[gmx-users] parallel run crashes only when shuffled
lindahl at stanford.edu
Thu Oct 3 10:26:04 CEST 2002
Mikko Huhtala wrote:
>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.
Yes - I've done that quite a lot for lipid bilayers when running in
Assume you have 256 DPPC lipids and 100 waters per lipid (just an
example, 100 is way too much).
The first time I run a new system I use the -shuffle option. The
resulting .gro file will then be shuffled.
Instead of keeping on deshuffling and reshuffling the files, I just
created a new topology
where the molecules section would look like (for 4 processors)
This order is the same as the shuffled .gro file, so then you can just
forget about the shuffling. grompp
won't split a molecule over processors if you are constraining ALL
bonds, and if you're not constraining
all bonds it's quite OK to split it...
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