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
**********************************************
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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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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