[gmx-users] Specs for GPU box

[Szilárd Páll]

Hi,

On Sat, Jan 7, 2017 at 3:20 AM, Alex <nedomacho at gmail.com> wrote:
> Hi Szilárd,
>
> Thanks for responding. Yes, those systems are indeed expensive, and our main
> objective here wasn't really bang for the buck.  What we want is the fastest
> possible single node for the money, and if that means an extra $5-10K, we're
> okay with that.

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? ;)

> The machine we want to build isn't dedicated to MD, but more
> of a general purpose number crunching beast.  For DFT calculations we want
> what you described, i.e. 1-2TB

FYI up to 1.54 TB you get even in dual-socket E5
https://ark.intel.com/products/91753/Intel-Xeon-Processor-E5-2698-v4-50M-Cache-2_20-GHz

> --  these benefit tremendously from massive
> amounts of RAM and CPU clock rate & cache amount.

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.

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?

> So, we want a _really_
> fast machine, which among other things will perform beautifully with GMX and
> LAMMPS. Yes, the K80 cards appear to be well outdated for our CPU selection.
> What would you recommend in terms of GPUs for an E7-based system?

GeForce TITAN X. (Money no issue? Get Tesla P40 or P100. Both will be
slower, tho).

> We will be working with a vendor, who, given the amount of money in
> question, will likely agree to assemble the machine and do benchmarks prior
> to sale. Given what you said already, can you suggest any GPUs to start
> with? If you guys are interested, I am 100% open to sharing the benchmark
> results.

Sounds good. We'll definitely be interested if you end up with
something really dense and packing a good punch.

Cheers,
--
Szilárd

> 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
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
>>> /Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>>>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
> mail to gmx-users-request at gromacs.org.