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

David van der Spoel spoel at xray.bmc.uu.se
Mon Jul 31 08:20:36 CEST 2006

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.

Please start by running some simpler, e.g. a water box on one processor 
without PME.
Then you can try to run this in parallel.
Then you try something more complicated.
Repeat all the steps with PME.

You can set the following enviroment variable for more output:
setenv LOG_BUFS 0
finally you can run the program with the -debug flag.

> Best wishes,
> Art
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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