[gmx-users] Problem with gromacs in Cluster

[Justin Lemkul]

On 4/25/13 8:28 AM, Sainitin Donakonda wrote:
> Hey all,
>
> I recently ran 20ns simulation of protein ligand complex on cluster i used
> following script to run simulation
>
> grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o
> md_test.tpr
>
> mpirun -n 8 mdrun -s md_test.tpr -deffnm md_test -np 8
>
> *I saved this as MD.sh And then submited to cluster using following script*
>
> #!/bin/bash
> #BSUB -J testgromacs             # the job's name/array job
> #BSUB -W 120:00                       # max. wall clock time in hh:mm
> #BSUB -n 8,8                          # number of processors Min,Max
> #BSUB -o test/output_%J.log             # output file
> #BSUB -e test/errors_%J.log             # error file
> #BSUB -M 8192     #Memory limit in MB
>
> echo "Started at `date`"
> echo
>
> cd test
>
> echo "Running gromacs test in `pwd`"
>
> ./MD.sh
>
> echo "Finished at `date`"
>
>
> It gave result but when checked files .xtc and created RMSD plots in that
> x-axis of this plot i see only 8ns ...but in MD.MDP file i specified 20ns..
>
> Cluster Output says that "TERM_RUNLIMIT: job killed after reaching LSF run
> time limit.
> Exited with exit code 140". i gave maximum cluster time 120 hours..still it
> is not sufficient ..
>
> Can any body tell me  how do it split script i such  that i will get all
> 20ns simulation
>

You specified a given time limit for the job, and the run exceeded it.  Either 
specify more run time (if allowed) or run your job in shorter intervals that 
will finish within the maximum time limit.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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