Hi Jason,
This is very helpful. Thanks a lot!
Best.
Ying-chieh
-----Original Message-----
From: Jason Swails [mailto:jason.swails.gmail.com]
Sent: Tuesday, August 5, 2014 10:03 PM
To: AMBER Mailing List
Subject: Re: [AMBER] pmemd.MPI of amber14: run MD twice with the same input but got different output (within statistical error)
On Mon, Aug 4, 2014 at 10:45 PM, Ying-Chieh Sun <sun.ntnu.edu.tw> wrote:
> Hi Brian,
> Thanks for the input.
>
> Ig issue is not our case. We did check that already.
>
This is certainly due to the dynamic load balancing in pmemd.MPI. What this means is that pmemd.MPI splits up the work between processors by analyzing how long each processor spent on the amount of work assigned to it and then redistributes the work in an attempt to get a more even distribution. Since there are always background processes taking up computational resources, the "optimal" load balance is almost never the same two different times. While this helps improve performance for obvious reasons, it also eliminates determinism.
As a result, the order of operations is never the same when running two different parallel calculations. If you want reproducibility, you'll need to use a program that uses a so-called "static load-balancing scheme"
(which means that the workload is distributed on the first step deterministically and never changed). Obviously serial versions of programs have static load balancing -- the single processor does all of the work. Also, pmemd.cuda, pmemd.cuda.MPI, and sander.MPI also all utilize static load balancing (I've personally seen sander.MPI generate identical results for the same number of processors for thousands of steps).
Of course this reproducibility relies on all input settings being _exactly_ the same (and ig must be a positive integer, _not_ -1).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Aug 05 2014 - 23:00:02 PDT
