[gmx-users] Spec'ing for new machines (again!)

[Szilárd Páll]

Hi,

Note that the new generation Ryzen2-based CPUs perform even better than
those we benchmarked for that paper. The 3900-series Threarippers are great
for workstations, unless you need the workstation form-factor, you are
better off with servers like the TYAN GA88B8021. If so, i  EPYC 1P is what
you should be looking at, e.g. EPYC 7402P.

GPU-wise, depending on your timeline you can expect NVIDIA to release
something this year, so you may want to time the purchase to either hit the
curren-gen GPUs discounted or go for the next gen.

Cheers,
--
Szilárd


On Sat, Apr 18, 2020 at 7:56 AM Alex <nedomacho at gmail.com> wrote:

>  From what I am seeing in this paper, we should just go with something
> along the lines of Ryzen 1950x + 4 x 2080 or 2080Ti. There are
> indications that Ryzen also rips (pun intended) Xeons in DFT/CC
> calculations, so overall this combination sounds quite reasonable for
> our purposes. This also outlines a path towards upgrading our existing
> nodes.
>
> Thanks Kevin, this is very informative.
>
> Alex
>
> On 4/17/2020 8:52 PM, Kevin Boyd wrote:
> > Yes, that's it. I think consumer-class Nvidia cards are still the best
> > value, unless you have other applications that need the benefits of
> > industrial cards.
> >
> > Cheers,
> >
> > Kevin
> >
> > On Fri, Apr 17, 2020 at 5:58 PM Alex <nedomacho at gmail.com> wrote:
> >
> >> *Message sent from a system outside of UConn.*
> >>
> >>
> >> Hi Kevin,
> >>
> >> Thanks for responding! RAM is mentioned for completeness. This amount is
> >> not for gmx -- we do other, much more RAM-intensive calculations, in
> >> fact 256 gigs is very modest for that. I have no doubt that AMD CPUs
> >> would work with Nvidia GPUs, was mainly wondering if there would be any
> >> additional speed boost if we also used AMD GPUs.
> >>
> >> Nope, haven't seen the paper, but quite interested in checking it out.
> >> Is this the latest version?
> >> https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.26011
> >>
> >> Thank you,
> >>
> >> Alex
> >>
> >> On 4/17/2020 6:29 PM, Kevin Boyd wrote:
> >>> Hi,
> >>>
> >>> AMD CPUs work fine with Nvidia GPUs, so feel free to use AMD as a base
> >>> regardless of the GPUs you end up choosing. In my experience AMD CPUs
> >> have
> >>> had great value.
> >>>
> >>> A ratio of ~4 cores/ GPU shouldn't be a problem. 256 GB of RAM is very
> >> much
> >>> overkill, but perhaps you have other uses for the machine that need it.
> >>>
> >>> Have you seen the updated "More bang for your buck" paper that goes
> into
> >>> optimizing compute nodes?
> >>>
> >>>
> >>> See
> >>>
> >>>
> >>>
> >>> On Fri, Apr 17, 2020 at 4:17 PM FAISAL NABI <fnabi at myamu.ac.in> wrote:
> >>>
> >>>> *Message sent from a system outside of UConn.*
> >>>>
> >>>>
> >>>> Gromacs is totally compatible with nvidia based gpu. You need to
> install
> >>>> cuda drivers and you can build easily with cmake. For amd gpu you
> would
> >> be
> >>>> needing openCL alongwith the sdk for amd gpu. I would suggest you to
> use
> >>>> nvidia acceleration for better performance.
> >>>>
> >>>> On Sat, Apr 18, 2020, 4:42 AM Alex <nedomacho at gmail.com> wrote:
> >>>>
> >>>>> Hello all,
> >>>>>
> >>>>> Hope you're staying safe & healthy! We are starting to spec new
> >> machines
> >>>>> and our end goal is two machines, each featuring:
> >>>>>
> >>>>> 1. ~16-18 CPU cores w/hyperthreading
> >>>>>
> >>>>> 2. Four GPUs
> >>>>>
> >>>>> 3. ~256 gigs of RAM.
> >>>>>
> >>>>> A very approximate allocation of money is ~$15-20K per unit, but we
> >>>>> could of course buy more if each machine turns out to be
> significantly
> >>>>> cheaper. All suggestions for CPUs and GPUs (esp. from Szilard) are
> >>>>> welcome. We are somewhat open to AMD-based solutions, but wonder what
> >>>>> the situation is with GPU acceleration, as so far we've been entirely
> >>>>> Intel-based. Will it work with NVIDIA cards? Will we have to install
> >> AMD
> >>>>> GPUs? Does current Gromacs perform well on AMD-based rigs?
> >>>>>
> >>>>> Thank you!
> >>>>>
> >>>>> Alex
> >>>>>
> >>>>> --
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> >>>>>
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> >>>>>
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