[gmx-users] MD workstation

[Szilárd Páll]

On Thu, Oct 16, 2014 at 3:35 PM, Hadházi Ádám <hadadam at gmail.com> wrote:
> May I ask why your config is better than e.g.
>
> 2x Intel Xeon E5-2620 CPUs (2x$405)
> 4x GTX 970(4x $330)
> 1x Z9PE-D8 WS ($449)
> 64 GB DDR3 ($600)
> PSU 1600W, ($250)
> standard 2TB 5400rpm drive, ($85)
> total: (~$3500)

Mirco's suggested setup will give much higher *aggregate* simulation
throughput. GROMACS uses both CPUs and GPUs and requires a balanced
resource mix to run efficiently (less so if you don't use PME). The
E5-2620 is rather slow and it will be a good match for a single GTX
970, perhaps even a 980, but it will be the limiting factor with two
GPUs per socket.

> As for your setup...can I use that 4 nodes in parallel for 1 long
> simulation or 1 FEP job?

Not without a fast network.

> What are the weak points of my workstation?

The CPU. Desktop IVB-E or HSW-E (e.g. i7 49XX, 59XX) will give much
better performance per buck.

Also note:
* your smaller 25k MD setup will not scale across multiple GPUs;
* in FEP runs you, by sharing a GPU between multiple runs you can
increase the aggregate throughput by quite a lot!

Cheers,
--
Szilárd

> Best,
> Adam
>
>
> 2014-10-16 23:00 GMT+10:00 Mirco Wahab <mirco.wahab at chemie.tu-freiberg.de>:
>
>> On 16.10.2014 14:38, Hadházi Ádám wrote:
>>
>>> Dear GMX Stuff and Users,
>>>>> I am planning to buy a new MD workstation with 4 GPU (GTX 780 or 970)
>>>>> or 3
>>>>> GPU (GTX 980) for 4000$.
>>>>> Could you recommend me a setup for this machine?
>>>>> 1 or 2 CPU is necessary? 32/64 GB memory? Cooling? Power?
>>>>>
>>>>
>>>> - What system (size, type, natoms) do you plan to simulate?
>>>>
>>>> - Do you have to run *only one single simulation* over long time
>>>>    or *some similar simulations* with similar parameters?
>>>>
>>>
>>> The systems are kind of mix:
>>> MD:
>>> smallest system: 25k atoms, spc/tip3p, 2fs/4fs, NPT, simulation time:
>>> 500-1000ns
>>> biggest system: 150k atoms, spc/tip3p, 2fs/4fs, NPT, simulation time:
>>> 100-1000ns
>>> FEP (free energy perturbation): ligand functional group mutation
>>> 25k-150k atoms, in complex and in water simulations, production
>>> simulation:
>>> 5ns for each lambda window (number of windows: 12)
>>>
>>
>> In this situation, I'd probably use 4 machines for $1000 each,
>> putting in each:
>>  - consumer i7/4790(K), $300
>>  - any 8GB DDR3, $75-$80
>>  - standard Z97 board, $100
>>  - standard PSU 450W, $40
>>  - standard 2TB 5400rpm drive, $85
>>
>> the rest of the money (4 x $395), I'd use for 4 graphics
>> cards, probably 3 GTX-970 ($330) and one GTX-980 ($550) -
>> depending on availability, the actual prices, and
>> your detailed budget.
>>
>> YMMV,
>>
>>
>> Regards
>>
>> M.
>>
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