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

[David van der Spoel]

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.
________________________________________________________________________
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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