Subject: Re: ...parallel computing

From: [email-masked] (Timothy G. Mattson)
Date: Wed, 4 Nov 92 09:07:41 EST

Workstation clusters are without a doubt going to be the 
dominant force in high performance computing for the next
decade (if not longer).  They will not completely replace 
the fancy MPP boxes which will always be needed for the 
most exotic grand challange problems, but lets face it -- 
many of us don't do grand challange problems.  A speedup of 
5 or 6 on 8 workstations is plenty.

With that preamble, I would like to point out some work with
the Linda parallel computing environment and computational 
chemistry.  There are a number of molecular modeling projects 
either completed or in late stages of development using Linda.

Klaus Schulten's group at the Beckman Institute has used Linda
(and PVM) in their molecular dynamics code, MD.  This code 
includes a parallel fast multipole algorithm and produces
really impressive results on the small sized (4) clusters I've
seen it run on (I will be running it soon on up to 16 RS/6000).

Richard Judsen at Sandia National laboratory has created a 
parallel version of the distance geometry code, DGEOM. This
is an embarassingly parallel code with speedups of about
27 on 32 SPARCstation 1's.  We have achieved even better
results (though I don't have them before me) running DGEOM
on the PVS machine from IBM (and now a word from my sponser...
Linda is portable from workstation clusters  all the way up
to MPP machines so I expended no additional effort in geting
the MPP DGEOM numbers).

Finally, there is MOPAC. I have been working with Kim Baldridge
of San Diego to create a Linda version of MOPAC (she did the
hard part in parallelizing the code for the iPSC/860). I hope
to have it done by the end of the year.  For now, all I have
done is the vibrational analysis portion of MOPAC (the easy 
part).  For Acetycholine I have numbers (in seconds):

          iPSC/860       Sparc 1
Nodes   Linda    Nx/2    Network

  1      768.8   766.6
  2      393.3   392.3     846.8
  4      210.6   208.5     452.1
  8      117.5   120.8     253.8
 16       74.7   75.4

(sorry that I don't have the sequential times for the SPARC 1).
Note that Linda and the native iPSC message passing numbers are
very similar.  Linda gets a bum rap for inefficiency which is
not always deserved (yes, thats another word form my sponser).

Kim Baldridge has finished the other pathways through the code and
has submitted a paper to some journal for publication (I don't
remember which).  Not surprisingly, the other pathways through 
MOPAC are not as parallel and therefore do not display such
nice speedups as above.   You'll have to ask Kim for those numbers.

Finally, I am trying to keep up on all the parallel computational
chemistry efforts going on around the world.  If you are doing
parallel computational chemistry and haven't spoken to me 
yet, please drop me a line -- especially if you are working
in molecular dynamics or MOPAC.  

I will be at SuperComputing'92 and urge you to come by and talk 
to me about parallel computational chemistry.  I will be at the
SCIENTIFIC Computing Booth (and SGI and HP and IBM and ...) so
I will be easy to find.  I might also add that on Tuesday
afternoon, there will be a workshop I organized with Cherri
Pancake of Oregon State University on "Mainstream tools for
parallel computing".  If you are thinking of entering the 
parallel computing game, this workshop should be most 
valuable).  

As computational chemists,  we are fortunate to be working in 
a field with so many algorithms that map rather well onto 
parallel architectures (though for the really big MPP systems
we need good eigenproblem software, as someone else pointed out).

--Tim

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Timothy G. Mattson, Ph.D.

Research Scientist                  Director of Product Engineering
Yale Computer Science Department    Scientific Computing Assoc. Inc.
[email-masked]                 [email-masked]
(203) 432-1203                      (203) 777-7442
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