Hi Aron,
> As one more thing to add, AMBER being run on a GPU, particularly the
> GTX
> ones, seems to often run into the problem where the coordinates and
> velocities get lost from one step to another. Maybe you've already
> done
> it, but Ross' response made me think that you should search your
> restart
> file for any 'NaN' entries.
This is worrying... Are you really seeing this occur on a regular basis?
If you are running the very latest version of the code (bugfix.20) You
shouldn't see such errors unless you have some kind of hardware issue. I
would suspect one of the following:
1) You are using an overclocked (or you overclocked yourself) GTX580.
2) Your card / computer is overheating.
3) Your power supply is underspecced for your machine running flat out.
4) Your GTX card is failing (happens - I've had several go bad, although
mostly due to fan failures).
You would also see NAN's etc occurring due to issues with your simulation,
if something is unstable, bad parameters, strained bonds etc etc. These sort
of errors should show up more frequently on a GTX card than a Tesla card
though.
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Mon Apr 02 2012 - 10:00:08 PDT
