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

[Alex]

 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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