rainy...@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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