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

From: Amit Aronovitch <>
Date: Fri 10 Feb 2006 - 15:53:47 GMT

Prof Brian Ripley wrote:

> On Fri, 10 Feb 2006, Amit Aronovitch wrote:
> You set the reply address to Martin Maechler! That's antisocial.
Sincere apologies. I certainly didn't intend to! (I probably misclicked while trying to put him on Cc: )

   Please ignore that header.

>> Hi,
>> Sorry for sending such a late reply, and for being abit OT.
>> I've been trying to compile 64 bit ATLAS for numpy
>> ( ), 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 F77FLAGS or MMFLAGS).
> Yes, that _is_ in the R-admin manual. I guess you have not read that
> - it describes how to install R. You can get it in the R tarball from
>> 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
> No, nor should you want to. If RHEL4 is like FC3/4 watch out, as RH
> have managed to get BLAS routines in liblapack and not liblas, and use
> incorrect patches to LAPACK 3.0. (Again, see the latest R-admin manual.)

Thanks for the tip - guess that means I'll have to compile my own lapack...

>> 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)
> ATLAS chose that. Since the real work is done by hand-tuned assembler
> code it should not matter.
>> 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?
> Depends on your ATLAS version. Again, ATLAS chose those.
> As it happens, I have been trying to build ATLAS on my new dual
> Opteron box this morning. The latest devel version (3.7.11) does not
> build, as at some point it says it expects the GNU x86-32 assembler.
> If it did it would use SSE3 and so be faster.
> Both 3.6.0 and 3.7.11 fail because my machine is too fast, and I had
> to increase the number of replications (1000) in make/Make.{mv,r1}tune
> and in tune/blas/level1/*.c. Even then I do not entirely trust the
> results (and the two versions report different L1 caches sizes ...).
> I got pretty exasperated with this (it needed about ten builds to get
> one that succeeded). Both ACML and the Goto BLAS work well out of the
> box on Opterons, but do have licence issues. (Again, see the R-admin
> manual for details.)
I'll certainly have to read the R-admin manual. Once I manage to get a working lib I'll try posting some of that info to ATLAS lists (should prbly be included in atlas errata or something).

  thanks alot,

      Amit A. mailing list Received on Sat Feb 11 02:56:10 2006

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