what software do biologists need?

Roy Omond omond at embl-heidelberg.de
Thu Mar 18 07:38:14 EST 1993

In article <33147 at castle.ed.ac.uk>, sss at castle.ed.ac.uk (S S Sturrock) writes:
> Just one thing for the computer scientists reading this, for the most part
> Teraflops (or Gigaflops at the moment) are really not very useful for the
> day to day biology task, ie sequence analysis.  Sure for modelling etc they
> become quite handy but integer arithmetic is where it is still at.  I
> originally wrote MPsrch for the CM-200 we have here at Edinburgh (oddly
> enough it was called CMsrch in those days, nothing like being predictable)
> and although the CM-200 claims to have 8 Gigaflops performance (I am sick
> and tired of people claiming it is the most powerful supercomputer in the
> UK) the it could barely manage 8 million cell updates (8K PEs) for the Smith
> Waterman algorithm.  That equates to the same performance as was attained
> on a 1024 PE DAP back in 1988!!  And the DAP dates back to the late 70's!
> Considering the CM-200 has 8K PEs this is really dreadful.  On the other
> hand, porting exactly the same C code onto a smallish MasPar with only 4K
> PEs brought about a 4 fold improvment in performance immediately, and
> within weeks the code was performing at just under 100 million cell
> updates.  This from a machine that costs *FAR* less than the MasPar.  Sure,
Presume you meant the CM-200 !

> for some tasks the CM (and other high Flop rating machines) is great but
> what we really need is a machine that can perform huge numbers of integer
> operations as well as floating point.  Now that I know a little more about
> programming the MasPar machines I have hiked the speed up to 180 million
> cell updates for proteins and 285 million for nucleic acid (4K PEs) scaling
> perfectly across all maspar machines (1-16K PEs).  Ah the power of mips V 
> flops!

Hear hear, Shane !

> MPsrch is still available on blitz at de.embl-heidelberg for protein searches

Just a small nitpick.  For most of the world, that should be :

	Blitz at EMBL-Heidelberg.DE

(*sigh*... ze British !)

> and the nucelic acid version is just about ready, just have to arrange
> exactly how to offer it as a mail service.

Real soon now :-)  Problem was/is manpower within EMBL;  Peter Rice has
agreed to help out with the DNA stuff.

> Shane Sturrock, Biocomputing Research Unit, Darwin Building, Mayfield Road,
> University of Edinburgh, Scotland, Commonwealth of Independent Kingdoms.  :-)
> Civilisation is a Haggis Supper with salt and sauce and a bottle of Irn Bru.

Re Civilisation:  Agreed !!!

Roy Omond
System Manager/PostMaster etc. etc.
European Molecular Biology Laboratory
Heidelberg, Germany.

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