PHYLIP on Crays

Joe Felsenstein joe at GENETICS.WASHINGTON.EDU
Mon Dec 3 12:58:52 EST 1990

Sarah Barron asked if PHYLIP has been ported to Cray Y-MPs.  It has, by
Ron DeBry (debry at ds1.scri.fsu.edu) and by Shan Duncan (duncan at csd4.csd.uwm.edu)
(the latter was actually an X-MP).

Both succeeded in getting it to work without difficulty.  But both reported
sufficiently slow running times that it was obviously not making use of
vector-processing very well.  The problem is that some of the interior
loops of the program use scalar quantities to store intermediate results.
If these scalars were made into vectors, there would, I suspect, be a big
speedup.  Also, in some programs there are IF statements inside the innermost
loops that can have results that come out differently for different
values of the index variable.  That would seem to be something that would
not vectorize well but might respond better to true parallel processing.

Programs that should do particularly well if the scalar temporary storage
variables are made vectors are DNAML, DNAMLK, and RESTML.  There are
pointers in the main documentation file under Cray, and I will try to
be responsive to inquiries.

Joe Felsenstein, Dept. of Genetics, Univ. of Washington, Seattle, WA 98195
 Internet/ARPANet: joe at genetics.washington.edu     (IP No.
 Bitnet/EARN:      felsenst at uwalocke
 UUCP:             ... uw-beaver!evolution.genetics!joe

More information about the Bio-soft mailing list

Send comments to us at biosci-help [At] net.bio.net