Re: amber-developers: Verlet update time and ntt=3 parallel scaling

From: Adrian Roitberg <>
Date: Wed, 07 May 2008 21:50:59 -0400

Bob and Dave,

I have had some discussions on some other stuff (electrostatics) with
Michael Mascagni at Florida State University, who has co-developed SPRNG

He is a nice guy and maybe Bob can chat with him a bit on parallel
random #s.


Robert Duke wrote:
> I think one problem that comes in is when you randomly seed multiple
> processors, you actually don't know when two sequences on two different
> processes will overlap, but at some point they will. If there is a lot
> of state to the generator, presumably any two random seed starting
> points won't overlap "soon", but apparently this can be a big enough
> problem that folks that do MC can spot interprocessor correlations. So
> we really have to be sure of what we are doing. It is interesting to
> me, and I'll pursue it as I get time, as long as Tom doesn't shoot me.
> Then we will be out of the space where we are worrying about provability.
> Regards - Bob
> ----- Original Message ----- From: "David A. Case" <>
> To: <>
> Sent: Wednesday, May 07, 2008 9:22 PM
> Subject: Re: amber-developers: Verlet update time and ntt=3 parallel
> scaling
>> On Wed, May 07, 2008, Ross Walker wrote:
>>> As far as I can tell if our random number generator is any good -
>>> which I
>>> don't know if we have properly checked or not - two sets of random
>>> numbers
>>> from different seeds should not have any correlation. Thus it should be
>>> equally correct (statistically) to do a Langevin run with each processor
>>> having its own random number stream - with simply different seeds for
>>> each
>>> mpi thread. This should be equivalent to having a single random number
>>> stream shared between all processors where each processor makes sure it
>>> doesn't use the same portion of the stream as other processors.
>> I agree with this, but (as Bob points out) it's not clear how you
>> prove it.
>> With the current method, one *assumes* that the single stream of
>> numbers (that
>> you would get with a serial code) is correct, then arranges to get the
>> same
>> results in parallel.
>> The only artifacts I know of have to do with reusing a particular part
>> of the
>> big stream of numbers. Since the period is very long, presumably
>> Ross' scheme
>> would have low probability of having this happen, but without a detailed
>> understanding of the scheme works, you might get fooled. But I think
>> it would
>> be worth the risk.
>> ...dac

                            Dr. Adrian E. Roitberg
                              Associate Professor
               Quantum Theory Project and Department of Chemistry
University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email
To announce that there must be no criticism of the president,
or that we are to stand by the president right or wrong,
is not only unpatriotic and servile, but is morally treasonable
to the American public."
   --  Theodore Roosevelt
Received on Sun May 11 2008 - 06:07:19 PDT
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