[gmx-users] GPU considerations for GROMACS

[Szilárd Páll]

Hi,

Whether investing in one of the fastest or two medium-high end GPU depends
on your workload: system size, type of run, single or multiple simulations,
etc. If you have multiple simulations you can run independently or coupled
only weakly in ensemble runs (e.g. using -multidir), multiple mid-tier GPUs
will be a better investment. On the other hand, if single simulation
performance is what you want to maximize and you have a relatively small
simulation system (e.g. 50k atoms), you will be better off with a single
fast GPU.

Regarding your CPU choice, I suggest you consider alternatives: e.g. a
Ryzen 3800X will cost a lot less and will be faster. Xeon generally does
not have much benefit for the use-case in question.

Cheers,
--
Szilárd


On Tue, Feb 18, 2020 at 3:21 PM 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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