Omega output with Debug mode?

Asked by Luc OGER on 2019-04-03

i need som ehelp:
in the latest yade git version (2019-04-01) when i compile with the DEBUG=OFF I got a correct output with a new window display for running the program BUT when I compile exactly the same trunk package on the same computer environnement but with DEBUG=ON, the program wants to use the Omega output mode and crashes immediatly

here the two runs outputs :

programme_yade/bouncing_ss_interaction% /usr/local/bin/yade-2019-04-01.git-aa31ef3 bouncing_sphere.py
Welcome to Yade 2019-04-01.git-aa31ef3
TCP python prompt on localhost:9000, auth cookie `ekadus'
XMLRPC info provider on http://localhost:21000
Running script bouncing_sphere.py
[[ ^L clears screen, ^U kills line. F12 controller, F11 3D view (press "h" in 3D view for help), F10 both, F9 generator, F8 plot. ]]

In [1]: Incident de segmentation (core dumped)
programme_yade/bouncing_ss_interaction% /usr/local/bin/yade-2019-04-01.git-aa31ef3 bouncing_sphere.py
Welcome to Yade 2019-04-01.git-aa31ef3
DEBUG /home/oger/Yade/trunk/core/Omega.hpp:106 Omega: Constructing Omega.
Incident de segmentation (core dumped)
programme_yade/bouncing_ss_interaction%

here the cmake output:
 cmake -DENABLE_PFVFLOW=OFF -DENABLE_TWOPHASEFLOW=OFF -DENABLE_LBMFLOW=OFF -DPYTHON_EXECUTABLE=/usr/bin/python2 -DCMAKE_VERBOSE_MAKEFILE=ON -DQGLVIEWER_INCLUDE_DIR=/usr/local/include/QGLViewer -Wno-error=deprecated -Wno-dev -DUSE_QT5=OFF -DDEBUG=ON ../trunk
-- Found OpenMP_C: -fopenmp
-- Found OpenMP_CXX: -fopenmp
-- Found OpenMP: TRUE
-- Found Qt4: /usr/bin/qmake (found version "4.8.7")
-- Version is set to 2019-04-01.git-aa31ef3
-- GTS using gts-config /usr/bin/gts-config
-- Using GTS from /usr
-- GCC Version >= 4.8. Adding -ftrack-macro-expansion=0
-- GCC Version >= 4.8. Adding -save-temps
-- GCC Version >= 4.9. Adding -fstack-protector-strong
-- Boost version: 1.66.0
-- Found the following Boost libraries:
-- python
-- thread
-- filesystem
-- iostreams
-- regex
-- serialization
-- system
-- date_time
-- chrono
-- Boost_VERSION: 106600
-- Boost_LIB_VERSION: 1_66
-- Boost_INCLUDE_DIRS: /usr/include
-- Boost_LIBRARIES: /usr/lib64/libboost_python.so/usr/lib64/libboost_thread.so/usr/lib64/libboost_filesystem.so/usr/lib64/libboost_iostreams.so/usr/lib64/libboost_regex.so/usr/lib64/libboost_serialization.so/usr/lib64/libboost_system.so/usr/lib64/libboost_date_time.so/usr/lib64/libboost_chrono.so
-- Found Eigen3, version: 3.3.4
-- Disable vectorization
-- Found VTK
-- Found OpenMP_C: -fopenmp
-- Found OpenMP_CXX: -fopenmp
-- Found OpenMP
-- GTS using gts-config /usr/bin/gts-config
-- Using GTS from /usr
-- Found GTS
-- USE QT4
-- Found Qt4: /usr/bin/qmake (found version "4.8.7")
-- Found GUI-LIBS
-- GMP libs: /usr/lib64/libgmp.so /usr/lib64/libgmpxx.so
-- GMP libs: /usr/lib64/libgmp.so /usr/lib64/libgmpxx.so
-- Found CGAL
-- Could NOT find Cholmod (missing: CHOLMOD_LIBRARIES CHOLMOD_INCLUDE_DIR AMD_LIBRARY CAMD_LIBRARY COLAMD_LIBRARY CCOLAMD_LIBRARY)
-- Missing dependency for LINSOLV, disabled
-- Found GL2PS
Yade will be installed to /usr/local
-- Suffix is set to -2019-04-01.git-aa31ef3
-- LIBRARY_OUTPUT_PATH is set to lib64
-- runtimePREFIX is set to /usr/local
-- Use system gts version
-- VTK version >7 is found
-- ===========================================================
-- Yade configured with following features: Odeint VTK OpenMP GTS GUI CGAL GL2PS
-- Disabled features: PFVFLOW LINSOLV TWOPHASEFLOW SPH DEFORM LIQMIGRATION LBMFLOW MASK_ARBITRARY THERMAL PROFILING PotentialParticles PotentialBlocks
-- Debug build
-- ===========================================================
-- Configuring done
-- Generating done
-- Build files have been written to: /home/oger/Yade/build

Question information

Language:
English Edit question
Status:
Solved
For:
Yade Edit question
Assignee:
No assignee Edit question
Solved by:
Luc OGER
Solved:
2019-04-08
Last query:
2019-04-08
Last reply:
2019-04-04
Chareyre (bruno-chareyre-9) said : #1

Omega is constructed anyway.
Does it crash if you don't execute that script?

Le mer. 3 avr. 2019 16:37, Luc OGER <email address hidden>
a écrit :

> New question #679750 on Yade:
> https://answers.launchpad.net/yade/+question/679750
>
> i need som ehelp:
> in the latest yade git version (2019-04-01) when i compile with the
> DEBUG=OFF I got a correct output with a new window display for running the
> program BUT when I compile exactly the same trunk package on the same
> computer environnement but with DEBUG=ON, the program wants to use the
> Omega output mode and crashes immediatly
>
> here the two runs outputs :
>
> programme_yade/bouncing_ss_interaction%
> /usr/local/bin/yade-2019-04-01.git-aa31ef3 bouncing_sphere.py
> Welcome to Yade 2019-04-01.git-aa31ef3
> TCP python prompt on localhost:9000, auth cookie `ekadus'
> XMLRPC info provider on http://localhost:21000
> Running script bouncing_sphere.py
> [[ ^L clears screen, ^U kills line. F12 controller, F11 3D view (press "h"
> in 3D view for help), F10 both, F9 generator, F8 plot. ]]
>
> In [1]: Incident de segmentation (core dumped)
> programme_yade/bouncing_ss_interaction%
> /usr/local/bin/yade-2019-04-01.git-aa31ef3 bouncing_sphere.py
> Welcome to Yade 2019-04-01.git-aa31ef3
> DEBUG /home/oger/Yade/trunk/core/Omega.hpp:106 Omega: Constructing Omega.
> Incident de segmentation (core dumped)
> programme_yade/bouncing_ss_interaction%
>
> here the cmake output:
> cmake -DENABLE_PFVFLOW=OFF -DENABLE_TWOPHASEFLOW=OFF
> -DENABLE_LBMFLOW=OFF -DPYTHON_EXECUTABLE=/usr/bin/python2
> -DCMAKE_VERBOSE_MAKEFILE=ON
> -DQGLVIEWER_INCLUDE_DIR=/usr/local/include/QGLViewer -Wno-error=deprecated
> -Wno-dev -DUSE_QT5=OFF -DDEBUG=ON ../trunk
> -- Found OpenMP_C: -fopenmp
> -- Found OpenMP_CXX: -fopenmp
> -- Found OpenMP: TRUE
> -- Found Qt4: /usr/bin/qmake (found version "4.8.7")
> -- Version is set to 2019-04-01.git-aa31ef3
> -- GTS using gts-config /usr/bin/gts-config
> -- Using GTS from /usr
> -- GCC Version >= 4.8. Adding -ftrack-macro-expansion=0
> -- GCC Version >= 4.8. Adding -save-temps
> -- GCC Version >= 4.9. Adding -fstack-protector-strong
> -- Boost version: 1.66.0
> -- Found the following Boost libraries:
> -- python
> -- thread
> -- filesystem
> -- iostreams
> -- regex
> -- serialization
> -- system
> -- date_time
> -- chrono
> -- Boost_VERSION: 106600
> -- Boost_LIB_VERSION: 1_66
> -- Boost_INCLUDE_DIRS: /usr/include
> -- Boost_LIBRARIES: /usr/lib64/
> libboost_python.so/usr/lib64/libboost_thread.so/usr/lib64/libboost_filesystem.so/usr/lib64/libboost_iostreams.so/usr/lib64/libboost_regex.so/usr/lib64/libboost_serialization.so/usr/lib64/libboost_system.so/usr/lib64/libboost_date_time.so/usr/lib64/libboost_chrono.so
> -- Found Eigen3, version: 3.3.4
> -- Disable vectorization
> -- Found VTK
> -- Found OpenMP_C: -fopenmp
> -- Found OpenMP_CXX: -fopenmp
> -- Found OpenMP
> -- GTS using gts-config /usr/bin/gts-config
> -- Using GTS from /usr
> -- Found GTS
> -- USE QT4
> -- Found Qt4: /usr/bin/qmake (found version "4.8.7")
> -- Found GUI-LIBS
> -- GMP libs: /usr/lib64/libgmp.so /usr/lib64/libgmpxx.so
> -- GMP libs: /usr/lib64/libgmp.so /usr/lib64/libgmpxx.so
> -- Found CGAL
> -- Could NOT find Cholmod (missing: CHOLMOD_LIBRARIES CHOLMOD_INCLUDE_DIR
> AMD_LIBRARY CAMD_LIBRARY COLAMD_LIBRARY CCOLAMD_LIBRARY)
> -- Missing dependency for LINSOLV, disabled
> -- Found GL2PS
> Yade will be installed to /usr/local
> -- Suffix is set to -2019-04-01.git-aa31ef3
> -- LIBRARY_OUTPUT_PATH is set to lib64
> -- runtimePREFIX is set to /usr/local
> -- Use system gts version
> -- VTK version >7 is found
> -- ===========================================================
> -- Yade configured with following features: Odeint VTK OpenMP GTS GUI CGAL
> GL2PS
> -- Disabled features: PFVFLOW LINSOLV TWOPHASEFLOW SPH DEFORM LIQMIGRATION
> LBMFLOW MASK_ARBITRARY THERMAL PROFILING PotentialParticles PotentialBlocks
> -- Debug build
> -- ===========================================================
> -- Configuring done
> -- Generating done
> -- Build files have been written to: /home/oger/Yade/build
>
>
>
> You received this question notification because your team yade-users is
> an answer contact for Yade.
>
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Luc OGER (luc-oger) said : #2

same crash:

programme_yade/bouncing_ss_interaction% /usr/local/bin/yade-2019-04-01.git-aa31ef3
Welcome to Yade 2019-04-01.git-aa31ef3
DEBUG /home/oger/Yade/trunk/core/Omega.hpp:106 Omega: Constructing Omega.
Incident de segmentation (core dumped)
programme_yade/bouncing_ss_interaction%

Chareyre (bruno-chareyre-9) said : #3

What is that «programme_yade...» part?

Le mer. 3 avr. 2019 19:58, Luc OGER <email address hidden>
a écrit :

> Question #679750 on Yade changed:
> https://answers.launchpad.net/yade/+question/679750
>
> Luc OGER posted a new comment:
> same crash:
>
> programme_yade/bouncing_ss_interaction%
> /usr/local/bin/yade-2019-04-01.git-aa31ef3
> Welcome to Yade 2019-04-01.git-aa31ef3
> DEBUG /home/oger/Yade/trunk/core/Omega.hpp:106 Omega: Constructing Omega.
> Incident de segmentation (core dumped)
> programme_yade/bouncing_ss_interaction%
>
> --
> You received this question notification because your team yade-users is
> an answer contact for Yade.
>
> _______________________________________________
> Mailing list: https://launchpad.net/~yade-users
> Post to : <email address hidden>
> Unsubscribe : https://launchpad.net/~yade-users
> More help : https://help.launchpad.net/ListHelp
>
>
>

Luc OGER (luc-oger) said : #4

everything before % is the part of the folder name so without interest here

the only command and result are :
/usr/local/bin/yade-2019-04-01.git-aa31ef3
Welcome to Yade 2019-04-01.git-aa31ef3
DEBUG /home/oger/Yade/trunk/core/Omega.hpp:106 Omega: Constructing Omega.
Incident de segmentation (core dumped)

Chareyre (bruno-chareyre-9) said : #5

It actually doesn't look like an output of a debug build, it should be more
verbose.
Can't you find some backtrace or something? (sorry I kind-of forgot details
of how to get debug info).

On Thu, 4 Apr 2019 at 10:03, Luc OGER <email address hidden>
wrote:

> Question #679750 on Yade changed:
> https://answers.launchpad.net/yade/+question/679750
>
> Luc OGER posted a new comment:
> everything before % is the part of the folder name so without interest
> here
>
> the only command and result are :
> /usr/local/bin/yade-2019-04-01.git-aa31ef3
> Welcome to Yade 2019-04-01.git-aa31ef3
> DEBUG /home/oger/Yade/trunk/core/Omega.hpp:106 Omega: Constructing Omega.
> Incident de segmentation (core dumped)
>
> --
> You received this question notification because your team yade-users is
> an answer contact for Yade.
>
> _______________________________________________
> Mailing list: https://launchpad.net/~yade-users
> Post to : <email address hidden>
> Unsubscribe : https://launchpad.net/~yade-users
> More help : https://help.launchpad.net/ListHelp
>
>
>

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Luc OGER (luc-oger) said : #6

it is the same !!!

here the begin of the previous debug version :

command : /usr/local/bin/yade-2019-03-14.git-8b073f5

results:

Welcome to Yade 2019-03-14.git-8b073f5
DEBUG /home/Yade/trunk/core/Omega.hpp:106 Omega: Constructing Omega.
DEBUG /home/Yade/trunk/core/Omega.cpp:209 loadPlugins: Loading plugin /usr/local/lib64/yade-2019-03-14.git-8b073f5/libyade.so
DEBUG /home/Yade/trunk/core/Omega.cpp:134 buildDynlibDatabase: called with 324 plugins.
DEBUG /home/Yade/trunk/core/Omega.cpp:140 buildDynlibDatabase: Factoring plugin Aabb
DEBUG /home/Yade/trunk/core/Omega.cpp:140 buildDynlibDatabase: Factoring plugin AxialGravityEngine
DEBUG /home/Yade/trunk/core/Omega.cpp:140 buildDynlibDatabase: Factoring plugin BicyclePedalEngine
DEBUG /home/Yade/trunk/core/Omega.cpp:140 buildDynlibDatabase: Factoring plugin Bo1_Box_Aabb
DEBUG /home/Yade/trunk/core/Omega.cpp:140 buildDynlibDatabase: Factoring plugin Bo1_ChainedCylinder_Aabb
DEBUG /home/Yade/trunk/core/Omega.cpp:140 buildDynlibDatabase: Factoring plugin Bo1_Cylinder_Aabb
DEBUG /home/Yade/trunk/core/Omega.cpp:140 buildDynlibDatabase: Factoring plugin Bo1_DeformableElement_Aabb
DEBUG /home/Yade/trunk/core/Omega.cpp:140 buildDynlibDatabase: Factoring plugin Bo1_Facet_Aabb
DEBUG /home/Yade/trunk/core/Omega.cpp:140 buildDynlibDatabase: Factoring plugin Bo1_GridConnection_Aabb
and so on...

and in both cases the libyade.so exists :
% ll /usr/local/lib64/yade-2019-04-01.git-aa31ef3/
total 1521428
-rwxr-xr-x 1 root root 1557894336 3 avril 16:07 libyade.so
drwxr-xr-x 3 root root 4096 3 avril 16:31 py

% ll /usr/local/lib64/yade-2019-03-14.git-8b073f5/
total 1521372
-rwxr-xr-x 1 root root 1557865488 28 mars 17:26 libyade.so
drwxr-xr-x 3 root root 4096 28 mars 17:51 py

Janek Kozicki (cosurgi) said : #7

Do you get somewhere a message: „ptrace: Operation not permitted” ? If yes, then check https://yade-dev.gitlab.io/trunk/introduction.html#fdbg

Luc OGER (luc-oger) said : #8

no sign of any ptrace message.

Janek Kozicki (cosurgi) said : #9

Hard to say. What is youe exact linux version? Maybe try reinstalling all the libraries, then recompiling? This can be a result of some previous misconfiguration of some system packages.

Can you run gdb without crash on a C++ hello world example?

Luc OGER (luc-oger) said : #10

I finally founded the problem about the DEBUG mode:

after testing so many runs of the yade in the debug mode, the /tmp folder was saturated and no more space was available to create a new /tmp/yade-TzyaFx/tmp-0 or similar directories..

sorry for the waste ofyour time for my own mystake!!