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

Chris Colbert sccolbert@gmail....
Sat Jun 6 12:46:27 CDT 2009


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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