[Zahra]

Hi @Binesh,

Thank you very much for sharing your codes. But, I again got the same errors using them.

I found out what is causing the previously mentioned errors: changing the value of “exportEveryNumberOfSteps” from zero to any other number in the ObjExporter. I do not need this option at this stage of my work, so I can just use the “exportAtEnd” and get the visual model at the end of the simulation. However, if you probably find out the solution for exporting the Obj file at every number of steps, I would appreciate if you kindly let me know about it.

Best wishes,

Zahra

[Zahra]

Dear @Binesh,

Thank you for your feedback. The ObjExporter code that I have sent to you is the original one and I did n’t change it.

Could you please explain what part of the code is incorrect?

Would you please share your ObjExporter files?

Best,

Zahra

[Zahra]

Dear @Binesh,

Thank you for your feedback. Please find the ObjExporter code files in the link below:

https://gist.github.com/zbounik/641aa66b47a0aa71e7bd745701013c7d

Best,
Zahra

[Zahra]

Dear @Binesh,

Thank you for your reply. I have used the objExporter to extract the visual model, but as I have mentioned before, it doesn’t work. I get this error when I use objExporter:

FROM SOFA [ERR] >> terminate called after throwing an instance of ‘std::out_of_range’
what(): basic_string::substr: __pos (which is 26) > this->size() (which is 21)

########## SIG 6 – SIGABRT: usually caused by an abort() or assert() ##########

FROM SOFA [OUT] >>

FROM SOFA [ERR] >> -> /home/zahra/sofa/build/v17.06/lib/libSofaHelper.so.17.06.02(sofa::helper::BackTrace::dump()+0x23) [0x7f49d3c5fc73]
-> /home/zahra/sofa/build/v17.06/lib/libSofaHelper.so.17.06.02(sofa::helper::BackTrace::sig(int)+0x19c) [0x7f49d3c5ffbc]
-> /lib/x86_64-linux-gnu/libc.so.6(+0x354b0) [0x7f49d32bc4b0]
-> /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x38) [0x7f49d32bc428]
-> /lib/x86_64-linux-gnu/libc.so.6(abort+0x16a) [0x7f49d32be02a]
-> /usr/lib/x86_64-linux-gnu/libstdc++.so.6(__gnu_cxx::__verbose_terminate_handler()+0x16d) [0x7f49d38f684d]
-> /usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x8d6b6) [0x7f49d38f46b6]
-> /usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x8d701) [0x7f49d38f4701]
-> /usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x8d919) [0x7f49d38f4919]
-> /usr/lib/x86_64-linux-gnu/libstdc++.so.6(std::__throw_out_of_range_fmt(char const*, …)+0x107) [0x7f49d391d3f7]
-> /home/zahra/sofa/build/v17.06/lib/libSofaExporter.so.17.06.02(sofa::component::misc::OBJExporter::writeOBJ()+0xee2) [0x7f49c6510d72]

FROM SOFA [ERR] >> -> /home/zahra/sofa/build/v17.06/lib/libSofaSimulationCore.so(sofa::simulation::InitVisitor::processNodeBottomUp(sofa::simulation::Node*)+0xd1) [0x7f49d5b59021]
-> /home/zahra/sofa/build/v17.06/lib/libSofaSimulationGraph.so.17.06.02(sofa::simulation::graph::DAGNode::executeVisitorBottomUp(sofa::simulation::Visitor*, std::__cxx11::list<sofa::simulation::graph::DAGNode*, std::allocator<sofa::simulation::graph::DAGNode*> >&)+0x57) [0x7f49d7985fd7]
-> /home/zahra/sofa/build/v17.06/lib/libSofaSimulationGraph.so.17.06.02(sofa::simulation::graph::DAGNode::doExecuteVisitor(sofa::simulation::Visitor*, bool)+0xc9) [0x7f49d7988c89]
-> /home/zahra/sofa/build/v17.06/lib/libSofaSimulationCore.so(sofa::simulation::Node::executeVisitor(sofa::simulation::Visitor*, bool)+0x144) [0x7f49d5b747e4]
-> /home/zahra/sofa/build/v17.06/lib/libSofaSimulationCore.so(sofa::simulation::Simulation::init(sofa::simulation::Node*)+0xeb) [0x7f49d5bc17cb]
-> /home/zahra/sofa/build/v17.06/bin/runSofa(main+0xe33) [0x407c53]
-> /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0) [0x7f49d32a7830]
-> /home/zahra/sofa/build/v17.06/bin/runSofa(_start+0x29) [0x408cd9]

please find the scene here:

https://gist.github.com/zbounik/579655d1d753ab749158d8cf89e830f1

Best,

Zahra

[Zahra]

Dear Hugo,

Thank you very much for your kind explanation.

Best,

Zahra

[Zahra]

Dear @Hugo,

Thank you very much for your advice, the mentioned SOFA examples are quite helpful.

It is a good news that SOFA would be usable in classical Python environments soon. Looking forward for it.

Best regards,

Zahra

[Zahra]

Dear @Hugo,

I did not try it yet.

Zahra

[Zahra]

Dear @egarcm,

Thank you for your explanation.

[Zahra]

Dear Marwa,

Thank you very much for your reply. This is not what exactly I want to do, but your reply gave me some hints. I tried to check it, however, I have a big problem here: how can I run “liver_controller.py”? Should I add it to the end of my script? It is not working!

Thank you in advance,

Zahra

[Zahra]

Dear Marwa,

Sorry I forgot to include the mesh files. Below please find the required files:

livertetra7509.msh :
https://gist.github.com/zbounik/1264c9cafe37b83438e854cd44881bd9

livertetra181.gmsh:

https://gist.github.com/zbounik/5a5c4105cbe7d98c6120c584bb7b6a13

Best,

Zahra

[Zahra]

Hi Noura,

Thank you, I try your hint.

Best,

Zahra

[Zahra]

Dear @Hugo,

Thank you for your explanation. At this level, yes, I think I understood their functionality.

best,

Zahra

[Zahra]

WOW! It is working now! Thank you so much dear @Hugo for your explanation, I am learning python scripting better now.

Cheers,

Zahra

[Zahra]

Hi @Hugo,

– I am using the stable version SOFA 17.06, and this is my generated python file:

https://gist.github.com/zbounik/b0043c19b817db11df45419c77afd645

Best,

Zahra

[Zahra]

Hi,

I am applying scn2python on my scenes and it translates correctly to a python script. But when I try to run it by runSofa, I get this error:

cannot create Scene, no “createScene(rootNode)” nor “createSceneAndController(rootNode)” module method found.

How can I run sofa in debug mode in Ubuntu to see at what line I got this error?

Best,

Zahra

[Zahra]

Dear @ELDiwiny,

Thank you. I do not have any problem on the installation, I just receive error when I run some scenes.
I have searched your skype ID, to send you a message via skype, but I could not find it. My skype ID is “zahra.bnk”. I appreciate if you kindly add me.
So I will be available on saturday, what time is appropriate for you?

Thank you for your time in advance.

Zahra

[Zahra]

Dear @ElDiwiny,

Thank you so much for your kind reply. For today, my internet has been disconnected, and now I am using a very low speed one which is not fine for online contact. I am wondering if you have a free time tomorrow, or any other day which is convenient for you?

Thank you again for your kind consideration,

Zahra

[Zahra]

Hi again,

I successfully rebuilt SOFA in a newly installed Ubuntu OS,however, I still get this error when running almost all of the scenes:

########## SIG 11 – SIGSEGV: segfault ##########
Segmentation fault (core dumped)

I used all the instructions mentioned in the build page, except the one for installing Qt. I did not use the Qt unified installer(it is not downloading for me). Instead, I used this: qt-opensource-linux-x64-5.6.0.run

https://download.qt.io/archive/qt/5.6/5.6.0/

Could it be the problem?

Would anyone kindly help me to solve this? I have no idea how to find the cause of this problem.

Best,

Zahra

[Zahra]

Hi @Hugo,

Thank you very much for your comment. I have removed previously installed python and reinstalled python 2.7, then ran cmake and recompiled to build sofa, but it still gives me SEG11 error. I am wondering if a history of python 3.5 may have some affects. I am thinking to clear everything and start from scratch to see if I receive this error again. I will inform you as soon as I reach a solution.

I will consider you hint regarding adding and configuring some .ini files while building sofa.

I highly appreciate your follow up 🙂

Zahra

[Zahra]

I should also add that, I had python 3.5 on my system, but I removed it and installed python 2.7 to work with sofa. can it be the cause of this error?

If I uninstall python and install a new one, should I build sofa again?

Thank you for your help.

Zahra

[Zahra]

Dear Hugo,

Thank you very much for your reply. The #1 is my major problem (SIG 11 – SIGSEGV: segfault error).

This is the properties of the python on my system:

Python 2.7.14 |Anaconda, Inc.| (default, Dec 7 2017, 17:05:42)
[GCC 7.2.0] on linux2

Should I use any other version?

Best regards,

Zahra

[Zahra]

Dear Hugo,

Thank you very much for letting me know. I hope to hear good news about SOFA.

Best wishes,

Zahra

[Zahra]

Thank you @Binesh, I have started a new topic regarding this error:

SIG 11 – SIGSEGV: segfault Segmentation fault (core dumped)

I appreciate your help and deeply wish you have a good luck with this error 🙂

[Zahra]

Hi @Binesh,

I know, I have changed it and I got that error.

BTW, as I have mentioned, my problem with extracting the surface has been resolved. I am now trying to figure out why the same code works for others and gives me the “SIG 11 – SIGSEGV: segfault” error. I encountered this error previously and I have thought it is because of my code. I may start a new topic about it as soon as I collect more evidences.

Best,

Zahra

[Zahra]

Hi @Binesh,

Thank you for your explanation. As Hugo mentioned, I think there is no need for implementing “Tetra2SurfaceTriangleMapping”.

Regarding the scene you have mentioned, I tried it: No .Obj file is created, and finally I receive this error:

FROM SOFA [ERR] >>
########## SIG 11 – SIGSEGV: segfault ##########

Best,

Zahra

[Author]

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