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.
>
>Iım 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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Received on Tue Sep 02 2014 - 10:30:02 PDT
