Gentoo Archives: gentoo-science

From: P Purkayastha <ppurka@×××××.com>
To: gentoo-science <gentoo-science@l.g.o>
Subject: [gentoo-science] sage on gentoo -- only use system atlas
Date: Wed, 21 Aug 2013 12:02:07
Message-Id: CADZU3NbnB7FKVE0=cZMqVOvPPYZo4khq+YeO=FkZrZf8-+NgrQ@mail.gmail.com
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=/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» emerge -pvq virtual/cblas virtual/lapack
[ebuild N ] virtual/cblas-2.0
[ebuild N ] virtual/lapack-3.4 USE="-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» 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.

Replies

Subject Author
Re: [gentoo-science] sage on gentoo -- only use system atlas Burcin Erocal <burcin@××××××.org>