[gmx-users] using gromacs in parallel
spoel at xray.bmc.uu.se
Thu Nov 13 23:15:01 CET 2003
On Thu, 2003-11-13 at 23:09, Madhuri Agashe wrote:
> I want to run Gromacs on a cluster of 46 processors. The Gromacs
> installed on these clusters is compiled with MPI.
> But when I ran gromacs MD run, we found that it was running only on a
> single node and all the other nodes were idle.
> The command I ran was the usual
> mdrun -s 2.tpr -o 1.trr -o 4.gro -e md01.edr
First off, please turn off HTML formatting in your mail program!
You have to create a multiprocessor topology with grompp (e.g. -np 2)
and then start mdrun using mpirun (or similar).
> What modifications does the command need to enable it to run on all
> available nodes??
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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