[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:
> Hello,
> 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
notes though...)

> 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.
> ________________________________________________________________________
> 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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