Mailman 3 February 2006 - SciPy-User

Where do I put site.cfg? What should it contain? Can I build w/o atlas?
by skip＠pobox.com Feb. 16, 2006

Feb. 16, 2006

I'm trying to build numpy an svn sandbox (just updated a couple minutes ago). If I grub around in numpy/distutils/system_info.py it says something about creating a site.cfg file with (for example) information about locating atlas. It says nothing about where this file belongs. I took a stab and placed it in my numpy source tree, right next to setup.py, with these lines: [atlas] library_dirs = /home/titan/skipm/src/ATLAS/lib/SunOS_Babe include_dirs = /home/titan/skipm/src/ATLAS/include/SunOS_Babe # for overriding the names of the atlas libraries atlas_libs = lapack, f77blas, cblas, atlas I then verified that those directories exist, contain apparently useful contents, and that I didn't have a conflicting environment variable named ATLAS: % ls /home/titan/skipm/src/ATLAS/lib/SunOS_Babe Make.inc libatlas.a libf77blas.a libtstatlas.a Makefile libcblas.a liblapack.a % ls /home/titan/skipm/src/ATLAS/include/SunOS_Babe atlas_buildinfo.h atlas_dmv.h atlas_smvT.h atlas_zr1.h atlas_cNCmm.h atlas_dmvN.h atlas_sr1.h atlas_zsysinfo.h atlas_cacheedge.h atlas_dmvS.h atlas_ssysinfo.h atlas_ztrsmXover.h atlas_cmv.h atlas_dmvT.h atlas_strsmXover.h cXover.h atlas_cmvN.h atlas_dr1.h atlas_trsmNB.h cmm.h atlas_cmvS.h atlas_dsysinfo.h atlas_type.h dXover.h atlas_cmvT.h atlas_dtrsmXover.h atlas_zNCmm.h dmm.h atlas_cr1.h atlas_sNCmm.h atlas_zmv.h sXover.h atlas_csysinfo.h atlas_smv.h atlas_zmvN.h smm.h atlas_ctrsmXover.h atlas_smvN.h atlas_zmvS.h zXover.h atlas_dNCmm.h atlas_smvS.h atlas_zmvT.h zmm.h % env | grep ATLAS % Then I tried "python setup.py build": Script started on Wed Feb 15 13:23:21 2006 babe:% python setup.py build Running from numpy source directory. No module named __svn_version__ F2PY Version 2_2110 blas_opt_info: blas_mkl_info: NOT AVAILABLE atlas_blas_threads_info: Setting PTATLAS=ATLAS Setting PTATLAS=ATLAS Setting PTATLAS=ATLAS FOUND: libraries = ['ptf77blas', 'ptcblas', 'atlas'] library_dirs = ['/opt/lib'] language = c include_dirs = ['/opt/include'] running build_src building extension "atlas_version" sources adding 'build/src/atlas_version_0x4568501b.c' to sources. running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext building 'atlas_version' extension compiling C sources gcc options: '-fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC' compile options: '-I/opt/include -Inumpy/core/include -I/opt/app/g++lib6/python-2.4/include/python2.4 -c' /opt/lang/gcc-3.4/bin/gcc -shared build/temp.solaris-2.8-i86pc-2.4/build/src/atlas_version_0x4568501b.o -L/opt/lib -lptf77blas -lptcblas -latlas -o build/temp.solaris-2.8-i86pc-2.4/atlas_version.so Text relocation remains referenced against symbol offset in file <unknown> 0x7 /opt/lib/libatlas.a(ATL_buildinfo.o) <unknown> 0xc /opt/lib/libatlas.a(ATL_buildinfo.o) <unknown> 0x11 /opt/lib/libatlas.a(ATL_buildinfo.o) <unknown> 0x16 /opt/lib/libatlas.a(ATL_buildinfo.o) How come distutils is ignoring my site.cfg file? Neither of these commands: python setup.py --help python setup.py build --help mention site.cfg. Failing all this, is there some way to build numpy/scipy without atlas? At this point I just want the damn thing to build. I'll worry about performance later (if at all). Thx, -- Skip Montanaro http://www.musi-cal.com/ skip(a)pobox.com

4 9

round off errors
by Ryan Krauss Feb. 15, 2006

Feb. 15, 2006

I am trying to understand the effects of round off error and floating point arithmetic on my research. I am reading through "What Every Computer Scientist Should Know About Floating-Point Arithmetic" and have some questions on my understanding of it and how it applies to SciPy/NumPy. My specific problem has to do with trying to find the roots of (sinh(b)+sin(b))**2-(sinh(b)-sin(b))**2 and other problematic expressions. (Acutually it is more like the determinant of mat[0,0]=(a/b)*(sinh(b)+sin(b) mat[0,1]=-a**2*d/(b**3)*(sinh(b)-sin(b)) mat[1,0]=b/d*(sinh(b)-sin(b)) mat[1,1]=-(a/b)*(sinh(b)-sin(b)) It turns out that with some symbolic manipulation, this can be rearranged to trying to find the roots of sinh(b)*sin(b) which is much better behaved. How will SciPy handle sinh(b)+ (or -) sin(b) when sinh(b) is very large and sin(b) is obviously between +/-1? As I understand it, the IEEE standard requires exact rounding for this operation which seems difficult and costly to me. What I am seeing is that when the determinant whose zeros I need to find is symbolically rearrange to sinh(b)*sin(b), the curve is smooth and has well defined places where it goes very near zero (I actually need to look for minima of the abs of this value in real problems because the results are complex valued). Note that this symbolic rearrangement might only be possible for simple systems. I am analyzing this simple system to get a handle on these errors. If I don't do the symbolic rearrangement, the determinant curve is very noisy for increasing b and the determinant might have a local minima, but that minima is not very close to zero. Is there a way to create a single precision number and do single precision math so that I can compare good and bad answers to each step in this problem (i.e. for a certain range of b, I could consider the double precision value to be "exact" and see what problems are arising because of round-off). I am trying to justify a pragmatic approach to this problem. Assuming that the expression is too complicated to look at and pick out floating-point problems and rearrange it, I want to be able to say that I can trust the roots (actually minima) if the following are true: 1. You plot the function you are trying to find minima of and it doesn't look noisy over the range of input values you are concerned with 2. The value of the expression at the minima is actually fairly small 3. Numerical searching starting at points in a region around the minima all converge to the same minima (basically there is a sort of numerical domain of attraction) Does this seem valid? I am a mechanical engineer and neither a computer scientist nor a mathematician. So, I don't know if I can or want to prove this rigidly, but I want to be convinced and convince my thesis committee at least that it is trust-worthy. My biggest fear is this: is there a case where floating-point precision problems would lead to well-behaved, stable, WRONG answers? Especially for cases involving trying to find small differences between large numbers like (a-b)**2-(a+b) for a>>>>b. Thanks for any thoughts on how to think about this, Ryan

2 1

Telling setup.py where to find stuff
by Otto Maddox Feb. 15, 2006

Feb. 15, 2006

I'm having a few troubles getting SciPy built, mostly due to mixing and matching compilers out of necessity. I installed Python 2.4.2 from source using Apple's GCC 4. Then, to get g77, installed GCC 3.4.5 from source into /opt/local/gcc34 (normally not in my PATH). Numpy 0.9.4 seemed to install fine by doing F77=/opt/local/gcc34/bin/g77 python setup.py install The problem is that the same thing doesn't work for getting SciPy's setup.py to find g77. Also, I do not know how to tell it where my fftw lives (under /opt/local/lib, /opt/local/include). Does anybody have any advice, please? -- http://www.fastmail.fm - Access all of your messages and folders wherever you are

3 2

scipy install fails: numpy.ndarray
by James K. Gruetzner Feb. 15, 2006

Feb. 15, 2006

Any ideas how to correct this? I've just installed scipy 0.4.4, and am having some problems with it. The key appears to be in the references to numpy.ndarray. When running scipy.test(level=0), numerous errors of: AttributeError: 'numpy.ndarray' object has no attribute 'dtypechar' Installation of scipy 0.4.4 does have many warnings, but appears to complete OK. - Many warnings that variables "might be used uninitialized" in various functions. - Many warnings that "ignoring return value of 'fscanf'" - Several warnings that "POSIX_C_SOURCE" redefined. - Many "unused variable" warnings Information follows below. Thanks in advance. James ---------------------------- system/platform: posix linux2 Fedora Core 4 python 2.4.1 numpy 0.9.4 LAPACK ATLAS 3.7.11 NOTE 1 gcc 4.0.2 fftw 3.0.1 1. Installed in the local tree. In ../scipy/Lib/linalg, the command python setup_atlas_version.py build_ext --inplace --force fails with the error message: /usr/lib/python2.4/site-packages/numpy/distutils/misc_util.py:896: UserWarning: Use Configuration('linalg','',top_path=None) instead of deprecated default_config_dict('linalg','',None) warnings.warn('Use Configuration(%s,%s,top_path=%s) instead of '\ Traceback (most recent call last): File "setup_atlas_version.py", line 29, in ? setup(**configuration()) File "setup_atlas_version.py", line 13, in configuration del config['fortran_libraries'] KeyError: 'fortran_libraries' ----------------- Output of python INSTALLDIR/numpy/distutils/system_info.py command: _pkg_config_info: NOT AVAILABLE agg2_info: ( src_dirs = .:/usr/local/src ) NOT AVAILABLE atlas_blas_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( paths: /usr/local/lib/atlas ) ( paths: /usr/lib/sse2 ) ( paths: /usr/local/lib/atlas/libf77blas.a ) ( paths: /usr/local/lib/atlas/libcblas.a ) ( paths: /usr/local/lib/atlas/libatlas.a ) ( include_dirs = /usr/local/include:/usr/include ) ( library_dirs = /usr/local/lib:/usr/lib ) ( paths: /usr/local/lib/atlas ) ( paths: /usr/lib/sse2 ) FOUND: libraries = ['f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/local/lib/atlas'] language = c atlas_blas_threads_info: Setting PTATLAS=ATLAS ( library_dirs = /usr/local/lib:/usr/lib ) ( paths: /usr/local/lib/atlas ) ( paths: /usr/lib/sse2 ) ( paths: /usr/local/lib/atlas/libatlas.a ) NOT AVAILABLE atlas_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( paths: /usr/local/lib/atlas ) ( paths: /usr/lib/sse2 ) ( paths: /usr/local/lib/atlas/libf77blas.a ) ( paths: /usr/local/lib/atlas/libcblas.a ) ( paths: /usr/local/lib/atlas/libatlas.a ) ( paths: /usr/local/lib/atlas/liblapack.a ) system_info.atlas_info ( include_dirs = /usr/local/include:/usr/include ) ( library_dirs = /usr/local/lib:/usr/lib ) ( paths: /usr/local/lib/atlas ) ( paths: /usr/lib/sse2 ) FOUND: libraries = ['lapack', 'f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/local/lib/atlas'] language = f77 atlas_threads_info: Setting PTATLAS=ATLAS ( library_dirs = /usr/local/lib:/usr/lib ) ( paths: /usr/local/lib/atlas ) ( paths: /usr/lib/sse2 ) ( paths: /usr/local/lib/atlas/libatlas.a ) system_info.atlas_threads_info NOT AVAILABLE blas_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( paths: /usr/local/lib/libblas.a ) ( library_dirs = /usr/local/lib:/usr/lib ) FOUND: libraries = ['blas'] library_dirs = ['/usr/local/lib'] language = f77 blas_mkl_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( include_dirs = /usr/local/include:/usr/include ) NOT AVAILABLE blas_opt_info: running build_src building extension "atlas_version" sources adding 'build/src/atlas_version_-0x32261224.c' to sources. running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext ( library_dirs = /usr/local/lib:/usr/lib ) FOUND: libraries = ['f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/local/lib/atlas'] language = c define_macros = [('ATLAS_INFO', '"\\"3.7.11\\""')] blas_src_info: ( src_dirs = .:/usr/local/src ) NOT AVAILABLE boost_python_info: ( src_dirs = .:/usr/local/src ) NOT AVAILABLE dfftw_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( include_dirs = /usr/local/include:/usr/include ) dfftw not found NOT AVAILABLE dfftw_threads_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( include_dirs = /usr/local/include:/usr/include ) dfftw threads not found NOT AVAILABLE djbfft_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( include_dirs = /usr/local/include:/usr/include ) NOT AVAILABLE fft_opt_info: fftw3_info: FOUND: libraries = ['fftw3'] library_dirs = ['/usr/local/lib'] define_macros = [('SCIPY_FFTW3_H', None)] include_dirs = ['/usr/local/include'] ( library_dirs = /usr/local/lib:/usr/lib ) FOUND: libraries = ['fftw3'] library_dirs = ['/usr/local/lib'] define_macros = [('SCIPY_FFTW3_H', None)] include_dirs = ['/usr/local/include'] fftw2_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( include_dirs = /usr/local/include:/usr/include ) fftw2 not found NOT AVAILABLE fftw_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( include_dirs = /usr/local/include:/usr/include ) ( paths: /usr/local/lib/libfftw3.a ) ( paths: /usr/local/include/fftw3.h ) ( library_dirs = /usr/local/lib:/usr/lib ) FOUND: libraries = ['fftw3'] library_dirs = ['/usr/local/lib'] define_macros = [('SCIPY_FFTW3_H', None)] include_dirs = ['/usr/local/include'] fftw_threads_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( include_dirs = /usr/local/include:/usr/include ) fftw threads not found NOT AVAILABLE freetype2_info: ( library_dirs = /usr/local/lib:/usr/lib ) FOUND: libraries = ['freetype', 'z'] define_macros = [('FREETYPE2_INFO', '"\\"9.7.3\\""'), ('FREETYPE2_VERSION_9_7_3', None)] include_dirs = ['/usr/include/freetype2'] gdk_2_info: ( library_dirs = /usr/local/lib:/usr/lib ) FOUND: libraries = ['gdk-x11-2.0', 'gdk_pixbuf-2.0', 'm', 'pangoxft-1.0', 'pangox-1.0', 'pango-1.0', 'gobject-2.0', 'gmodule-2.0', 'dl', 'glib-2.0'] define_macros = [('GDK_2_INFO', '"\\"2.6.10\\""'), ('GDK_VERSION_2_6_10', None), ('XTHREADS', None), ('_REENTRANT', None), ('XUSE_MTSAFE_API', None)] include_dirs = ['/usr/include/gtk-2.0', '/usr/lib/gtk-2.0/include', '/usr/X11R6/include', '/usr/include/pango-1.0', '/usr/include/freetype2', '/usr/include/freetype2/config', '/usr/include/glib-2.0', '/usr/lib/glib-2.0/include'] gdk_info: ( library_dirs = /usr/local/lib:/usr/lib ) FOUND: libraries = ['gdk', 'Xi', 'Xext', 'X11', 'm', 'glib'] library_dirs = ['/usr/X11R6/lib'] define_macros = [('GDK_INFO', '"\\"1.2.10\\""'), ('GDK_VERSION_1_2_10', None)] include_dirs = ['/usr/include/gtk-1.2', '/usr/X11R6/include', '/usr/include/glib-1.2', '/usr/lib/glib/include'] gdk_pixbuf_2_info: ( library_dirs = /usr/local/lib:/usr/lib ) FOUND: libraries = ['gdk_pixbuf-2.0', 'm', 'gobject-2.0', 'gmodule-2.0', 'dl', 'glib-2.0'] define_macros = [('GDK_PIXBUF_2_INFO', '"\\"2.6.10\\""'), ('GDK_PIXBUF_VERSION_2_6_10', None)] include_dirs = ['/usr/include/gtk-2.0', '/usr/include/glib-2.0', '/usr/lib/glib-2.0/include'] gdk_pixbuf_xlib_2_info: ( library_dirs = /usr/local/lib:/usr/lib ) FOUND: libraries = ['gdk_pixbuf_xlib-2.0', 'gdk_pixbuf-2.0', 'm', 'gobject-2.0', 'gmodule-2.0', 'dl', 'glib-2.0'] extra_link_args = ['-Wl,--export-dynamic'] define_macros = [('GDK_PIXBUF_XLIB_2_INFO', '"\\"2.6.10\\""'), ('GDK_PIXBUF_XLIB_VERSION_2_6_10', None)] include_dirs = ['/usr/include/gtk-2.0', '/usr/include/glib-2.0', '/usr/lib/glib-2.0/include'] gdk_x11_2_info: ( library_dirs = /usr/local/lib:/usr/lib ) FOUND: libraries = ['gdk-x11-2.0', 'gdk_pixbuf-2.0', 'm', 'pangoxft-1.0', 'pangox-1.0', 'pango-1.0', 'gobject-2.0', 'gmodule-2.0', 'dl', 'glib-2.0'] define_macros = [('GDK_X11_2_INFO', '"\\"2.6.10\\""'), ('GDK_X11_VERSION_2_6_10', None), ('XTHREADS', None), ('_REENTRANT', None), ('XUSE_MTSAFE_API', None)] include_dirs = ['/usr/include/gtk-2.0', '/usr/lib/gtk-2.0/include', '/usr/X11R6/include', '/usr/include/pango-1.0', '/usr/include/freetype2', '/usr/include/freetype2/config', '/usr/include/glib-2.0', '/usr/lib/glib-2.0/include'] gtkp_2_info: ( library_dirs = /usr/local/lib:/usr/lib ) FOUND: libraries = ['gtk-x11-2.0', 'gdk-x11-2.0', 'atk-1.0', 'gdk_pixbuf-2.0', 'm', 'pangoxft-1.0', 'pangox-1.0', 'pango-1.0', 'gobject-2.0', 'gmodule-2.0', 'dl', 'glib-2.0'] define_macros = [('GTKP_2_INFO', '"\\"2.6.10\\""'), ('GTK_VERSION_2_6_10', None), ('XTHREADS', None), ('_REENTRANT', None), ('XUSE_MTSAFE_API', None)] include_dirs = ['/usr/include/gtk-2.0', '/usr/lib/gtk-2.0/include', '/usr/X11R6/include', '/usr/include/atk-1.0', '/usr/include/pango-1.0', '/usr/include/freetype2', '/usr/include/freetype2/config', '/usr/include/glib-2.0', '/usr/lib/glib-2.0/include'] gtkp_x11_2_info: ( library_dirs = /usr/local/lib:/usr/lib ) FOUND: libraries = ['gtk-x11-2.0', 'gdk-x11-2.0', 'atk-1.0', 'gdk_pixbuf-2.0', 'm', 'pangoxft-1.0', 'pangox-1.0', 'pango-1.0', 'gobject-2.0', 'gmodule-2.0', 'dl', 'glib-2.0'] define_macros = [('GTKP_X11_2_INFO', '"\\"2.6.10\\""'), ('GTK_X11_VERSION_2_6_10', None), ('XTHREADS', None), ('_REENTRANT', None), ('XUSE_MTSAFE_API', None)] include_dirs = ['/usr/include/gtk-2.0', '/usr/lib/gtk-2.0/include', '/usr/X11R6/include', '/usr/include/atk-1.0', '/usr/include/pango-1.0', '/usr/include/freetype2', '/usr/include/freetype2/config', '/usr/include/glib-2.0', '/usr/lib/glib-2.0/include'] lapack_atlas_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( paths: /usr/local/lib/atlas ) ( paths: /usr/lib/sse2 ) ( paths: /usr/local/lib/atlas/libf77blas.a ) ( paths: /usr/local/lib/atlas/libcblas.a ) ( paths: /usr/local/lib/atlas/libatlas.a ) system_info.lapack_atlas_info NOT AVAILABLE lapack_atlas_threads_info: Setting PTATLAS=ATLAS ( library_dirs = /usr/local/lib:/usr/lib ) ( paths: /usr/local/lib/atlas ) ( paths: /usr/lib/sse2 ) ( paths: /usr/local/lib/atlas/libatlas.a ) system_info.lapack_atlas_threads_info NOT AVAILABLE lapack_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( paths: /usr/local/lib/liblapack.a ) ( library_dirs = /usr/local/lib:/usr/lib ) FOUND: libraries = ['lapack'] library_dirs = ['/usr/local/lib'] language = f77 lapack_mkl_info: mkl_info: NOT AVAILABLE NOT AVAILABLE lapack_opt_info: running build_src building extension "atlas_version" sources adding 'build/src/atlas_version_0x39ddef23.c' to sources. running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext customize GnuFCompiler customize GnuFCompiler customize GnuFCompiler using build_ext ( library_dirs = /usr/local/lib:/usr/lib ) FOUND: libraries = ['lapack', 'f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/local/lib/atlas'] language = f77 define_macros = [('ATLAS_INFO', '"\\"3.7.11\\""')] lapack_src_info: ( src_dirs = .:/usr/local/src ) ( paths: /usr/local/src/LAPACK/SRC ) ( library_dirs = /usr/local/lib:/usr/lib ) FOUND: sources = ['/usr/local/src/LAPACK/SRC/sbdsdc.f', '/usr/local/src/LAPAC ... ... /LAPACK/SRC/izmax1.f', '/usr/local/src/LAPACK/SRC/dzsum1.f'] language = f77 numarray_info: ( include_dirs = /usr/include/python2.4 ) ( paths: /usr/include/python2.4/numarray/arrayobject.h ) ( library_dirs = ) FOUND: define_macros = [('NUMARRAY_VERSION', '"\\"1.5.1\\""'), ('NUMARRAY', None)] include_dirs = ['/usr/include/python2.4'] numpy_info: ( include_dirs = /usr/include/python2.4 ) ( library_dirs = ) FOUND: define_macros = [('NUMPY_VERSION', '"\\"0.9.4\\""'), ('NUMPY', None)] sfftw_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( include_dirs = /usr/local/include:/usr/include ) sfftw not found NOT AVAILABLE sfftw_threads_info: ( library_dirs = /usr/local/lib:/usr/lib ) ( include_dirs = /usr/local/include:/usr/include ) sfftw threads not found 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/lib ) ( include_dirs = /usr/X11R6/include:/usr/include ) ( paths: /usr/X11R6/lib/libX11.so ) ( paths: /usr/X11R6/include/X11/X.h ) ( library_dirs = /usr/X11R6/lib:/usr/lib ) FOUND: libraries = ['X11'] library_dirs = ['/usr/X11R6/lib'] include_dirs = ['/usr/X11R6/include'] xft_info: ( library_dirs = /usr/local/lib:/usr/lib ) FOUND: libraries = ['Xft', 'X11', 'freetype', 'Xrender', 'fontconfig'] library_dirs = ['/usr/X11R6/lib'] define_macros = [('XFT_INFO', '"\\"2.1.2.2\\""'), ('XFT_VERSION_2_1_2_2', None)] include_dirs = ['/usr/X11R6/include', '/usr/include/freetype2', '/usr/include/freetype2/config']

3 4

scipy_base
by Bruce Feb. 14, 2006

Feb. 14, 2006

Hi, Im new to scipy. I installed it and it seems to work, at least I can >>> import scipy The tutorial at scipy.org/Wiki immediately start talking about the package scipy_base but I can`t seem to find it. What`s that about? thx

2 2

SciPy on mandriva
by manouchk Feb. 14, 2006

Feb. 14, 2006

I'm wondering if there are SciPy mandriva users. I'm quite new to python and SciPy. It seems that mandriva have obsolete scientific related python packages. python-SciPy-0.3.2-5mdk.src.rpm python-numarray-1.5.1-1mdk.src.rpm python-scientific-2.4.9-5mdk.src.rpm python-numeric-24.0-2mdk.src.rpm aparently mandriva still didn't switch to NumPy, it seems that matplotlib is not included etc... I've seen numpy provides a src.rpm packages that could be probably installed. Can NumPy be installed in conjonction with numeric? or must replace numeric? I'm wondering if there are some "clean" src.rpm for mandriva somewhere for all thoose packages (matplotlib, NumPy, SciPy) in their recent version? (if not I could work on them!) thank you, Emmanuel Favre-Nicolin

2 3

Re: [SciPy-user] Sparse matrix questions
by Ed Schofield Feb. 14, 2006

Feb. 14, 2006

Nils Wagner wrote: >from scipy.sparse import * >from scipy import * > >A = rand(4,4) >sparseA = csc_matrix(A) ># ># How can I build the norm of a sparse matrix without using todense ? ># >eps = linalg.norm(sparseA.todense()) > > This is a non-trivial problem, and I don't think we have a function for it. Could you write one and contribute it? ;) ># How do I scale a sparse matrix object ? ># >#sparseA = sparseA/0.5 # doesn't work > > > Interesting. I'll fix this in SVN. For now, just use multiplication instead: >>> sparseA *= 2.0 ># How do I initialize a sparse matrix of order n \times m with zeros ># >B = zeros((4,5),Float) >#sparseB = csc_matrix(B) # doesn't work > > It's filled with zeros already. Just use >>> sparseB = csc_matrix((4,5)) But for efficiency I suggest you use dok_matrix to construct and manipulate matrices, then convert to csc or csr for solvers or matrix multiplication. For diagonals, you can use dok_matrix.setdiag(): >>> sparseB = dok_matrix((5,5)) >>> sparseB.setdiag([1]*5) >>> sparseB.todense() array([[ 1., 0., 0., 0., 0.], [ 0., 1., 0., 0., 0.], [ 0., 0., 1., 0., 0.], [ 0., 0., 0., 1., 0.], [ 0., 0., 0., 0., 1.]]) I hope this helps. In the future, please post questions like these on the scipy-user list, not on scipy-dev :) -- Ed

2 1

Using C code in scipy-best practice
by Jose Luis Gomez Dans Feb. 14, 2006

Feb. 14, 2006

Hi! After using f2py to be able to call some Fortran 77 code from Python, I now have a need to do the same with some C function. I was wondering what the best practice is to wrap this function into some Python callable object. I read a number of different approaches are possible, but while with f2py I know what to expect, with C, it appears that SWIG, or Pyrex, or...? Many thanks! -- 10 GB Mailbox, 100 FreeSMS/Monat http://www.gmx.net/de/go/topmail +++ GMX - die erste Adresse f�r Mail, Message, More +++

2 2

wiki problem
by Gary Ruben Feb. 14, 2006

Feb. 14, 2006

The AstroPy link on the Topical_Software page is broken. The original AstroPy page says "AstroPy has moved to this page on SciPy's wiki site (at their request)." but it isn't there. Gary R.

2 1

Variable precision
by Ryan Krauss Feb. 13, 2006

Feb. 13, 2006

Is there anyway to constrain optimize.fmin to use single precision or even fewer digits in its internal calculations? I am trying to show that one approach to a problem is less prone to round off errors than another approach, but the results aren't all that dramatic with double precision numbers. Thanks, Ryan

1 0