[gmx-users] mdrun hangs on nodes of P655+ aix 5.2

Carsten Kutzner ckutzne at gwdg.de
Mon Jul 31 10:21:29 CEST 2006

Hi Art,

you run a small system (4800 atoms) on a lot of CPUs (64). In the md.log file
it says that you have 2 grid points per CPU for the parallel FFT (local_nx).
There is indeed one limitation to the PME code in 3.3.1: you need at least
0.5*pme_order grid points per CPU. Your pme_order is 6. So you should try to
either reduce the pme order to 4 or to reduce the number of CPUs for that
system, or reduce the fourierspacing to get a larger grid :) Unfortunately
in the 3.3.1 PME code it is not checked if the number of grid points per CPU
is enough.


Arthur Roberts wrote:
> Hi, all,
> I am trying to run Gromacs on a P655+ with Aix 5.2. 
> Initially, mdrun appears to work, but always hangs. 
> Eventually, I get timed out from the supercomputer
> with no data to show for it.  Below is a link
> detailing the problem:
> http://cetus.mchem.washington.edu/pub/supercomputer/Mdrun-hangs-without-showing-steps.html
> I appreciate your input.  Your previous suggestions
> have been very helpful.
> Best wishes,
> Art
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Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics Department
Am Fassberg 11
37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302

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