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

[Dongsheng Zhang]

Dear Art,

Thank you for sharing your tips. In my case, there is no COUL term in my
coarse-grained force field. I just can't understand why the program
stops without finding any error (It can continue by tpbconv).

All the best!

Dongsheng


On Sat, 2006-08-05 at 11:16 -0700, Arthur Roberts wrote:
> 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
> > 
> 
> _______________________________________________
> 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