[gmx-users] grompp allocating 0 atoms to a node
Justin A. Lemkul
jalemkul at vt.edu
Fri Dec 7 15:46:42 CET 2007
Just to clarify something in my previous message - using grompp with and without
-shuffle gave the same output, which is given in my first message.
Sorry for any confusion.
Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
> Hi all,
> I'm running a very simple system consisting of a globular protein with a
> in a box of SPC water with counterions (ffG43a1 for all components). I ran
> normal routine of minimization, equilibration, and production, but I've been
> getting poor scaling and decided to try again with a different number of
> processors. The system contains roughly 39,000 atoms, and I initially used
> processors. Now I would like to try 36. When I run grompp, it allocates 0
> atoms to the first node:
> Division over nodes in atoms:
> 0 3135 1059 1059 1059 1059 1059 1059 1059
> 1059 1059 1059 1059 1059 1059 1059 1059 1059
> 1059 1059 1059 1056 1059 1056 1059 1056 1059
> 1059 1056 1059 1056 1059 1056
> I tried the -shuffle option, just to see if it would change anything,
> although I
> didn't expect that it would do much since my system is so simple.
> The Gromacs version is 3.3, and I have not tried newer versions for
> consistency's sake with some older simulations we have done.
> Has anyone ever experienced anything like this? Is there anything wrong? It
> seems odd to allow zero atoms to be on one node.
> Thanks for any insights,
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul at vt.edu | (540) 231-9080
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
jalemkul at vt.edu | (540) 231-9080
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