Hi I think i begin to see how things have to work.... Just to make sure i understood correctly: - the directories /usr/lib64/blas/reference/ and /usr/lib64/lapack/reference/ and the libraries they contained are irrelevant for the science overlay - generally one compiles an application using cblas with `pkg-config --cflags cblas` and links it with `pkg-config --libs cblas` (and similarly for blas and lapack) Is this correct? Thank You Jody On Tue, Sep 3, 2013 at 11:57 AM, jody wrote: > 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 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 >>> >> >> >