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Optimizing CNS

David Konerding dek at nano.ucsf.edu
Sun Feb 28 20:25:29 EST 1999

On 28 Feb 1999 11:58:15 GMT, Steffen Graether
<steffen at protein.biochem.queensu.ca> wrote:
>Could someone suggest how I could optimize cns on a linux pc running
>redhat 5.2? I find the three-fold execution time difference between our
>overused R10000-250 MHz Octane and underused PentiumII-333 Mhz PC rather

Dear Steffen,

There are a few possibilities I can think of:

1) The Octane is using SGI-specific math libraries which are highly

2) You are running out of physical RAM and the machine is swapping.

3) f2c (which CNS uses to compile on linux) does not optimize as well as

There's not much you can do about #1, you should definitely observe the
machine to see whether #2 is true, and #3- well, try to convince the CNS authors
to change CNS so it compiles with g77 rather than f2c.  

Additionally, one final possibility- hack CNS so it compiles with a professional
fortran compiler like PGF77 (from Portland Group).  It can optimize much better
than g77.

Good luck.
Email: dek at cgl.ucsf.edu    David Konerding     WWW: http://picasso.ucsf.edu/~dek
Snail: Graduate Group in Biophysics
Medical Sciences 926, Box 0446
University of California
San Francisco, CA 94143

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