[gmx-users] system reshaped on itanium II
David van der Spoel
spoel at xray.bmc.uu.se
Fri Mar 4 10:08:07 CET 2005
On Fri, 2005-03-04 at 10:05 +0100, Jens Krüger wrote:
> David wrote:
> > On Thu, 2005-03-03 at 18:04 +0100, Jens Krüger wrote:
> > > Hello,
> > >
> > > I observed a strange behavior of my simulation systems on a new Itanium
> > > II Cluster. Whatever system I use, it behaves well on a normal P4, but
> > > when transferred to the Cluster, the box expands along the z-axis and
> > > the water molecules "regroup" from typical brick shape to an
> > > octahedral-bipyramidal shape. After ca. 50 ps the whole system crashes.
> > > I varied all parameters and rebuilt the systems from scratch but the
> > > problem still remains.
> > >
> > Which gromacs version is this? The latest CVS has optimized Itanium
> > routines which work fine for me.
> It's Gromacs 3.2.1. Haven't tried the CVS, maybe it solves the problem. Can
> you please give me some hints about the compiler flags, configure options,
> etc. that might be of importance during installation?
Nothing special, I used the intel C compiler with a specific MPI version
(Quadrics). No fortran is needed anymore.
Be careful with the CVS code as well, i.e. do the same tests you have
run with the current version.
> > Have you compared the tpr files on the P4 and Itanium? Run the P4 tpr
> > file on the Itanium?
> The unmodified P4 tpr runs at the Itanium, but shows exactly the same
> failure; "Brick turns into diamond" killing the simulation.
> > In general we need a problem to be reduced as much as possible to be
> > able to look into it.
> The failure also occurs with the benchmark systems, so I believe, that it is
> not related to the simulation system or settings.
> Jens Krüger
> Jens Krueger
> mercutio at uni-paderborn.de
> Warburger Str. 100 * 33098 Paderborn * Tel.:05251-602183
> Warburger Str. 64 * 33098 Paderborn * Tel.:05251-2025608
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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://xray.bmc.uu.se/~spoel
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