Re: [AMBER] PHI Intel Compilation

From: Ross Walker <ross.rosswalker.co.uk>
Date: Tue, 02 Sep 2014 10:34:15 -0700

Hi Jacopo,

No you have to use Intel MPI - The Xeon Phi cards only work with Intel's
compilers and Intel's MPI.

All the best
Ross


On 9/2/14, 10:16 AM, "Jacopo Sgrignani" <sgrigna.gmail.com> wrote:

>Dear Ross
>Thanks for your reply.
>Do I have to use intel-mpi or can I Also use openmpi ?
>
>Thanks
>
>Jacopo
>
>> Il giorno 02/set/2014, alle ore 19:11, Ross Walker
>><ross.rosswalker.co.uk> ha scritto:
>>
>> Hi Jacopo,
>>
>> You are using the serial version of the code - this only runs on 1 out
>>of
>> the 61 cores on a Xeon Phi - hence why it is so slow.
>>
>> You need to also build the parallel (MPI) version and the run that with
>> mpirun specifying the number of cores on the Xeon Phi model you have.
>>
>> All the best
>> Ross
>>
>>
>>
>>> On 9/2/14, 6:40 AM, "Jacopo Sgrignani" <sgrigna.gmail.com> wrote:
>>>
>>> Dear all
>>> I compiled pmemd for a PHI intel accelerator in the native mode.
>>>
>>> To run the calculation I use this command: ssh mic0 "export
>>> LD_LIBRARY_PATH=/tmp/; cd /tmp; ./pmemd.mic_native -O -i md.in -p
>>> letroamber2.prmtop -c letroamber2.inpcrd -o prova.outę¸ &
>>>
>>> The simulation starts but it is extremely slow 0.05 ns/day.
>>>
>>> Ię÷m new in using this hardware, so I would like to ask some advices for
>>> speeding up my simulation.
>>> Do I need intel_mpi libraries also for running in native mode?
>>> Is my command line correct?
>>>
>>> Thanks in advance
>>>
>>> Jacopo
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
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Received on Tue Sep 02 2014 - 11:00:02 PDT
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