Hi Scott,
I compiled pmemd.cuda_SPFP for Patrick and ran make test.cuda. All tests
passed, apart from a few (6 I think) that only had minor differences in
values (different 4th digit).
The CUDA Toolkit:
$ nvcc -V
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2012 NVIDIA Corporation
Built on Thu_Apr__5_00:24:31_PDT_2012
Cuda compilation tools, release 4.2, V0.2.1221
The driver was freshly installed today:
devdriver_4.0_linux_64_270.41.19
Cards on the node where both test.cuda and Patrick's jobs ran:
$ nvidia-smi -L
GPU 0: Tesla M2050 (S/N: 0322310084063)
GPU 1: Tesla M2050 (S/N: 0322310082367)
Hope this helps,
Marc
On 4 September 2012 19:44, Scott Le Grand <varelse2005.gmail.com> wrote:
> 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
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Tue Sep 04 2012 - 13:30:03 PDT
