Hi,
some more technical things come to mind from your mdin:
- run an NPT simulation only if you really have to, NVT is faster
- using the berendsen thermostate with a higher coupling constant may also
help
- have auto error correction (ECC?) on the GPUs disabled if you can, I
think this adds nothing to simulation stability and costs up to 10% in
speed...
On Wed, April 18, 2012 6:52 am, Albert wrote:
> 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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>
>
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>
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 - 04:30:03 PDT
