From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from lists.gentoo.org ([140.105.134.102] helo=robin.gentoo.org) by nuthatch.gentoo.org with esmtp (Exim 4.62) (envelope-from ) id 1HM45x-0004zh-Cq for garchives@archives.gentoo.org; Tue, 27 Feb 2007 15:18:26 +0000 Received: from robin.gentoo.org (localhost [127.0.0.1]) by robin.gentoo.org (8.14.0/8.14.0) with SMTP id l1RFHarj030392; Tue, 27 Feb 2007 15:17:36 GMT Received: from rwcrmhc11.comcast.net (rwcrmhc11.comcast.net [216.148.227.151]) by robin.gentoo.org (8.14.0/8.14.0) with ESMTP id l1RFHZX7030381 for ; Tue, 27 Feb 2007 15:17:36 GMT Received: from [24.22.125.13] (c-24-22-125-13.hsd1.or.comcast.net[24.22.125.13]) by comcast.net (rwcrmhc11) with ESMTP id <20070227151731m1100jeq7be>; Tue, 27 Feb 2007 15:17:31 +0000 Message-ID: <45E44B84.9070401@cesmail.net> Date: Tue, 27 Feb 2007 07:17:24 -0800 From: "M. Edward (Ed) Borasky" User-Agent: Thunderbird 2.0b2 (X11/20070208) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-science@gentoo.org Reply-to: gentoo-science@lists.gentoo.org MIME-Version: 1.0 To: gentoo-science@lists.gentoo.org Subject: Re: [gentoo-science] lapack 3.0? (rkward) References: <200702241007.46155.gentoo@matthewlee.org> <45E0B340.9050204@a3.epfl.ch> <200702251718.21765.gentoo@matthewlee.org> <45E22C1F.8040805@cesmail.net> <45E3E7E3.1090507@centrum.cz> In-Reply-To: <45E3E7E3.1090507@centrum.cz> Content-Type: text/plain; charset=ISO-8859-2; format=flowed Content-Transfer-Encoding: quoted-printable X-MIME-Autoconverted: from 8bit to quoted-printable by robin.gentoo.org id l1RFHas9030392 X-Archives-Salt: ea1af5a0-7189-4502-802a-abfb12dd14a7 X-Archives-Hash: 24fac3baf75df411e4f725bdf414ac29 Honza Mach=E1=E8ek wrote: > On 26.02.2007 01:38, M. Edward (Ed) Borasky wrote: > =20 >> I'm a little curious about something ... does "rkward" actually requir= e >> 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 deprecat= ed >> linking against external Lapack libraries! >> =20 > > I think I recall some discussion at the bugzilla to the point that al= l > 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: > > =20 >> This goes against modularity, *the* fundamental principle of any good=20 >> Linux distribution. >> =20 Well, here's the logic of the R developers (from=20 http://cran.fhcrc.org/doc/manuals/R-admin.html): "A.3.2 LAPACK Provision is made for using an external LAPACK library, principally to=20 cope with BLAS libraries which contain a copy of LAPACK (such as=20 |libsunperf| on Solaris, |vecLib| on Mac OS X and ACML on=20 `ix86'/`x86_64' Linux). However, the likely performance gains are=20 thought to be small (and may be negative), and the default is not to=20 search for a suitable LAPACK library, and this is definitely *not*=20 recommended. [snip] "For problems compiling LAPACK using recent versions of |gcc| on `ix86'=20 Linux, see New platforms=20 : these=20 problems have surfaced in Fedora Core 3's distribution, for example. "Please *do* bear in mind that using --with-lapack is `definitely *not*=20 recommended': it is provided *only* because it is necessary on some=20 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 happ= en when I just use the Atlas BLAS, so I don't use the external LAPACK wit= h R. --=20 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 rabb= its fire. --=20 gentoo-science@gentoo.org mailing list