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

[Alex]

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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