Hi All,
Just a note, I don't want to get everyone's hopes up prematurely but we
'may' have a possible solution to this. Mark Williamson is currently working
on it / testing that it does indeed work around the problem. At least for
GTX580 which is what we currently have access to.
I will provide an update once as soon as I can.
All the best
Ross
> -----Original Message-----
> From: Sergio R Aragon [mailto:aragons.sfsu.edu]
> Sent: Friday, December 10, 2010 10:16 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Fwd: simulation terminates for no apparent reason
>
> Hello Gabriel,
>
> The error you are encountering has been the subject of a large amount of
> discussion in this list. Unfortunately there is no fix for this problem
at the
> present time. It appears that all GTX 400 series cards AND the 580 have
this
> error. Nvidia is working on it, but we have no assurance of a workaround.
> We are hopeful that one will be found.
>
> Meanwhile, we cannot use these cards to run pmemd.cuda. If you can,
> move over to the Tesla cards such as the C2050 to do your work.
>
> Sincerely,
>
> Sergio Aragon
> Professor of Chemistry
> San Francisco State University
>
>
> -----Original Message-----
> From: Gabriel Urquiza [mailto:urquizagabes.gmail.com]
> Sent: Friday, December 10, 2010 5:14 AM
> To: AMBER Mailing List
> Subject: [AMBER] Fwd: simulation terminates for no apparent reason
>
> Greetings amberists,
>
> I am having some problems running PMEMD simulations of a protein in a
> water
> box. The system has around 60.000 atoms and I'm running it CUDA on a
> GeForce
> GTX 480 1.4Ghz board with a global memory size of 1535 MB. I am running
> several short dynamics with this system and it turns out that when I check
> at the human-readable output files I notice that some of them just
> abnormally terminated. The step in which the simulations finish doesn't
> follow any apparent pattern, some terminate near the end, others right at
> the beginning. Most of the simulations runs through though but if I remove
> every file, restart the machine and resubmit all the simulations, using
the
> same script, in the same order, it is almost certain that the simulations
> that crashed earlier won't be exactly the ones that will crash now. It
seems
> a very random thing and I find it very weird. I am placing my bets on the
> narrow memory size of the board I'm using, but I've decided to ask for
some
> light on the matter.
>
> The machine is running on double precision and it has an i7 processor. The
> nohup pops one out of two error messages down below, whenever a
> dynamic
> crashes:
>
> Error: the launch timed out and was terminated launching kernel
> kCalculatePMENonbondForces
> Error: the launch timed out and was terminated launching kernel
> kPMEGetGridWeights
>
> I hope you can assist me with this.
>
>
> Gabriel Urquiza
>
> ----------------
>
> Universidade Federal da Paraíba - UFPB
> Departamento de Química - Programa de Pós-Graduação
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Received on Fri Dec 10 2010 - 11:30:08 PST
