> >> 1. What presently is available (or seen coming in the near
> >> future) on parallel machines that would aid molecular biology
> >> research?
> >
> >There is a program called BigNet written for the Cray, CM200, and CM5
>> Of course, there are other machines that might be considered....the
> Maspar machine has an excellent $-per-CPU-minute ratio when kept busy on
> very large problems....I don't happen to know it for the Convex products
> but I'll bet it's good also.
I agree, however the question asked what software was available. BigNet
currently runs on these machines without any rewriting or alteration.
Do you know of any molecular bio software written for the MasPar or
Convex? If not, then one needs to consider 1) porting with possible
restructuring 2) writing from scratch. The original posting suggests
that they are looking for code ready to roll...
> Let's put this the other way around: if one has an algorithm which is
> purely synchronous (each processor in the machine is executing the same
> line of FORTRAN at the same moment), then you may be home free! The
> implementation of the algorithm on your machine-of-choice may be greatly
> simplified (and I know of at least one major sequence classification
> algorithm that falls into this category).
The numerical arguement I gave in my previous posting is based on a
synchronous *SIMD* construct. It is NOT true to assume that one can
bypass the communication issue in SIMD.
> For some categories of algorithms, massively parallel is the way to go!
> And for other categories, it may be the pits. :^) [ I'm thinking of the
> contrast in two crop process modeling presentations a few years ago....the
> guy that grew FORTRAN "supercomputed" corn had a gut-wrenching experience,
> whereas the guy that threw away COMAX (FORTRAN Cotton Model) and grew cotton
> in LISP from first principles thought it was a breeze to do. ]
>>> Steve Modena
Right! :-)
Cheers!
-Rogene
******************************************************************************* Rogene M. Eichler West
Neuroscience Program Minnesota Supercomputer Institute
University of Minnesota Army High Performance Computing Research Center
AHPCRC: (612)626-8082 1100 Washington Ave South
Home: (612)292-0573 Suite 101 MN Tech Center
Fax: (612)626-1596 MPLS, MN 55415
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