Hi Nils, no, I compiled with gcc 3.x, therefore I didn't run into that problem. Hanno On Feb 28, 2006, at 8:28 PM, Nils Wagner wrote:
On Tue, 28 Feb 2006 18:49:06 +0100 "Hanno Klemm" <klemm@phys.ethz.ch> wrote:
Hi Christian,
you output looks like a problem I had:
On my 64bit architecture I had to modify the make file for atlas and append an -fPIC at the compiler flags (I tired that at the architecture flags, the g77 and the c flags. That did the job). Otherwise it seems not possible to use the libraries with scipy.
Good luck, Hanno
Hi Hanno,
Thank you for your valuable comment. Did you also apply the patch to ATLAS/bin/uumtst.c ? The sanity_test failed here. http://math-atlas.sourceforge.net/errata.html#gcc4
Cheers,
Nils
Christian Kristukat <ckkart@hoc.net> said:
On Tue, 28 Feb 2006 19:20:55 +0900 Christian Kristukat <ckkart@hoc.net> 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
Nils Wagner wrote: 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
Nils Wagner wrote: 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
-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",
592, in add_subpackage config_list = self.get_subpackage(subpackage_name,subpackage_path) File "/usr/local/svn/numpy/numpy/distutils/misc_util.py",
582, in get_subpackage subpackage_path) File "/usr/local/svn/numpy/numpy/distutils/misc_util.py",
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",
592, in add_subpackage config_list = self.get_subpackage(subpackage_name,subpackage_path) File "/usr/local/svn/numpy/numpy/distutils/misc_util.py",
582, in get_subpackage subpackage_path) File "/usr/local/svn/numpy/numpy/distutils/misc_util.py",
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",
636, in add_data_dir self.add_data_files((ds,filenames)) File "/usr/local/svn/numpy/numpy/distutils/misc_util.py",
build/temp.linux-x86_64-2.4/build/src/ atlas_version_0x5b360788cdd9eddc.o line line line line line line line line
702, in add_data_files dist.data_files.extend(data_dict.items()) AttributeError: 'NoneType' object has no attribute 'extend'
I can't say more than that I followed exactly the instructions here: http://pong.tamu.edu/tiki/tiki-view_blog_post.php?blogId=6&postId=97 (the full LAPACK issue is covered there, too) and it worked.
Christian
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-- Hanno Klemm klemm@phys.ethz.ch
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-- Hanno Klemm klemm@itp.phys.ethz.ch ETH Zurich tel: +41-1-6332580 Institute for theoretical physics mobile: +41-79-4500428 http://www.mth.kcl.ac.uk/~klemm