[gmx-users] Re: Question about parallazing Gromacs (Qiao Baofu)

[Cesar Araujo]

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" <qiaobf at gmail.com>
> Subject: [gmx-users] Question about parallazing Gromacs
> To: gmx-users at gromacs.org
> Message-ID:
> <6a91f07b0609130342j5f2f5f8di482c48c9a0e9fb2d at mail.gmail.com>
> 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
> **********************************************
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