[gmx-users] Workstation choice

[Szilárd Páll]

Hi,

Are you intending to use it mostly/only for running simulations or also as
a desktop computer?

Starting with the 2018 release we offload more work to the GPU to account
for the increase in the gap between the performance of CPUs and GPUs and
the prevalence of (especially workstations) with >1 GPU per CPU (socket).
As a result, fewer CPU cores are needed to keep a GPU busy. For "regular"
biomolecular simulations (decent amount of water, no pulling, no free
energy, etc.), the rule of thumb is that 3-4 workstation cores are enough
to get up to 90% of the peak performance. If you have more non-offloaded
work (i.e. not pair-interactions or PME), you might need a a few more cores
to avoid CPU-bound simulations.

Given the above, and assuming you generally have multiple simulations you
can do concurrently (and you don't need to scale these to multiple GPUs),
you are generally better off with two GPUs (e.g. second or third from the
highest-end consumer GPU, e.g. a GTX 1080 or 1070) and a decent 8+ core
CPU. That will also result in a more cost-effective setup as well as higher
aggregate performance.

Now, when it comes to the best absolute performance, the Intel i9's or the
Threadripper 2's are hard to beat, but for your case those are probably too
pricey and an overkill for a 1-2 GPU setup (fast enough to drive 3+ GPUs).
I'd suggest looking at Ryzen 7's or possibly Threadripper 1's; the Intel i7
8600k/8700k are also good options, but likely more pricey and less value
for money than the Ryzen 7's.

I'm not on the top of pricing details so you should probably look at some
configs and get back with concrete CPU + GPU (+price) combinations and we
might be able to guesstimate what's best.

Cheers,
--
Szilárd


On Thu, Sep 6, 2018 at 7:10 PM Olga Selyutina <olga.gluschenko at gmail.com>
wrote:

>  Thank you,
>
> to use these tests isn’t a problem, but available workstation are too old,
> so test results won’t be helpful in choosing actual components. I have an
> access to high-performance cluster, but it also couldn’t be the basis
> because of its high cost. If it is hard to give the certain recommendation,
> I would to know at least how do performance correlate with the number of
> cores/threads and core frequency? What is more important the core frequency
> or number of cores? What is preferable, Intel or AMD? How should be
> correlated GPU and CPU performance?
>
> In the previous letters in mail-list I found recommendations on purchase of
> Threadripper 1950X+GeForce GTX-1080Ti, I think that more cheap and similar
> effective choice is TR 1950X+GeForce GTX-*1080*. Will there be significant
> differences with 1)TR 19*20*X+GeForce GTX-1080 2) Intel 7900x+GeForce
> GTX-1080?
>
> 2018-09-05 20:53 GMT+07:00 Benson Muite <benson.muite at ut.ee>:
>
> > Hi Olga,
> >
> > The authors of:
> >
> > https://github.com/bio-phys/MDBenchmark/tree/version-1.3.2
> >
> > https://zenodo.org/record/1318123
> >
> > May be helpful. If your data is not confidential, you may consider
> running
> > Gromacs remotely on a cloud high performance computing resource, or
> > benchmarking remotely and then purchasing a suitable configuration.
> >
> > Some other information:
> > http://manual.gromacs.org/documentation/current/user-guide/
> > mdrun-performance.html#
> > http://www.gromacs.org/GPU_acceleration
> > https://extras.csc.fi/chem/courses/gmx2007/Erik_Talks/buildi
> > ng_clusters.pdf
> > http://www.gromacs.org/Documentation/Performance_checklist
> >
> > On 09/05/2018 12:02 PM, Olga Selyutina wrote:
> >
> >>   Hello,
> >>
> >> I need help in choice of the workstation for MD simulations using
> GROMACS.
> >> It is supposed to study systems consisting from 30-50k atoms, in
> >> particular, lipid bilayer models. Since the last generation of Intel and
> >> Ryzen CPU has made a big leap in performance, available workstation
> can’t
> >> be taken as a basis. Please, help to choose components of the
> workstation,
> >> particularly, GPU and CPU with total cost about $2000. What is better,
> to
> >> buy two GPUs(sli) or one GPU but more effective?
> >>
> >>
> > --
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> >
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>
>
>
> --
> Best regards, Olga Selyutina
> --
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