Re: [AMBER] NaN error in .rst files

From: Ross Walker <>
Date: Mon, 24 Jan 2011 19:54:03 -0800

Hi Peter,

Before you check into this any further can I just confirm that you have
iwrap=1 set in the &cntrl namelist. If not then this is the problem and it
is a pmemd / sander issue, completely unrelated to cuda. It will, in
principal go away if we move to netcdf restart files.

If you can confirm this only occurs with PMEMD.cuda and you have iwrap=1 set
then it warrants investigating and the next step will be to see if anyone
has seen this problem on any of the Tesla cards or it is confined to GTX
series cards.

All the best

> -----Original Message-----
> From: peker milas []
> Sent: Monday, January 24, 2011 2:42 PM
> To: AMBER Mailing List
> Subject: [AMBER] NaN error in .rst files
> Dear Amber coders/users
> We had a discussion about this problem couple days ago. Briefly at
> some point of simulations pmemd.cuda creates NaN s in the restart
> files. Then the next step of simulation messes up. This is sort of a
> problem which happens in totally random way. As some users already
> pointed out, part of it can be related with heating problem because
> GTX 470/480 cards were not designed for this kind of intense
> calculations. Although i totally agree with this, i couldn't find an
> easy way of observing this behavior. In fact there is only nvidia-smi
> command which shows me the current state of the card (like its
> temperature, etc...). So i really want to go little bit deep with this
> problem and i would like to know if anybody knows a good indicator for
> checking cards behavior in detail. It can be a command or any sort
> additional package/program for monitoring it.
> Any help will be appreciated
> regards
> peker milas
> _______________________________________________
> AMBER mailing list

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Received on Mon Jan 24 2011 - 20:00:04 PST
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