[gmx-users] Problems with parallel runs with special topology (SEGV 11)

[David van der Spoel]

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
version.

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
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>