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

[Alex]

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 <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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