[gmx-users] Increasing performance of siumulation in cluster

[Sainitin Donakonda]

Hi Mark,

I forgot to mention about simulation it is protein ligand simulation which
contains one protein and ligand with 20000 solute molecules..and regarding
hardware of cluster which is in my university as follows

CPUs  AMD Opteron 6274   number of cores  5888   th. peak performance  51.8
TFlops   compute nodes  4-way nodes *Saxonid* with 64 cores   nodes with 64
GB RAM  48   nodes with 128 GB RAM  24   nodes with 256 GB RAM  12   nodes
with 512 GB RAM  8
Can you now suggest some methods which i can use to optimize to increase
performance

Thanks,
Nitin


On Fri, May 31, 2013 at 10:54 AM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> 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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