[gmx-users] Gromacs GPU system question

[Mirco Wahab]

On 22.06.2013 22:18, Mare Libero wrote:
> The vendor I contacted was pushing for one of the
> high end i7 processors with hyper-threading. But from what I can read,
> most of the MD software don't make any use of it. So, using a the
> multi-cores AMD (like your  FX-8350) can be a cheaper and more
> advantageous option.

Your vendor is, in my opinion, right. The AMD consumer multicores
(Piledriver) aren't actually eight-core cpus, but rather similar
to 4 core cpus (they are called 'modules').

For testing a user-defined potential, I once compiled performance
figures over a range of actual commodity hardware (available to me).
These are all workstations and usually overclocked somehow by the
students (but only if there's no crash at all in a year ;-)
This is all *without GPU*, only the plain and raw CPU processing
power for Gromacs is checked for (last column).

  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

  Test case:
  Two coarse-grained implicit-solvent vesicles bumping into each other
  SD integrator
  480,000 particles
  Box (110nm)³
  User-defined potential (rc=0.8225nm)
  dt=0.020ps
   --------------------------------------------
     CPU            	Arch	Cores	ns/day
   --------------------------------------------
   - X6/1090T;3.3GHz	SSE2	6C/6T	19.130
   - FX-8350;4.5GHz	AVX_FMA	4M/8T	34.175
   - i7/2600K;4.2GHz	AVX_256	4C/8T	39.073
   - i7/3770K;4.4GHz	AVX_265	4C/8T	41.931
   - i7/3930K;4.2GHz	AVX_256 6c/12T	56.891

  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

You can see here, for CPU performance, you can't
really choose anything different from the 6-core i7/3930K.
It costs some bucks more than the 4-core-CPUs but will run
significantly faster the time you use it.

> Most of what we do is protein-protein interactions and protein stability
> studies with explicit water/ions. One of our projects now has <100,000
> atoms in a 100 Ang water box (7,800 protein atoms + 67,000 water). It's
> difficult to be more specific on the parameters since each project is
> different, but in general we do not deviate much from a standard NPT run.

10nm box/75K atoms is not very large. I guess you'd use a time step
of 0.002 ps and a united atom model + spc or spc/e water? 100ns/day
seem possible with any GPU from GTX-660 or higher. If you buy a mighty
GPU (Titan), the question will be: can your n-core-CPU saturate such a
fast GPU monster? A good compromise would be, probably, the GTX-780
which is a slightly reduced Titan for half the price and all options
open.

my € 0.02

M.