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 C337C1381F3 for ; Wed, 21 Aug 2013 12:02:07 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id E1F9BE0E8A; Wed, 21 Aug 2013 12:02:04 +0000 (UTC) Received: from mail-pd0-f169.google.com (mail-pd0-f169.google.com [209.85.192.169]) (using TLSv1 with cipher ECDHE-RSA-RC4-SHA (128/128 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 03FB1E0D08 for ; Wed, 21 Aug 2013 12:02:03 +0000 (UTC) Received: by mail-pd0-f169.google.com with SMTP id r10so365414pdi.0 for ; Wed, 21 Aug 2013 05:02:02 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:date:message-id:subject:from:to:content-type; bh=xUbQZJPXPUaMrlWjlS68dBQXOFGgKkOPR6rcXpwweTw=; b=En17NkvifYJMjhZ8ay9biT1vU7lemFe8t4WUsuhwOLP5bCv0maOoZJjuOqsZtOJ7GN ub4JZ+WoT4f4jSD2qRBBriLyXTIEkVlL8pfo8igGaQ1Dp+LBmrSslr7iZ5COwkiS5xWI XFCIXrXKwvUfvWtYi0ZFI7belc51e4Czjst4/oJ9gA4Y9IbW5mO+YWWA4gQZSsBt+jOz TaXDvmJ/OF2bokxudEo46NrShFl1NwjjVPk/RLIRSxkG5F9Y5sxcsJITyN4vbc5Jy82X dl195mliAyr58EFGmb87eD2LPV6yaEcin0wurHiPaHsrUMy8kYHC+DESK6BvUkCXVWLm +Q+Q== 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 X-Received: by 10.68.225.42 with SMTP id rh10mr7350563pbc.176.1377086522748; Wed, 21 Aug 2013 05:02:02 -0700 (PDT) Received: by 10.70.73.8 with HTTP; Wed, 21 Aug 2013 05:02:02 -0700 (PDT) Date: Wed, 21 Aug 2013 20:02:02 +0800 Message-ID: Subject: [gentoo-science] sage on gentoo -- only use system atlas From: P Purkayastha To: gentoo-science Content-Type: multipart/alternative; boundary=e89a8ff243c10375ef04e473f149 X-Archives-Salt: d3d8e8c0-d763-40dc-9249-a4c5d145352e X-Archives-Hash: 93d8d5712b5f1cb60b3eb3f4dd45121d --e89a8ff243c10375ef04e473f149 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi all, 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=3D/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. I looked at the dependencies of sci-mathematics/sage in the sage-on-gentoo overlay, and I see that virtual/cblas and virtual/lapack is pulled in by sci-libs/fflas-ffpack. This ebuild is pulled in by sci-libs/linbox, and finally linbox is pulled in by sage. However, the following command only pulls in the virtual packages, which means that I already have lapack installed, but probably under a different library name. ~/tmp/sage-on-gentoo=BB emerge -pvq virtual/cblas virtual/lapack [ebuild N ] virtual/cblas-2.0 [ebuild N ] virtual/lapack-3.4 USE=3D"-doc" Can anyone tell me which library name corresponds to liblapack.so? I can then make a symlink and proceed with building my personal copy of sage. Here is an output of equery files: ~/tmp/sage-on-gentoo=BB equery files atlas | grep '/usr/lib.*lapack' /etc/env.d/alternatives/lapack/atlas-threads/usr/lib64/pkgconfig/lapack.pc /etc/env.d/alternatives/lapack/atlas/usr/lib64/pkgconfig/lapack.pc /usr/lib64/libatlclapack.so /usr/lib64/libatlclapack.so.3 /usr/lib64/libatllapack.so /usr/lib64/libatllapack.so.3 /usr/lib64/libptclapack.so /usr/lib64/libptclapack.so.3 /usr/lib64/libptlapack.so /usr/lib64/libptlapack.so.3 /usr/lib64/pkgconfig/atlas-clapack-threads.pc /usr/lib64/pkgconfig/atlas-clapack.pc /usr/lib64/pkgconfig/atlas-lapack-threads.pc /usr/lib64/pkgconfig/atlas-lapack.pc Thanks and regards, basu. --e89a8ff243c10375ef04e473f149 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi all,

=A0 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.

=A0 To do so, I added the science overlay and emerged sci-libs/atlas[l= apack,fortran,threads]. Thereafter, I added the environment variable
<= div>
SAGE_ATLAS_LIB=3D/usr/lib

and p= roceeded to compile sage in my home directory. Atlas fails with the error t= hat it can not find liblapack. The exact error message is given below:

Cannot find liblapack.* in /usr/lib
Unable to find o= ne of liblapack, libcblas, libatlas or libf77blas
in the directory None<= br>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://sa= gemath.org/doc/installation/source.html#environment-variables
Unset SAGE_ATLAS_LIB to build ATLAS from source.

I looked at the dependencies of sci-mathematics/sage in the sage-on-gent= oo overlay, and I see that virtual/cblas and virtual/lapack is pulled in by= sci-libs/fflas-ffpack. This ebuild is pulled in by sci-libs/linbox, and fi= nally linbox is pulled in by sage.

However, the following command only pulls in the virtua= l packages, which means that I already have lapack installed, but probably = under a different library name.

~/tmp/sage-on-gent= oo=BB emerge -pvq virtual/cblas virtual/lapack
[ebuild N ] virtual/cblas-2.0
[ebuild N ] virtual/lapack-3.4 U= SE=3D"-doc"

Can anyone tell me which li= brary name corresponds to liblapack.so? I can then make a symlink and proce= ed with building my personal copy of sage. Here is an output of equery file= s:

~/tmp/sage-on-gentoo=BB equery files atlas | grep '= /usr/lib.*lapack'
/etc/env.d/alternatives/lapack/atlas-threads/usr/l= ib64/pkgconfig/lapack.pc
/etc/env.d/alternatives/lapack/atlas/usr/lib64/= pkgconfig/lapack.pc
/usr/lib64/libatlclapack.so
/usr/lib64/libatlclapack.so.3
/usr/lib64/= libatllapack.so
/usr/lib64/libatllapack.so.3
/usr/lib64/libptclapack.= so
/usr/lib64/libptclapack.so.3
/usr/lib64/libptlapack.so
/usr/lib= 64/libptlapack.so.3
/usr/lib64/pkgconfig/atlas-clapack-threads.pc
/usr/lib64/pkgconfig/atlas= -clapack.pc
/usr/lib64/pkgconfig/atlas-lapack-threads.pc
/usr/lib64/p= kgconfig/atlas-lapack.pc

Thanks and regards,
=A0 =A0 basu.

--e89a8ff243c10375ef04e473f149--