Re: [AMBER] NaN question

From: Jason Swails <>
Date: Fri, 19 Oct 2012 10:49:50 -0400

On Fri, Oct 19, 2012 at 10:36 AM, <> wrote:

> Hello and thank you in advance for your help,
> I have a NaN error that does not seem to respond to the posted
> fixes/suggestions. I will provide as much information as would be helpful.
> My guess of what is helpful follows.
> I am operating Amber12 on a 2 GPU system that follows the Ross Walker
> recommendation for all hardware. The command nvidia-smi returns a
> temperature of 80 C for GPU0 and 85 C for GPU1.
> My bugfixes are current through bugfix.24.

There are two sets of bug fixes available. One is for Amber and the other
for AmberTools. When reporting patch levels (which is important in this
case), give us the result of the following command:

cd $AMBERHOME && ./ --patch-level

This will tell us how many patches have been applied to both packages. For
reference, the fully-updated tree should return this:

$ ./ --patch-level
Latest patch applied to AmberTools12: 25
Latest patch applied to Amber12: 11

Note, you can also use to quickly check for available
updates using "./ --check" (see a full listing of options
using --help).

Most notably, bugfix.11 for Amber12 I believe fixes parallel GPU
simulations which may have given NaNs before.


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Fri Oct 19 2012 - 08:00:04 PDT
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