> I've been contacted by a member of the Geosciences Dept.
> wanting to know if I would support his request to the University
> Adminstration for matching funds to obtain parallel computing
> capabilities. Clearly this group needs lots of crunching power
> and I support their efforts. My questions to my more knowledgable
> collegues are:
> 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
that is a backprop neural net for protein tertiary structure prediction.
Contact George Wilcox [ george at lenti.med.umn.edu ].
Much of the problem with parallel algorithms is that they are machine
specific. There have been attempts at standardization of the parallel
languages (F90, Fortran D, CMFortran), but communication calls are
far from standard. If you are porting code between very different
architectures, often the datasets will need to be restructured to insure
reasonable performance. When you ask about code already written, you
should also inquire as to which platform it was developed on.
> 2. Is parallel computing on campus something we would use?
You might want to sent mail to Andrei Malevsky. [malevsky at ahpcrc.umn.edu]
He has been developing geophysical models on hetereogeneous platforms.
In general, if you have a problem that requires a significant amount
of interprocessor communication, a serial machine might give you better
performance.
Cheers!
-Rogene
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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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