Segmentation fault

[lomlrn]

Hi there, iam trying to get the newest 12.2.r1 to run. All what i get on my Debian box is


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Segmentation fault


I am using the current stable release of Debian 64 bit Linux:

Linux theo 2.6.32-5-amd64 #1 SMP Fri Sep 9 20:23:16 UTC 2011 x86_64 GNU/Linux

However. May it be possible that there is a mixing with a current installation of the intel compiler / mkl ?

Best regards. 

[Anders Blom]

Segmentation faults are unusual in ATK, but can occur in VNL if the proper graphics drivers are not present. I assume you are trying to launch "vnl"?

ATK is independent of other libraries and installed software so that is very rarely a problem. Your "uname" statement doesn't give away precisely which Debian version you have, that is found by "cat /etc/debian_version". It would be useful, then we can see if the problem can be reproduced by us.

That might take some time, however. Do you have another resource available for VNL, for the moment?

There might be a "crashlog.txt" file in the directory where you typed "vnl", if so, please send its contents to us.

[perfetti]

I got the same error when I am using this newly released ATK.

But I am using ubuntu. On the other hand, I've got a crashlog.txt, whose content is:
===================================================
 Traceback (most recent call last):
  File "./zipdir/NL/GUI/Main/Main.py", line 40, in main
  File "./zipdir/NL/GUI/MainWindow/MainWindow.py", line 16, in <module>
  File "./zipdir/NL/GUI/ResultBrowser/ResultViewer.py", line 21, in <module>
  File "./zipdir/NL/GUI/Graphics/Plots/NEB.py", line 8, in <module>
  File "./zipdir/NL/GUI/Graphics/NewPlot2D/NewPlot2D.py", line 3, in <module>
  File "./build/vnl/lib/python2.7/site-packages/matplotlib/__init__.py", line 133, in <module>
  File "./build/vnl/lib/python2.7/site-packages/matplotlib/rcsetup.py", line 19, in <module>
  File "./build/vnl/lib/python2.7/site-packages/matplotlib/colors.py", line 54, in <module>
  File "./build/vnl/lib/python2.7/site-packages/matplotlib/cbook.py", line 15, in <module>
  File "new.py", line 10, in <module>
    vector_a = [10.0, 0.0, 0.0]*Angstrom
NameError: name 'Angstrom' is not defined.



==================================================
new.py is a file I created long ago, and this error is the same old error that cause my atk cannot run on linux.  But I don't know how to clean it.

[Anders Blom]

Which Ubuntu version, exactly? We have seen some problems on 11.10, may be the same thing that occurs on Debian.

[Anders Blom]

Oh, wait, hang on. "perfetti", your problem may be completely trivial and different (or not).

What is this file "new.py"? Where is it located, what are you trying to do, precisely, when you get this error?

A Python file called new or new.py is a very dangerous thing that should be avoided at all times. It can only cause problems.

[lomlrn]

> cat /etc/debian_version
>> 6.0.2

The problem arises when trying to launching vnl, yes. It does also happen, if i want to run a test job with atk-python just at the console. I have also realized, that atk-python seems to be linked against libGLU* (and others). May be this is causing the trouble.

Using that platform

> cat /etc/redhat-release
>> Scientific Linux SL release 5.5 (Boron)

let run the very same ATK version without problems.


 

[Anders Blom]

We will look into it.

[perfetti]

new.py is a file that I created before, and I just named it casually.
The software stopped working that time: After I click the desktop icon, it appears for two seconds, and then disappear.
The new.py was in the home directory of QuantumWise, however, after i move it , either to the trash can, or to the desktop, the software can show up as normal after clicking. The only problem has changed to segmentation fault.

I am using ubuntu linux 2.6.38-8-generic.

Oh, wait, hang on. "perfetti", your problem may be completely trivial and different (or not).

What is this file "new.py"? Where is it located, what are you trying to do, precisely, when you get this error?

A Python file called new or new.py is a very dangerous thing that should be avoided at all times. It can only cause problems.

[Anders Blom]

Ok, so one should never use a Python file called new or new.py, we learned that

As for the segfault, can you please check the output of

locate libGL

and esp. look for libGLU. Which Ubuntu are you using (perfetti)? It may be necessary to install libGLU manually; we cannot ship it with ATK since it's licensed under GPL.

[Anders Blom]

It would be of great help for us, when troubleshooting this issue, to know the output of

Code

ldd atkpython/lib/python2.7/_NLEngine.so

Issue the command in the ATK 12.2 installation directory.

[perfetti]

It would be of great help for us, when troubleshooting this issue, to know the output of

Code

ldd atkpython/lib/python2.7/_NLEngine.so

Issue the command in the ATK 12.2 installation directory.

The output is like this: linux-vdso.so.1 =>  (0x00007fff053ff000)    libintlc.so.5 => not found    libsocorro.so => not found    libmkl_intel_lp64.so => not found    libmkl_intel_thread.so => not found    libmkl_lapack.so => not found    libmkl_core.so => not found    libiomp5.so => not found    libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007fd5ed4c9000)    libRocketFuel2.so => not found    librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007fd5ed2c1000)    libpng12.so.0 => /lib/x86_64-linux-gnu/libpng12.so.0 (0x00007fd5ed099000)    libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007fd5ece81000)    libjpeg.so.62 => /usr/lib/x86_64-linux-gnu/libjpeg.so.62 (0x00007fd5ecc5d000)    libGLU.so.1 => /usr/lib/libGLU.so.1 (0x00007fd5ec9ed000)    libGL.so.1 => /usr/lib/fglrx/libGL.so.1 (0x00007fd5ec7e8000)    libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007fd5ec4e2000)    libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fd5ec25c000)    libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007fd5ec046000)    libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fd5ebcb1000)    /lib64/ld-linux-x86-64.so.2 (0x00007fd5eebd6000)    libXext.so.6 => /usr/lib/x86_64-linux-gnu/libXext.so.6 (0x00007fd5eba9e000)    libX11.so.6 => /usr/lib/x86_64-linux-gnu/libX11.so.6 (0x00007fd5eb764000)    libxcb.so.1 => /usr/lib/x86_64-linux-gnu/libxcb.so.1 (0x00007fd5eb547000)    libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007fd5eb343000)    libXau.so.6 => /usr/lib/x86_64-linux-gnu/libXau.so.6 (0x00007fd5eb140000)    libXdmcp.so.6 => /usr/lib/x86_64-linux-gnu/libXdmcp.so.6 (0x00007fd5eaf3a000)

[perfetti]

Ok, so one should never use a Python file called new or new.py, we learned that

As for the segfault, can you please check the output of

locate libGL

and esp. look for libGLU. Which Ubuntu are you using (perfetti)? It may be necessary to install libGLU manually; we cannot ship it with ATK since it's licensed under GPL.

The output of locate libGL is like this
/home/student/XCrySDen-1.5.25-bin-semishared/external/lib/libGL.so
/home/student/XCrySDen-1.5.25-bin-semishared/external/lib/libGL.so.1
/home/student/XCrySDen-1.5.25-bin-semishared/external/lib/libGL.so.1.5.070200
/home/student/XCrySDen-1.5.25-bin-semishared/external/lib/libGL.so.1.5.071000
/home/student/XCrySDen-1.5.25-bin-semishared/external/lib/libGLU.so
/home/student/XCrySDen-1.5.25-bin-semishared/external/lib/libGLU.so.1
/home/student/XCrySDen-1.5.25-bin-semishared/external/lib/libGLU.so.1.3.070200
/home/student/XCrySDen-1.5.25-bin-semishared/external/lib/libGLU.so.1.3.071000
/usr/lib/libGL.so
/usr/lib/libGLEW.so.1.5
/usr/lib/libGLEW.so.1.5.2
/usr/lib/libGLEWmx.so.1.5
/usr/lib/libGLEWmx.so.1.5.2
/usr/lib/libGLU.so.1
/usr/lib/libGLU.so.1.3.071000
/usr/lib/fglrx/libGL.so
/usr/lib/fglrx/libGL.so.1
/usr/lib/fglrx/libGL.so.1.2
/usr/lib/mesa/libGL.so.1
/usr/lib/mesa/libGL.so.1.2
/usr/lib32/libGL.so
/usr/lib32/libGLU.so
/usr/lib32/libGLU.so.1
/usr/lib32/libGLU.so.1.3.071000
/usr/lib32/fglrx/libGL.so.1
/usr/lib32/fglrx/libGL.so.1.2
/usr/lib32/mesa/libGL.so.1
/usr/lib32/mesa/libGL.so.1.2
(now the new.py problem is gone, and I only got this segmentation fault problem)

[Anders Blom]

Nothing out of the ordinary here, the unresolved dependencies are ATK libraries which are included in the package, so they will be found when ATK loads. And anyway, missing libraries don't result in segfaults, so the reason for checking this is to see if it finds some incompatible library. Our developers will take a look at this.

A few other questions:

• Is this Ubuntu 11.10 or which version?
• Can you run "glxgears"?
• What graphics card is installed, with which drivers? I would have expected to see links to NVidia or ATI drivers, but perhaps for Mesa drivers you wouldn't anyway; ATK should run anyway...
• This is on the same machine where 11.8.2 runs fine?

[perfetti]

A few other questions:

• Is this Ubuntu 11.10 or which version?

It's Ubuntu 11.04.

• Can you run "glxgears"?

Yes.

• What graphics card is installed, with which drivers? I would have expected to see links to NVidia or ATI drivers, but perhaps for Mesa drivers you wouldn't anyway; ATK should run anyway...

It's ATI Technologies Inc FirePro V4800.

• This is on the same machine where 11.8.2 runs fine?

This one doesn't work,neither.
[/list]

And I got this on the terminal when it crashed:QGLShader::link: "Vertex shader(s) linked, fragment shader(s) linked.
"
QGLShader::link: "Vertex shader(s) linked, fragment shader(s) linked.
"
QGLShader::link: "Vertex shader(s) linked, fragment shader(s) linked.
"
QGLShader::link: "Vertex shader(s) linked, fragment shader(s) linked.
"
QGLShader::link: "Vertex shader(s) linked, fragment shader(s) linked.
"
QGLShader::link: "Vertex shader(s) linked, fragment shader(s) linked.
"
Segmentation fault

Thanks everyone.

[Anders Blom]

I see - well, in some sense that's good news, it means at least we didn't do anything special in 12.2 that caused this. Thus, more likely it's a problem with your graphics driver. You have a good graphics card, but are you making the most of it, meaning, are you running with vendor drivers, or those which came with Ubuntu? The difference (esp. for 3D) is huge.

This problem has been reported elsewhere for the ATI 4800 card: https://bugs.launchpad.net/mixxx/+bug/656241/ Comment 76 here (pointing to comment 65) has some tips that seemed to work for that user (and indeed, the real advise is above to install the latest vendor graphics driver).

http://mixxx.org/forums/viewtopic.php?f=3&t=2464&start=10#p9371 might be useful too...

Sorry about this - 3D graphics and Linux can be a bit challenging, but it's not really anything to do with ATK...