[gmx-users] Problems with parallel runs with special topology (SEGV 11)
David van der Spoel
spoel at xray.bmc.uu.se
Tue Oct 12 14:17:16 CEST 2004
On Tue, 2004-10-12 at 12:23, Peter Ahlström wrote:
> At present I try to run parallell runs of 21 polymeric molecules (using GMX 3.2.1), each one consisting of 945 atoms and traversing several boxes. I have got a problem with SEGV error if a molecule happens to be split between 2 processors. (This problem I have sean also with Gromacs 1.6.*, 2.* and further on)
This might be related to the "no water on processor 0" problem which was
fixed recently, IIRC that was before 3.2.1 (doesn't say in the release
> Also, the mdrun appears to have problems to finish when running in parallel, after most of the results and final files are printed the
> program appears to get stuck.
> Gromacs was recompiled and run on a Linux-cluster using mpich.
The not finishing problem is worked around for MPICH in the next
You could try the cvs code.
> 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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