[gmx-users] Mdrun box nan error

David spoel at xray.bmc.uu.se
Fri May 7 20:15:02 CEST 2004

On Fri, 2004-05-07 at 20:01, Nathalie R. Basdevant wrote:
> David,
> So I have tried your suggestion to launch the same tpr twice. The error (box
> nan) is NOT reproducible. That's the only error I get, the 'atoms' thing
> referred to the accompanying LINCS error.
> So that leaves compiler and hardware then. I'll investigate...

See if there are compiler flags for IEEE compatible floating point
calculations and turn it on. You can also try to turn off (some)
optimizations in the compiler. One would hope that Itanium priced
hardware does not have hardware problems. Does the machine have ECC
(error correcting) memory? Finally, some OS store messages about
hardware failure in the system logs...

> Thank you
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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