[gmx-users] grompp allocating 0 atoms to a node

[Justin A. Lemkul]

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.

-Justin

Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:

> Hi all,
>
> I'm running a very simple system consisting of a globular protein with a
> ligand
> in a box of SPC water with counterions (ffG43a1 for all components).  I ran
> my
> 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
> 24
> 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    1059    1059    1056    1059    1056    1059    1056    1059
> 1056
>  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
>
>
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul at vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>
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========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

========================================