[gmx-users] Fwd: Question about GPU acceleration in GROMACS 5

[Mark Abraham]

Hi,

Only the short-ranged non-bonded work is offloaded to the GPU, but that's
almost all the force-based work you are doing. So it is entirely
unsurprising that the work done on the GPU takes a lot longer than it does
on the CPU. That warning is aimed at the more typical PME-based simulation
where the long-ranged part is done on the CPU, and now there is load to
balance. Running constraints+update happens only on the CPU, which is
always a bottleneck, and worse in your case.

Ideally, we'd share some load that your simulations are doing solely on the
GPU with the CPU, and/or do the update on the GPU, but none of the
infrastructure is there for that.

Mark

On Fri, Dec 12, 2014 at 2:00 PM, Tomy van Batis <tomyvanbatis at gmail.com>
wrote:
>
> Dear all
>
> I am working with a system of about 200.000 particles. All the non-bonded
> interactions on the system are Lennard-Jones type (no Coulomb). I constrain
> the bond-length with Lincs. No torsion or bending interactions are taken
> into account.
>
>
> I am running the simulations on a 4-core Xeon® E5-1620 vs @ 3.70GHz
> together with an NVIDIA Tesla K20Xm. I observe a strange behavior when
> looking to performance of the simulations:
>
>
> 1. Running in 4 cores+gpu
>
> GPU/CPU force evaluation time=9.5 and GPU usage=58% (I see that with the
> command nvidia-smi)
>
>
> [image: Inline image 1]
>
>
>
> 2. Running in 2 cores+gpu
>
> GPU/CPU force evaluation time=9.9 and GPU usage=45-50% (Image is not
> included due to size restrictions)
>
>
>
> The situation doesn't change if I include the option -nd gpu (or gpu_cpu)
> in the mdrun.
>
>
> I can see in the mailing list that the force evaluation time should be
> about 1, that means that I am far away from the optimal performance.
>
>
> Does anybody have any suggestions about how to improve the computational
> speed?
>
>
> Thanks in advance,
>
> Tommy
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
>