Thanks Scott,
The driver was installed by the sysadmin - I don't have root access on this
cluster.
He wrote to me that it was "the latest driver", but apparently not. I'll
ask him to download a fresh driver from nvidia.
Can pmemd.cuda post-bugfix.9 still be compiled with the 4.0 toolkit? I
initially tried this, but got an error saying I needed to use 4.2.
Thanks,
--Marc
On 4 September 2012 21:15, Scott Le Grand <varelse2005.gmail.com> wrote:
> 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 - 13:30:04 PDT
