Re: [gentoo-science] Fwd: sci-lib/atlas, static libraries, cblas, lapack

[jody]

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@××××××××××××.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
>>
>
>