[gmx-users] Workstation configuration advices?

[Szilárd Páll]

On Fri, Nov 10, 2017 at 9:53 AM, Javier Luque Di Salvo
<jluquedisalvo at outlook.com.ar> wrote:
> Dear users and developers,
>
>
> I am about to acquire a Workstation to mainly run GROMACS. In choosing the right configuration that fits the budget, I came out with this basic arrange (from Dell - Precision 7820 Tower):
>
> - Processor: Intel Xeon Gold 6130 2.1 GHz 3.7 GHz Turbo, 16Core 10.4 GT/s 2 UPI, 22MB cache, HT (125W) DDR-2666. Or any other similar of the Intel Xenon (R) type.

That's going to be really expensive. You can get far better
performance with a i9-7980XE for similar price or far better
performance/price with 12-14 core i9s; However, you'll get even better
performance/price with a Threadripper 1950X which should be around the
same performance as the 12-14-core Intel (for lower price than
either).

> - Graphic card: NVIDIA Quadro P4000, 8GB, 4DP (7x20TB): even if I would like a Tesla P100, anyone has used Quadro cards or knows about its acceleration in GROMACS? Also, are Raedon graphic cards compatible/ tested for GROMACS (I didn't check if they support CUDA).

That's a rather low-end card in terms of compute-performance. I'd
recommend 1070 Ti / 1080 or 1080 Ti (two of each perhaps?). The Quadro
P4000 is in terms of compute performance slower than the GTX 1070 for
half the price.

> - Memory 32 GB (2x16 GB or 4x8GB?) It wont be better 16GB of RAM and maybe 18Cores, 20Cores? The price rises very easy when adding only two-four cores! The same for the graphic card!

For MD simulations you won't need more than 16 Gb, but do get at least
four modules because otherwise you won't get the full bandwidth.

> - Primary Hard disk: Solid state (SSD) Class 50 of 512 GB.
>
> About the primary hard disk, should it be NVMe or SATA SSDs? I saw that NVMe has much better I/O communication but since its relative new tech, I don't know if GROMACS can fully run here, I believe it does.

What do you mean by "fully run"? Simulations won't make use of the
fast I/O, but if you'll do large-scale analysis, that might. It boils
down to the price, but if it comes to deciding whether to get 14 cores
+ NVMe or 16 cores + SSD, I'd choose the latter unless your analysis
will last days longer ;)

> Also, NVMe it doesn't support RAID (is RAID a must for GROMACS?), and I'm afraid to encounter basic problems such as not being able to properly install the OS and the right dependencies/ libraries/ related tools-software. http://info.grcooling.com/nvme-vs-sata-ssd

Not sure what issues you're referring to, but I've been running my
Linux OS on NVMe without issues.

> - Secondary disk: SATA 3.5'' 1TB 7200 rpm.
>
>
> I'm intended to simulate polyelectrolyte hydrocarbon-polymers, its water uptake and ion-diffusion, in simulation boxes of a maximum about 10x10x10 nm, but most of the work would be in much smaller dimensions.

I assume that's far less dense than e.g water, right? Otherwise you'll
have ~100M atoms which would not be very fast on a single node even
with 18 cores + 2 GPUs.

Cheers,
--
Szilárd



>
> Any comments are highly appreciated.
>
> Best regards
>
>
> ________________________________________
>
> Javier Luque Di Salvo
>
> Dipartamento di Ingegneria Chimica
>
> Universitá Degli Studi di Palermo
>
> Viale delle Scienze, Ed. 6
> 90128 PALERMO (PA)
> +39.09123867503
>
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