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.out² &
>>
>> The simulation starts but it is extremely slow 0.05 ns/day.
>>
>> I¹m 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
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>
>
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Received on Tue Sep 02 2014 - 10:30:03 PDT
