From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) by finch.gentoo.org (Postfix) with ESMTP id AE8871381F3 for ; Thu, 22 Aug 2013 00:39:49 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id EDD95E0C71; Thu, 22 Aug 2013 00:39:47 +0000 (UTC) Received: from mailfilter2.tranzpeer.net (mailfilter-227.tranzpeer.net [202.180.66.227]) by pigeon.gentoo.org (Postfix) with ESMTP id 364F7E0C57 for ; Thu, 22 Aug 2013 00:39:47 +0000 (UTC) Received: from webmail.slingshot.co.nz (webmailfe1.prv.callplus.co.nz [202.189.160.41]) by mailfilter2.tranzpeer.net (Postfix) with ESMTP id E7BE375 for ; Thu, 22 Aug 2013 12:39:44 +1200 (NZST) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-science@lists.gentoo.org Reply-to: gentoo-science@lists.gentoo.org MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 7bit Date: Thu, 22 Aug 2013 12:39:44 +1200 From: =?UTF-8?Q?Fran=C3=A7ois_Bissey?= To: gentoo-science@lists.gentoo.org Subject: Re: [gentoo-science] sage on gentoo -- only use system atlas In-Reply-To: <20130821141942.7add4823@carl.erocal.org> References: <20130821141942.7add4823@carl.erocal.org> Message-ID: X-Sender: fbissey@slingshot.co.nz User-Agent: Roundcube Webmail/0.9.2 X-Spam-Status: No, score=0.1 required=5.0 tests=LOCAL_SLINGSHOT_TEST, UNPARSEABLE_RELAY autolearn=no version=3.3.2 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on spamsrv2 X-Archives-Salt: 6c991d64-f3d9-456f-a589-91c9d7944d5c X-Archives-Hash: b04d454b1a3ff7c568b76beb4e2916eb On 2013-08-22 00:19, Burcin Erocal wrote: > Hi, > > On Wed, 21 Aug 2013 20:02:02 +0800 > P Purkayastha wrote: > >> I need to have a personal installation of Sage to do development >> work. However, I also want to reduce my upgrade times by installing a >> system atlas. >> >> To do so, I added the science overlay and emerged >> sci-libs/atlas[lapack,fortran,threads]. Thereafter, I added the >> environment variable >> >> SAGE_ATLAS_LIB=/usr/lib >> >> and proceeded to compile sage in my home directory. Atlas fails with >> the error that it can not find liblapack. The exact error message is >> given below: >> >> Cannot find liblapack.* in /usr/lib >> Unable to find one of liblapack, libcblas, libatlas or libf77blas >> in the directory None >> Set SAGE_ATLAS_LIB to the directory containing liblapack, libcblas, >> libatlas and libf77blas (either .a, .so, .dylib extensions) if >> you wish to use existing ATLAS libraries. For more details, see >> http://sagemath.org/doc/installation/source.html#environment-variables >> Unset SAGE_ATLAS_LIB to build ATLAS from source. > > if you make Sage believe that the atlas package was installed properly, > the installation proceeds without trouble. So as a quick workaround, > just do > > touch spkg/installed/atlas- > > I always do this on my system. It would be good to find out the proper > solution of course. :) > The main problem here is that Gentoo support the installation of multiple BLAS/LAPACK at once. For that reason there is no libraries on the system installed with the names: libcblas.* libf77blas.* liblapack.* My recommendation for you is to create a folder in your home directory and link all the libraries you need with the appropriate name in a lib subfolder and pass the parent directory to SAGE_ATLAS_LIB. Francois