[gmx-users] Increasing performance of siumulation in cluster

[Mark Abraham]

There are lots of things you might do, but when we don't know what's in the
simulation or anything about the hardware, nobody can tell.

Mark


On Thu, May 30, 2013 at 2:16 PM, Sainitin Donakonda <saigro16 at gmail.com>wrote:

> 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
> MD_first10.tpr
>
> 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
>
> #!/bin/bash
> #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`"
> echo
>
> cd /home/sample/
>
> echo "Running gromacs test in `pwd`"
>
> ./MD.sh
>
> 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
> simulation*
>
> Thanks
>
> Nitin
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