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.
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