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 - 14:00:03 PDT
