[gmx-users] More Athlon talk
feenstra at chem.vu.nl
Mon Feb 24 08:11:15 CET 2003
Lynne E. Bilston wrote:
> I haven't had much time to test single cpu jobs, so I can't answer this
> one other than to say I haven't had a problem with them. I also have ECC
> memory. However, I do still have occasional crashes in gromacs which
> show up as settle errors in the logs. There are no odd things happening
> as far as I can tell from the simulation data. If I restart from just
> before the crash, they don't occur again. This is often several
> nanoseconds into a run. If I look at the coordinate files from the step
> before the crash, some of the bits of the protein are missing. I'm not
> sure if any of this is helpful or relevant.
Just a note to avoid confusion. When you restart a run, even using the
.trr file and tpbconv, your continuation will not be *completely* identical
to the original, the difference lies in the effects of temperature coupling.
And even a very slight change will cause your simulation to diverge rapidly.
So it is not surprising that you do not reproduce the settle errors in your
restarted run, and you cannot conclude from this that you must have hardware
Do the missing bits of the protein have 'nan' coordinates (check the
.gro/.pdb file with a simple text viewer/editor)?
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
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