[gmx-users] Question about parallazing Gromacs

Qiao Baofu qiaobf at gmail.com
Wed Sep 13 12:42:37 CEST 2006

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

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

The following is one of the the job scripts on the cluster:

# MD NTP(Berendsen&Berendsen, T=425&P=1bar),200ps tau_p=4
#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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