Re: amber-developers: weirdnesses in Langevin dynamics code

From: Robert Duke <>
Date: Tue, 24 May 2005 10:59:54 -0700

Folks -
Maybe there are some issues I am unaware of here, but a sequence of
pseudorandom numbers, starting with the same initial seed, should be very
deterministic, and I don't immediately see the problem with relying on
The only way I could see problems, given that the code is all provided in
the app (as opposed to in libraries), would be if you had a heterogeneous
parallel run; ie., you were running on different types of platform. That
course would be disastrous, but I can think of lots of things that will
break if you do that (anywhere you rely on the same calculation on
nodes producing the same result).
Regards - Bob

----- Original Message -----
From: "John Mongan" <>
To: <>
Sent: Tuesday, May 24, 2005 1:45 PM
Subject: Re: amber-developers: weirdnesses in Langevin dynamics code

>> John Mongan has code for multiple "streams" of random numbers (I
>> that
>> might be implemented here. But basically, there is probably nothing
>> wrong
>> with the code as it stands.
> Yes, I reorganized amrand a couple years ago such that it's fairly easy
> create your own "private" sequence of random numbers. Hopefully it's
> how to use it from the code, or the constant pH code can be used as an
> example; if not, I'll explain.
> Constant pH needs to be able to generate the same random number on all
> nodes so that the Monte Carlo step can be synchronized without needing
> comms (I gather that NEB has a similar requirement). I ended up
> implementing the "private streams" approach because depending on the
> generator to remain synchronized between nodes seemed to be a fragile
> solution.
> John
Received on Wed Apr 05 2006 - 23:49:56 PDT
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