[gmx-users] Gromacs on a Power8 machine

[Szilárd Páll]

Hi,

On Thu, Jun 18, 2015 at 2:46 PM, Baker D.J. <D.J.Baker at soton.ac.uk> wrote:
> Hello,
>
> I'm not sure that this is the correct place to send my question, however please bear with me and help me to redirect my enquiry if necessary.
>
> We recently received delivery of two Power8 machines-one of the machines has a K40 GPU installed. I have read that interesting reports that Gromacs performs well on Power8 systems, especially if there's a GPU card available. I have been doing some experiments, and so far I've have been very disappointed by the performance of Gromacs.

Can you please elaborate? Something quantifiable would be useful. Have
you compared to some other platform? Which one? How?

> At this stage I am just working on one of the "water" examples (1536). I am working with the very latest gromacs (5.1) and I have tried configuring with GMX_SIMD=IBM_VSX, however when I try a parallel run I still get this warnng:
>
> WARNING: Using the slow plain C kernels. This should
> not happen during routine usage on supported platforms.

As mentioned on your other gmx-dev post, the non-bonded kernels (which
represent most of the i/flops in a run) have not been ported to
IBM_VSX yet, but the rest of the code should AFAIK have SIMD support,
so without GPUs don't expect great performance. However, with GPU
acceleration (where the not yet SIMD ported non-bondeds are
offloaded), you should get decent performance.

> Could someone please advise how I should configure and install Gromacs to get the best out of our Power8 machines.

Notes:
- You'll likely need at least a K40 @875MHz per socket (for the
high-end 12C Power8 CPUs);
- The balance of ranks to threads and threads/core will need tweaking;
somewhere around 4 threads/socket and 8-12 threads per rank were AFAIR
optimal. Don't even try to run one rank with 96 threads/socket (it
won't even work :).
- I recommend using the FFTW version form github
(https://github.com/FFTW/fftw3) where Erik Lindahl has recently added
VSX implementation (among others).

Cheers,
--
Szilárd

> Best regards,
>
> David.
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