[SciPy-user] ATLAS and gcc v4.0.2

Nils Wagner nwagner at mecha.uni-stuttgart.de
Tue Feb 28 05:32:34 CST 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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