[gmx-users] GPU-accelerated EM

[Alex]

Mark,

I agree with you 100%, given how I've always used particle-based simulation
tools. It is my understanding that my colleague is optimizing custom
forcefields based on EM, followed by short MD. The work is also unrelated
to what most of the GMX community does, so I stay away from this part.
What happens then is also perception-dependent. On our older boxes without
GPU acceleration, he'd see equally sluggish performance from EM and MD,
while now his EM (when submitted incorrectly) runs slowly and the MD
portion completes in a quick burst. This can be perceived as EM being the
bottleneck. Before my initial post, we already decided on CPU-only EM and
your advice to move the EM portion elsewhere (e.g. our old machines) is
even better.

Thanks,

Alex


On Fri, Sep 8, 2017 at 4:27 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> The em log files report using the GPUs, and they do. It just isn't very
> useful because the EM implementations do a lot more neighbour search
> stages, which doesn't use the GPUs.
>
> So, if there's other work for the GPUs to do, then I would plan to run a
> workflow heavily dominated by EM, on a non-GPU resource.
>
> We're not aware of a use case that would justify thinking about how to make
> a correct implementation of EM that could do less searching, because in
> most cases the time spent in EM is a tiny fraction of the time spent in MD.
> Is the workflow useful to optimize in this way?
>
> Mark
>
> On Fri, Sep 8, 2017 at 11:53 PM Alex <nedomacho at gmail.com> wrote:
>
> > Hi all,
> >
> > I tend to run one fat node-wise simulation, but we have another user
> whose
> > use case is different. He runs a bunch of small jobs at the same time and
> > in his case most of the time is taken up by the EM. We have two
> > hyperthreaded Xeons E5 (44 cores total) and 3 GPUs.
> >
> > So, we try to run 10 jobs using 4 cores each. Each mdrun line includes
> >
> > -ntomp 4 -pin on -pinoffset x -pinstride 1 -gpu_id y
> >
> > where pinoffset is 0, 4, 8, etc for the first, second, etc, simulation
> and
> > y changes from 0 to 2 so that the first two GPUs are subscribed three
> > times, while the third one is subscribed four times.
> >
> > Upon submitting this batch, each mdrun instance utilizes something like
> 10%
> > of CPU and the EM jobs proceed slowly. Removing GPU and setting -nb cpu
> > seems to fix that. With MD, everything works properly, but with EM
> there's
> > no GPU acceleration and low CPU usage. Is this correct behavior?
> >
> > Thanks,
> >
> > Alex
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