[gmx-users] Question about parallazing Gromacs

[David van der Spoel]

Qiao Baofu wrote:
> Hi all,
> 
> I have a question about parallazing gromacs: I run the same system on a 
> cluster of my institute and my local computer,
>      Cluster:* * dual processor boards AMD Opteron 270 (Dual-Core), 2.0 GHz
>      Local computer: AMD X86-64 Cpu, double precision
> 
> 1. The cluster (nodes=3:ppn=4) runs  87950 MD steps  for one hour
> 2. The cluster (nodes=5:ppn=4) runs  42749 MD  steps  for one hour
> 3. The cluster (nodes=11:ppn=4) runs  5962 MD  steps  for one hour
> 3. My local computer runs  179090 MD steps  For 1hour 51 mintues.
> 
> It is verry strange that the more cpus I use, the slowest the gromacs 
> runs.!!
> 
> Who knows what's wrong with my job?   And for paralleled gromacs, how 
> many cpus is prefered?
> 
> 
> 
> The grompp command is:   grompp -np 12 -o md3.mdp -c md3in.gro -p 
> MCl.top -o md3.tpr
> 
> The following is one of the the job scripts on the cluster:
> 
> #
> # MD NTP(Berendsen&Berendsen, T=425&P=1bar),200ps tau_p=4
> #
> #
> #!/bin/bash
> #PBS -N "md3"
> #
> #PBS -l walltime=01:00:00,nodes=3:ppn=4
> #
> #PBS -m abe
> #
> #PBS -o md3.out
> #
> #PBS -e md3.err
> #
> #
> cd /work/fias/qiao/time_checking/nodes3/
> /usr/local/Cluster-Apps/lam/gcc/64/7.1.1/bin/lamboot $PBS_NODEFILE
> /usr/local/Cluster-Apps/lam/gcc/64/7.1.1/bin/mpirun -np 12 mdrun -v -s 
> md3.tpr -x md3 -e md3 -c md3 -g md3
> exit 0
> 
>  
> -- 
> Sincerely yours,
> **********************************************
> Baofu Qiao, PhD
> Frankfurt Institute for Advanced Studies
> **********************************************
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
try running on one quad node.

gromacs 3.3 does not scale very well, we're working on improving that 
for 4.0.

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++