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

[Dongsheng Zhang]

Dear Erik,

I had the same problem as Arthur Roberts. So I downloaded your new
version of gmx_system_xdr.h and gmx_system_xdr.c from
http://bugzilla.gromacs.org/show_bug.cgi?id=55

Before I recompile gromacs, I checked the difference between your new
version and the old one. The result is as follows:

diff gmx_system_xdr.c gmx_system_xdr-n.c
2c2
<  * $Id: gmx_system_xdr.c,v 1.5.4.1 2006/03/09 08:12:16 lindahl Exp $
---
>  * $Id: gmx_system_xdr.c,v 1.5 2004/01/23 17:23:13 lindahl Exp $

 diff gmx_system_xdr.h gmx_system_xdr-n.h
2c2
<  * $Id: gmx_system_xdr.h,v 1.3.4.1 2006/03/09 08:12:09 lindahl Exp $
---
>  * $Id: gmx_system_xdr.h,v 1.3 2003/11/17 21:50:40 spoel Exp $

Both differences are in documentation. I am confused how your
modification can solve the problem.

I had the same problem and posted in the mailing list before (
http://www.gromacs.org/pipermail/gmx-users/2006-June/022493.html ) I
also found Jason O'Young had asked the similar question at
http://www.gromacs.org/pipermail/gmx-users/2006-May/021605.html

I think this problem sounds common, could you please investigate what's
wrong? Thank you very much for your help!

By the way, I can continue the simulation by tpbconv, but hangs soon
without any error message. The "top" command shows the programs is
running, but no more output data.

 
All the best!

Dongsheng


On Mon, 2006-07-31 at 08:36 +0200, Erik Lindahl wrote:
> Hi,
> 
> It _might_ be solved by the fix attachment at
> 
> http://bugzilla.gromacs.org/show_bug.cgi?id=55
> 
> (also in CVS)
> 
> Cheers,
> 
> Erik
> 
> On Jul 31, 2006, at 8:11 AM, 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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