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Hi |
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I think i begin to see how things have to work.... |
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Just to make sure i understood correctly: |
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- the directories /usr/lib64/blas/reference/ and |
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/usr/lib64/lapack/reference/ and the libraries they contained are |
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irrelevant for the science overlay |
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- generally one compiles an application using cblas with `pkg-config |
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--cflags cblas` and links it with `pkg-config --libs cblas` (and similarly |
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for blas and lapack) |
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Is this correct? |
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|
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Thank You |
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Jody |
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|
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|
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On Tue, Sep 3, 2013 at 11:57 AM, jody <jody.xha@×××××.com> wrote: |
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|
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> Hi Francois |
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> Thanks for your reply. |
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> |
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> I already had eselect from the science overlay: version 1.3.7-r100[1] ([1] |
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> refers to the science overlay) |
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> and eselect-blas, eselect-cblas and eselect-lapack were already removed (i |
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> had to do this to emerge atlas). |
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> |
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> Now I unmasked and emerged the virtuals cblas, blas and lapack from the |
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> science overlay. |
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> |
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> when i look at the lib64 directory, i see |
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> aim-octopus ~ # ls -l /usr/lib64/liblapack.* |
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> lrwxrwxrwx 1 root root 28 Aug 20 09:43 /usr/lib64/liblapack.a -> |
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> lapack/reference/liblapack.a |
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> lrwxrwxrwx 1 root root 29 Aug 20 09:43 /usr/lib64/liblapack.so -> |
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> lapack/reference/liblapack.so |
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> lrwxrwxrwx 1 root root 31 Aug 20 09:43 /usr/lib64/liblapack.so.0 -> |
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> lapack/reference/liblapack.so.0 |
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> aim-octopus ~ # ls -l /usr/lib64/libcblas.* |
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> |
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> lrwxrwxrwx 1 root root 13 Aug 20 10:54 /usr/lib64/libcblas.a -> |
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> libgslcblas.a |
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> lrwxrwxrwx 1 root root 14 Aug 20 10:54 /usr/lib64/libcblas.so -> |
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> libgslcblas.so |
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> lrwxrwxrwx 1 root root 16 Aug 20 10:54 /usr/lib64/libcblas.so.0 -> |
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> libgslcblas.so.0 |
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> aim-octopus ~ # ls -l /usr/lib64/libblas.* |
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> lrwxrwxrwx 1 root root 24 Aug 19 18:07 /usr/lib64/libblas.a -> |
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> blas/reference/libblas.a |
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> lrwxrwxrwx 1 root root 25 Aug 19 18:07 /usr/lib64/libblas.so -> |
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> blas/reference/libblas.so |
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> lrwxrwxrwx 1 root root 27 Aug 19 18:07 /usr/lib64/libblas.so.0 -> |
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> blas/reference/libblas.so.0 |
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> |
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> I found .pc files in /usr/lib64/blas/reference/ and |
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> /usr/lib64/lapack/reference/ but there is no directory |
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> /usr/lib64/cblas/reference. How can i get the cblas from the science |
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> overlay? |
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> |
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> I noticed that i have sci-libs/*-reference for blas and lapack emerged |
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> (even though none of them are from the science overlay) but no |
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> sci-libs/cblas-reference: |
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> aim-octopus ~ # eix blas-reference |
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> [I] sci-libs/blas-reference |
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> Available versions: 20070226 ~20070226-r2 **20070226-r3 ~20120925[1] |
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> **99999999[1] {{doc static-libs test}} |
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> Installed versions: 20070226(18:07:30 08/19/13)(-doc) |
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> Homepage: http://www.netlib.org/lapack/ |
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> Description: Reference implementation of BLAS |
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> |
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> aim-octopus ~ # eix lapack-reference |
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> [I] sci-libs/lapack-reference |
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> Available versions: 3.1.1-r1 ~3.2.1-r1 **3.2.1-r3 ~3.4.2[1] |
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> **9999[1] {{doc static-libs test xblas}} |
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> Installed versions: 3.1.1-r1(09:43:40 08/20/13)(-doc) |
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> Homepage: http://www.netlib.org/lapack/ |
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> Description: Reference implementation of LAPACK |
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> |
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> [1] "science" /var/lib/layman/science |
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> |
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> aim-octopus ~ # eix cblas-reference |
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> * sci-libs/cblas-reference |
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> Available versions: 20030223-r4 ~20030223-r5 ~20110218[1] |
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> {{static-libs}} |
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> Homepage: http://www.netlib.org/blas/ |
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> Description: C wrapper interface to the F77 reference BLAS |
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> implementation |
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> |
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> [1] "science" /var/lib/layman/science |
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> |
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> |
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> Do i need to emerge sci-libs/cblas-reference? |
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> Do i need to unmask and emerge the overlay versions for all |
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> sci-libs/*-reference as well? |
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> |
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> |
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> I am sorry, but i don't understand what you said about the .pc files. |
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> In what situation and how should i use the .pc file? |
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> |
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> Thanks |
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> Jody |
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> |
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> |
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> |
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> On Tue, Sep 3, 2013 at 12:57 AM, François Bissey <fbissey@××××××××××××.nz>wrote: |
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> |
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>> Hi Jody, |
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>> |
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>> The mechanism for handling multiple BLAS/LAPACK in the science overlay |
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>> is incompatible with the one used in the main tree. |
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>> In particular the science overlay stack doesn't create link link to |
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>> libcblas, |
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>> libblas and liblapack. |
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>> You have to unmask eselect from the science overlay as well as the |
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>> virtuals |
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>> (cblas,blas and lapack) and remove all the tree eselect-blas, |
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>> eselect-cblas |
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>> and eselect-lapack modules. |
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>> No packages in Gentoo, in the tree or the overlay, should use libblas, |
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>> libcblas or |
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>> liblapack directly but configure it throught pkg-config. |
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>> All BLAS/LAPACK implementation in Gentoo provide .pc file for that |
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>> purpose. With |
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>> the new science overlay structure you create a link for which .pc file is |
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>> the default. |
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>> |
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>> So once you have completed your move to the science overlay stack you |
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>> need to remove |
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>> those links if they still exist. |
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>> |
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>> Francois |
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>> |
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>> |
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>> On 2013-09-02 19:04, jody wrote: |
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>> |
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>>> Hi |
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>>> I have successfully installed sci-libs/atlas from the science overlay. |
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>>> |
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>>> Now there are some points which are somewhat unclear. |
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>>> |
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>>> I have been redirected here from the gentoo forum. |
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>>> |
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>>> 1. cblas implementation |
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>>> Even though |
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>>> |
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>>> # eselect cblas list |
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>>> Available providers for cblas: |
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>>> [1] atlas * |
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>>> [2] atlas-threads |
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>>> |
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>>> all cblas libraries are pointing to gsl implementations: |
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>>> |
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>>> ls -l /usr/lib64/libcblas.* |
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>>> lrwxrwxrwx 1 root root 13 Aug 20 10:54 /usr/lib64/libcblas.a -> |
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>>> libgslcblas.a |
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>>> lrwxrwxrwx 1 root root 14 Aug 20 10:54 /usr/lib64/libcblas.so -> |
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>>> libgslcblas.so |
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>>> lrwxrwxrwx 1 root root 16 Aug 20 10:54 /usr/lib64/libcblas.so.0 -> |
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>>> libgslcblas.so.0 |
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>>> |
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>>> Shouldn't the '/usr/lib64/libcblas.so' point to |
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>>> '/usr/lib64/libatlcblas.so' etc.? |
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>>> |
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>>> 2. static libs for cblas |
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>>> The installation of sci-libs/atlas did not create any static libs: |
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>>> |
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>>> ls -l /usr/lib64/libatl* |
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>>> lrwxrwxrwx 1 root root 13 Aug 22 09:11 /usr/lib64/libatlas.so |
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>>> -> libatlas.so.3 |
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>>> -rwxr-xr-x 1 root root 5961968 Aug 22 09:11 /usr/lib64/libatlas.so.3 |
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>>> lrwxrwxrwx 1 root root 16 Aug 22 09:11 |
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>>> /usr/lib64/libatlcblas.so -> libatlcblas.so.3 |
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>>> -rwxr-xr-x 1 root root 142504 Aug 22 09:11 |
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>>> /usr/lib64/libatlcblas.so.3 |
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>>> |
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>>> And i have at least one 3rd party code which requires the cblas |
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>>> libraries to be linked statically. |
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>>> |
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>>> 3. eselect lapack |
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>>> I found that 'app-admin/eselect-lapack' is blocking 'sci-libs/atlas', |
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>>> |
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>>> but atlas did not pull in eselect for lapack: |
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>>> |
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>>> # eselect lapack list |
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>>> !!! Error: Can't load module lapack |
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>>> exiting |
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>>> |
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>>> eselect-cblas is also blocking 'sci-libs/atlas', but apparently atlas |
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>>> pulls in eselect for cblas. |
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>>> |
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>>> 4. Shouldn't there also be a lapack implementation from atlas? |
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>>> |
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>>> Could somebody clarify or help out? |
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>>> Jody |
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>>> |
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>> |
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>> |
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> |