Hi,
On Jun 6, 2009 3:11pm, Chris Colbert <[email protected]> wrote:
it definately found your threaded atlas libraries. How do you know
it's numpy is using lapack_lite?
I don't, actually. But it is importing it. With python -v, this is the
error I get if I don't set LD_LIBRARY_PATH to my scipy_build directory
import numpy.linalg.linalg # precompiled from
/data10/users/rich/usr/galois/lib64/python/numpy/linalg/linalg.pyc
dlopen("/data10/users/rich/usr/galois/lib64/python/numpy/linalg/lapack_lite.so",
2);
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/data10/users/rich/usr/galois//lib64/python/numpy/__init__.py", line
130, in <module>
import add_newdocs
File "/data10/users/rich/usr/galois//lib64/python/numpy/add_newdocs.py",
line 9, in <module>
from lib import add_newdoc
File "/data10/users/rich/usr/galois//lib64/python/numpy/lib/__init__.py",
line 13, in <module>
from polynomial import *
File "/data10/users/rich/usr/galois//lib64/python/numpy/lib/polynomial.py",
line 18, in <module>
from numpy.linalg import eigvals, lstsq
File "/data10/users/rich/usr/galois//lib64/python/numpy/linalg/__init__.py",
line
47, in <module>
from linalg import *
File "/data10/users/rich/usr/galois//lib64/python/numpy/linalg/linalg.py",
line 22, in <module>
from numpy.linalg import lapack_lite
ImportError: liblapack.so: cannot open shared object file: No such file or
directory
Here blas_opt_info seems to be missing ATLAS version.
numpy.show_config()
atlas_threads_info:
libraries = ['lapack', 'lapack', 'f77blas', 'cblas', 'atlas']
library_dirs = ['/usr/local/rich/src/scipy_build/lib']
language = f77
blas_opt_info:
libraries = ['lapack', 'f77blas', 'cblas', 'atlas']
library_dirs = ['/usr/local/rich/src/scipy_build/lib']
define_macros = [('NO_ATLAS_INFO', 2)]
language = c
atlas_blas_threads_info:
libraries = ['lapack', 'f77blas', 'cblas', 'atlas']
library_dirs = ['/usr/local/rich/src/scipy_build/lib']
language = c
lapack_opt_info:
libraries = ['lapack', 'lapack', 'f77blas', 'cblas', 'atlas']
library_dirs = ['/usr/local/rich/src/scipy_build/lib']
define_macros = [('NO_ATLAS_INFO', 2)]
language = f77
lapack_mkl_info:
NOT AVAILABLE
blas_mkl_info:
NOT AVAILABLE
mkl_info:
NOT AVAILABLE
when I do:
python
>>import numpy
>>numpy.show_config()
atlas_threads_info:
libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas']
library_dirs = ['/usr/local/lib']
language = f77
blas_opt_info:
libraries = ['ptf77blas', 'ptcblas', 'atlas']
library_dirs = ['/usr/local/lib']
define_macros = [('ATLAS_INFO', '"\\"3.8.3\\""')]
language = c
atlas_blas_threads_info:
libraries = ['ptf77blas', 'ptcblas', 'atlas']
library_dirs = ['/usr/local/lib']
language = c
lapack_opt_info:
libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas']
library_dirs = ['/usr/local/lib']
define_macros = [('NO_ATLAS_INFO', 2)]
language = f77
lapack_mkl_info:
NOT AVAILABLE
blas_mkl_info:
NOT AVAILABLE
mkl_info:
NOT AVAILABLE
also try:
>>> a = numpy.random.randn(6000, 6000)
>>> numpy.dot(a,a)
and make sure all your cpu cores peg at 100%
Unfortunately only one cpu. What does that mean? Threaded libraries not
used?
from top:
Cpu0 :100.0%us, 0.0%sy, 0.0%ni, 0.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st
Cpu1 : 0.0%us, 0.2%sy, 0.0%ni, 99.4%id, 0.0%wa, 0.2%hi, 0.2%si, 0.0%st
Cpu2 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st
Cpu3 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st
Thanks much for the help.
Rich
On Sat, Jun 6, 2009 at 3:35 PM, [email protected]> wrote:
> Oops. Thanks, that makes more sense:
>
> http://pastebin.com/m7067709b
>
> On Jun 6, 2009 12:15pm, Chris Colbert [email protected]> wrote:
>> 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 [email protected]>
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 [email protected]>
>> > 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 [email protected]>
>> >> 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
[email protected]>
>>
>> >> > 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
[email protected]>
>>
>> >> >> 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
[email protected]>
>>
>> >> >>> 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
>>
>> >> >>> > [email protected]
>>
>> >> >>> > http://mail.scipy.org/mailman/listinfo/numpy-discussion
>>
>> >> >>> >
>>
>> >> >>> >
>>
>> >> >>> _______________________________________________
>>
>> >> >>> Numpy-discussion mailing list
>>
>> >> >>> [email protected]
>>
>> >> >>> http://mail.scipy.org/mailman/listinfo/numpy-discussion
>>
>> >> >>
>>
>> >> >>
>>
>> >> >> _______________________________________________
>>
>> >> >> Numpy-discussion mailing list
>>
>> >> >> [email protected]
>>
>> >> >> http://mail.scipy.org/mailman/listinfo/numpy-discussion
>>
>> >> >>
>>
>> >> >>
>>
>> >> >
>>
>> >> _______________________________________________
>>
>> >> Numpy-discussion mailing list
>>
>> >> [email protected]
>>
>> >> http://mail.scipy.org/mailman/listinfo/numpy-discussion
>>
%
_______________________________________________
Numpy-discussion mailing list
[email protected]
http://mail.scipy.org/mailman/listinfo/numpy-discussion
