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

[Dongsheng Zhang]

Dear Erik,

Thank you. My gmx is 3.3.1. Maybe that's the reason there is no
difference except documentation part. To my understanding to your email,
gmx 3.3.1  has solved that problem. I don't know why I still encounter
it. In fact, there is no COUL term in my coarse-grained FF. I don't know
what is the cause in my case. If you need more information, please let
me know.


All the best!


Dongsheng




On Mon, 2006-08-07 at 07:45 +0200, Erik Lindahl wrote:
> Hi,
> 
> I'm certainly seeing lots of differences between 1.5 and 1.5.4.1 when  
> I run diff in my cvs tree.
> 
> However, I think we made the 3.3.1 release after march 9, in which  
> case it is included there.
> 
> Cheers,
> 
> Erik
> 
> On Aug 5, 2006, at 12:05 AM, Dongsheng Zhang wrote:
> 
> > 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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