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

[Zahra]

Hi,

This is the error I sometimes get when I run some SOFA scenes, including runSofa itself.

I tried it in 3 versions of sofa. Here is the results:

In sofa 16.12 (and also 17.06), when I execute:

home/zahra/sofa/sofa-16.12/build/bin/runSofa , it gives me different results even if I make no change:

result #1:

The scene animates truely but when I close the runSofa window, it results in the SIG 11 error as follows:

[INFO]    [SofaPython] Added '/home/zahra/sofa/sofa-16.12/src/applications/plugins/SofaPython/python' to sys.path
[INFO]    [SofaPython] Added '/home/zahra/sofa/sofa-16.12/src/applications/plugins/SofaTest/python' to sys.path
[INFO]    [PluginManager] Loaded plugin: /home/zahra/sofa/sofa-16.12/build/lib/libSofaPython.so

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

result #2:
The scene animates an I receive no error:

[INFO]    [SofaPython] Added '/home/zahra/sofa/sofa-16.12/src/applications/plugins/SofaPython/python' to sys.path
[INFO]    [SofaPython] Added '/home/zahra/sofa/sofa-16.12/src/applications/plugins/SofaTest/python' to sys.path
[INFO]    [PluginManager] Loaded plugin: /home/zahra/sofa/sofa-16.12/build/lib/libSofaPython.so

result #3:
If I try to grasp the snake and move it, or even if I want to just change the position of it, sometimes I receive no error, but more times I receive this kinds of errors:

[ERROR]   [Mat] invertMatrix finds too small determinant, matrix = [-11.1054 -3.66721 -0,2.8 0 -0,1.52427 7.95794 -0]
[ERROR]   [Mat] invertMatrix finds too small determinant, matrix = [-0.58616 10.5192 -0,0 -2.8 -0,1.52427 0 -0]
...

or

 No convergence in  unbuilt nlcp gaussseidel function : error =13.9639 after1000 iterations

 No convergence in  unbuilt nlcp gaussseidel function : error =11.7298 after1000 iterations
...

These all happen when I try runSofa successively without any change.

By executing runSofa in v18.06, I receive this:

Before animating:

[INFO]    [runSofa] Loading automatically plugin list in /home/zahra/sofa/sofa18.06/build/v18.06/lib/plugin_list.conf.default
[INFO]    [SofaPython] Added '/home/zahra/sofa/sofa18.06/src/applications/plugins/SofaPython/python' to sys.path
[INFO]    [PluginManager] Loaded plugin: /home/zahra/sofa/sofa18.06/build/v18.06/lib/libSofaPython.so
[INFO]    [PluginManager] Loaded plugin: /home/zahra/sofa/sofa18.06/build/v18.06/lib/libCImgPlugin.so
[INFO]    [PluginManager] Loaded plugin: /home/zahra/sofa/sofa18.06/build/v18.06/lib/libSofaMiscCollision.so
[INFO]    [PluginManager] Loaded plugin: /home/zahra/sofa/sofa18.06/build/v18.06/lib/libSofaAllCommonComponents.so
The constructor with a QGLFormat is deprecated, use the regular contructor instead.
[ERROR]   [FileRepository] File icons/back.png NOT FOUND in :/home/zahra/sofa/sofa18.06/build/v18.06:/home/zahra/sofa/sofa18.06/build/v18.06:/home/zahra/sofa/sofa18.06/build/v18.06
[ERROR]   [FileRepository] File icons/home.png NOT FOUND in :/home/zahra/sofa/sofa18.06/build/v18.06:/home/zahra/sofa/sofa18.06/build/v18.06:/home/zahra/sofa/sofa18.06/build/v18.06

[ERROR]   [FileRepository] File docs/runsofa.html NOT FOUND in :/home/zahra/sofa/sofa18.06/build/v18.06:/home/zahra/sofa/sofa18.06/build/v18.06:/home/zahra/sofa/sofa18.06/build/v18.06

and after I hit the animate button:

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

I should also mention that “docs/runsofa.html”, “icons/home.png” and “icons/back.png” do exist.

I hope anyone can help me regarding this, it became a big problem and I do not know how to deal with it…

Is it possible that this error results from Ubuntu?

Thanks in advance,

Zahra

[Hugo]

Hi Zahra,

I noticed some of your errors as well. This is preoccupying that such an issue passed through the SOFA contributions.
We will investigate, thank you very much for your notice. If you don’t here from us, please poke us again by the end of next week.

Cheers,

Hugo

[Zahra]

Dear Hugo,

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

Best wishes,

Zahra

[Hugo]

Hi Zahra,

First of all, now SOFA v16.12 starts being a bit old. It’s good to remain a bit up-to-date, but I understand the need of stable release for simulation development.

Regarding your result #1 and #2, this looks strange and never occured with me. This may be due to your Python version, what do you have?

result #3:
– the invertMatrix error : it warns that the inverse of the system matrix includes very small values. This might come from a too strong sollicitation and FEM elements might have collapsed
– the nlcp gaussseidel error : it is a normal output if the constraint resolution (GaussSeider is the solver used to compute the solution of the constraint problem) did not find a solution with the tolerance and nb max of iterations given by the user.

Regarding the error from [FileRepository], it seems to be fixed in the latest master version.
But when animating, I never got a crash. I will try to recompile from scratch the v18.06 on my machine.

Best,

Hugo

[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]

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

[Hugo]

Hi Zahra,

Yes have you tried ?
You’re suppose to run cmake again (configure and generate) then recompile.
Keep us updated.

Hugo

[Hugo]

Dear @zahra,

as you noticed (with the [FileRepository] error) there was an issue caused by the fact that SofaGuiQt and runSofa had no idea were to find their resources (if not installed).
Adding and configuring some .ini files will fix that.

See the PR#758

Any upate about your issue #1 & #2?

Hugo

[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]

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

[ElDiwiny]

Hi Zahra,

I would be happy to try help you, I have faced many problems like that before, I can help you step by step. My skype ID is marwaeldiwiny1991.

[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

[ElDiwiny]

Hi Zahra,

You are so welcome, I will try to do my best, I will do a video about installation SOFA, and if doesnot help you, we can possibly do it on Saturday.

[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

[ElDiwiny]

Hi Zahra,

Kindly I have sent you an invitation. I will do my best as much as I can.

Best,
Marwa

[Hugo]

Thank you for your strong involvement @meldiwiny
Do not hesitate to let us know about the outcome of your discussion

Cheers

Hugo

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