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

Richard Llewellyn llewelr@gmail....
Sat Jun 6 13:32:24 CDT 2009


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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> >>
> >>
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