[gmx-users] Problem with gromacs in Cluster
fracarb at myopera.com
Thu Apr 25 14:58:08 CEST 2013
You can split the simulation in different part (for example 5 ns each),
every time you'll finish one you will extend it adding more time.
My cluster uses a different "script system" than yours so I can't help
with it, but basically you have to submit more than 1 job with different
command to execute:
1) first production
mpirun -n 8 mdrun -s md_test.tpr -deffnm md_test -np 8
2) modify the tpr file
tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
3) next X ns
mpirun -n 8 mdrun -s next.tpr -cpi previous.cpt
4) modify the tpr file
5) production md
and so on
with qsub you can submit a depending job (-hold_jid) that will run only
when the previous step will finish, in your case there should be a
similar way to do it.
On Thu, 25 Apr 2013, at 12:28 PM, Sainitin Donakonda wrote:
> Hey all,
> I recently ran 20ns simulation of protein ligand complex on cluster i
> following script to run simulation
> grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o
> 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
> #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`"
> cd test
> echo "Running gromacs test in `pwd`"
> 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
> Cluster Output says that "TERM_RUNLIMIT: job killed after reaching LSF
> time limit.
> Exited with exit code 140". i gave maximum cluster time 120 hours..still
> is not sufficient ..
> Can any body tell me how do it split script i such that i will get all
> 20ns simulation
> Thanks in advance ,
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fracarb at myopera.com
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