[gmx-users] Parallel Problem
spoel at xray.bmc.uu.se
Mon Jun 14 06:32:39 CEST 2004
On Mon, 2004-06-14 at 00:37, Ashish Misra wrote:
> Hi all,
> I am having a problem getting Gromacs to run in parallel. When running
> as a serial job, the system runs fine.
> While running in parallel, I get the following error lines when running
> grompp It seems to me that there is a problem when atoms are being
> distributed across the nodes.
> Moltype PEG SOL #atoms
> CPU 0 2 2591 8013
> CPU 1 2 2591 8013
> CPU 2 2 2590 8010
> CPU 3 2 2590 8010
> Made a shuffling table with 10370 entries [molecules]
> processing coordinates...
> Shuffling coordinates...
> Entering shuffle_xv
> Sorting coordinates for 8 copies of molecule PEG
> Sorting coordinates for 10362 copies of molecule SOL
Have you manually shuffled the coordinates before you ran grompp?
The order of the atoms does not match between topology and coords. What
happens when you run without -shuffle?
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
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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