[gmx-users] Segmentation fault while running MD simulation

[rainy908 at yahoo.com]

Hi,

The relevant lines of my script are the following:

line 27: # Run MD and write output to /nas2 disk
line 28: $MDRUN -v -nice 0 -np $NSLOTS -s npg3_4.tpr -o npg3_4.trr -c
confout.gro -g npg3_4.log -x npg3_4.xtc -e npg3_4.edr
line 29:
line 30: # MDRUN completes: now make the next run file for a further 200 ps,
to be run by next job
line 31: $TPBCONV -s npg3_4.tpr -f npg3_4.trr -e npg3_4.edr -o npg3_4_2.tpr
-extend 200000


Since line 31 would be carried out after line 28, I'm not sure why the
comment "-s: command not found" is relevant?

Lily

2009/11/13 Mark Abraham <Mark.Abraham at anu.edu.au>

> rainy908 at yahoo.com wrote:
>
>> Hi all,
>>
>> I've encountered a problem while trying to run Gromacs on my
>> coarse-grained molecule.  I've already performed the initial energy
>> minimization.  I tried to run the inital MD simulation, but the job was cut
>> short due to a segmentation fault, as mentioned in the output file:
>>
>> ^Mstep 0^Mstep 100, will finish Wed Dec 16 16:55:17 2009^Mstep 200, will
>> finish Wed Dec 16 07:04:11 2009^Mstep 300, will finish Wed Dec 16 12:59:33
>> 2009^Mstep 400, will finish Wed Dec 16 09:02:03 2009^Mstep 500, will finish
>> Wed Dec 16 12:12:01 2009^Mstep 600, will finish Wed Dec 16 14:18:47
>> 2009^Mstep 700, will finish Wed Dec 16 15:49:22 2009^Mstep 800, will finish
>> Wed Dec 16 13:29:16 2009^Mstep 900, will finish Wed Dec 16 14:45:15
>> 2009^Mstep 1000, will finish Wed Dec 16 15:46:03 2009
>>
>> /opt/gridengine/default/spool/
>> compute-0-7/job_scripts/182710: line 28: 18851 Segmentation fault
>>  (core dumped) $MDRUN -v -nice 0 -np $NSLOTS -s npg3_4.tpr -o npg3_4.trr -c
>> confout.gro -g npg3_4.log -x npg3_4.xtc -e npg3_4.edr
>> /opt/gridengine/default/spool/compute-0-7/job_scripts/182710: line 31: -s:
>> command not found
>>
>
> So what's on line 31 of your submission script? The above is just stderr
> and stdout, which are not the main output. What's in the .log file?
>
> Mark
>
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