Hi Francois

Thanks for your reply.

I already had eselect from the science overlay: version 1.3.7-r100[1] ([1] refers to the science overlay)

and eselect-blas, eselect-cblas and eselect-lapack were already removed (i had to do this to emerge atlas).

Now I unmasked and emerged the virtuals cblas, blas and lapack from the science overlay.

when i look at the lib64 directory, i see

aim-octopus ~ # ls -l /usr/lib64/liblapack.*
lrwxrwxrwx 1 root root 28 Aug 20 09:43 /usr/lib64/liblapack.a -> lapack/reference/liblapack.a
lrwxrwxrwx 1 root root 29 Aug 20 09:43 /usr/lib64/liblapack.so -> lapack/reference/liblapack.so
lrwxrwxrwx 1 root root 31 Aug 20 09:43 /usr/lib64/liblapack.so.0 -> lapack/reference/liblapack.so.0
aim-octopus ~ # 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

aim-octopus ~ # ls -l /usr/lib64/libblas.*
lrwxrwxrwx 1 root root 24 Aug 19 18:07 /usr/lib64/libblas.a -> blas/reference/libblas.a
lrwxrwxrwx 1 root root 25 Aug 19 18:07 /usr/lib64/libblas.so -> blas/reference/libblas.so
lrwxrwxrwx 1 root root 27 Aug 19 18:07 /usr/lib64/libblas.so.0 -> blas/reference/libblas.so.0

I found .pc files in /usr/lib64/blas/reference/ and /usr/lib64/lapack/reference/ but there is no directory

/usr/lib64/cblas/reference. How can i get the cblas from the science overlay?

I noticed that i have sci-libs/*-reference for blas and lapack emerged (even though none of them are from the science overlay) but no sci-libs/cblas-reference:
aim-octopus ~ # eix blas-reference
[I] sci-libs/blas-reference
     Available versions:  20070226 ~20070226-r2 **20070226-r3 ~20120925[1] **99999999[1] {{doc static-libs test}}
     Installed versions:  20070226(18:07:30 08/19/13)(-doc)
     Homepage:            http://www.netlib.org/lapack/
     Description:         Reference implementation of BLAS

aim-octopus ~ # eix lapack-reference
[I] sci-libs/lapack-reference
     Available versions:  3.1.1-r1 ~3.2.1-r1 **3.2.1-r3 ~3.4.2[1] **9999[1] {{doc static-libs test xblas}}
     Installed versions:  3.1.1-r1(09:43:40 08/20/13)(-doc)
     Homepage:            http://www.netlib.org/lapack/
     Description:         Reference implementation of LAPACK

[1] "science" /var/lib/layman/science

aim-octopus ~ # eix cblas-reference
* sci-libs/cblas-reference
     Available versions:  20030223-r4 ~20030223-r5 ~20110218[1] {{static-libs}}
     Homepage:            http://www.netlib.org/blas/
     Description:         C wrapper interface to the F77 reference BLAS implementation

[1] "science" /var/lib/layman/science

Do i need to emerge sci-libs/cblas-reference?

Do i need to unmask and emerge the overlay versions for all sci-libs/*-reference as well?

I am sorry, but i don't understand what you said about the .pc files.

In what situation and how should i use the .pc file?

Thanks

  Jody

On Tue, Sep 3, 2013 at 12:57 AM, François Bissey <fbissey@slingshot.co.nz> wrote:

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