[gmx-users] Specs for GPU box

Alex nedomacho at gmail.com
Sat Jan 7 03:20:22 CET 2017

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. 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 --  these 
benefit tremendously from massive amounts of RAM and CPU clock rate & 
cache amount. 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appear to be well outdated for our CPU selection.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?

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.

Thank you!


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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