[gmx-users] system reshaped on itanium II
spoel at xray.bmc.uu.se
Thu Mar 3 18:21:08 CET 2005
On Thu, 2005-03-03 at 18:04 +0100, Jens Krüger wrote:
> 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.
Have you compared the tpr files on the P4 and Itanium? Run the P4 tpr
file on the Itanium?
In general we need a problem to be reduced as much as possible to be
able to look into it.
> What I have tried so far:
> - changed the number of nodes
> - varied pcoupltype (none, isotropic, ...) with different coupling
> - varied Tcoupl
> - varied coulombtype (cut-off and PME) with different parameters
> - tried all variations of grompp with or without -shuffle -sort
> - double checked, if I am really using a cubic/tric system and NOT a
> - used clean protein/water, DPPC/water and protein/POPE/water, each
> running stable on a Linux P4
> - energy minimization cg and steep
> All of them did not had any influence on that strange failure.
> Has anybody an idea what might by the reason?
> 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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