[Rd] ATLAS threaded 64 bit Opteron build for R: need -fPIC

From: Amit Aronovitch <aronovitch_at_gmail.com>
Date: Fri 10 Feb 2006 - 10:29:39 GMT


 Sorry for sending such a late reply, and for being abit OT.

  I've been trying to compile 64 bit ATLAS for numpy (http://numeric.scipy.org/ ),
and so far this thread is the most useful one I could google up - thanks!.   I encountered similiar problems, and so far could not get a .a linkable to numpy
(comparing to your post - it seems I might have forgotten to add the -fPIC for the

 Also, I'm having trouble with the ATLAS lapack. To get a usable lib, one has to
merge it with a full lapack implementation (as described in the ATLAS errata).
 However, I'm using RHEL4, and their installed liblapack.a seems to have been compiled
without -fPIC, so the merged library is unlinkable to numpy's .so. Is there a way to use Redhat's
installed liblapack.so?

 Few questions about your compiler flags:

  1. Is there a reason to compile with -O rather than -O3? (did you try and encounter some problem, or found no major performance difference)
  2. I see you use -mfpmath=387 - does this work better than sse2 (which seems to be the default)? How about the "sse,387" option - should I try that?

Martin Maechler wrote:

>>>>>/ "PD" == Peter Dalgaard <p.dalgaard at biostat.ku.dk <https://www.stat.math.ethz.ch/mailman/listinfo/r-devel>>
/>>>>>/ >>>>>> "PD" == Peter Dalgaard <p.dalgaard at biostat.ku.dk>
>>>>>> on 26 Feb 2004 15:44:16 +0100 writes:
> PD> Douglas Bates <bates at stat.wisc.edu> writes:
> >> Have you tried configuring R with Goto's BLAS
> >> http://www.cs.utexas.edu/users/kgoto/
> >>
> >> I haven't worked with Opteron or Athlon64 computers but I understand
> >> that Goto's BLAS are very effective on those machines. Furthermore
> >> Goto's BLAS are (only) available as .so libraries so you don't need to
> >> mess with creating the .so version.
> PD> I tried it, yes. Somewhat to my surprise, it seemed to be not quite as
> PD> fast as the threaded ATLAS, but I wasn't very systematic about the
> PD> benchmarking.
> PD> (and the Goto items have license issues, which get in the way for
> PD> binary distributions.)
>Thanks a lot, Peter, Brian, Doug, for your feedbacks!
>In the mean time, I have three running versions of R(-devel) on
>the 64-Opteron
>- "plain"
>- linked against threaded GOTO
>- linked against threaded (static) ATLAS (using -fPIC for compilation;
> "large" Rlapack)
>and I find that GOTO is faster than ATLAS
>consistently (between ~ 5-20%) for several tests
>(square matrices; %*% and solve).
>ATLAS is still an order of magnitude faster than "plain" for
>3000x3000 matrices.
>Here are somewhat repeatable "ATLAS for R" build instructions:
> 1. get ATLAS source; unpack
> 2. make : use defaults and "express" installation
> 3. Before "make install ...", edit the Make.<ARCHITECTURE> file:
> add "-fPIC" to three places, namely F77FLAGS, CCFLAG0, and MMFLAGS:
> which in case of the "threaded Opteron" architecture, leads to
> the three new lines
> F77FLAGS = -fPIC -fomit-frame-pointer -O -m64
> CCFLAG0 = -fPIC -fomit-frame-pointer -O -mfpmath=387 -m64
> MMFLAGS = -fPIC -fomit-frame-pointer -O -mfpmath=387 -m64
> in the file Make.Linux_HAMMER64SSE2_2
> 4. make install arch=Linux_HAMMER64SSE2_2
> 5. Sym.link the ATLAS libraries into /usr/local/lib:
> cd /usr/local/lib
> ln -s <ATLAS_build_dir>/lib/Linux_HAMMER64SSE2_2/lib* .
> 6. (needed for runtime!):
> Use environment variable LD_LIBRARY_PATH=/usr/local/lib
>Note that I haven't built *.so (shared) libraries yet.

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https://stat.ethz.ch/mailman/listinfo/r-devel Received on Fri Feb 10 21:35:15 2006

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