Mailman 3 November 2007 - SciPy-User

weave inline compile error
by Michael ODonnell 28 Nov '07

28 Nov '07

I have been trying to use scipy.weave.inline on Windows XP via cygwin. Ultimately, I need to use weave.inline for compiling c++ code nested in python program. However, I have been extremely unsuccessful at getting this to work. I recently posted some errors on this site, which are subject under "weave and compiler install help". Basically, I have not been able to find out anything else, but let me summarize: First, I am using these versions, but note I have tried to use the most recent stable release of python enthought: I created a distutils.cfg file specifying [build_ext] compiler=mingw32 python-2.4.1.msi scipy-0.6.0.win32-py2.4.exe Numeric-24.2.win32-py2.4.exe numpy-1.04.win32-py2.4.exe wxPython2.8-win32-unicode-2.8.6.1-py24.exe and wxPython2.8-win32-docs-demos-2.8.6.1.exe As well as a couple other packages cygwin: setup.exe (current) mingw-install-20060210.tar (MSYS) and MinGW-5.1.3.exe (I read online that these do not work with 2.4.1 so I am focusing with cygwin) An example of weave that I am trying to get to work is: a = 1 weave.inline('printf("%d\\n",a);',['a'], verbose=2, type_converters=converters.blitz, compiler='gcc') #I have tried numerous versions of this The error seems to be in the code written in the numpy\distutils\exec_command.py: s,o = exec_command(cmd) The best I can tell, is that the code is trying to execute the above command wich is failing to write output to s,o. These variables are then written to files, which cannot be read. The program jumps around between exec_command and _exec_command. I don't know python well enough to know what is causing the error. It appears to me that the code is being compiled, but this one line is not working. I also tried running the script written by exec_command.py directly (commented out the os.remove() in exec_command.py, but this did not work. It did help me identify that the problem is with s and o variables. Does anyone have any thoughts on what I should try to do. I appreciate any suggestions and ideas one can provide. Thanks! Michael Here is an example of my errors: running build_ext running build_src building extension "sc_552cccf5dbf4f6eadd273cdcbd5860525" sources customize Mingw32CCompiler customize Mingw32CCompiler using build_ext customize Mingw32CCompiler customize Mingw32CCompiler using build_ext building 'sc_552cccf5dbf4f6eadd273cdcbd5860525' extension compiling C++ sources C compiler: g++ -mno-cygwin -O2 -Wall compile options: '-IC:\Python24\lib\site-packages\scipy\weave -IC:\Python24\lib\site-packages\scipy\weave\scxx -IC:\Python24\lib\site-packages\numpy\core\include -IC:\Python24\include -IC:\Python24\PC -c' g++ -mno-cygwin -O2 -Wall -IC:\Python24\lib\site-packages\scipy\weave -IC:\Python24\lib\site-packages\scipy\weave\scxx -IC:\Python24\lib\site-packages\numpy\core\include -IC:\Python24\include -IC:\Python24\PC -c c:\temp\Michael\python24_compiled\sc_552cccf5dbf4f6eadd273cdcbd5860525.cpp -o c:\temp\Michael\python24_intermediate\compiler_c8350d870e6c54e8f29dd7094c2bfb45\Release\temp\michael\python24_compiled\sc_552cccf5dbf4f6eadd273cdcbd5860525.o Traceback (most recent call last): File "C:\Python24\Lib\site-packages\pythonwin\pywin\framework\scriptutils.py", line 310, in RunScript exec codeObject in __main__.__dict__ File "C:\Documents and Settings\Michael\Application Data\ESRI\ArcToolbox\scripts\test_weave.py", line 251, in ? main() File "C:\Documents and Settings\Michael\Application Data\ESRI\ArcToolbox\scripts\test_weave.py", line 205, in main weave.inline('printf("%d\\n",a);',['a'], verbose=2, type_converters=converters.blitz) #, compiler = 'gcc', verbpse=2, type_converters=converters.blitz, auto_downcast=0) #'msvc' or 'gcc' or 'mingw32' File "C:\Python24\Lib\site-packages\scipy\weave\inline_tools.py", line 338, in inline auto_downcast = auto_downcast, File "C:\Python24\Lib\site-packages\scipy\weave\inline_tools.py", line 447, in compile_function verbose=verbose, **kw) File "C:\Python24\Lib\site-packages\scipy\weave\ext_tools.py", line 365, in compile verbose = verbose, **kw) File "C:\Python24\Lib\site-packages\scipy\weave\build_tools.py", line 269, in build_extension setup(name = module_name, ext_modules = [ext],verbose=verb) File "C:\Python24\Lib\site-packages\numpy\distutils\core.py", line 176, in setup return old_setup(**new_attr) File "C:\Python24\lib\distutils\core.py", line 159, in setup raise SystemExit, error CompileError: error: c:\temp\tmpgnzrbr\buunmb.txt: No such file or directory ____________________________________________________________________________________ Be a better pen pal. Text or chat with friends inside Yahoo! Mail. See how. http://overview.mail.yahoo.com/

1 0

install numpy/scipy with Intel Compilers
by Laurence Viry 27 Nov '07

27 Nov '07

Hi! I try to install numpy 1.0.4 and scipy 0.6.0 with INTEL C/C++ and Fortran compilers and SCSL scientific library with python2.4.4 on Itanium with linux OS. (Altix SGI with SUSE linux) I didn't success to configure the construct of build_ext for scipy with the fortran INTEL compiler (--fcompiler=intele) * First, I set LD_LIBRARY_PATH and LD_RUN_PATH with directories which contains c/c++, fortran and SCSL libraries export LD_LIBRARY_PATH=/opt/intel/intel_cc/9.0.024/lib:/opt/intel/intel_fc/9.0.021/lib:/usr/lib Export LD_RUN_PATH=/opt/intel/intel_cc/9.0.024/lib:/opt/intel/intel_fc/9.0.021/lib:/usr/lib * I put in the file "site.cfg" : [DEFAULT] library_dirs = /usr/lib:/usr/local/lib/:/usr/local/stow/fftw-3.1.2/lib include_dirs = /usr/include:/usr/local/include:/usr/local/stow/fftw-3.1.2/include [blas] library_dirs = /usr/lib include_dirs=/usr/include blas_libs= scs [lapack] library_dirs = /usr/lib include_dirs=/usr/include lapack_libs = scs [fftw] libraries = fftw3 * Compile and install numpy with: python setup.py config --compiler=intel build_clib --compiler=intel build_ext --compiler=intel install It's Ok for numpy, it doesn'tt need fortran compiler but for scipy python setup.py -v config_cc --compiler=intele config_fc --fcompiler=intele build_clib --compiler=intele --fcompiler=intele build_ext --compiler=intele --fcompiler=intele install It's Ok for build_clib, the python script find c and fortran compiler it doesn't find fortran compiler for build_ext, first I had a warning warning: build_ext: f77_compiler=intele is not available, it was available for the construct of build_clib? ???? then warning: build_ext: extension 'scipy.fftpack._fftpack' has Fortran libraries but no Fortran linker found, using default linker for the construct of build_ext, the python script use the default fortran compiler g77 and the construct stoped with the message error: "extension 'scipy.interpolate.dfitpack' has Fortran sources but no Fortran compiler found" why --fcompiler=intele option of build_ext doesn't operate????????? I show this option of build_ext command with the python command python setup.py build_ext --help-fcompiler I set the variables F77, F90 , F77FLAGS with the intel compiler, I had the same error How can I configure the construct of build_ext for scipy with the Intel fortran compiler The solutions I found on the scipy archives didn't work Thank for your help -- Laurence Viry CRIP UJF - Projet MIRAGE ( http://mirage.imag.fr ) Laboratoire de Modélisation et Calcul - IMAG tel: 04 76 63 56 34 fax: 04 76 63 12 63 e-mail: Laurence.Viry(a)imag.fr

3 3

pdf of multivariate normal
by John Reid 27 Nov '07

27 Nov '07

Am I right that this doesn't exist in scipy/numpy? Obviously it isn't too hard to code myself but I was surprised it wasn't there. If it is there, how could I have found it easily? John.

5 5

Installation of time series failed on windows
by Tim Michelsen 26 Nov '07

26 Nov '07

Hello, I tried to install the time-series package from the sandbox on my windows. It failed while maskarray was installed nicely. May someone please help me here? Here's a log from IPython when running the setup.py install Ignoring attempt to set 'name' (from 'timeseries' to 'timeseries.lib') Warning: Assuming default configuration (.\tests/{setup_tests,setup}.py was not found) Appending timeseries.tests configuration to timeseries Ignoring attempt to set 'name' (from 'timeseries' to 'timeseries.tests') running install running build running config_cc unifing config_cc, config, build_clib, build_ext, build commands --compiler options running config_fc unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options running build_src building extension "timeseries.cseries" sources running build_py copying .\ipython_log.py -> build\lib.win32-2.5\timeseries running build_ext No module named msvccompiler in numpy.distutils, trying from distutils.. <type 'exceptions.SystemExit'>: error: Python was built with Visual Studio 2003; extensions must be built with a compiler than can generate compatible binaries. Visual Studio 2003 was not found on this system. If you have Cygwin installed, you can try compiling with MingW32, by passing "-c mingw32" to setup.py. WARNING: Failure executing file: <setup.py> Thanks. Tim

2 1

scipy 0.6 installation problem
by Yutec Sun 25 Nov '07

25 Nov '07

Hello, I'd like to ask your favor for helping me install scipy 0.6. I have a problem importing scipy. In fact, importing doesn't show an error message, but scipy.test produces failures. My OS is Ubuntu 7.10 (Gutsy Gibbon) amd64. Following the installation instruction, I attach the messages for further information. Please understand that I'm new to linux system and scipy, and let me know how to successfully install scipy step by step. I thank you for your help. Best regards, Yutec -------------------------------------------------------------------------------------------------------------- 1. Error message -------------------------------------------------------------------------------------------------------------- yutec@yutec-laptop:/usr/lib/python2.5/site-packages/numpy/distutils$ python Python 2.5.1 (r251:54863, Oct 5 2007, 13:50:07) [GCC 4.1.3 20070929 (prerelease) (Ubuntu 4.1.2-16ubuntu2)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import scipy >>> scipy.test(level=1) Found 9/9 tests for scipy.cluster.vq Found 18/18 tests for scipy.fftpack.basic Found 4/4 tests for scipy.fftpack.helper Found 20/20 tests for scipy.fftpack.pseudo_diffs Found 1/1 tests for scipy.integrate Found 10/10 tests for scipy.integrate.quadpack Found 3/3 tests for scipy.integrate.quadrature Found 6/6 tests for scipy.interpolate Found 6/6 tests for scipy.interpolate.fitpack Found 4/4 tests for scipy.io.array_import Found 28/28 tests for scipy.io.mio Found 13/13 tests for scipy.io.mmio Found 5/5 tests for scipy.io.npfile Found 4/4 tests for scipy.io.recaster Found 16/16 tests for scipy.lib.blas Found 128/128 tests for scipy.lib.blas.fblas Found 42/42 tests for scipy.lib.lapack Found 41/41 tests for scipy.linalg.basic <module 'scipy.linalg.fblas' from '/usr/lib/python2.5/site-packages/scipy/linalg/fblas.so'> Found 16/16 tests for scipy.linalg.blas Found 72/72 tests for scipy.linalg.decomp Found 128/128 tests for scipy.linalg.fblas Found 6/6 tests for scipy.linalg.iterative Found 4/4 tests for scipy.linalg.lapack Found 7/7 tests for scipy.linalg.matfuncs Found 9/9 tests for scipy.linsolve.umfpack Found 2/2 tests for scipy.maxentropy Found 3/3 tests for scipy.misc.pilutil Found 399/399 tests for scipy.ndimage Found 5/5 tests for scipy.odr Found 8/8 tests for scipy.optimize Found 1/1 tests for scipy.optimize.cobyla Found 10/10 tests for scipy.optimize.nonlin Found 4/4 tests for scipy.optimize.zeros Found 5/5 tests for scipy.signal.signaltools Found 4/4 tests for scipy.signal.wavelets Found 152/152 tests for scipy.sparse Found 342/342 tests for scipy.special.basic Found 3/3 tests for scipy.special.spfun_stats Found 107/107 tests for scipy.stats Found 73/73 tests for scipy.stats.distributions Found 10/10 tests for scipy.stats.morestats Found 0/0 tests for __main__ /usr/lib/python2.5/site-packages/scipy/cluster/vq.py:477: UserWarning: One of the clusters is empty. Re-run kmean with a different initialization. warnings.warn("One of the clusters is empty. " ...exception raised as expected: One of the clusters is empty. Re-run kmean with a different initialization. ................................................Residual: 1.05006987327e-07 ..................../usr/lib/python2.5/site-packages/scipy/interpolate/fitpack2.py:458: UserWarning: The coefficients of the spline returned have been computed as the minimal norm least-squares solution of a (numerically) rank deficient system (deficiency=7). If deficiency is large, the results may be inaccurate. Deficiency may strongly depend on the value of eps. warnings.warn(message) ...... Don't worry about a warning regarding the number of bytes read. Warning: 1000000 bytes requested, 20 bytes read. .........................................................................caxpy:n=4 ..caxpy:n=3 ....ccopy:n=4 ..ccopy:n=3 .............cscal:n=4 ....cswap:n=4 ..cswap:n=3 .....daxpy:n=4 ..daxpy:n=3 ....dcopy:n=4 ..dcopy:n=3 .............dscal:n=4 ....dswap:n=4 ..dswap:n=3 .....saxpy:n=4 ..saxpy:n=3 ....scopy:n=4 ..scopy:n=3 .............sscal:n=4 ....sswap:n=4 ..sswap:n=3 .....zaxpy:n=4 ..zaxpy:n=3 ....zcopy:n=4 ..zcopy:n=3 .............zscal:n=4 ....zswap:n=4 ..zswap:n=3 ................................................................................................................................................................................caxpy:n=4 ..caxpy:n=3 ....ccopy:n=4 ..ccopy:n=3 .............cscal:n=4 ....cswap:n=4 ..cswap:n=3 .....daxpy:n=4 ..daxpy:n=3 ....dcopy:n=4 ..dcopy:n=3 .............dscal:n=4 ....dswap:n=4 ..dswap:n=3 .....saxpy:n=4 ..saxpy:n=3 ....scopy:n=4 ..scopy:n=3 .............sscal:n=4 ....sswap:n=4 ..sswap:n=3 .....zaxpy:n=4 ..zaxpy:n=3 ....zcopy:n=4 ..zcopy:n=3 .............zscal:n=4 ....zswap:n=4 ..zswap:n=3 .............Result may be inaccurate, approximate err = 1.56163357201e-08 ...Result may be inaccurate, approximate err = 1.25221600096e-10 ......Use minimum degree ordering on A'+A. ..Use minimum degree ordering on A'+A. ...Use minimum degree ordering on A'+A. ............................................................................................................./usr/lib/python2.5/site-packages/scipy/ndimage/interpolation.py:41: UserWarning: Mode "reflect" may yield incorrect results on boundaries. Please use "mirror" instead. warnings.warn('Mode "reflect" may yield incorrect results on ' ........................................................................................................................................................................................................................................................................................................F..F.........................................................Use minimum degree ordering on A'+A. .....................................Use minimum degree ordering on A'+A. .....................................Use minimum degree ordering on A'+A. ................................Use minimum degree ordering on A'+A. ....................................................................................................................................................................................................................................................................................................................................................0.2 0.2 0.2 ......0.2 ..0.2 0.2 0.2 0.2 0.2 .........................................................................................................................................................................................................Ties preclude use of exact statistic. ..Ties preclude use of exact statistic. ...... ====================================================================== FAIL: test_explicit (scipy.tests.test_odr.test_odr) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.5/site-packages/scipy/odr/tests/test_odr.py", line 50, in test_explicit -8.7849712165253724e-02]), File "/usr/lib/python2.5/site-packages/numpy/testing/utils.py", line 232, in assert_array_almost_equal header='Arrays are not almost equal') File "/usr/lib/python2.5/site-packages/numpy/testing/utils.py", line 217, in assert_array_compare assert cond, msg AssertionError: Arrays are not almost equal (mismatch 100.0%) x: array([ 1.26462971e+03, -5.42545890e+01, -8.64250389e-02]) y: array([ 1.26465481e+03, -5.40184100e+01, -8.78497122e-02]) ====================================================================== FAIL: test_multi (scipy.tests.test_odr.test_odr) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.5/site-packages/scipy/odr/tests/test_odr.py", line 191, in test_multi 0.5101147161764654, 0.5173902330489161]), File "/usr/lib/python2.5/site-packages/numpy/testing/utils.py", line 232, in assert_array_almost_equal header='Arrays are not almost equal') File "/usr/lib/python2.5/site-packages/numpy/testing/utils.py", line 217, in assert_array_compare assert cond, msg AssertionError: Arrays are not almost equal (mismatch 100.0%) x: array([ 4.31272063, 2.44289312, 7.76215871, 0.55995622, 0.46423343]) y: array([ 4.37998803, 2.43330576, 8.00288459, 0.51011472, 0.51739023]) ---------------------------------------------------------------------- Ran 1728 tests in 3.660s FAILED (failures=2) <unittest._TextTestResult run=1728 errors=0 failures=2> -------------------------------------------------------------------------------------------------------------- 2. System check -------------------------------------------------------------------------------------------------------------- yutec@yutec-laptop:~$ python -c 'import os,sys;print os.name,sys.platform' posix linux2 yutec@yutec-laptop:~$ uname -a Linux yutec-laptop 2.6.22-14-generic #1 SMP Sun Oct 14 21:45:15 GMT 2007 x86_64 GNU/Linux yutec@yutec-laptop:~$ gcc -v Using built-in specs. Target: x86_64-linux-gnu Configured with: ../src/configure -v --enable-languages=c,c++,fortran,objc,obj-c++,treelang --prefix=/usr --enable-shared --with-system-zlib --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --enable-nls --with-gxx-include-dir=/usr/include/c++/4.1.3 --program-suffix=-4.1 --enable-__cxa_atexit --enable-clocale=gnu --enable-libstdcxx-debug --enable-mpfr --enable-checking=release x86_64-linux-gnu Thread model: posix gcc version 4.1.3 20070929 (prerelease) (Ubuntu 4.1.2-16ubuntu2) yutec@yutec-laptop:~$ g77 --version GNU Fortran (GCC) 3.4.6 (Ubuntu 3.4.6-6ubuntu2) Copyright (C) 2006 Free Software Foundation, Inc. GNU Fortran comes with NO WARRANTY, to the extent permitted by law. You may redistribute copies of GNU Fortran under the terms of the GNU General Public License. For more information about these matters, see the file named COPYING or type the command `info -f g77 Copying'. yutec@yutec-laptop:~$ python -c 'import sys;print sys.version' 2.5.1 (r251:54863, Oct 5 2007, 13:50:07) [GCC 4.1.3 20070929 (prerelease) (Ubuntu 4.1.2-16ubuntu2)] yutec@yutec-laptop:~$ python -c 'import numpy;print numpy.__version__' 1.0.4 yutec@yutec-laptop:~$ cd /usr/lib/python2.5/site-packages/scipy/ yutec@yutec-laptop:/usr/lib/python2.5/site-packages/scipy$ cd linalg yutec@yutec-laptop:/usr/lib/python2.5/site-packages/scipy/linalg$ yutec@yutec-laptop:/usr/lib/python2.5/site-packages/scipy/linalg$ python setup_atlas_version.py build_ext --inplace --force Traceback (most recent call last): File "setup_atlas_version.py", line 7, in <module> from numpy.distutils.misc_util import get_path, default_config_dict ImportError: cannot import name get_path yutec@yutec-laptop:/usr/lib/python2.5/site-packages/scipy/linalg$ python -c 'import atlas_version' ATLAS version 3.6.0 built by root on Thu Jun 3 21:13:07 UTC 2004: UNAME : Linux ravel 2.6.5 #3 SMP Tue Apr 13 13:41:54 UTC 2004 x86_64 GNU/Linux INSTFLG : MMDEF : /home/camm/atlas3-3.6.0/CONFIG/ARCHS/HAMMER64SSE2/gcc/gemm ARCHDEF : /home/camm/atlas3-3.6.0/CONFIG/ARCHS/HAMMER64SSE2/gcc/misc F2CDEFS : -DAdd__ -DStringSunStyle CACHEEDGE: 720896 F77 : /home/camm/usr/bin/g77, version GNU Fortran (GCC) 3.3.3 (Debian 20040422) F77FLAGS : -fomit-frame-pointer -O -m64 CC : /usr/bin/gcc, version gcc (GCC) 3.3.3 (Debian 20040422) CC FLAGS : -fomit-frame-pointer -O -mfpmath=387 -m64 MCC : /usr/bin/gcc, version gcc (GCC) 3.3.3 (Debian 20040422) MCCFLAGS : -fomit-frame-pointer -O -mfpmath=387 -m64 yutec@yutec-laptop:/usr/lib/python2.5/site-packages/scipy/linalg$ cd .. yutec@yutec-laptop:/usr/lib/python2.5/site-packages/scipy$ cd .. yutec@yutec-laptop:/usr/lib/python2.5/site-packages$ cd numpy yutec@yutec-laptop:/usr/lib/python2.5/site-packages/numpy$ cd distutils/ yutec@yutec-laptop:/usr/lib/python2.5/site-packages/numpy/distutils$ python system_info.py lapack_info: libraries lapack not found in /usr/local/lib FOUND: libraries = ['lapack'] library_dirs = ['/usr/lib'] language = f77 lapack_opt_info: lapack_mkl_info: mkl_info: libraries mkl,vml,guide not found in /usr/local/lib libraries mkl,vml,guide not found in /usr/lib NOT AVAILABLE NOT AVAILABLE atlas_threads_info: Setting PTATLAS=ATLAS libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib libraries lapack_atlas not found in /usr/local/lib libraries ptf77blas,ptcblas,atlas not found in /usr/lib/atlas libraries lapack_atlas not found in /usr/lib/atlas libraries ptf77blas,ptcblas,atlas not found in /usr/lib __main__.atlas_threads_info NOT AVAILABLE atlas_info: libraries f77blas,cblas,atlas not found in /usr/local/lib libraries lapack_atlas not found in /usr/local/lib libraries f77blas,cblas,atlas not found in /usr/lib/atlas libraries lapack_atlas not found in /usr/lib/atlas __main__.atlas_info FOUND: libraries = ['lapack', 'f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/lib'] language = f77 include_dirs = ['/usr/include'] customize GnuFCompiler Found executable /usr/bin/g77 gnu: no Fortran 90 compiler found gnu: no Fortran 90 compiler found customize GnuFCompiler gnu: no Fortran 90 compiler found gnu: no Fortran 90 compiler found customize GnuFCompiler using config FOUND: libraries = ['lapack', 'f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/lib'] language = f77 define_macros = [('ATLAS_INFO', '"\\"?.?.?\\""')] include_dirs = ['/usr/include'] lapack_atlas_info: libraries lapack_atlas,f77blas,cblas,atlas not found in /usr/local/lib libraries lapack_atlas not found in /usr/local/lib libraries lapack_atlas,f77blas,cblas,atlas not found in /usr/lib/atlas libraries lapack_atlas not found in /usr/lib/atlas __main__.lapack_atlas_info FOUND: libraries = ['lapack', 'lapack_atlas', 'f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/lib'] language = f77 include_dirs = ['/usr/include'] umfpack_info: libraries umfpack not found in /usr/local/lib libraries umfpack not found in /usr/lib NOT AVAILABLE _pkg_config_info: Found executable /usr/bin/pkg-config NOT AVAILABLE lapack_atlas_threads_info: Setting PTATLAS=ATLAS libraries lapack_atlas,ptf77blas,ptcblas,atlas not found in /usr/local/lib libraries lapack_atlas not found in /usr/local/lib libraries lapack_atlas,ptf77blas,ptcblas,atlas not found in /usr/lib/atlas libraries lapack_atlas not found in /usr/lib/atlas libraries lapack_atlas,ptf77blas,ptcblas,atlas not found in /usr/lib __main__.lapack_atlas_threads_info NOT AVAILABLE x11_info: libraries X11 not found in /usr/lib64 NOT AVAILABLE blas_info: libraries blas not found in /usr/local/lib FOUND: libraries = ['blas'] library_dirs = ['/usr/lib'] language = f77 fftw_info: libraries fftw3 not found in /usr/local/lib FOUND: libraries = ['fftw3'] library_dirs = ['/usr/lib'] define_macros = [('SCIPY_FFTW3_H', None)] include_dirs = ['/usr/include'] f2py_info: FOUND: sources = ['/usr/lib/python2.5/site-packages/numpy/f2py/src/fortranobject.c'] include_dirs = ['/usr/lib/python2.5/site-packages/numpy/f2py/src'] gdk_pixbuf_xlib_2_info: NOT AVAILABLE dfftw_threads_info: libraries drfftw_threads,dfftw_threads not found in /usr/local/lib libraries drfftw_threads,dfftw_threads not found in /usr/lib dfftw threads not found NOT AVAILABLE atlas_blas_info: libraries f77blas,cblas,atlas not found in /usr/local/lib libraries f77blas,cblas,atlas not found in /usr/lib/atlas FOUND: libraries = ['f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/lib'] language = c include_dirs = ['/usr/include'] fftw3_info: libraries fftw3 not found in /usr/local/lib FOUND: libraries = ['fftw3'] library_dirs = ['/usr/lib'] define_macros = [('SCIPY_FFTW3_H', None)] include_dirs = ['/usr/include'] blas_opt_info: blas_mkl_info: libraries mkl,vml,guide not found in /usr/local/lib libraries mkl,vml,guide not found in /usr/lib NOT AVAILABLE atlas_blas_threads_info: Setting PTATLAS=ATLAS libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib libraries ptf77blas,ptcblas,atlas not found in /usr/lib/atlas libraries ptf77blas,ptcblas,atlas not found in /usr/lib NOT AVAILABLE customize GnuFCompiler gnu: no Fortran 90 compiler found gnu: no Fortran 90 compiler found customize GnuFCompiler gnu: no Fortran 90 compiler found gnu: no Fortran 90 compiler found customize GnuFCompiler using config FOUND: libraries = ['f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/lib'] language = c define_macros = [('ATLAS_INFO', '"\\"?.?.?\\""')] include_dirs = ['/usr/include'] sfftw_info: libraries srfftw,sfftw not found in /usr/local/lib libraries srfftw,sfftw not found in /usr/lib sfftw not found NOT AVAILABLE xft_info: NOT AVAILABLE fft_opt_info: djbfft_info: NOT AVAILABLE FOUND: libraries = ['fftw3'] library_dirs = ['/usr/lib'] define_macros = [('SCIPY_FFTW3_H', None)] include_dirs = ['/usr/include'] gdk_x11_2_info: NOT AVAILABLE agg2_info: NOT AVAILABLE numarray_info: NOT AVAILABLE blas_src_info: NOT AVAILABLE fftw2_info: libraries rfftw,fftw not found in /usr/local/lib FOUND: libraries = ['rfftw', 'fftw'] library_dirs = ['/usr/lib'] define_macros = [('SCIPY_FFTW_H', None)] include_dirs = ['/usr/include'] fftw_threads_info: libraries rfftw_threads,fftw_threads not found in /usr/local/lib FOUND: libraries = ['rfftw_threads', 'fftw_threads'] library_dirs = ['/usr/lib'] define_macros = [('SCIPY_FFTW_THREADS_H', None)] include_dirs = ['/usr/include'] _numpy_info: FOUND: define_macros = [('NUMERIC_VERSION', '"\\"24.2\\""'), ('NUMERIC', None)] include_dirs = ['/usr/include/python2.5'] wx_info: Could not locate executable wx-config File not found: None. Cannot determine wx info. NOT AVAILABLE gdk_info: NOT AVAILABLE gtkp_x11_2_info: NOT AVAILABLE sfftw_threads_info: libraries srfftw_threads,sfftw_threads not found in /usr/local/lib libraries srfftw_threads,sfftw_threads not found in /usr/lib sfftw threads not found NOT AVAILABLE boost_python_info: NOT AVAILABLE freetype2_info: NOT AVAILABLE gdk_2_info: NOT AVAILABLE dfftw_info: libraries drfftw,dfftw not found in /usr/local/lib libraries drfftw,dfftw not found in /usr/lib dfftw not found NOT AVAILABLE lapack_src_info: NOT AVAILABLE gtkp_2_info: NOT AVAILABLE gdk_pixbuf_2_info: NOT AVAILABLE amd_info: libraries amd not found in /usr/local/lib libraries amd not found in /usr/lib NOT AVAILABLE Numeric_info: FOUND: define_macros = [('NUMERIC_VERSION', '"\\"24.2\\""'), ('NUMERIC', None)] include_dirs = ['/usr/include/python2.5'] numerix_info: numpy_info: FOUND: define_macros = [('NUMPY_VERSION', '"\\"1.0.4\\""'), ('NUMPY', None)] FOUND: define_macros = [('NUMPY_VERSION', '"\\"1.0.4\\""'), ('NUMPY', None)]

4 3

sparse BLAS in scipy?
by Anand Patil 24 Nov '07

24 Nov '07

Hi all, Is there a set of python-callable sparse BLAS out there yet? I haven't found one, and not for lack of Googling. I'm willing to work on swigging a library if the need exists, but would like some guidance from someone with more experience with these things. First, it looks like there are three implementations that would be good for this purpose: - NIST sparse BLAS - SparseLib++ (superseded by above?) - Boost's ublas with sparse template parameters. Questions: - Do I need to do this, or are wrappers already available? - If so, which library would be best? I lean toward Boost, just because it's so broadly templatized that scripting a wrapper for all all the sparse-sparse and sparse-dense versions should be relatively easy. - What should the calling conventions from Python be like? - Any other pointers? (things I should know about numpy.i, for example). Anand

1 0

Installation of Python/mpl/numpy/scipy/Ipython for students
by Mark Bakker 24 Nov '07

24 Nov '07

A question was posted a week or so ago on the scipy list about installing Python/mpl/numpy/scipy/Ipython by David Arnold (both Windows and Mac). He was interested in a simple install for students (and others that are less computer-savy). We had a little off-list correspondence, but thought to bring it back to the list, also posting on mpl (cause I read that list and it seems pretty responsive) and the numpy Google discussion group (they respond VERY quickly). On the scipy list it was suggested to use Sage reply, but that sounds like a little overkill to me. I have used the enthought package on windows successfully in class in the past, but I understand that they have now switched to eggs, which is not convenient (yet). I also don't like all the other things I have to set myself. A switch on the IDLE GUI to get mpl to work interactively (which is now seems impossible to do), and setting my PYTHONPATH with environment variables. It is all easy to do, but not for students, especially students without much knowledge of how computers work let alone access to set these variables and options. At one point I was reading about making a superpack (or a name like that) installation for Python with our favorite packages as mentioned above. I am not sure where that is going. Are others dreaming about such a superpack? What needs to be done to get it going? Mark

1 0

Building with a non-standard gfortran
by Adam Mercer 23 Nov '07

23 Nov '07

Hi Using MacPorts, the gfortran compiler, from gcc-4.2.x, is installed as gfortran-mp-4.2. I have been trying to build scipy with this compiler and found that that numpy I need to build and install with $ python setup.py config_fc --fcompiler gnu95 \ --f77exec /opt/local/bin/gfortran-mp-4.2 \ --f90exec /opt/local/bin/gfortran-mp-4.2 build $ python setup.py install --prefix=${NUMPY_LOCATION} however using the above for scipy fails on the install phase with it being unable to locate a fortran compiler. I therefore need to install scipy with $ python setup.py config_fc --fcompiler gnu95 \ --f77exec /opt/local/bin/gfortran-mp-4.2 \ --f90exec /opt/local/bin/gfortran-mp-4.2 install --prefix=${SCIPY_LOCATION} Is this expected, as I would have expected install to inherit the options that where used during the build phase? Cheers Adam PS: I'm using numpy-1.0.4 and scipy-0.6.0

4 4

this must sound stupid ... (how to delete and destroy an AUI-pane ?)
by Stef Mientki 23 Nov '07

23 Nov '07

hello, I want to dynamically create, modify and delete AUI-panes in a AUI_DockingWindowMgr, Now I can create panes: self._mgr.AddPane( self.CreateHTMLCtrl(), wx.aui.AuiPaneInfo(). Name("test3").Caption("Client Size Reporter"). Left(). CloseButton ( False ). MaximizeButton ( False ) ) I can find the pane again pane = self._mgr.GetPane("test2") but how do I delete and destroy a pane ? The next statements all returns errors :-( pane.Close() self._mgr.DetachPane(pane) thanks, Stef

1 1

Read an array from a file using io.read_array
by Nils Wagner 22 Nov '07

22 Nov '07

Hi all, Is it possible to use io.read_array for the following task. I have an ascii file realeig.pmat. The essential information in this file is a table with 4 columns and several lines corresponding to the number of computed eigenvalues. The task is to read that information from a file. Empty lines and lines beginning with "!", "$" should be skipped. How can I handle the delimiter "&" which is used to continue lines ? Any pointer would be appreciated. Nils

2 3