Hi,
On Wed, Jul 12, 2017 at 9:45 AM, Robinson, Roger
<Roger.Robinson.evotec.com> wrote:
>
> The interconnects aren't great on the HPC system.
Unless you have something like Infiniband your scaling across nodes is
going to be poor at best.
> There are some benchmarks here->
> http://ambermd.org/amber10.bench1.html
Those benchmarks are for pmemd,MPI, which is the performance-tuned MD
engine. Sander has a lot more functionality but does not scale nearly
as well (as you are finding out).
> But I thought I would ask for some advice here.
> I am running in groups of 8 processes per node (8ppn).
>
> Would running in smaller/larger groups be better / worse.
A long time ago I remember sometimes getting better scaling by running
with fewer processors per node, the idea being to reduce the IO
bandwidth across the interconnect. You could experiment with that.
-Dan
>
> Should I expect a speed up ?
>
> Anyother common errors ?
>
> Roger
>
>
>
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Received on Wed Jul 12 2017 - 07:30:04 PDT
