Well, can your sysadmin give me account on the machine in question?
Or please point him to
http://developer.nvidia.com/cuda/cuda-downloads
It indicates 295.41 as the latest driver...
Your point about passing test.cuda is valid, but since it runs at my end,
there's not much else I can suggest...
On Tue, Sep 4, 2012 at 1:31 PM, Marc van der Kamp
<marcvanderkamp.gmail.com>wrote:
> PS As pmemd.cuda essentially passed make test.cuda completely, I'd think
> the driver shouldn't be the issue?
> It is only Patrick's test cases with transition metals in co-factors that
> are failing. So you can run these same test cases without problems?
> --Marc
>
> On 4 September 2012 21:21, Marc van der Kamp <marcvanderkamp.gmail.com
> >wrote:
>
> > 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 - 15:00:03 PDT
