[Numpy-discussion] is my numpy installation using custom blas/lapack?

Chris Colbert sccolbert@gmail....
Sat Jun 6 14:15:44 CDT 2009


i need the full link to pastebin.com in order to view your post.

It will be something like http://pastebin.com/m6b09f05c


chris


On Sat, Jun 6, 2009 at 2:32 PM, Richard Llewellyn<llewelr@gmail.com> wrote:
> I posted the setup.py build output to pastebin.com, though missed the
> uninteresting stderr (forgot tcsh command to redirect both).
> Also, used setup.py build --fcompiler=gnu95.
>
>
> To be clear, I am not certain that my ATLAS libraries are not found. But
> during the build starting at line 95 (pastebin.com) I see a compilation
> failure, and then NO_ATLAS_INFO, 2.
>
> I don't think I can use ldconfig without root, but have set LD_LIBRARY_PATH
> to point to the scipy_build/lib until I put them somewhere else.
>
> importing numpy works, though lapack_lite is also imported. I wonder if this
> is normal even if my ATLAS was used.
>
> Thanks,
> Rich
>
> On Sat, Jun 6, 2009 at 10:46 AM, Chris Colbert <sccolbert@gmail.com> wrote:
>>
>> and where exactly are you seeing atlas not found? during the build
>> process, are when import numpy in python?
>>
>> if its the latter, you need to add a .conf file  in /etc/ld.so.conf.d/
>>  with the line /usr/local/rich/src/scipy_build/lib  and then run  sudo
>> ldconfig
>>
>> Chris
>>
>>
>> On Sat, Jun 6, 2009 at 1:42 PM, Chris Colbert<sccolbert@gmail.com> wrote:
>> > can you run this and post the build.log to pastebin.com:
>> >
>> > assuming your numpy build directory is /home/numpy-1.3.0:
>> >
>> > cd /home/numpy-1.3.0
>> > rm -rf build
>> > python setup.py build &&> build.log
>> >
>> >
>> > Chris
>> >
>> >
>> > On Sat, Jun 6, 2009 at 1:37 PM, Richard Llewellyn<llewelr@gmail.com>
>> > wrote:
>> >> Hi Chris,
>> >>  thanks much for posting those installation instructions.  Seems
>> >> similar to
>> >> what I pieced together.
>> >>
>> >> I gather ATLAS not found.  Oops, drank that beer too early.
>> >>
>> >> I copied Atlas libs to /usr/local/rich/src/scipy_build/lib.
>> >>
>> >> This is my site.cfg.  Out of desperation I tried search_static_first =
>> >> 1,
>> >> but probably of no use.
>> >>
>> >> [DEFAULT]
>> >> library_dirs = /usr/local/rich/src/scipy_build/lib:$HOME/usr/galois/lib
>> >> include_dirs =
>> >> /usr/local/rich/src/scipy_build/lib/include:$HOME/usr/galois/include
>> >> search_static_first = 1
>> >>
>> >> [blas_opt]
>> >> libraries = f77blas, cblas, atlas
>> >>
>> >> [lapack_opt]
>> >> libraries = lapack, f77blas, cblas, atlas
>> >>
>> >> [amd]
>> >> amd_libs = amd
>> >>
>> >> [umfpack]
>> >> umfpack_libs = umfpack, gfortran
>> >>
>> >> [fftw]
>> >> libraries = fftw3
>> >>
>> >>
>> >> Rich
>> >>
>> >>
>> >>
>> >>
>> >> On Sat, Jun 6, 2009 at 10:25 AM, Chris Colbert <sccolbert@gmail.com>
>> >> wrote:
>> >>>
>> >>> when you build numpy, did you use site.cfg to tell it where to find
>> >>> your atlas libs?
>> >>>
>> >>> On Sat, Jun 6, 2009 at 1:02 PM, Richard Llewellyn<llewelr@gmail.com>
>> >>> wrote:
>> >>> > Hello,
>> >>> >
>> >>> > I've managed a build of lapack and atlas on Fedora 10 on a quad
>> >>> > core,
>> >>> > 64,
>> >>> > and now (...) have a numpy I can import that runs tests ok. :]    I
>> >>> > am
>> >>> > puzzled, however, that numpy builds and imports lapack_lite.  Does
>> >>> > this
>> >>> > mean
>> >>> > I have a problem with the build(s)?
>> >>> > Upon building numpy, I see the troubling output:
>> >>> >
>> >>> > ########################
>> >>> >
>> >>> > C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe
>> >>> > -Wall
>> >>> > -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protecto
>> >>> > r --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC
>> >>> > -fPIC
>> >>> >
>> >>> > compile options: '-c'
>> >>> > gcc: _configtest.c
>> >>> > gcc -pthread _configtest.o -L/usr/local/rich/src/scipy_build/lib
>> >>> > -llapack
>> >>> > -lptf77blas -lptcblas -latlas -o _configtest
>> >>> > /usr/bin/ld: _configtest: hidden symbol `__powidf2' in
>> >>> > /usr/lib/gcc/x86_64-redhat-linux/4.3.2/libgcc.a(_powidf2.o) is
>> >>> > reference
>> >>> > d by DSO
>> >>> > /usr/bin/ld: final link failed: Nonrepresentable section on output
>> >>> > collect2: ld returned 1 exit status
>> >>> > /usr/bin/ld: _configtest: hidden symbol `__powidf2' in
>> >>> > /usr/lib/gcc/x86_64-redhat-linux/4.3.2/libgcc.a(_powidf2.o) is
>> >>> > reference
>> >>> > d by DSO
>> >>> > /usr/bin/ld: final link failed: Nonrepresentable section on output
>> >>> > collect2: ld returned 1 exit status
>> >>> > failure.
>> >>> > removing: _configtest.c _configtest.o
>> >>> > Status: 255
>> >>> > Output:
>> >>> >   FOUND:
>> >>> >     libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas']
>> >>> >     library_dirs = ['/usr/local/rich/src/scipy_build/lib']
>> >>> >     language = f77
>> >>> >     define_macros = [('NO_ATLAS_INFO', 2)]
>> >>> >
>> >>> > ##########################
>> >>> >
>> >>> > I don't have root on this machine, but could pester admins for
>> >>> > eventual
>> >>> > temporary access.
>> >>> >
>> >>> > Thanks much for any help,
>> >>> > Rich
>> >>> >
>> >>> > _______________________________________________
>> >>> > Numpy-discussion mailing list
>> >>> > Numpy-discussion@scipy.org
>> >>> > http://mail.scipy.org/mailman/listinfo/numpy-discussion
>> >>> >
>> >>> >
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