[SciPy-user] ATLAS and gcc v4.0.2
Nils Wagner
nwagner at mecha.uni-stuttgart.de
Tue Feb 28 06:32:34 EST 2006
On Tue, 28 Feb 2006 19:20:55 +0900
Christian Kristukat <ckkart at hoc.net> wrote:
> Nils Wagner wrote:
>>>>
>>>> SuSE 10.0 comes with gcc-fortran
>>>>
>>>> Name : gcc-fortran Relocations:
>>> You're right. But the executable is called 'gfortran'. I
>>> mixed that up.
>>>
>> I have already build blas and lapack libraries using g77
>> according to the installation hints.
>>
>> Can I use them or must I recompile blas and lapack with
>> gfortran ?
>
> I'm not an expert on this subject, just sharing my
>experiences. If you're using
> ATLAS you don't need BLAS as far as I understood. I
>followed the instructions in
> the link I posted before. Compared to the compilation
>time of ATLAS, LAPACK
> builds almost instantaneously, so it doesn't hurt to
>rebuild LAPACK, I just
> don't know wether g77 built LAPACK works together with
>gfortran ATLAS.
> At least I know, that if you're using gfrotran all the
>time, everything works
> fine on SuSE 10.0.
>
> Good luck, Christian
>
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I followed your advice and rebuilt blas and lapack using
gfortran. Compilation of ATLAS seems to work. Also
I have build a complete lapack
http://math-atlas.sourceforge.net/errata.html#completelp
I am on SuSE 10.0 x86_64 GNU/Linux
However
python setup.py build failed
Running from numpy source directory.
Warning: not existing path in numpy/distutils: site.cfg
No module named __svn_version__
F2PY Version 2_2179
blas_opt_info:
blas_mkl_info:
/usr/local/svn/numpy/numpy/distutils/system_info.py:531:
UserWarning: Library error: libs=['mkl', 'vml', 'guide']
found_libs=[]
warnings.warn("Library error: libs=%s found_libs=%s" %
\
NOT AVAILABLE
atlas_blas_threads_info:
Setting PTATLAS=ATLAS
/usr/local/svn/numpy/numpy/distutils/system_info.py:531:
UserWarning: Library error: libs=['ptf77blas', 'ptcblas',
'atlas'] found_libs=[]
warnings.warn("Library error: libs=%s found_libs=%s" %
\
/usr/local/svn/numpy/numpy/distutils/system_info.py:531:
UserWarning: Library error: libs=['ptf77blas', 'ptcblas',
'atlas'] found_libs=['/usr/local/lib/atlas/libatlas.a']
warnings.warn("Library error: libs=%s found_libs=%s" %
\
NOT AVAILABLE
atlas_blas_info:
/usr/local/svn/numpy/numpy/distutils/system_info.py:531:
UserWarning: Library error: libs=['f77blas', 'cblas',
'atlas'] found_libs=[]
warnings.warn("Library error: libs=%s found_libs=%s" %
\
FOUND:
libraries = ['f77blas', 'cblas', 'atlas']
library_dirs = ['/usr/local/lib/atlas']
language = c
running build_src
building extension "atlas_version" sources
creating build
creating build/src
adding 'build/src/atlas_version_0x5b360788cdd9eddc.c'
to sources.
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
building 'atlas_version' extension
compiling C sources
gcc options: '-pthread -fno-strict-aliasing -DNDEBUG -O2
-fmessage-length=0 -Wall -D_FORTIFY_SOURCE=2 -g -fPIC'
creating build/temp.linux-x86_64-2.4
creating build/temp.linux-x86_64-2.4/build
creating build/temp.linux-x86_64-2.4/build/src
compile options: '-Inumpy/core/include
-I/usr/include/python2.4 -c'
gcc: build/src/atlas_version_0x5b360788cdd9eddc.c
gcc -pthread -shared
build/temp.linux-x86_64-2.4/build/src/atlas_version_0x5b360788cdd9eddc.o
-L/usr/local/lib/atlas -lf77blas -lcblas -latlas -o
build/temp.linux-x86_64-2.4/atlas_version.so
/usr/lib64/gcc/x86_64-suse-linux/4.0.2/../../../../x86_64-suse-linux/bin/ld:
/usr/local/lib/atlas/libatlas.a(ATL_buildinfo.o):
relocation R_X86_64_32 against `a local symbol' can not be
used when making a shared object; recompile with -fPIC
/usr/local/lib/atlas/libatlas.a: could not read symbols:
Bad value
collect2: ld returned 1 exit status
/usr/lib64/gcc/x86_64-suse-linux/4.0.2/../../../../x86_64-suse-linux/bin/ld:
/usr/local/lib/atlas/libatlas.a(ATL_buildinfo.o):
relocation R_X86_64_32 against `a local symbol' can not be
used when making a shared object; recompile with -fPIC
/usr/local/lib/atlas/libatlas.a: could not read symbols:
Bad value
collect2: ld returned 1 exit status
##### msg: error: Command "gcc -pthread -shared
build/temp.linux-x86_64-2.4/build/src/atlas_version_0x5b360788cdd9eddc.o
-L/usr/local/lib/atlas -lf77blas -lcblas -latlas -o
build/temp.linux-x86_64-2.4/atlas_version.so" failed with
exit status 1
error: Command "gcc -pthread -shared
build/temp.linux-x86_64-2.4/build/src/atlas_version_0x5b360788cdd9eddc.o
-L/usr/local/lib/atlas -lf77blas -lcblas -latlas -o
build/temp.linux-x86_64-2.4/atlas_version.so" failed with
exit status 1
FOUND:
libraries = ['f77blas', 'cblas', 'atlas']
library_dirs = ['/usr/local/lib/atlas']
language = c
define_macros = [('NO_ATLAS_INFO', 2)]
Warning: distutils distribution has been initialized, it
may be too late to add an extension _dotblas
Traceback (most recent call last):
File "setup.py", line 76, in ?x86_64 GNU/Linux
setup_package()
File "setup.py", line 63, in setup_package
config.add_subpackage('numpy')
File
"/usr/local/svn/numpy/numpy/distutils/misc_util.py", line
592, in add_subpackage
config_list =
self.get_subpackage(subpackage_name,subpackage_path)
File
"/usr/local/svn/numpy/numpy/distutils/misc_util.py", line
582, in get_subpackage
subpackage_path)
File
"/usr/local/svn/numpy/numpy/distutils/misc_util.py", line
539, in _get_configuration_from_setup_py
config = setup_module.configuration(*args)
File "/usr/local/svn/numpy/numpy/setup.py", line 10, in
configuration
config.add_subpackage('core')
File
"/usr/local/svn/numpy/numpy/distutils/misc_util.py", line
592, in add_subpackage
config_list =
self.get_subpackage(subpackage_name,subpackage_path)
File
"/usr/local/svn/numpy/numpy/distutils/misc_util.py", line
582, in get_subpackage
subpackage_path)
File
"/usr/local/svn/numpy/numpy/distutils/misc_util.py", line
539, in _get_configuration_from_setup_py
config = setup_module.configuration(*args)
File "numpy/core/setup.py", line 217, in configuration
config.add_data_dir('tests')
File
"/usr/local/svn/numpy/numpy/distutils/misc_util.py", line
636, in add_data_dir
self.add_data_files((ds,filenames))
File
"/usr/local/svn/numpy/numpy/distutils/misc_util.py", line
702, in add_data_files
dist.data_files.extend(data_dict.items())
AttributeError: 'NoneType' object has no attribute
'extend'
Any suggestion ?
Nils
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