[gmx-users] two questions on multiple simulations and stochastic dynamics

David van der Spoel spoel at xray.bmc.uu.se
Mon Apr 26 15:09:01 CEST 2004

On Mon, 2004-04-26 at 14:31, F.Hao at chem.rug.nl wrote:
> Hi, all:
>     I have two questions. 
> 1) I want to perform multiple simulation on one system and run them in 
> parallel with gmx3.2.1. What I did is:
> grompp -v -f md0.mdp -c pr.gro -p x.top -o topol0.tpr
> grompp -v -f md1.mdp -c pr.gro -p x.top -o topol1.tpr
> grompp -v -f md2.mdp -c pr.gro -p x.top -o topol2.tpr
> grompp -v -f md3.mdp -c pr.gro -p x.top -o topol3.tpr
> Then I sunmit this job to a cluster which had one processor on each node
> by using "qsub myjob". myjob is a script:
> #PBS -l nodes=4,walltime=240:00:00
> cd working_directory/
> lamboot
> mpirun -np 4 mdrun -multi -np 4 -s topol.tpr
> It did produce four trajectories. But all four simulations were running 
> on the first processor and leave the rest three nodes idle. Is it possible 
> to let one subjob run on one of the four processors or I should do 
> grompp -np 4 -v -f md0.mdp -c pr.gro -p x.top -o topol0.tpr ...?
> Any hints will be sincerely appreciated!

It is a recently discovered bug. I think Berk has fixed it in CVS.

David van der Spoel, PhD, Assist. 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://xray.bmc.uu.se/~spoel

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