/pkg/dem/SpherePack.cpp:129 makeCloud: 3. 0.425, cdf=0.7, cdf2=1467,4861723291381
DEBUG /home/son/Desktop/myYade/trunk/pkg/dem/SpherePack.cpp:129 makeCloud: 4. 0.5, cdf=0.7, cdf2=1467,4861723291381
DEBUG /home/son/Desktop/myYade/trunk/pkg/dem/SpherePack.cpp:129 makeCloud: 5. 0.7, cdf=1, cdf2=1590,2628427143145
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/pkg/common/InsertionSortCollider.cpp:207 action: Resize bounds containers from 0 to 612, will std::sort.
DEBUG /home/son/Desktop/myYade/trunk/core/ForceContainerParallel.cpp:224 resize: Resize ForceContainer from the size 0 to the size 712
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
INFO  /home/son/Desktop/myYade/trunk/core/Omega.cpp:265 saveSimulation: Saving file 1kPacking.yade
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:635 run: RUN (1000 to go)!
DEBUG /home/son/Desktop/myYade/trunk/py/wrapper/yadeWrapper.cpp:641 wait: WAIT!
SIGSEGV/SIGABRT handler called; gdb batch file is `/tmp/yade-aCNfzm/tmp-0'
GNU gdb (Ubuntu 7.7.1-0ubuntu5~14.04.3) 7.7.1
Copyright (C) 2014 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-linux-gnu".
Type "show configuration" for configuration details.
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>.
Find the GDB manual and other documentation resources online at:
<http://www.gnu.org/software/gdb/documentation/>.
For help, type "help".
Type "apropos word" to search for commands related to "word".
Could not attach to process.  If your uid matches the uid of the target
process, check the setting of /proc/sys/kernel/yama/ptrace_scope, or try
again as the root user.  For more details, see /etc/sysctl.d/10-ptrace.conf
/tmp/yade-aCNfzm/tmp-0:1: Error in sourced command file:
ptrace: Operation not permitted.
(gdb) quit
Segmentation fault (core dumped)

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https://bugs.launchpad.net/bugs/1732210

Title:
  getNeighbors_Segmentation fault (core dumped)

Status in Yade:
  New

Bug description:
  Hi,

  I got an error "Segmentation fault (core dumped)". I have narrowed
  down to find out that the problem is about the function
  getNeighbors(). But this error does not always happen. I got error
  when num_spheres = 50,100,200,250,300 but when num_spheres = 150 there
  will be no error with getNeighbors()

  My system info:
  Ubuntu 14.04 LTS
  Yade is compiled using packaged version yade-2017.01a

  Regards,
  Son

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References

[Bug 1732210] [NEW] getNeighbors_Segmentation fault (core dumped)
From: Son Pham Thai, 2017-11-14