Computer Systems for the Life Sciences !?!?!

sss3 at ukc.ac.uk sss3 at ukc.ac.uk
Sat May 11 05:42:25 EST 1991


Our department has access to an AMT DAP 32x32 processor array which
is used for DNA and Protein sequence analysis using software produced
by Dr. J.Collins and Dr. A.Coulson of Edinburgh University.

My research is aimed at a similar program using Kent's MIMD Meiko
Compting Surface.  My speciality is in OCCAM programming on
transputers.  I have no desire to go back to sequential programming
because I feel it hinders my thinking, yes I am a bit of a CSP fan.
There is a lot of talk about using functional languages with implicit
parallelism, or using sequential languages with parallel extensions.
I feel this to be a mistake, OCCAM is proving itself to be easy,
logical and secure, and also offers a higher degree of performance due
to it's explicit parallel nature.  On the question of ADA, that
language, although closely realated to CSP as is OCCAM it is proving to
be less efficient than OCCAM because it takes 60-100 times as long to
perform a context switch between concurrent processes, and allows
output guards on channels which consumes a lot of bandwidth slowing
down the communication process for example.

Results so far are promising, I am using the Needleman/Wunsch
alogorithm at present just to test various topologies.  In the case of
the Meiko I can reconfigure the processors from software allowing
great flexibility and control over the distribution of data.  I am six
months into the project and have achieved a speed of 12000 comparisons
a minute on a pipeline of 16 workers.  I have access to 90
transputers, soon to be increased to nearly 200 when we get the new
daemon fitted to our sun host allowing us to use both our cabinets.

With the arrival of the T9000 series I envisage at least an order or
magnitude increase in performance being within reach, not to mention
the ability to write software that is no longer dependant on the
number of links associated with the transputer design.  If all goes
according to plan we should get an array of 32 T9000 when they reach
the production stage, at least that is the aim.  A new version of
OCCAM has been produced (OCCAM 91) to take advantage of the increased
performance.

At the moment BioComputing here at Kent does not have much priority, I
am the only postgraduate working in the field, I hope to see interest
grow as more people realise the potential of the transputer and OCCAM.


************************************************************************

Shane Sturrock, BioComputing,
Biological Laboratory,
University of Kent,                   \
Canterbury,                         (}:-(   That is Biological Captain.
Great Britain.                        /

************************************************************************

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