Well, there is a common misconception with parallel computing. Usually, you
will have an optimun number of processors that guarantees the best
performance. More or less than that number will result in a decreased
performance and longer computation times. The optimum number of processors
will depend on the particular problem and the hardware/software
configuration of your cluster, but for instance, in my case for docking
experiments I've found that 4 cpu's is Ok. If I try to use more than 4 cpus
the performance is worst. The same is for less than 4 cpu's. You have to
find your optimum making some tests with your settings. To do that you can
start your simulation and interrupt after a while to have some data logged
in the log file. Then, from the information in that log file you can
estimate the time that the whole task will take and compare using more or
less number of processors until you find your optimum value.
I hope it helps.
Regards,
César.-
----------------------------------------------------------------------
Message: 1
Date: Wed, 13 Sep 2006 12:42:37 +0200
From: "Qiao Baofu" <[EMAIL PROTECTED]>
Subject: [gmx-users] Question about parallazing Gromacs
To: gmx-users@gromacs.org
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset="iso-8859-1"
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
**********************************************
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
http://www.gromacs.org/pipermail/gmx-users/attachments/20060913/fdee271a/attachment-0001.html
_______________________________________________
gmx-users mailing list gmx-users@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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
