From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from pigeon.gentoo.org ([208.92.234.80] helo=lists.gentoo.org) by finch.gentoo.org with esmtp (Exim 4.60) (envelope-from <gentoo-science+bounces-1391-garchives=archives.gentoo.org@lists.gentoo.org>) id 1QSmrL-000222-Qg for garchives@archives.gentoo.org; Sat, 04 Jun 2011 09:09:32 +0000 Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 563771C157; Sat, 4 Jun 2011 09:08:53 +0000 (UTC) Received: from homiemail-a38.g.dreamhost.com (caiajhbdccac.dreamhost.com [208.97.132.202]) by pigeon.gentoo.org (Postfix) with ESMTP id 1505D1C136 for <gentoo-science@lists.gentoo.org>; Sat, 4 Jun 2011 09:08:52 +0000 (UTC) Received: from homiemail-a38.g.dreamhost.com (localhost [127.0.0.1]) by homiemail-a38.g.dreamhost.com (Postfix) with ESMTP id 2DED610AFAB for <gentoo-science@lists.gentoo.org>; Sat, 4 Jun 2011 02:08:52 -0700 (PDT) DomainKey-Signature: a=rsa-sha1; c=nofws; d=velodius.com; h=date:from:to :subject:message-id:in-reply-to:references:mime-version: content-type; q=dns; s=velodius.com; b=otcFt+BZqCAU220GrLIEMDX9X J2czfetVW2OIt4Z+XMkArbgTMwNL0ms+GVEnSKigNS1dzdmLaYvoIB12GYn/P9lf TmsH7YigrBiR0su7xICggfL5+2mBzZagG/DkjcFV4NaPsMjvKOfGGsdD3OlQ178j g4qdvB2rQg34SMOxKg= DKIM-Signature: v=1; a=rsa-sha1; c=relaxed; d=velodius.com; h=date:from :to:subject:message-id:in-reply-to:references:mime-version: content-type; s=velodius.com; bh=XZTpTgC0W4GsfvQPnD0SRUQlkL4=; b=sK/cZuB2Lt4KPpGl0XKaYtrRDmEbYtiU/Zg8cXX20zv09HXa0NuT8rWmPSPZf mvbZxKlXab23YH2VfbJ5qVCa0WhOQjG1vLS1uWBvCw98T/8dUhgauq5Z+OSlgSYE qN0gVEKarOvf+SP5BXdv+Td8yPDLxCq9SUJ5B4E3BZ7luw= Received: from pcbox-marc (136.Red-213-97-163.staticIP.rima-tde.net [213.97.163.136]) (using TLSv1 with cipher DHE-RSA-AES128-SHA (128/128 bits)) (No client certificate requested) (Authenticated sender: timer@velodius.com) by homiemail-a38.g.dreamhost.com (Postfix) with ESMTPSA id 6783110AFA5 for <gentoo-science@lists.gentoo.org>; Sat, 4 Jun 2011 02:08:51 -0700 (PDT) Date: Sat, 4 Jun 2011 11:08:46 +0200 From: Marc Vinyals <marcvinyals@velodius.com> To: gentoo-science@lists.gentoo.org Subject: Re: [gentoo-science] sci-libs/scipy-0.9.0-r1 undefined symbol: clapack_sgesv Message-ID: <20110604110846.4e788c2e@pcbox-marc> In-Reply-To: <201106041215.18808.fbissey@slingshot.co.nz> References: <20110531154403.0d6f08fd@pcbox-marc> <201106020722.18860.fbissey@slingshot.co.nz> <20110602123250.57b5071c@pcbox-marc> <201106041215.18808.fbissey@slingshot.co.nz> X-Mailer: Claws Mail 3.7.9 (GTK+ 2.24.3; x86_64-pc-linux-gnu) Precedence: bulk List-Post: <mailto:gentoo-science@lists.gentoo.org> List-Help: <mailto:gentoo-science+help@lists.gentoo.org> List-Unsubscribe: <mailto:gentoo-science+unsubscribe@lists.gentoo.org> List-Subscribe: <mailto:gentoo-science+subscribe@lists.gentoo.org> List-Id: Gentoo Linux mail <gentoo-science.gentoo.org> X-BeenThere: gentoo-science@lists.gentoo.org Reply-to: gentoo-science@lists.gentoo.org Mime-Version: 1.0 Content-Type: multipart/signed; micalg=PGP-SHA1; boundary="Sig_/vPepQ+gqbVlyKHRN6a0EuvK"; protocol="application/pgp-signature" X-Archives-Salt: X-Archives-Hash: b36e581c31d00a356e89096603a8f9e4 --Sig_/vPepQ+gqbVlyKHRN6a0EuvK Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable EL Sat, 4 Jun 2011 12:15:18 +1200 Francois Bissey <fbissey@slingshot.co.nz> escrigu=C3=A9: > > Here are my logs. You'll find some warnings in the configuration > > stage, I hope they'll mean something to you. Also, there's no trace > > of libclapack.so in > > ldd /usr/lib64/python2.7/site-packages/scipy/linalg/clapack.so. >=20 > The output of > ldd /usr/lib64/python2.7/site-packages/scipy/linalg/clapack.so is > very suspicious with Atlas it should look like this: > ldd /usr/lib/python2.7/site-packages/scipy/linalg/clapack.so > linux-gate.so.1 =3D> (0xb7890000) liblapack.so.0 > =3D> /usr/lib/liblapack.so.0 (0xb732a000) libpython2.7.so.1.0 > =3D> /usr/lib/libpython2.7.so.1.0 (0xb71bb000) libc.so.6 > =3D> /lib/libc.so.6 (0xb7035000) libblas.so.0 > =3D> /usr/lib/blas/atlas/libblas.so.0 (0xb7014000) libcblas.so.0 > =3D> /usr/lib/blas/atlas/libcblas.so.0 (0xb6ff2000) libatlas.so.0 > =3D> /usr/lib/libatlas.so.0 (0xb6933000) libgfortran.so.3 > =3D> /usr/lib/gcc/i686-pc-linux- gnu/4.5.2/libgfortran.so.3 (0xb6871000) > libm.so.6 =3D> /lib/libm.so.6 (0xb684b000) > libgcc_s.so.1 > =3D> /usr/lib/gcc/i686-pc-linux-gnu/4.5.2/libgcc_s.so.1 (0xb682d000) > libpthread.so.0 =3D> /lib/libpthread.so.0 (0xb6813000) > libdl.so.2 =3D> /lib/libdl.so.2 (0xb680f000) > libutil.so.1 =3D> /lib/libutil.so.1 (0xb680b000) > /lib/ld-linux.so.2 (0xb7891000) >=20 > So nothing from blas/cblas/lapack was linked into your scipy which is > very worrying. It may be that there is a problem with your current > blas&co setup. what's the output of > ls -la /usr/lib64/libcblas.so >=20 > Francois >=20 ls -la /usr/lib64/libcblas.so lrwxrwxrwx 1 root root 26 2 jun 13:44 /usr/lib64/libcblas.so -> blas/reference/libcblas.so ls -la /usr/lib64/libblas.so lrwxrwxrwx 1 root root 25 2 jun 13:43 /usr/lib64/libblas.so -> blas/reference/libblas.so ls -la /usr/lib64/liblapack.so lrwxrwxrwx 1 root root 29 2 jun 13:47 /usr/lib64/liblapack.so -> lapack/reference/liblapack.so It looks reasonable to me. --Sig_/vPepQ+gqbVlyKHRN6a0EuvK Content-Type: application/pgp-signature; name=signature.asc Content-Disposition: attachment; filename=signature.asc -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) iEYEARECAAYFAk3p9h8ACgkQu4rFT+k3kmQR6wCfTz5ATGXQBRtvrdgWEcggQ1+S tewAnAw/vRb5trXtNcDZAseE+og8TVMW =UoCv -----END PGP SIGNATURE----- --Sig_/vPepQ+gqbVlyKHRN6a0EuvK--