[gmx-users] GPU considerations for GROMACS

[Kevin Boyd]

Hi,

A CPU:GPU ratio of 4:1 is fairly well balanced these days (depending on the
quality of the hardware), so you should expect to roughly double your
throughput adding a second GPU to your current system. However, that
doesn't mean
your single simulation performance will double - it's a lot more efficient
to run multiple simulations in parallel with these setups, because multiple
GPUs don't scale perfectly.

We can't make absolute statements about the performance you should expect,
it depends a lot on workload among other things. Have you seen the "More
bang for your buck" paper?.
https://arxiv.org/abs/1903.05918

Kevin


On Tue, Feb 18, 2020 at 6:21 AM hairul.ikmal at gmail.com <
hairul.ikmal at gmail.com> wrote:

> Hello,
>
> Previously, I have helped building a workstation for my fellow
> researcher who heavily uses GROMACS for his MD simulations, with the
> following base specs:
>
> -CPU: 8 cores (Xeon E2278G)
> -RAM: 32GB
> -GPU: 1x RTX2080Ti
>
>
> With this setup, he managed to shrink down each simulation runtime to,
> say approximately 12 hours, compared to previous system (purely CPU
> only, no GPU support), which took days to complete.
>
>
> 1) Based on the current progress, we plan to build another system
> (which will also run GROMACS most of the time) using the existing
> workstation as reference. But currently we are unsure which setup
> (Option 1 vs Option 2) will GENERALLY give shortest/fastest runtime,
> when running the same set of GROMACS simulation :
>
>
> Option 1:
> Retain same CPU, RAM and GPU specs (1x RTX2080Ti)
>
>
> Option 2:
> Retain same CPU and RAM specs, but GPU wise, use 2x RTX 2070S instead
> of 1x RTX2080Ti
>
>
> 2) Besides building another system, we are considering to upgrade the
> existing system, too. For example, assuming the system has the
> expansion capability (enough PCI-e 16x slots, power supply), will
> adding another card (making it 2x RTX2080Ti instead of 1x RTX2080Ti)
> into existing setup will significantly cut down current runtime?  If
> yes, by how much time reduction can we expect generally with this
> upgrade?
>
>
> Appreciate if someone can share their thoughts and experience.
> Thank you!
>
>
> -Hairul
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