Re: [PyMOL] Linux FC3 upgrade causing pymol core dump

[Stefano T. <tr...@vm...>]

Do you have nvidia drivers?
If so, may be you came across the same problem I have:

I have installed the latest version of Mandriva Linux on a AMD 
Athlon(tm) MP 2400+ PC with
a Quadro4 900 XGL graphich card and the NVIDIA-Linux-x86-1.0-7174 driver

When I run pymol and load a pdb file, the program crashes with the 
following message:

 CmdLoad: "GLGA/sup_models/pdb1rzu.ent" loaded as "pdb1rzu".
*** glibc detected *** double free or corruption (!prev): 0x08a76ba0 ***
/usr/local/pymol-0.98-precompiled/pymol.com: line 14: 16877 
Aborted                 (core dumped) $PYMOL_PATH/pymol.exe $*

However, if I set auto_show_lines=off and auto_show_nonbonded=off BEFORE 
loading the molecule, the program loads the PDB file without crashing 
(and without showing any graphical object, of course). Then, I can use 
the "show" command/button for any type of representation (ribbons, 
nonbonded, sticks, ...) EXCEPT the "lines" representation, which causes 
a program crash.

This happens with both distributed binary and self compiled PyMol 
versions. I have tried version 0.97 and 0.98 with the same results.

Then, browsing the internet, I came across the following message from 
Warren:

http://sourceforge.net/mailarchive/message.php?msg_id=11735911

and I decided to try the 0_99beta01 version 
(http://delsci.com/beta/pymol-0_99beta01-bin-linux-x86-nvidia-test.tgz), 
which seems to solve my problem for the moment.



gerwald jogl wrote:

> Hi everyone,
>
> Just wanted to send in a description of the following situation:
> I was using pymol 0.98 precompiled on FC3 today and did an automatic 
> update during the day (therefore, sorry but I don't know which 
> packages where upgraded :-(
> Afterwards, pymol would start up, but core dump immediately after 
> loading a pdb file.
> The same is happening with the 0.97 precompiled version and with my 
> own compile of the 0.98 source code.
> This is what I get:
> /xsoft/pymol-0.97precompiled/pymol.com: line 14: 19692 Segmentation 
> fault      (core dumped) $PYMOL_PATH/pymol.exe $*
>
> or my compile:
> /xsoft/pymol-0.98/pymol.com: line 2: 19785 Segmentation fault      
> (core dumped) /usr/bin/python 
> /usr/lib/python2.3/site-packages/pymol/__init__.py $*
>
>
> Any comments on this would be greatly appreciated...
> Gerwald
>
>
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-- 

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Stefano Trapani, PhD

Laboratoire de Virologie Moleculaire & Structurale
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