R devel - Feb 2000 - forwarded message from Dirk Eddelbuettel <edd@debian.org>

Dirk's mail to r-devel bounced because of his peculiar return
address.  He asked me to forward this for him.

P.S. I have tried building R with atlas2 on a Debian GNU/Linux 2.2
system but I have not yet managed to out-fox the configure script to
get it to use the desired shared object library.
-- 
Douglas Bates                            bates@stat.wisc.edu
Statistics Department                    608/262-2598
University of Wisconsin - Madison        http://www.stat.wisc.edu/~bates/
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Date: Wed,  9 Feb 2000 08:52:01 -0500 (EST)
To: r-devel@lists.r-project.org
Subject: Atlas 
From: Dirk Eddelbuettel <edd@debian.org>
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Congrats on getting 0.99 out, and on the rapid convergence towards 1.0.
Attached below is the latest email in a very interesting thread about
building GNU Octave with the 'Atlas' (Automatically Tuned Linear Algebra
Software) libraries that are drop-in replacements for (parts of) Lapack and
the Blas. Speed increases of up to 10 have been reported for simple matrix
multiplication (this is over Lapack/Blas used by Octave).  You can find the
whole thread at http://www.che.wisc.edu/octave/mailing-lists/help-octave/2000/ 

Regards, Dirk


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From: "John W. Eaton" <jwe@bevo.che.wisc.edu>
To: R Clint Whaley <rwhaley@cs.utk.edu>
cc: help-octave@bevo.che.wisc.edu
Subject: Re: ATLAS and octave
Date: Wed, 9 Feb 2000 03:05:13 -0600 (CST)

Here is all I did to build a copy of Octave that uses ATLAS:

  1. build ATLAS

  2. merge all four of the libraries that the ATLAS build creates into
     a single libatlas.a and install it in /some/dir.

  3. relink Octave by running

       make SPECIAL_MATH_LIB=/some/dir/libatlas.a

That seems to be all that is needed.

Would it be possible to modify the ATLAS makefiles to just build a
libatlas.a?  Then Octave could simply have

  AC_CHECK_LIB(atlas, ATL_xerbla)

in the configure script, and set SPECIAL_MATH_LIB accordingly.

Things might get a little more complicated for shared libraries.  Some
systems seem to barf when multiple shared libraries define the same
symbol.  But it would probably be possible to solve that, either by
doing whatever is necesary to tell the dynamic linker not to barf, or
by omitting the duplicate symbols from libcruft.

BTW, I see the following speedup on my system (266MHz Pentium II):

  octave:1> a = rand (1000); b = rand (1000); 
  octave:2> t = cputime (); a * b; cputime () - t

  without ATLAS:  94.4 seconds
  with ATLAS:     10.5 seconds

Wow!

Thanks,

jwe



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>>>>> "DB" == Douglas Bates <bates@stat.wisc.edu>
writes:
    DB> P.S. I have tried building R with atlas2 on a Debian GNU/Linux
    DB> 2.2 system but I have not yet managed to out-fox the configure
    DB> script to get it to use the desired shared object library.  --

Note that the Debian Atlas libraries are tuned for a P2-350 with 512
cache; which for us is fine, since our MOSIX cluster is full of them.
It might be less optimal for P3's and P1's, since it's supposed to
be
(according to the documentation at the original site, as well as the
Debian docs, last I looked) built on the configuration at hand... 

Nonetheless, it might be a worthwhile thing to explore...

best,
-tony

-- 
A.J. Rossini		       Research Assistant Professor of Biostatistics 
Biostatistics/Univ. of Washington  (Th)	Box 357232   206-543-1044 (3286=fax)
Center for AIDS Research/HMC/UW	  (M/F)	Box 359931   206-731-3647 (3693=fax)
VTN/SCHARP/FHCRC		 (Tu/W)	Box 358080   206-667-7025 (4812=fax)
rossini@(biostat.washington.edu|u.washington.edu|hivnet.fhcrc.org)
http://www.biostat.washington.edu/~rossini

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