[gmx-users] Increasing performance of siumulation in cluster

Sainitin Donakonda saigro16 at gmail.com
Fri May 31 10:34:13 CEST 2013

Hi all,

I recently ran 20ns simulation in linux cluster.

Used following script for MD simulation

#This is the first simulation MD.mdp file contains 20 ns setup
grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o

mpirun -n 16 mdrun -s MD_first10.tpr -deffnm MD_first10 -np 16

#This extends 10 ns simulation
tpbconv -s MD_first10.tpr  -o md_extended.tpr -extend 10000

mpirun -n 16 mdrun -s md_extended.tpr -deffnm MD_first10 -cpi
MD_first10.cpt -append -np 16

and bsub file

#BSUB -J testgromacs             # the job's name/array job
#BSUB -W 120:00                       # max. wall clock time in hh:mm
#BSUB -n 16,16                          # number of processors Min,Max
#BSUB -o /home/sample/output_%J.log             # output file
#BSUB -e /home/sample/errors_%J.log             # error file
#BSUB -M 8192     #Memory limit in MB

echo "Started at `date`"

cd /home/sample/

echo "Running gromacs test in `pwd`"


echo "Finished at `date`"
*It ran for total 5 days but didnt give all 20ns simulation ..So i checked
log file for performance *
*Parallel run - timing based on wallclock.*
*               NODE (s)   Real (s)      (%)*
*       Time: 359019.178 359019.178    100.0*
*                       4d03h43:39*
*                      (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)*
*Performance:    445.015     24.708      2.407      9.973*
*It looks like this gave very performance 2.4 ns per 9 hours..this looks
very low for me.. Can any body tell me how to increase performance of



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