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
--
========================================
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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