[gmx-users] Gromacs does not fully utilize CPU

[Mark Abraham]

Hi,

Such node sharing is definitely going to hurt your throughput - mdrun is
designed to saturate the CPU cores you run it on. Just starting both
processes naively will give terrible performance. You have to keep both
processes on separate cores (e.g. with Linux taskset or similar tools to
set the *affinity* of the threads to cores). mdrun can also be managed
along the lines of
http://manual.gromacs.org/documentation/2016/user-guide/mdrun-performance.html#examples-for-mdrun-on-one-node
but
your other process will need some other kind of management, so you might as
well use the same for mdrun (which by default it will respect).

Mark

On Tue, Aug 16, 2016 at 2:44 PM Irem Altan <irem.altan at duke.edu> wrote:

> Hi,
>
> I have a system with an nVidia Tesla K20 and 12 cores with
> hyper-threading. It normally runs with %2400 CPU. However, when there is
> another process working, taking up 50% CPU, Gromacs ends up using 1500% CPU
> instead. This results in only 67% of the total CPU being utilized. Is this
> expected behavior? If so, what is the best way to optimize the system?
>
> Best,
> Irem
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