Does your build of pmemd.cuda pass a make test.cuda?
Also what CUDA Toolkit/Display driver are you using?
On Tue, Sep 4, 2012 at 10:27 AM, Patrick von Glehn <
patrickvonglehn.gmail.com> wrote:
> Hi Jason and Scott,
>
> Unfortunately bugfix 9 has not solved the problem.
>
> To reiterate for anyone else who is interested, molecular dynamics on
> my system of interest runs smoothly with pmemd but the system blows up
> when run with pmemd.cuda on GPUs (a few atoms in the region of the
> hexacoordinated cobalt fly off in different directions). This happens
> with either a 0.002ps timestep or a 0.000002ps timestep.
>
> I initially ran the calculations on NVIDIA Tesla M2090 GPUs with
> pmemd.cuda_SPDP and then I tried again on Nvidia Fermi M2050 GPUs with
> bufix.9 applied.
>
> Input files can be found attached to the first message in this thread.
>
> Any help would be greatly appreciated,
>
> Patrick von Glehn
> PhD student in the Harvey and Mulholland groups
> Centre for Computational Chemistry
> University of Bristol
>
> On 22 August 2012 15:50, Jason Swails <jason.swails.gmail.com> wrote:
> > On Wed, Aug 22, 2012 at 10:28 AM, Patrick von Glehn <
> > patrickvonglehn.gmail.com> wrote:
> >
> >> Hi Scott,
> >>
> >> Thanks for your reply.
> >>
> >> Do you have reason to believe that the new patch will resolve this
> >> error? Were you able to reproduce the error with an unpatched version
> >> of amber? Also, forgive my ignorance, but what does TOT mean?
> >>
> >
> > Top Of Tree, I think :). What this means is that he doesn't see the
> error
> > with the soon-to-be-released pmemd.cuda upgrade (I don't think the
> current
> > version of amber was tested, but the upcoming patch is known to have
> fixed
> > a handful of bugs).
> >
> >
> >> What sort of timescale are we talking about here for the new patch
> >> release? Days/weeks/months? I am very keen to get my GPU simulations
> >> going!
> >>
> >
> > No promises here, but in conversations I've had with Ross, I would say
> > we're aiming for 'days'. The patch is a large one, and has to be handled
> > with care, but we're taking a crack at generating the patch tonight. If
> > the merge goes smoothly and everything tests out correctly the first time
> > through, you probably will not have more than a few days to wait.
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
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>
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Received on Tue Sep 04 2012 - 12:00:04 PDT
