[gmx-users] Gromacs: Cloud Vs. Boinc Server?

[Matt Larson]

>From the Gromacs on GPU page
(http://www.gromacs.org/Downloads/Installation_Instructions/GPUs)

These are the compatible GPU cards (Basically buy NVidia for now):

v2.0
Compatible NVIDIA CUDA versions (also see OpenMM version compatibility above):

v3.x
Compatible hardware (for details consult the NVIDIA CUDA GPUs list):

G92/G94:
GeForce 9800 GX2/GTX/GTX+/GT
GeForce 9800M GT
GeForce GTS 150, 250
GeForce GTX 280M, 285M
Quadro FX 4700
Quadro Plex 2100 D4
GT200:
GeForce GTX 260, 270, 280, 285, 295
Tesla C1060, S1070, M1060
Quadro FX 4800, 5800
Quadro CX
Quadro Plex 2200 D2, 2200 S4
GF1xx (Fermi)
GeForce GTX 460, 465, 470, 480, 570, 580
Tesla C2050, C2070, M2050, M2070

---

 I got an EVGA Geforce GTX 580, which is about $450 for trying out GPU
based MD, and has 512 GPU cores and a high clock rate, 1.5 gigs of
memory.  Having more cores and more memory are both important things
for the GPU side of molecular dynamics (cores = more parallel, memory
= more atoms and less memory transferring).  I think you have some
limitations with the GPU sims, like atoms < 100,000.  It is amazing
that with implicit solvent you can really see a huge benefit and
perhaps that might open some new doors.

-Matt Larson


On Wed, Oct 12, 2011 at 9:54 AM, Szilárd Páll <szilard.pall at cbr.su.se> wrote:
> Dear Stephan,
>
>> Radeons work as well.  You can put a 3-4 GPU board together with the highest end AMD or Intel chip for 3K, plus 16G RAM if you look around for a day or two, but the cooling is the main problem (with 1/4 the price radeons Vs. GTI cards), so one has to take cooling into account (h20 cost another 800$, or investing in 4-6 good fans/cooling an additional 2-300$).  If you have a slightly higher budget you can get multi CPU boards with 4 GPU slots, ie 4 or 8 CPU's (direct via mail from Taiwan), but the CPU's and GPU's is where the money is spent.
>
> No, Radeons don't work and won't work in the near future - Gromacs
> doesn't support OpenCL. Cooling needs attention, but in reality it's
> nowhere near $2-300 extra - unless you want the fans with funky leds.
>
> Btw, what software is the above hardware description targeting? To me
> it sounds more like a gaming rig and not something specifically aiming
> at maximum performance with Gromacs 4.5 (nor 4.6 which is yet to be
> released).
>
>> As far as I have seen GPU Gromacs runs at around 1 Teraflop per Radeon 5900 series (double percission, single is supposed to run around 4 tera flops per GPU, so depends on your needs, desires as far as simulations), and the latest Intel 970's are around 400-500 Gflops/chip.
>
> Again, I might be missing something, but how exactly does Gromacs run
> on Radeons? I assume when referring to the i7 970 (?) above you meant
> 40-50 GFlops/chip - the i7 970 should have 70 GFlops peak. Also note
> that Flops are not every useful, what matters is time to solution for
> the specific problem one wants to solve.
>
> Cheers,
> --
> Szilárd
>
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