Hello Adrian,
sorry I forgot to mention that: yes regular MD does work with 2 GPUs with our cluster.
Best regards,
Florian
> Am 15.02.2017 um 15:15 schrieb Adrian Roitberg <roitberg.ufl.edu>:
>
> Hi Florian
>
> Before we go further, have you checked regular MD with 2 GPUS? Does that
> work ok in your setup ?
>
> Thanks
>
> adrian
>
>
>
> On 2/15/17 7:50 AM, Hofer, Florian wrote:
>> Dear AMBER Developers,
>> we are using the constant pH calculation algorithm in AMBER, espacially the newly implemented version for pmemd.CUDA in AMBER 16. Calculations of the same system using a single GPU and the pmemd.cuda executable work fine, however when we were trying to do the calcualtion with 2 GPUs and using the pmemd.cuda.MPI executable we noticed that the calculations get halted at about 15000 steps.
>> The caluclations produce regular outputfiles until they stop and the jobs drop from the GPU, without any error messages. However the jobs remain active on the CPU with 100% each.
>>
>> The caluclations are done on a GPU cluster with the following specs:
>>
>> MPI program: mpich-3.2
>> AMBER version: AMBER 16 updated on 10 Feb 2017
>> Queue system: SGE-6.2u5p3
>>
>> Hardware:
>> Peer to Peer: Enabled
>> GeForce GTX 780 2x or GeForce GTX TITAN X 2x
>> Intel(R) Xeon(R) CPU E5-2609 v2 2x
>>
>> Has anyone else noted similar behavior or can help us figure out the problem?
>>
>> Really appreciating your help and best wishes,
>> Florian Hofer
>> _______________________________________________
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> Dr. Adrian E. Roitberg
> University of Florida Research Foundation Professor.
> Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
>
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Received on Wed Feb 15 2017 - 06:30:03 PST
