Your driver is far too old for 4.2. Either install a newer driver or use
the 4.0 toolkit...
On Sep 4, 2012 1:08 PM, "Marc van der Kamp" <marcvanderkamp.gmail.com>
wrote:
> 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
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Received on Tue Sep 04 2012 - 13:30:03 PDT
