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.abra...@anu.edu.au> > 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 > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php