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

[Kevin Boyd]

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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