Assigning 0 atoms to a node does not seem very useful.
But your protein seems to have 3135 atoms and you are
probably using constraints, then grompp can not split the protein.
So you should not run on more nodes than the total number of atoms
divided by 3135: 12 nodes.
Gromacs 4 will solve all these issues.
Berk.
From: "Justin A. Lemkul" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <[email protected]>
To: Discussion list for GROMACS users <[email protected]>
Subject: Re: [gmx-users] grompp allocating 0 atoms to a node
Date: Fri, 7 Dec 2007 09:46:42 -0500
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" <[EMAIL PROTECTED]>:
> 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
> [EMAIL PROTECTED] | (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
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
========================================
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