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 - 11:00:08 PDT
