[gmx-users] Specs for GPU box

[Alex]

Szilárd, I think I am starting to understand and appreciate your 
argument. In essence, you are warning me against building a beast of 
stupidity. : )


> Sounds like you're in a situation that's not too bad. Just for the
> $5-10k extra you'd get decent MD server! ;)
> (Have you considered donating the leftover $ e.g. to GROMACS? ;)
Trust me when I say that my employer's donation to GMX would bring tears 
to both your eyes and mine. Those would not be tears of joy, 
unfortunately. : (
> Seems like you want to have the cake and eat it. Especially clock rate
> and cache are somewhat orthogonal in all but the crazy-priced E7 chips
> (like E7-8890/91). Even if you'd get the E7-8890 in a 4-socket setup,
> I you'll be able to plug in at most 4 GPUs, probably no GeForce.
> Supermicro has some large 5U up to 8S servers, no idea what other
> vendors have as I'm mostly used to 2S GPU.
Well, I'd like to have the cake and eat it, yes. However, now that I 
went into more detail looking at the differences between E5 and E7, your 
point is quite clear.

> Insisting on a single E7 + GPU server will most probably not give the
> best of both worlds. You will likely end up with a machine that's
> mediocre for many if not most tasks. Why not split the
> responsibilities and get two separate machines e.g. a large memory
> 4-socket CPU-only and a separate 2S (or 4S) with GPUs?
>
> BTW, E5-4xxx does 4S, do you really _need_ E7?
Not much of an insistence. We were leaning against multiple low core 
count nodes to avoid dealing with interconnects. However, your point 
about two E5-based machines (one with GPUs, one without) is perfectly 
attractive.
If you were to build an E5-based GPU-accelerated _high-core_ count MD 
server with a budget of $20-25K, what would you go with?
> GeForce TITAN X. (Money no issue? Get Tesla P40 or P100. Both will be
> slower, tho).
What do you mean "both will be slower?"
> Sounds good. We'll definitely be interested if you end up with
> something really dense and packing a good punch.
>
I will be happy to share the results, once I have something to share. 
Especially if it's something good!

Thanks,

Alex

>
>> Thank you!
>>
>> Alex
>>
>>
>>
>> On 1/6/2017 6:05 AM, Szilárd Páll wrote:
>>> Hi Alex,
>>>
>>> Benchmarks of quad-socket Intel machines are rare because AFAIK such
>>> systems are mighty expensive and you will not get good bang for buck with
>>> them, especially if you combine these pricey nodes/CPUs with the old and
>>> slow K80s.
>>>
>>> The only reason to get E7 is if >=4 sockets or >1.5 TB memory per node is
>>> a
>>> must. Furthermore, the only reason to buy K80s today (for GROMACS) if they
>>> are dirt-cheap (e.g. free :).
>>>
>>> You'll be much better off with:
>>> - 1-2-socket Broadwell nodes
>>> - P100 if you need Tesla, GeForce 1070/1080
>>>
>>> However, more importantly, what kind of simulations you want to run? For
>>> 50K you might be able to get multiple nodes with optimal price/perf.
>>>
>>> Cheers,
>>> --
>>> Szilárd
>>>
>>> On Tue, Dec 27, 2016 at 9:24 PM, Alex <nedomacho at gmail.com> wrote:
>>>
>>>> Hi all,
>>>>
>>>> We've got some dedicated funding (~50K) for a computing box. GMX will be
>>>> one of the applications used there (the other MD package would be LAMMPS,
>>>> which has similar requirements). Other applications would be ab initio
>>>> and
>>>> DFT packages, so, aside from a ton of RAM and possibly a fast SSD for
>>>> scratch, there aren't too many requirements.
>>>>
>>>> My question is about an "optimal" CPU-GPU combination. Initially, we
>>>> wanted
>>>> something like a quad-Xeon (something relatively senior in the E7 family,
>>>> ~48-64 cores total) with two K80 cards, but I can't find anything like
>>>> this
>>>> in your benchmark documents.
>>>>
>>>> Can someone help spec this thing?
>>>>
>>>> Thanks a lot,
>>>>
>>>> Alex
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