Re: [gentoo-science] lapack 3.0? (rkward)

["M. Edward (Ed) Borasky" <znmeb@cesmail.net>]

Honza Macháček wrote:
> On 26.02.2007 01:38, M. Edward (Ed) Borasky wrote:
>   
>> I'm a little curious about something ... does "rkward" actually require
>> an external Lapack, or is this optional? The reason I ask is that R
>> itself *contains* a copy of Lapack, and the R developers have deprecated
>> linking against external Lapack libraries!
>>     
>
>   I think I recall some discussion at the bugzilla to the point that all
> multimedia packages that compile their own libraries instead of linking
> to external ones should be hardmasked, allegedly for the sake of
> maintainability. Moreover in my mailbox I've found an old discussion
> (28. 8. 2006) of Freemat 2.0 and problems with its dependency on matio,
> when accidentally I myself called to attention that Freemat sources
> contained their own copy of the matio library, and Andrey G. Grozin
> dismissed the option of using them rather fiercely, reasoning:
>
>   
>> This goes against modularity, *the* fundamental principle of any good 
>> Linux distribution.
>>     
Well, here's the logic of the R developers (from 
http://cran.fhcrc.org/doc/manuals/R-admin.html):


        "A.3.2 LAPACK

Provision is made for using an external LAPACK library, principally to 
cope with BLAS libraries which contain a copy of LAPACK (such as 
|libsunperf| on Solaris, |vecLib| on Mac OS X and ACML on 
`ix86'/`x86_64' Linux). However, the likely performance gains are 
thought to be small (and may be negative), and the default is not to 
search for a suitable LAPACK library, and this is definitely *not* 
recommended.

[snip]

"For problems compiling LAPACK using recent versions of |gcc| on `ix86' 
Linux, see New platforms 
<http://cran.fhcrc.org/doc/manuals/R-admin.html#New-platforms>: these 
problems have surfaced in Fedora Core 3's distribution, for example.

"Please *do* bear in mind that using --with-lapack is `definitely *not* 
recommended': it is provided *only* because it is necessary on some 
platforms."

In any event, when I have beta-tested R releases on my Athlon Thunderbird, when I use the "with-lapack" option and link R with the external Atlas LAPACK I get many failures in the "make check-all" pass. These don't happen when I just use the Atlas BLAS, so I don't use the external LAPACK with R.
-- 
M. Edward (Ed) Borasky, FBG, AB, PTA, PGS, MS, MNLP, NST, ACMC(P)
http://borasky-research.blogspot.com/

If God had meant for carrots to be eaten cooked, He would have given rabbits fire.

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