Re: [AMBER] cuda job not working

From: Daniel Roe <>
Date: Sat, 4 Jan 2014 11:14:47 -0700


On Sat, Jan 4, 2014 at 8:59 AM, Jio M <> wrote:

> 1) I get this: so looks like its not updated?

No; this code is actually way out of date and you need to update. Simply
re-run configure, apply all available patches, and re-compile the code.

> 3) Another thing I noted: job needs to be exclusive in a node. I use bsub
> submission scripts and with that -x flag allows to use node exclusively for
> one job but when I don't use this and submit on free GPU in some node with
> some job already running on it, my AMBER job kills with same error.

I'm not 100% sure, but it sounds like whatever queuing software you are
using isn't properly allocating GPUs by e.g. setting CUDA_VISIBLE_DEVICES.
An Amber CUDA job should have exclusive access to the GPUs it is using. It
is not recommended for jobs to share GPUs; this can lead to unexpected and
bad behavior. If you haven't already, see more information on running CUDA

Hope this helps,


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Sat Jan 04 2014 - 10:30:02 PST
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