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

[Peter Ahlström]

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)

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 force field contains standard interactions but uses a Buckingham like nonbonded interaction defined in the pairs list.

Enclosed are one topology file (21PO45s.top for the system), the force field files (smith..), the scripts and corresponding output (PO45s_mdA2* for two processors and PO45s_mdB7_2 for seven processors).
Due to size limitations the topology file for one molecule is not attached but can be found at 
http://www.adm.hb.se/~ahl/1PO45s.itp

I am very grateful if the gromacs-community could make me understand what goes on since I intend to run more mixed systems so that I can't split my molecules evenly over processors.

Regards
Peter

Dr. Peter Ahlström
School of Engineering
University College of Borås 
SE-501 90 Borås
Ph. +46-33-435 46 75 Fax +46-33-435 40 08
peter.ahlstrom at hb.se
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