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.
Regards,
Carsten
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
http://www.mpibpc.mpg.de/research/dep/grubmueller/
http://www.gwdg.de/~ckutzne
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