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

From: Amit Aronovitch <aronovitch_at_gmail.com>
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
>> (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 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
>
> ftp://ftp.stat.math.ethz.ch/Software/R/R-devel.tar.bz2
>
>
>> 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?
>
>
> 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.



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https://stat.ethz.ch/mailman/listinfo/r-devel Received on Sat Feb 11 02:56:10 2006

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