[gmx-users] Mdrun box nan error
lindahl at csb.stanford.edu
Mon May 10 10:48:18 CEST 2004
> On Fri, 2004-05-07 at 20:01, Nathalie R. Basdevant wrote:
>> 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'
>> referred to the accompanying LINCS error.
>> So that leaves compiler and hardware then. I'll investigate...
Just to get this clear - are you launching *exactly* the same command
twice, with *exactly* the same input files, but you get different
In that case it cannot be a compiler issue, since it should be running
the same code. It is either a bug in the operating system, or in the
hardware. However, a lower level of compiler optimization might avoid
triggering the bug...
I have contacts both HP and Intel, so I'm sure we can get some help to
debug it. What we would need from you is:
1. A simple (small) system where it happens, and preferrably after a
small number of steps. You can use gmxdump to compare trajectories and
see if they differ.
2. Every single piece of information you have about your operating
system, version, hardware, memory, compiler (+version), etc.
More information about the gromacs.org_gmx-users