Hi Jody,
The mechanism for handling multiple BLAS/LAPACK in the science overlay
is incompatible with the one used in the main tree.
In particular the science overlay stack doesn't create link link to
libcblas,
libblas and liblapack.
You have to unmask eselect from the science overlay as well as the
virtuals
(cblas,blas and lapack) and remove all the tree eselect-blas,
eselect-cblas
and eselect-lapack modules.
No packages in Gentoo, in the tree or the overlay, should use libblas,
libcblas or
liblapack directly but configure it throught pkg-config.
All BLAS/LAPACK implementation in Gentoo provide .pc file for that
purpose. With
the new science overlay structure you create a link for which .pc file
is the default.
So once you have completed your move to the science overlay stack you
need to remove
those links if they still exist.
Francois
On 2013-09-02 19:04, jody wrote:
Hi
I have successfully installed sci-libs/atlas from the science overlay.
Now there are some points which are somewhat unclear.
I have been redirected here from the gentoo forum.
1. cblas implementation
Even though
# eselect cblas list
Available providers for cblas:
[1] atlas *
[2] atlas-threads
all cblas libraries are pointing to gsl implementations:
ls -l /usr/lib64/libcblas.*
lrwxrwxrwx 1 root root 13 Aug 20 10:54 /usr/lib64/libcblas.a ->
libgslcblas.a
lrwxrwxrwx 1 root root 14 Aug 20 10:54 /usr/lib64/libcblas.so ->
libgslcblas.so
lrwxrwxrwx 1 root root 16 Aug 20 10:54 /usr/lib64/libcblas.so.0 ->
libgslcblas.so.0
Shouldn't the '/usr/lib64/libcblas.so' point to
'/usr/lib64/libatlcblas.so' etc.?
2. static libs for cblas
The installation of sci-libs/atlas did not create any static libs:
ls -l /usr/lib64/libatl*
lrwxrwxrwx 1 root root 13 Aug 22 09:11 /usr/lib64/libatlas.so
-> libatlas.so.3
-rwxr-xr-x 1 root root 5961968 Aug 22 09:11 /usr/lib64/libatlas.so.3
lrwxrwxrwx 1 root root 16 Aug 22 09:11
/usr/lib64/libatlcblas.so -> libatlcblas.so.3
-rwxr-xr-x 1 root root 142504 Aug 22 09:11
/usr/lib64/libatlcblas.so.3
And i have at least one 3rd party code which requires the cblas
libraries to be linked statically.
3. eselect lapack
I found that 'app-admin/eselect-lapack' is blocking 'sci-libs/atlas',
but atlas did not pull in eselect for lapack:
# eselect lapack list
!!! Error: Can't load module lapack
exiting
eselect-cblas is also blocking 'sci-libs/atlas', but apparently atlas
pulls in eselect for cblas.
4. Shouldn't there also be a lapack implementation from atlas?
Could somebody clarify or help out?
Jody
