Re: [gentoo-science] sage on gentoo -- only use system atlas

[P Purkayastha]

On Thu, Aug 22, 2013 at 8:39 AM, François Bissey <fbissey@××××××××××××.nz>wrote:

> On 2013-08-22 00:19, Burcin Erocal wrote:
>
>> Hi,
>>
>> On Wed, 21 Aug 2013 20:02:02 +0800
>> P Purkayastha <ppurka@×××××.com> wrote:
>>
>>    I need to have a personal installation of Sage to do development
>>> work. However, I also want to reduce my upgrade times by installing a
>>> system atlas.
>>>
>>>   To do so, I added the science overlay and emerged
>>> sci-libs/atlas[lapack,fortran,threads]. Thereafter, I added the
>>> environment variable
>>>
>>> SAGE_ATLAS_LIB=/usr/lib
>>>
>>> and proceeded to compile sage in my home directory. Atlas fails with
>>> the error that it can not find liblapack. The exact error message is
>>> given below:
>>>
>>> Cannot find liblapack.* in /usr/lib
>>> Unable to find one of liblapack, libcblas, libatlas or libf77blas
>>> in the directory None
>>> Set SAGE_ATLAS_LIB to the directory containing liblapack, libcblas,
>>> libatlas and libf77blas (either .a, .so, .dylib extensions) if
>>> you wish to use existing ATLAS libraries. For more details, see
>>> http://sagemath.org/doc/installation/source.html#environment-variables
>>> Unset SAGE_ATLAS_LIB to build ATLAS from source.
>>>
>>
>> if you make Sage believe that the atlas package was installed properly,
>> the installation proceeds without trouble. So as a quick workaround,
>> just do
>>
>> touch spkg/installed/atlas-<version_number>
>>
>> I always do this on my system. It would be good to find out the proper
>> solution of course. :)
>>
>
Thanks! This makes the compilation proceed further. FYI, in sage-git, the
corresponding directory is SAGE_ROOT/local/var/lib/sage/installed


One question though: can this trick be used with the other packages such as
R, givaro, etc. If this can be done, then it will be so much easier to
upgrade sage! I wouldn't have to rely on luck on whether the build finishes
in some finite time. :-)



>>  The main problem here is that Gentoo support the installation of
> multiple BLAS/LAPACK at once.
> For that reason there is no libraries on the system installed with the
> names:
> libcblas.*
> libf77blas.*
> liblapack.*
>
> My recommendation for you is to create a folder in your home directory and
> link all the libraries you need with the appropriate name in a lib
> subfolder
> and pass the parent directory to SAGE_ATLAS_LIB.
>
>  Francois


Actually I do have those libraries. Only missing one is liblapack.*. It is
probably one of the similarly named libraries, except I don't know which. I
don't want to find out by hit and trial given how finicky atlas is.

~» ll /usr/lib/{libcblas.so,libf77blas.so,libatlas.so}
lrwxrwxrwx 1 root root 13 Aug 20 19:39 /usr/lib/libatlas.so -> libatlas.so.3
lrwxrwxrwx 1 root root 14 Sep 15 2012 /usr/lib/libcblas.so -> libgslcblas.so
lrwxrwxrwx 1 root root 15 Aug 20 19:39 /usr/lib/libf77blas.so ->
libf77blas.so.3