Hi Szilárd,

We haven't decided yet on what price point& performance level we would be 
settling on, but this is overall great advice, thanks a lot.

Alex

On 4/21/2020 4:32 PM, Szilárd Páll wrote:
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 <nedoma...@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 <nedoma...@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 <fn...@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 <nedoma...@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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