hello:
thank you very much for your kind reply. Does anybody else have any
idea how to improve it?
here is my md.in file:
production dynamics
&cntrl
imin=0, irest=1, ntx=5,
nstlim=250000000, dt=0.002,
ntc=2, ntf=2,
cut=10.0, ntb=2, ntp=1, taup=2.0,
ntpr=1000, ntwx=1000, ntwr=50000,
ntt=3, gamma_ln=2.0,
temp0=300.0,
/
thank you very much
On 04/18/2012 09:36 AM, steinbrt.rci.rutgers.edu wrote:
> Hi,
>
>> some test for a 50,000 atoms protein/water system,
>> command:
>> 1X8 16.44
> I am not part of the CUDA developers, but to me, that looks not unusual,
> depending on your GPUs. Compare to
>
> http://ambermd.org/gpus/benchmarks.htm#Benchmarks
>
> I assume that 1X8 means 1 8core node with a single GPU, right? 10-20ns/d
> for a medium-large system is what I'd expect.
>
>> 1X6 17.98
>> 2X6 19.41
>> 3X6 20.13
>> 4X6 19.70
>> 5X6 19.62
>> 6X6 19.03
>> 10X6 18.33
>> It seems that the efficiency is not so high and the best one is 3X6 with
>> around 20.1 ns/day. Since I am going to run hundreds of ns, it would
>> take such a long time to be finished.....
> I would argue that you gain almost nothing from scaling to a third GPU, so
> 2 or even 1 GPU is the optimal spot to run your simulation. Adding 50%
> more resources to gain 5% more efficiency seems wasteful to me. You see
> that multi-GPU scaling is not very efficient, which would depend on your
> machine setup.
>
> As for the long time your simulation would then take: *are you kidding
> me?* I hate to sound exceptionally old here, but when I started doing MD
> (say 5 years ago) I'd have killed for multinanosecond simulations on a
> single machine, especially when waiting for a three-week 1 ns
> equilibration to finish. So I guess the efficiency you see is the best one
> could get at the moment and it is actually very very impressive!
>
> Please imagine last paragraph wrapped in<rant> tags ;-)
>
> Thomas
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
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Received on Wed Apr 18 2012 - 04:00:04 PDT
