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

[Arthur Roberts]

Hi, all,

I was able to fix the problem by:

1) Reducing my PME order from 6 to 4
2) Reducing my Fourier spacing from 0.12 to 0.06
3) Also, I had to do comm_grps = System or comm_grps =
Protein

Best wishes,
Art

--- Dongsheng Zhang <dong at pampas.chem.purdue.edu>
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
> > > _______________________________________________
> > > gmx-users mailing list    gmx-users at gromacs.org
> > >
> http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please don't post (un)subscribe requests to the
> list. Use the
> > > www interface or send it to
> gmx-users-request at gromacs.org.
> > > Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
> > 
> > _______________________________________________
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the
> list. Use the 
> > www interface or send it to
> gmx-users-request at gromacs.org.
> > Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the
> list. Use the 
> www interface or send it to
> gmx-users-request at gromacs.org.
> Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
>