[gmx-users] parallel run crashes only when shuffled

Mikko Huhtala mhuhtala at abo.fi
Thu Oct 3 10:17:09 CEST 2002

David van der Spoel writes:
 > I forgot to add, yes shuffle coordinates manually and topology manually.

How does this add to what you wrote before? :-)

I guess the question is what does 'shuffle manually' mean? How does
grompp decide what to put on which processor? It reads the topology
file in the order it is written and divides the system in chunks of
approximately equal size (without breaking molecules), correct? So
manual shuffling means reordering the lines in the [ molecules ]
section of the topology and making the coordinate file match.


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