VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue May 11 2010 - 22:07:03 CDT

Hi,
  Yes, I know (compute-exclusive), but since he didn't mention having
set the devices to anything but normal mode, I doubt this is the reason
he's encountering the problem.

I'm guessing that what is happening is that ACEMD is
getting a failed memory allocation if it is running at the moment
VMD goes through its startup memory allocation/clear/deallocation.

If it's just an issue of compute-exclusive mode, there are a number
of ways of dealing with it.

I haven't added code to VMD to allow a "gpu subset" to be specified thus
far, but it wouldn't be too hard to do so for people that want this
capability. I could probably implement such a feature in one of the
alpha VMD builds in a few days. I'm traveling off and on from
Wednesday until Monday, but I could probably have a new test build
with such a feature available shortly thereafter.

Cheers,
  John

On Tue, May 11, 2010 at 09:08:25PM -0400, Axel Kohlmeyer wrote:
> On Tue, 2010-05-11 at 19:23 -0500, John Stone wrote:
>
> john,
>
> if the GPUs are configured for "compute-exclusive" mode,
> then you cannot access them with any other code for as
> long as VMD is running. i have seen this behavior on our
> 6-GPU node for example with the latest drivers, VMD cvs v
> ersion, CUDA-3.0 etc.
>
> cheers,
> axel.
>
> > Hi,
> > VMD doesn't "lock" any of the devices. When it starts up it does
> > clear the GPU memory and do a brief allocation/clear/deallocation cycle
> > designed to catch any unusual GPU behavior during startup. Does ACEMD fail
> > while VMD is starting up? What happens if you do a "kill -STOP" on ACEMD,
> > then start VMD, than do a "kill -CONT" on ACEMD after VMD prints the startup
> > messages?
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Wed, May 12, 2010 at 12:49:54AM +0200, Joakim Swedberg wrote:
> > > Hi everybody,
> > >
> > > I have a problem where I need to run another CUDA accelerated software's
> > > at the same time as VMD 1.8.7. The other software ACEMD lets me specify
> > > which devices I want to use but I have not been able to find a way to do
> > > that in VMD and it locks all devices, As a result the other software
> > > always crashes if I run VMD 1.8.7.
> > >
> > > Any help would be useful
> > >
> > > Regards
> > >
> > > Joakim Swedberg
> > > BSc (Honours)
> > > PhD student
> > >
> > > ----------------------------------------------------------------------
> > >
> > > Institute of Health and Biomedical Innovation (IHBI)
> > > 60 Musk Avenue
> > > Kelvin Grove
> > > Queensland 4059
> > > Australia
> > >
> > > http://www.ihbi.qut.edu.au/
> > >
> > > Phone +61 (0)7 3138 6222
> > > Mobile +61 (0)413 165 805
> > > Email j.swedberg_at_student.qut.edu.au
> > > joakim_swedberg_at_hotmail.com
> > >
> > > ----------------------------------------------------------------------
> > >
> > >
> >
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> http://sites.google.com/site/akohlmey/
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA. 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078