Re: Segmentation fault (core dumped) in MDAnalysis

[Oliver Beckstein]

Hi,

could you please let us know

1) which version of MDAnalysis did you download
2) how did you compile and install it

Then start fresh:

python setup.py clean
python setup.py build 2>&1 build.log
python setup.py install 2>&1 install.log

Show us the output from the build and install stage (in the log files).

Please reply to the mailing list address because there are more people there that can help, in particular people who use RHEL (which I don't have personally available).

Thanks,
Oliver

On 30 Mar, 2012, at 15:19, xianqiang sun wrote:

> Dear Dr. Orbeckst,
>
> I have successfully installed the MDAnalysis according to the installation guide. My system is: RHEL-2.6.32-220.el6.x86_64, and the python is Python 2.6.6. However, A error information which shows Segmentation fault happens. The detail information is as following:
>
> [leos@leost420 ~]$ python
> Python 2.6.6 (r266:84292, Sep 12 2011, 14:03:14)
> [GCC 4.4.5 20110214 (Red Hat 4.4.5-6)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import MDAnalysis
> Segmentation fault (core dumped)
>
>
> I am confused with this bug. Is there any possible way that I can solve this bug to make sure that I can use MDAnalysis?
>
> Thanks so much for your kind help and your reply is appreciated,
>
> Best regards,
> Xianqiang
>
> --
> Xianqiang Sun
> Division of Theoretical Chemistry and Biology
> School of Biotechnology
> Royal Institute of Technology
> S-106 91 Stockholm, Sweden

--
Oliver Beckstein * orbe...@gmx.net
skype: orbeckst * orbe...@gmail.com

[leo]

Dear all,

I have successfully installed the MDAnalysis according to the
installation guide. My system is: RHEL-2.6.32-220.el6.x86_64, and the

python is Python 2.6.6. However, error information which shows

Segmentation fault happens. The detail information is as following:

[leos@leost420 ~]$ python
Python 2.6.6 (r266:84292, Sep 12 2011, 14:03:14)
[GCC 4.4.5 20110214 (Red Hat 4.4.5-6)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import MDAnalysis
Segmentation fault (core dumped)


I am confused with this bug. Is there any possible way that I can
solve this bug to make sure that I can use MDAnalysis?

Best regards,
Xianqiang

[Oliver Beckstein]

Hi,

I only realised a few minutes after I sent my first email that you also posted to the mailing list, so I really did not have to remind you to do so.

In addition to the information I asked for in my previous email you could also try to run python in the gdb debugger; possibly that tells us in which library the segfault occurs.

Try the following:

$ which python

That gives the full path to your python (perhaps /usr/bin/python, mine is /opt/local/bin/python).

Then start gdb

$ gdb

Inside gdb we'll try to run python and the import command. In the following, "(gdb)" is the debugger prompt, only type commands on the (gdb) line but without the prompt, everything else is the output I get:

Use whatever path you got for your python for the 'file' command below.

#----------
(gdb) file /opt/local/bin/python
(gdb) run -c "import MDAnalysis; print MDAnalysis.__version__"
Starting program: /opt/local/bin/python -c "import MDAnalysis; print MDAnalysis.__version__"

Program received signal SIGTRAP, Trace/breakpoint trap.
0x00007fff5fc01028 in __dyld__dyld_start ()
(gdb) continue
Continuing.
....
.... lots of warnings about Could not find object file ...
....
....
Reading symbols for shared libraries . done
Reading symbols for shared libraries . done
Reading symbols for shared libraries . done
0.7.6-devel

Program exited normally.

#-----------

With a bit of luck the debugger stops where the segfault occurs and using the 'where' command

(gdb) where

you might be able to pinpoint the shared library. That would be a necessary first step in debugging.

Maybe someone else has a better idea how to do this – I never came across this problem before.

Oliver

[xianqiang sun]

Hi Oliver,

Thanks so much for your kind help. I tried to check these the installation according to your suggestion. However, I didn't run the check successfully. Therefore, I have reinstalled python, numpy and scipy et. al. Then, MDAnalysis_0.7.5.1 works now.

Thanks and regards,

Xianqiang

--
You received this message because you are subscribed to the Google Groups "MDnalysis discussion" group.
To post to this group, send email to mdnalysis-...@googlegroups.com.
To unsubscribe from this group, send email to mdnalysis-discus...@googlegroups.com.
For more options, visit this group at http://groups.google.com/group/mdnalysis-discussion?hl=en.

[Oliver Beckstein]

On Thursday, 3 May 2012 07:36:29 UTC-7, leo wrote:

Thanks so much for your kind help. I tried to check these the installation according to your suggestion. However, I didn't run the check successfully. Therefore, I have reinstalled python, numpy and scipy et. al. Then, MDAnalysis_0.7.5.1 works now.

Thanks so much for reporting back; this might be useful for anyone else who might encounter the same problem. I am glad it is working now.

Oliver