[Chimera-users] segmentation fault

Greg Couch gregc at cgl.ucsf.edu
Fri Mar 2 11:09:22 PST 2012

On Fri, 2 Mar 2012, nauton lionel wrote:

> Hello
> I send this Email, because I can't used chimera-1.6 for linux 64 bits ( 
> 2-29-2012 version) it crash with this comment "segmentation fault", 
> everytime I tried to load pdb or mol2 files.
> and I don't have this problem with chimera-1.6rc for linux-32 bits
> or chimera-1.6( 2-29-2012 version)
> and chimera-1.5.3 for linux 64bits works well on the same PC
> I used fedora 16...


To help me debug this, please send email to chimera-bugs with (1) the 
output of CHIMERA/bin/linuxdist, (2) the output of /usr/bin/glxinfo, and 
(3) a backtrace of where the segmentation fault occurs.  Substitute for 
CHIMERA, the actual path to your chimera installation.

To get the backtrace, use a terminal window, and enable core dumps by 
(assuming you are using the bash shell):

 	ulimit -c unlimited

then run chimera in debug mode:

 	CHIMERA/bin/chimera --debug

and do what you need to do to get a segmentation fault.  That should 
produce a core file.  The name of the core file varies with the Linux 
distribution, traditionally it is named "core", but it might be named 
"core.PID" where PID was the process identifier of the chimera process, or 
it might be placed in a different directory, like /tmp.  Once you have 
located the core file, run gdb on it:

 	gdb CHIMERA/bin/python2.7 core

and at the gdb prompt, type bt to get the backtrace.  Then copy & paste 
the backtrace into your email.

 	Thank you,


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