Hi Jason,
Thank you so much for this information. I had not
tried using NETCDF trajectories and restart files,
but will definitely try it now.
Thank you very much again!
Best regards,
Shan-Ho
-----------------------------
Shan-Ho Tsai
GACRC/EITS, University of Georgia, Athens GA
On Tue, 21 May 2013, Jason Swails wrote:
> On Mon, May 20, 2013 at 4:11 PM, Shan-ho Tsai <tsai.hal.physast.uga.edu>wrote:
>
>>
>> Hi Ross,
>>
>> Thank you so much for your prompt and detailed response.
>> It all makes perfect sense. We had enabled the Persistence
>> Mode and set the Compute Mode to Exclusive_Process. But we
>> have been having occasional storage latency issues on one
>> mounted file system. Following your suggestion, I just ran
>> a few tests with a larger NSTLIM and the results are
>> consistent with the values reported in the URL.
>>
>> I really appreciate your detailed explanation and kind
>> suggestions.
>>
>
> I'll share another nugget of wisdom I've gleaned from running pmemd.cuda on
> machines with potentially poor latency on mounted file systems. Use NetCDF
> EVERYTHING. Set ioutfm=1 to get NetCDF trajectories and set ntxo=2 to get
> NetCDF restart files.
>
> In one of my tests, setting ntxo=2 nearly tripled my performance (I've
> always used ioutfm=1).
>
> A few disclaimers there:
> 1) the default restart frequency is way too high (every ~500 steps). If you
> only print 5 to 10 restarts a simulation, the performance would probably
> not matter much.
> 2) The JAC benchmark does not print any restarts IIRC.
> 3) The test system was extremely small (<10K atoms with a 15 Angstrom
> solvent buffer). Simulation efficiency of small systems tend to be highly
> sensitive to small changes like this. Larger systems are unlikely to be as
> affected.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Tue May 21 2013 - 07:30:02 PDT
