Mailman 3 June 2004 - SciPy-Dev

installation problems with SciPy
by Giovanni Samaey June 25, 2004

June 25, 2004

Hi, just changing LD_LIBRARY_PATH did not make a difference. I tried reinstalling scipy with the LD_LIBRARY_PATH set, and somehow this installation crashed with the following final lines: building extension "scipy.io.numpyio" sources building extension "scipy.linalg.fblas" sources generating fblas interface 20 error: build/src/atlas321/fblas.pyf: No such file or directory Now I am confused again... How did I break this? Giovanni -- Giovanni Samaey http://www.cs.kuleuven.ac.be/~giovanni/ Katholieke Universiteit Leuven email: giovanni(a)cs.kuleuven.ac.be Departement Computerwetenschappen phone: +32-16-327081 Celestijnenlaan 200A, B-3001 Heverlee, Belgium fax: +32-16-327996 Office: A04.36

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installation problems with SciPy
by Giovanni Samaey June 25, 2004

June 25, 2004

Thank you for the help. Putting /usr/lib/3dnow in LD_LIBRARY_PATH made the tests run better. The state has progressed: Running scipy.test() now gives no errors (on all levels). The only things that go "wrong" now is two warnings. I don't know if they are worth bothering about: **************************************************************** WARNING: cblas module is empty ----------- See scipy/INSTALL.txt for troubleshooting. Notes: * If atlas library is not found by scipy/system_info.py, then scipy uses fblas instead of cblas. **************************************************************** **************************************************************** WARNING: clapack module is empty ----------- See scipy/INSTALL.txt for troubleshooting. Notes: * If atlas library is not found by scipy/system_info.py, then scipy uses flapack instead of clapack. **************************************************************** However, import atlas_version still gives an error. I don't know if I should care? bash-2.05a$ python -c 'import atlas_version' Traceback (most recent call last): File "<string>", line 1, in ? ImportError: ./atlas_version.so: undefined symbol: ATL_buildinfo Best, and thanks already! I would never have found this LD_LIBRARY_PATH stuff. Giovanni -- Giovanni Samaey http://www.cs.kuleuven.ac.be/~giovanni/ Katholieke Universiteit Leuven email: giovanni(a)cs.kuleuven.ac.be Departement Computerwetenschappen phone: +32-16-327081 Celestijnenlaan 200A, B-3001 Heverlee, Belgium fax: +32-16-327996 Office: A04.36

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installation problems with SciPy
by Giovanni Samaey June 25, 2004

June 25, 2004

Hi, I seem to have some problems installing SciPy. I installed SciPy from the latest (?) source that I downloaded following the instructions at http://www.scipy.org/documentation/buildscipy.txt I took advantage of the fact that ATLAS is already installed here under /usr/lib/3dnow. I don't have root access to my system. The test() routine runs, but gives 15 errors of the type ====================================================================== ERROR: check_sh_legendre (scipy.special.basic.test_basic.test_sh_legendre) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/giovanni/bin/lib/python2.3/site-packages/scipy/special/tests/test_basic.py", line 1806, in check_sh_legendre Ps1 = sh_legendre(1) File "/home/giovanni/bin/lib/python2.3/site-packages/scipy/special/orthogonal.py", line 593, in sh_legendre x,w,mu0 = ps_roots(n,mu=1) File "/home/giovanni/bin/lib/python2.3/site-packages/scipy/special/orthogonal.py", line 584, in ps_roots return js_roots(n,1.0,1.0,mu=mu) File "/home/giovanni/bin/lib/python2.3/site-packages/scipy/special/orthogonal.py", line 205, in js_roots val = gen_roots_and_weights(n,an_Js,sbn_Js,mu0) File "/home/giovanni/bin/lib/python2.3/site-packages/scipy/special/orthogonal.py", line 121, in gen_roots_and_weights eig = get_eig_func() File "/home/giovanni/bin/lib/python2.3/site-packages/scipy/special/orthogonal.py", line 91, in get_eig_func eig = scipy.linalg.eig AttributeError: 'module' object has no attribute 'eig' ---------------------------------------------------------------------- Moreover, functions from the packages "integrate" and "linalg" are simply not found... I generated the information that is requested by the INSTALL.text file; it is attached to this mail... The command $ python scipy_core/scipy_distutils/command/build_flib.py could not be executed because for some reason "build_flib.py" is not present; maybe the info in attachment might tell why? If these problems could be solved, I would be thrilled, because SciPy really looks to a promising tool. Thanks already in advance, Best, Giovanni -- Giovanni Samaey http://www.cs.kuleuven.ac.be/~giovanni/ Katholieke Universiteit Leuven email: giovanni(a)cs.kuleuven.ac.be Departement Computerwetenschappen phone: +32-16-327081 Celestijnenlaan 200A, B-3001 Heverlee, Belgium fax: +32-16-327996 Office: A04.36 ------ os.name='posix' ------ sys.platform='linux2' ------ sys.version: 2.3.4 (#3, Jun 24 2004, 11:19:27) [GCC 2.95.4 20011002 (Debian prerelease)] ------ sys.prefix: /home/giovanni/bin ------ sys.path=':/home/giovanni/bin/lib/python23.zip:/home/giovanni/bin/lib/python2.3:/home/giovanni/bin/lib/python2.3/plat-linux2:/home/giovanni/bin/lib/python2.3/lib-tk:/home/giovanni/bin/lib/python2.3/lib-dynload:/home/giovanni/bin/lib/python2.3/site-packages:/home/giovanni/bin/lib/python2.3/site-packages/Numeric' ------ Failed to import numarray: No module named numarray Found Numeric version '23.3' in /home/giovanni/bin/lib/python2.3/site-packages/Numeric/Numeric.pyc Found f2py2e version '2.39.235_1693' in /home/giovanni/bin/lib/python2.3/site-packages/f2py2e/f2py2e.pyc Found scipy_distutils version '0.3.0_27.455' in '/home/giovanni/bin/lib/python2.3/site-packages/scipy_distutils/__init__.pyc' ------ Importing scipy_distutils.command.build_flib ... error: No module named build_flib ------ Checking availability of supported Fortran compilers: error: local variable 'build_flib' referenced before assignment ------ Importing scipy_distutils.fcompiler ... ok ------ Checking availability of supported Fortran compilers: customize CompaqFCompiler customize AbsoftFCompiler Could not locate executable ifort Could not locate executable ifc Could not locate executable efort Could not locate executable efc Could not locate executable ifort customize IntelFCompiler customize GnuFCompiler customize SunFCompiler customize VastFCompiler customize IbmFCompiler customize LaheyFCompiler customize IntelVisualFCompiler customize IntelItaniumFCompiler customize PGroupFCompiler customize CompaqVisualFCompiler customize MipsFCompiler customize HPUXFCompiler customize IntelItaniumVisualFCompiler customize NAGFCompiler List of available Fortran compilers: --fcompiler=gnu GNU Fortran Compiler (0.5.25) List of unavailable Fortran compilers: --fcompiler=absoft Absoft Corp Fortran Compiler --fcompiler=compaq Compaq Fortran Compiler --fcompiler=compaqv DIGITAL|Compaq Visual Fortran Compiler --fcompiler=hpux HP Fortran 90 Compiler --fcompiler=ibm IBM XL Fortran Compiler --fcompiler=intel Intel Fortran Compiler for 32-bit apps --fcompiler=intele Intel Fortran Compiler for Itanium apps --fcompiler=intelev Intel Visual Fortran Compiler for Itanium apps --fcompiler=intelv Intel Visual Fortran Compiler for 32-bit apps --fcompiler=lahey Lahey/Fujitsu Fortran 95 Compiler --fcompiler=mips MIPSpro Fortran Compiler --fcompiler=nag NAGWare Fortran 95 Compiler --fcompiler=pg Portland Group Fortran Compiler --fcompiler=sun Sun|Forte Fortran 95 Compiler --fcompiler=vast Pacific-Sierra Research Fortran 90 Compiler List of unimplemented Fortran compilers: --fcompiler=f Fortran Company/NAG F Compiler For compiler details, run 'config_fc --verbose' setup command. ------ Importing scipy_distutils.command.cpuinfo ... error: No module named cpuinfo Importing scipy_distutils.cpuinfo ... ok ------ CPU information: getNCPUs has_mmx has_sse has_sse2 is_Intel is_Pentium is_PentiumIV is_singleCPU ------ _pkg_config_info: NOT AVAILABLE agg2_info: ( src_dirs = .:/usr/local/src ) NOT AVAILABLE atlas_blas_info: ( library_dirs = /home/giovanni/bin/lib:/usr/local/lib:/usr/lib ) ( paths: /usr/lib/3dnow ) ( paths: /usr/lib/3dnow/libf77blas.so ) ( paths: /usr/lib/3dnow/libcblas.so ) ( paths: /usr/lib/3dnow/libatlas.so ) ( paths: /usr/lib/3dnow/atlas ) system_info.atlas_blas_info ( include_dirs = /usr/local/include:/usr/include:/home/giovanni/bin/include ) ( paths: /usr/include/atlas_enum.h,/usr/include/atlas_misc.h ) ( paths: /usr/include/cblas.h ) FOUND: libraries = ['f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/lib/3dnow'] language = c include_dirs = ['/usr/include'] atlas_blas_threads_info: ( library_dirs = /home/giovanni/bin/lib:/usr/local/lib:/usr/lib ) ( paths: /usr/lib/3dnow ) ( paths: /usr/lib/3dnow/libatlas.so ) ( paths: /usr/lib/3dnow/libatlas.a ) system_info.atlas_blas_threads_info NOT AVAILABLE atlas_info: ( library_dirs = /home/giovanni/bin/lib:/usr/local/lib:/usr/lib ) ( paths: /usr/lib/3dnow ) ( paths: /usr/lib/3dnow/libf77blas.so ) ( paths: /usr/lib/3dnow/libcblas.so ) ( paths: /usr/lib/3dnow/libatlas.so ) ( paths: /usr/lib/3dnow/liblapack_atlas.so ) ( paths: /usr/lib/3dnow/atlas ) ( paths: /usr/lib/3dnow/atlas/liblapack.so ) system_info.atlas_info ( include_dirs = /usr/local/include:/usr/include:/home/giovanni/bin/include ) ( paths: /usr/include/atlas_enum.h,/usr/include/atlas_misc.h ) ( paths: /usr/include/cblas.h ) FOUND: libraries = ['lapack', 'f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/lib/3dnow/atlas', '/usr/lib/3dnow'] language = f77 include_dirs = ['/usr/include'] atlas_threads_info: ( library_dirs = /home/giovanni/bin/lib:/usr/local/lib:/usr/lib ) ( paths: /usr/lib/3dnow ) ( paths: /usr/lib/3dnow/libatlas.so ) ( paths: /usr/lib/3dnow/libatlas.a ) ( paths: /usr/lib/3dnow/liblapack_atlas.so ) system_info.atlas_threads_info NOT AVAILABLE blas_info: ( library_dirs = /home/giovanni/bin/lib:/usr/local/lib:/usr/lib ) ( paths: /usr/lib/libblas.so ) FOUND: libraries = ['blas'] library_dirs = ['/usr/lib'] language = f77 blas_opt_info: running build_src building extension "atlas_version" sources adding 'build/src/atlas_version_0x8bd9e760.c' to sources. running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext Command: /home/giovanni/bin/bin/python -c "import imp;imp.load_dynamic(\"atlas_version\",\"atlas_version.so\")" Status: 1 Output: Traceback (most recent call last): File "<string>", line 1, in ? ImportError: libatlas.so.2: cannot open shared object file: No such file or directory FOUND: libraries = ['f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/lib/3dnow'] language = c define_macros = [('NO_ATLAS_INFO', 2)] include_dirs = ['/usr/include'] blas_src_info: ( src_dirs = .:/usr/local/src ) NOT AVAILABLE boost_python_info: ( src_dirs = .:/usr/local/src ) NOT AVAILABLE dfftw_info: ( library_dirs = /home/giovanni/bin/lib:/usr/local/lib:/usr/lib ) ( include_dirs = /usr/local/include:/usr/include:/home/giovanni/bin/include ) NOT AVAILABLE dfftw_threads_info: ( library_dirs = /home/giovanni/bin/lib:/usr/local/lib:/usr/lib ) ( include_dirs = /usr/local/include:/usr/include:/home/giovanni/bin/include ) NOT AVAILABLE djbfft_info: ( library_dirs = /home/giovanni/bin/lib:/usr/local/lib:/usr/lib ) ( include_dirs = /usr/local/include:/usr/include:/home/giovanni/bin/include ) NOT AVAILABLE fftw_info: ( library_dirs = /home/giovanni/bin/lib:/usr/local/lib:/usr/lib ) ( include_dirs = /usr/local/include:/usr/include:/home/giovanni/bin/include ) ( paths: /usr/lib/librfftw.so ) ( paths: /usr/lib/libfftw.so ) ( paths: /usr/include/fftw.h,/usr/include/rfftw.h ) FOUND: libraries = ['rfftw', 'fftw'] library_dirs = ['/usr/lib'] define_macros = [('SCIPY_FFTW_H', None)] include_dirs = ['/usr/include'] fftw_threads_info: ( library_dirs = /home/giovanni/bin/lib:/usr/local/lib:/usr/lib ) ( include_dirs = /usr/local/include:/usr/include:/home/giovanni/bin/include ) ( paths: /usr/lib/librfftw_threads.so ) ( paths: /usr/lib/libfftw_threads.so ) ( paths: /usr/include/fftw_threads.h,/usr/include/rfftw_threads.h ) FOUND: libraries = ['rfftw_threads', 'fftw_threads'] library_dirs = ['/usr/lib'] define_macros = [('SCIPY_FFTW_THREADS_H', None)] include_dirs = ['/usr/include'] freetype2_info: NOT AVAILABLE gdk_pixbuf_2_info: FOUND: libraries = ['gdk_pixbuf-2.0', 'm', 'gobject-2.0', 'gmodule-2.0', 'dl', 'glib-2.0'] define_macros = [('GDK_PIXBUF_2_INFO', '"\\"2.0.2\\""'), ('GDK_PIXBUF_VERSION_2_0_2', None)] gdk_pixbuf_xlib_2_info: FOUND: libraries = ['gdk_pixbuf_xlib-2.0', 'gdk_pixbuf-2.0', 'm', 'gobject-2.0', 'gmodule-2.0', 'dl', 'glib-2.0'] define_macros = [('GDK_PIXBUF_XLIB_2_INFO', '"\\"2.0.2\\""'), ('GDK_PIXBUF_XLIB_VERSION_2_0_2', None)] gdk_x11_2_info: FOUND: libraries = ['gdk-x11-2.0', 'gdk_pixbuf-2.0', 'm', 'pangox-1.0', 'pangoxft-1.0', 'pango-1.0', 'gobject-2.0', 'gmodule-2.0', 'dl', 'glib-2.0'] define_macros = [('GDK_X11_2_INFO', '"\\"2.0.2\\""'), ('GDK_X11_VERSION_2_0_2', None)] gtkp_2_info: FOUND: libraries = ['gtk-x11-2.0', 'gdk-x11-2.0', 'atk-1.0', 'gdk_pixbuf-2.0', 'm', 'pangox-1.0', 'pangoxft-1.0', 'pango-1.0', 'gobject-2.0', 'gmodule-2.0', 'dl', 'glib-2.0'] define_macros = [('GTKP_2_INFO', '"\\"2.0.2\\""'), ('GTK_VERSION_2_0_2', None)] gtkp_x11_2_info: FOUND: libraries = ['gtk-x11-2.0', 'gdk-x11-2.0', 'atk-1.0', 'gdk_pixbuf-2.0', 'm', 'pangox-1.0', 'pangoxft-1.0', 'pango-1.0', 'gobject-2.0', 'gmodule-2.0', 'dl', 'glib-2.0'] define_macros = [('GTKP_X11_2_INFO', '"\\"2.0.2\\""'), ('GTK_X11_VERSION_2_0_2', None)] lapack_atlas_info: ( library_dirs = /home/giovanni/bin/lib:/usr/local/lib:/usr/lib ) ( paths: /usr/lib/3dnow ) ( paths: /usr/lib/3dnow/liblapack_atlas.so ) ( paths: /usr/lib/3dnow/libf77blas.so ) ( paths: /usr/lib/3dnow/libcblas.so ) ( paths: /usr/lib/3dnow/libatlas.so ) ( paths: /usr/lib/3dnow/liblapack_atlas.so ) ( paths: /usr/lib/3dnow/atlas ) ( paths: /usr/lib/3dnow/atlas/liblapack.so ) system_info.lapack_atlas_info ( include_dirs = /usr/local/include:/usr/include:/home/giovanni/bin/include ) ( paths: /usr/include/atlas_enum.h,/usr/include/atlas_misc.h ) ( paths: /usr/include/cblas.h ) FOUND: libraries = ['lapack', 'lapack_atlas', 'f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/lib/3dnow/atlas', '/usr/lib/3dnow'] language = f77 include_dirs = ['/usr/include'] lapack_atlas_threads_info: ( library_dirs = /home/giovanni/bin/lib:/usr/local/lib:/usr/lib ) ( paths: /usr/lib/3dnow ) ( paths: /usr/lib/3dnow/liblapack_atlas.so ) ( paths: /usr/lib/3dnow/libatlas.so ) ( paths: /usr/lib/3dnow/liblapack_atlas.a ) ( paths: /usr/lib/3dnow/libatlas.a ) ( paths: /usr/lib/3dnow/liblapack_atlas.so ) system_info.lapack_atlas_threads_info NOT AVAILABLE lapack_info: ( library_dirs = /home/giovanni/bin/lib:/usr/local/lib:/usr/lib ) ( paths: /usr/lib/liblapack.so ) FOUND: libraries = ['lapack'] library_dirs = ['/usr/lib'] language = f77 lapack_opt_info: running build_src building extension "atlas_version" sources adding 'build/src/atlas_version_0xfef664c6.c' to sources. running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext customize GnuFCompiler customize GnuFCompiler customize GnuFCompiler using build_ext Command: /home/giovanni/bin/bin/python -c "import imp;imp.load_dynamic(\"atlas_version\",\"atlas_version.so\")" Status: 1 Output: Traceback (most recent call last): File "<string>", line 1, in ? ImportError: libatlas.so.2: cannot open shared object file: No such file or directory FOUND: libraries = ['lapack', 'f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/lib/3dnow/atlas', '/usr/lib/3dnow'] language = f77 define_macros = [('NO_ATLAS_INFO', 2)] include_dirs = ['/usr/include'] lapack_src_info: ( src_dirs = .:/usr/local/src ) NOT AVAILABLE numarray_info: NOT AVAILABLE numpy_info: ( include_dirs = /home/giovanni/bin/include/python2.3 ) ( paths: /home/giovanni/bin/include/python2.3/Numeric/arrayobject.h ) FOUND: define_macros = [('NUMERIC_VERSION', '"\\"23.3\\""')] include_dirs = ['/home/giovanni/bin/include/python2.3'] sfftw_info: ( library_dirs = /home/giovanni/bin/lib:/usr/local/lib:/usr/lib ) ( include_dirs = /usr/local/include:/usr/include:/home/giovanni/bin/include ) NOT AVAILABLE sfftw_threads_info: ( library_dirs = /home/giovanni/bin/lib:/usr/local/lib:/usr/lib ) ( include_dirs = /usr/local/include:/usr/include:/home/giovanni/bin/include ) NOT AVAILABLE wx_info: Could not locate executable wx-config File not found: wx-config. Cannot determine wx info. NOT AVAILABLE x11_info: ( library_dirs = /usr/X11R6/lib:/usr/X11/lib:/usr/lib ) ( include_dirs = /usr/X11R6/include:/usr/X11/include:/usr/include ) ( paths: /usr/X11R6/lib/libX11.so ) ( paths: /usr/X11R6/include/X11/X.h ) FOUND: libraries = ['X11'] library_dirs = ['/usr/X11R6/lib'] include_dirs = ['/usr/X11R6/include'] xft_info: NOT AVAILABLE bash-2.05a$ python setup_atlas_version.py build_ext --inplace --force atlas_threads_info: scipy_distutils.system_info.atlas_threads_info NOT AVAILABLE atlas_info: scipy_distutils.system_info.atlas_info FOUND: libraries = ['lapack', 'f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/lib/3dnow/atlas', '/usr/lib/3dnow'] language = f77 include_dirs = ['/usr/include'] running build_ext building 'atlas_version' extension gcc options: '-pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC' creating build creating build/temp.linux-i686-2.3 creating build/temp.linux-i686-2.3/amd creating build/temp.linux-i686-2.3/amd/gauss creating build/temp.linux-i686-2.3/amd/gauss/export creating build/temp.linux-i686-2.3/amd/gauss/export/home3 creating build/temp.linux-i686-2.3/amd/gauss/export/home3/giovanni creating build/temp.linux-i686-2.3/amd/gauss/export/home3/giovanni/Downloads creating build/temp.linux-i686-2.3/amd/gauss/export/home3/giovanni/Downloads/SciPy_complete-0.3 creating build/temp.linux-i686-2.3/amd/gauss/export/home3/giovanni/Downloads/SciPy_complete-0.3/Lib creating build/temp.linux-i686-2.3/amd/gauss/export/home3/giovanni/Downloads/SciPy_complete-0.3/Lib/linalg compile options: '-I/home/giovanni/bin/include/python2.3 -c' gcc: /amd/gauss/export/home3/giovanni/Downloads/SciPy_complete-0.3/Lib/linalg/atlas_version.c gcc -pthread -shared build/temp.linux-i686-2.3/amd/gauss/export/home3/giovanni/Downloads/SciPy_complete-0.3/Lib/linalg/atlas_version.o -L/usr/lib/3dnow/atlas -L/usr/lib/3dnow -latlas -o atlas_version.so bash-2.05a$ python -c 'import atlas_version' Traceback (most recent call last): File "<string>", line 1, in ? ImportError: libatlas.so.2: cannot open shared object file: No such file or directory

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Hello
by Maxim Shemanarev June 20, 2004

June 20, 2004

Hello All, I'm Maxim Shemanarev and I will work on the new graphic back-end in Kiva. It's based on my Anti-Grain Geometry (http://antigrain.com). I can perfectly do the C++ part of the job, and Eric and I have lots of new ideas, but I also will need to do some job in Python and SWIG. I'm still not very good in those things, so, please forgive me possible stupid questions. I will gratefully appreciate your help. Currently I'm working on improving alpha-blending in AGG (very basic things), so it will be a while before I ask you of some help. Thank you in advance. McSeem

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interest in xplt bug reports?
by Arnd Baecker June 17, 2004

June 17, 2004

Dear all, I would like to know if there is any interest in bug reports concerning scipy.xplt? During the last months a couple of issues/features/bugs and differences between linux/windows were found by the students of our computational physics course with python/Numeric/scipy. The xplt issues caused the largest amount of complaints (shortly followed by documentation ;-). If there is sufficient interest, we have some money for a student who could compile a list of problems (with short examples). As xplt derives from pygist, should we better address the questions to the pygist people and hope that any fixes will get incorporated into scipy.xplt at some point? If so, whom should we contact (Michiel de Hoon?)? Best, Arnd

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slicing using Index and Mask arrays
by Travis Oliphant June 10, 2004

June 10, 2004

I have just added a feature to scipy in CVS This feature lets a[a > 3] = 10 a[indexarray] = 3 and so forth to function. Currently a[maskarray] and a[indexarray] always return a 1-d array (multidimensional returns not yet supported) while a[maskarray] = obj and a[indexarray]= obj will keep the shape of a To enable the new feature you must type (we will do this by default on scipy import at some point) scipy.alter_numeric() You can get back old numeric behavior using scipy.restore_numeric() Please report any bugs you find... -Travis O.

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any FreeBSD user here ?
by Ying-Chieh Liao June 9, 2004

June 9, 2004

I'd like to use SciPy on FreeBSD I've installed all the dependencies (all from FreeBSD ports collection): python 2.3.4 py-numeric 23.1 atlas 3.6.0 fftw 2.1.5 djbfft 0.76 But when I build scipy, there are many error messages (attached below) looks like it cannot find the lapack and blas lib I think maybe because FreeBSD changes it's name ... 195:-lalapack.1 => /usr/local/lib/libalapack.so.1 197:-lcblas.1 => /usr/local/lib/libcblas.so.1 198:-lf77blas.1 => /usr/local/lib/libf77blas.so.1 200:-lalapack_r.1 => /usr/local/lib/libalapack_r.so.1 202:-lcblas_r.1 => /usr/local/lib/libcblas_r.so.1 203:-lf77blas_r.1 => /usr/local/lib/libf77blas_r.so.1 205:-lptcblas.1 => /usr/local/lib/libptcblas.so.1 206:-lptf77blas.1 => /usr/local/lib/libptf77blas.so.1 How can I let scipy find these libs ? lapack_opt_info: atlas_threads_info: scipy_distutils.system_info.atlas_threads_info scipy_core/scipy_distutils/system_info.py:595: UserWarning: ********************************************************************* Could not find lapack library within the ATLAS installation. ********************************************************************* warnings.warn(message) FOUND: libraries = ['ptf77blas', 'ptcblas', 'atlas'] library_dirs = ['/usr/local/lib'] language = c define_macros = [('ATLAS_WITHOUT_LAPACK', None)] include_dirs = ['/usr/local/include'] running build_src building extension "atlas_version" sources adding 'build/src/atlas_version_0x1f56736.c' to sources. running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext lapack_info: NOT AVAILABLE scipy_core/scipy_distutils/system_info.py:916: UserWarning: Lapack (http://www.netlib.org/lapack/) libraries not found. Directories to search for the libraries can be specified in the scipy_distutils/site.cfg file (section [lapack]) or by setting the LAPACK environment variable. warnings.warn(LapackNotFoundError.__doc__) lapack_src_info: NOT AVAILABLE scipy_core/scipy_distutils/system_info.py:919: UserWarning: Lapack (http://www.netlib.org/lapack/) sources not found. Directories to search for the sources can be specified in the scipy_distutils/site.cfg file (section [lapack_src]) or by setting the LAPACK_SRC environment variable. warnings.warn(LapackSrcNotFoundError.__doc__) NOT AVAILABLE Traceback (most recent call last): File "setup.py", line 110, in ? setup_package(ignore_packages) File "setup.py", line 83, in setup_package ignore_packages = ignore_packages) File "scipy_core/scipy_distutils/misc_util.py", line 459, in get_subpackages config = setup_module.configuration(*args) File "/tmp/py-scipy/work/SciPy_complete-0.3/Lib/linalg/setup_linalg.py", line 40, in configuration raise NotFoundError,'no lapack/blas resources found' scipy_distutils.system_info.NotFoundError: no lapack/blas resources found -- Pi seconds is a nanocentury. --- Tom Duff

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Citing SciPy
by Prabhu Ramachandran June 4, 2004

June 4, 2004

Hi, I cite SciPy in my Thesis and need to specify the authors and a year. This is what I have so far: @Misc{, title = {{SciPy}: Open source scientific tools for {Python}}, url = "http://www.scipy.org/" } The bibliography style I use (natbib) requires a year and author names. Any recommendations for these fields? FWIW, this is what I use for SWIG and Python: @Misc{, author = {Guido van Rossum and others}, title = {The {Python} programming language}, year = {1991--}, url = "http://www.python.org/" } @Misc{, author = {David Beazley and others}, title = {{SWIG}: Simplified Wrapper and Interface Generator}, year = {1995--}, url = "http://www.swig.org" } Thanks. prabhu

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One test failed in current CVS
by Fernando Perez June 3, 2004

June 3, 2004

Hi all, after Robert's help, I got current CVS to successfully build on a Fedora Core 2 box, using the scipy ATLAS libs for P4 with HT. Running the level=10 tests gives me a single failure: ====================================================================== FAIL: check_expon (scipy.stats.morestats.test_morestats.test_anderson) ---------------------------------------------------------------------- Traceback (most recent call last): File "scipy/stats/tests/test_morestats.py", line 55, in check_expon assert_array_less(A, crit[-2:]) File "scipy_test/testing.py", line 705, in assert_array_less assert cond,\ AssertionError: Arrays are not less-ordered (mismatch 100.0%): Array 1: 3.20099820806 Array 2: [ 1.587 1.9339999999999999] ---------------------------------------------------------------------- Ran 950 tests in 106.527s FAILED (failures=1) I figured it was worth reporting it here. Best, f

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Problem with shared libraries
by Fernando Perez June 3, 2004

June 3, 2004

Hi all, today I tried to build current CVS scipy on a new Fedora Core 2 system, and I'm running into a problem. I think the gist of it has already been seen by Eric here: http://www.scipy.net/pipermail/scipy-dev/2002-April/000836.html albeit in a slightly different incarnation. The symptom is: In [1]: import linalg --------------------------------------------------------------------------- ImportError Traceback (most recent call last) /usr/local/installers/src/scipy/build/lib.linux-i686-2.3/scipy/<console> /usr/local/installers/src/scipy/build/lib.linux-i686-2.3/scipy/scipy/linalg/__init__.py 6 --------------------- 7 ----> 8 """ 9 # Modules to import under the scipy namespace 10 from scipy_version import scipy_version as __version__ /usr/local/installers/src/scipy/build/lib.linux-i686-2.3/scipy/scipy/linalg/basic.py /usr/local/installers/src/scipy/build/lib.linux-i686-2.3/scipy/scipy/linalg/lapack.py ImportError: linalg/clapack.so: undefined symbol: clapack_sgesv And I think I know why it's happening: I installed the ATLAS binaries from scipy.org on my system, putting them in /usr/lib, _including_ the modified lapack/blas libraries. However, in /usr/lib Fedora also provides shared libraries (.so) for lapack and blas. I guess that the build is getting confused, picking up the shared libraries at build time. I can't put the libs from the Atlas pack in /usr/local/lib, because this directory is NFS-shared by several clients, all with different architectures (Pentium-3, P-4 wihout HT, P-4 with HT, dual-P4, etc). So I want the Atlas library set provided by scipy to go into each client's own /usr/lib, leaving /usr/local/lib for things which aren't so cpu-sensitive as Atlas. Can anyone suggest a way out of this problem? Thanks in advance for any suggestions, Fernando

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