LINKAGE speed up

Mats Sundvall sundvall at perrier.embnet.se
Wed Apr 15 03:54:16 EST 1992


In article 11258 at gazette.bcm.tmc.edu, bwc at raven.mbir.bcm.tmc.edu (Robert Cottingham) writes:
>
>
>First I want to thank all of the people who responded to my request
>last month for information regarding LINKAGE in C.  The upshot is that
>using p2c to translate the code seems to be totally successful in our
>experience so far.  Several of the respondents also related their
>surprize at how well p2c worked.  To date I am unaware of any human
>modification necessary to use the C code out of p2c.  We are working
>in a Sun environment.

We came to the same conclusion a year ago. We were as surprised as you!

[Suggested change to the code deleted]

>Dont take my word for the accuracy of this code as I havent tried it
>in Pascal yet, but it works in C.  This one change makes about a
>factor of 2 speed improvement.  Again, keep in mind that this code
>change needs to be made in all of the various -seg--- routines that
>contain the *** line of code, in order to see the speed up in all
>situations.

Here you spot a problem with the way the code is organized today without
suggesting the obvious solution. At least 90% of the code in the different
programs (MLINK, ILINK, LINKMAO...) are exactly the same, or with very little
differences. We did run a series of diffs and 3diff on the code and was
able to merge most of the code. Actually you can see the the same change
has been done at several places in the Pascal code, with subtle differences
between the programs. This code is a nightmare to maintain. It should be
easy to merge all these routines into a library of callable routines
without to much work. We did it but did not finish it because we choked
on some routines were we could not understand the code ;-{

To make such a library would make it possible to then go in and optimize
routines and just relink the programs. Of course you do not want to
do it all over again when the next release of Pascal LINKAGE comes out.
That was the other reason we did not finish the work.

Regards,

Mats Sundvall
Dept of Medical Genetics,
Uppsala University
Sweden



>
>If you are going to try p2c and/or the above code changes, I recommend
>that you rerun any final results with the original programs before
>publishing them.
>
>Regards,
>Bob
>
>	------------------------------------------------------------
>	Bob Cottingham          	Phone:  713/798-4275
>	Cell Biology, M301          	Fax:        798-5386
>	Baylor College of Medicine	Email: bwc at bcm.tmc.edu
>	Houston, TX   77030
>	------------------------------------------------------------



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