Mailman 3 June 2002 - SciPy-User

ImportError: No module named fastumath
by Carl Staelin Aug. 15, 2002

Aug. 15, 2002

I grabbed scipy from CVS and built it last night, and I get an error when I try to use it: ImportError: No module named fastumath Some details on my system: OS: Linux, Mandrake 8.1 Python: python-2.1 Numerical: latest from CVS as of last night, 22.0a fypy2e: latest from CVS as of last night, 2.1.13.175.1250 ATLAS: 3.3.14 LAPACK: 3.0 When I look in /usr/lib/python2.1/site-packages/scipy_base, there is a file fastumath.so, so I am puzzled as to why the statement 'import scipy_base.fastumath' fails in scipy_base/__init__.py. Any suggestions welcome... Thanks, Carl Here is the debugging output: [staelin@firewall scipy]$ python -v # /usr/lib/python2.1/site.pyc matches /usr/lib/python2.1/site.py import site # precompiled from /usr/lib/python2.1/site.pyc # /usr/lib/python2.1/os.pyc matches /usr/lib/python2.1/os.py import os # precompiled from /usr/lib/python2.1/os.pyc import posix # builtin # /usr/lib/python2.1/posixpath.pyc matches /usr/lib/python2.1/posixpath.py import posixpath # precompiled from /usr/lib/python2.1/posixpath.pyc # /usr/lib/python2.1/stat.pyc matches /usr/lib/python2.1/stat.py import stat # precompiled from /usr/lib/python2.1/stat.pyc # /usr/lib/python2.1/UserDict.pyc matches /usr/lib/python2.1/UserDict.py import UserDict # precompiled from /usr/lib/python2.1/UserDict.pyc Python 2.1.1 (#1, Aug 30 2001, 17:36:05) [GCC 2.96 20000731 (Mandrake Linux 8.1 2.96-0.61mdk)] on linux-i386 Type "copyright", "credits" or "license" for more information. import readline # dynamically loaded from /usr/lib/python2.1/lib-dynload/readline.so >>> import scipy import scipy # directory /usr/lib/python2.1/site-packages/scipy # /usr/lib/python2.1/site-packages/scipy/__init__.pyc matches /usr/lib/python2.1/site-packages/scipy/__init__.py import scipy # precompiled from /usr/lib/python2.1/site-packages/scipy/__init__.pyc # /usr/lib/python2.1/site-packages/scipy/scipy_version.pyc matches /usr/lib/python2.1/site-packages/scipy/scipy_version.py import scipy.scipy_version # precompiled from /usr/lib/python2.1/site-packages/scipy/scipy_version.pyc # /usr/lib/python2.1/site-packages/scipy/__cvs_version__.pyc matches /usr/lib/python2.1/site-packages/scipy/__cvs_version__.py import scipy.__cvs_version__ # precompiled from /usr/lib/python2.1/site-packages/scipy/__cvs_version__.pyc # /usr/lib/python2.1/site-packages/Numeric/Numeric.pyc matches /usr/lib/python2.1/site-packages/Numeric/Numeric.py import Numeric # precompiled from /usr/lib/python2.1/site-packages/Numeric/Numeric.pyc # /usr/lib/python2.1/site-packages/Numeric/numeric_version.pyc matches /usr/lib/python2.1/site-packages/Numeric/numeric_version.py import numeric_version # precompiled from /usr/lib/python2.1/site-packages/Numeric/numeric_version.pyc import _numpy # dynamically loaded from /usr/lib/python2.1/site-packages/Numeric/_numpy.so import multiarray # dynamically loaded from /usr/lib/python2.1/site-packages/Numeric/multiarray.so import umath # dynamically loaded from /usr/lib/python2.1/site-packages/Numeric/umath.so # /usr/lib/python2.1/site-packages/Numeric/Precision.pyc matches /usr/lib/python2.1/site-packages/Numeric/Precision.py import Precision # precompiled from /usr/lib/python2.1/site-packages/Numeric/Precision.pyc # /usr/lib/python2.1/string.pyc matches /usr/lib/python2.1/string.py import string # precompiled from /usr/lib/python2.1/string.pyc import strop # dynamically loaded from /usr/lib/python2.1/lib-dynload/strop.so # /usr/lib/python2.1/types.pyc matches /usr/lib/python2.1/types.py import types # precompiled from /usr/lib/python2.1/types.pyc import math # dynamically loaded from /usr/lib/python2.1/lib-dynload/math.so # /usr/lib/python2.1/site-packages/Numeric/ArrayPrinter.pyc matches /usr/lib/python2.1/site-packages/Numeric/ArrayPrinter.py import ArrayPrinter # precompiled from /usr/lib/python2.1/site-packages/Numeric/ArrayPrinter.pyc # /usr/lib/python2.1/pickle.pyc has bad mtime import pickle # from /usr/lib/python2.1/pickle.py # can't create /usr/lib/python2.1/pickle.pyc # /usr/lib/python2.1/copy_reg.pyc matches /usr/lib/python2.1/copy_reg.py import copy_reg # precompiled from /usr/lib/python2.1/copy_reg.pyc import marshal # builtin import struct # dynamically loaded from /usr/lib/python2.1/lib-dynload/struct.so# /usr/lib/python2.1/re.pyc matches /usr/lib/python2.1/re.py import re # precompiled from /usr/lib/python2.1/re.pyc # /usr/lib/python2.1/sre.pyc matches /usr/lib/python2.1/sre.py import sre # precompiled from /usr/lib/python2.1/sre.pyc # /usr/lib/python2.1/sre_compile.pyc matches /usr/lib/python2.1/sre_compile.py import sre_compile # precompiled from /usr/lib/python2.1/sre_compile.pyc import _sre # builtin # /usr/lib/python2.1/sre_constants.pyc matches /usr/lib/python2.1/sre_constants.py import sre_constants # precompiled from /usr/lib/python2.1/sre_constants.pyc # /usr/lib/python2.1/sre_parse.pyc matches /usr/lib/python2.1/sre_parse.py import sre_parse # precompiled from /usr/lib/python2.1/sre_parse.pyc # /usr/lib/python2.1/StringIO.pyc has bad mtime import StringIO # from /usr/lib/python2.1/StringIO.py # can't create /usr/lib/python2.1/StringIO.pyc import errno # dynamically loaded from /usr/lib/python2.1/lib-dynload/errno.so # /usr/lib/python2.1/copy.pyc matches /usr/lib/python2.1/copy.py import copy # precompiled from /usr/lib/python2.1/copy.pyc import scipy_base # directory scipy_base # scipy_base/__init__.pyc matches scipy_base/__init__.py import scipy_base # precompiled from scipy_base/__init__.pyc Traceback (most recent call last): File "<stdin>", line 1, in ? File "/usr/lib/python2.1/site-packages/scipy/__init__.py", line 29, in ? from scipy_base import * File "scipy_base/__init__.py", line 4, in ? import scipy_base.fastumath ImportError: No module named fastumath >>>

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Please confirm your request to join FlyLadyMentors
by Yahoo!Groups June 30, 2002

June 30, 2002

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problems with scipy.io.readarray
by Remco.Strijbos＠jdsu.com June 28, 2002

June 28, 2002

I try to read a file into an array in with from scipy import io x=io.read_array('test.dat') but get the following traceback Traceback (most recent call last): File "<interactive input>", line 1, in ? File "C:\Python22\Lib\site-packages\scipy\io\array_import.py", line 319, in read_array colsize, collist = getcolumns(ascii_object, columns, sep) File "C:\Python22\Lib\site-packages\scipy\io\array_import.py", line 247, in getcolumns val = process_line(firstline, separator, collist, [Numeric.Float]*N, 0) File "C:\Python22\Lib\site-packages\scipy\io\array_import.py", line 227, in process_line vals[k] = extract_columns(arlist, collist[k], atype[k], missing) File "C:\Python22\Lib\site-packages\scipy\io\array_import.py", line 205, in extract_columns return numpyio.convert_objectarray(toconvlist, atype, missing) SystemError: D: \trentm\main\Apps\ActivePython-2_2\src\Core\Objects\methodobject.c:33: bad argument to internal function I used: SciPy-0_2_0_alpha_102_3553_win32-py2_2.exe on Win NT Any idea what is going wrong? Best regards, Remco Strijbos This email contains information that may be confidential and privileged. Unless you are the addressee (or authorized to receive for the addressee), you may not use, copy or disclose this message to anybody or the information contained herein. If you have received this email in error, please notify the sender and delete this message. Thank you.

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scipy workshop
by Andrew Ptak June 27, 2002

June 27, 2002

Hello, I submitted a registration form for the scipy workshop (about a week ago, I think) but I haven't gotten any email since then. Has the 50 person limit been reached? Thanks, Andy Ptak

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[ANN] SciPy '02 - Python for Scientific Computing Workshop
by Travis N. Vaught June 24, 2002

June 24, 2002

Apologies if you are receiving this a second time. (mailing list problems should be fixed now) ---------------------------------------- Python for Scientific Computing Workshop ---------------------------------------- CalTech, Pasadena, CA Septemer 5-6, 2002 http://www.scipy.org/site_content/scipy02 This workshop provides a unique opportunity to learn and affect what is happening in the realm of scientific computing with Python. Attendees will have the opportunity to review the available tools and how they apply to specific problems. By providing a forum for developers to share their Python expertise with the wider industrial, academic, and research communities, this workshop will foster collaboration and facilitate the sharing of software components, techniques and a vision for high level language use in scientific computing. The two-day workshop will be a mix of invited talks and training sessions in the morning. The afternoons will be breakout sessions with the intent of getting standardization of tools and interfaces. The cost of the workshop is $50.00 and includes 2 breakfasts and 2 lunches on Sept. 5th and 6th, one dinner on Sept. 5th, and snacks during breaks. There is a limit of 50 attendees. Should we exceed the limit of 50 registrants, the 50 persons selected to attend will be invited individually by the organizers. Discussion about the conference may be directed to the SciPy-user mailing list: mailto:scipy-user@scipy.org http://www.scipy.org/MailList ------------- Co-Hosted By: ------------- The National Biomedical Computation Resource (NBCR, SDSC, San Diego, CA) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ http://nbcr.sdsc.edu The mission of the National Biomedical Computation Resource at the San Diego Supercomputer Center is to conduct, catalyze, and enable biomedical research by harnessing advanced computational technology. The Center for Advanced Computing Research (CACR, CalTech, Pasadena, CA) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ http://nbcr.sdsc.edu CACR is dedicated to the pursuit of excellence in the field of high-performance computing, communication, and data engineering. Major activities include carrying out large-scale scientific and engineering applications on parallel supercomputers and coordinating collaborative research projects on high-speed network technologies, distributed computing and database methodologies, and related topics. Our goal is to help further the state of the art in scientific computing. Enthought, Inc. (Austin, TX) ^^^^^^^^^^^^^^^ http://enthought.com Enthought, Inc. provides business and scientific computing solutions through software development, consulting and training. Enthought also fosters the development of SciPy, an open source library of scientific tools for Python.

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[ANN] SciPy '02 - Python for Scientific Computing Workshop
by Travis N. Vaught June 17, 2002

June 17, 2002

---------------------------------------- Python for Scientific Computing Workshop ---------------------------------------- CalTech, Pasadena, CA Septemer 5-6, 2002 http://www.scipy.org/site_content/scipy02 This workshop provides a unique opportunity to learn and affect what is happening in the realm of scientific computing with Python. Attendees will have the opportunity to review the available tools and how they apply to specific problems. By providing a forum for developers to share their Python expertise with the wider industrial, academic, and research communities, this workshop will foster collaboration and facilitate the sharing of software components, techniques and a vision for high level language use in scientific computing. The two-day workshop will be a mix of invited talks and training sessions in the morning. The afternoons will be breakout sessions with the intent of getting standardization of tools and interfaces. The cost of the workshop is $50.00 and includes 2 breakfasts and 2 lunches on Sept. 5th and 6th, one dinner on Sept. 5th, and snacks during breaks. There is a limit of 50 attendees. Should we exceed the limit of 50 registrants, the 50 persons selected to attend will be invited individually by the organizers. Discussion about the conference may be directed to the SciPy-user mailing list: mailto:scipy-user@scipy.org http://www.scipy.org/MailList ------------- Co-Hosted By: ------------- The National Biomedical Computation Resource (NBCR, SDSC, San Diego, CA) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ http://nbcr.sdsc.edu The mission of the National Biomedical Computation Resource at the San Diego Supercomputer Center is to conduct, catalyze, and enable biomedical research by harnessing advanced computational technology. The Center for Advanced Computing Research (CACR, CalTech, Pasadena, CA) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ http://nbcr.sdsc.edu CACR is dedicated to the pursuit of excellence in the field of high-performance computing, communication, and data engineering. Major activities include carrying out large-scale scientific and engineering applications on parallel supercomputers and coordinating collaborative research projects on high-speed network technologies, distributed computing and database methodologies, and related topics. Our goal is to help further the state of the art in scientific computing. Enthought, Inc. (Austin, TX) ^^^^^^^^^^^^^^^ http://enthought.com Enthought, Inc. provides business and scientific computing solutions through software development, consulting and training.

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failure of scipy.test(level=5)
by damian June 10, 2002

June 10, 2002

Hello, The result I get from the test are : .................................................................................................................... ====================================================================== ERROR: check_exceptions (test_inline_tools.test_inline) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib/python2.2/site-packages/scipy/weave/tests/test_inline_tools.py", line 25, in check_exceptions result = inline_tools.inline(code,['a']) File "/usr/local/lib/python2.2/site-packages/scipy/weave/inline_tools.py", line 327, in inline auto_downcast = auto_downcast, File "/usr/local/lib/python2.2/site-packages/scipy/weave/inline_tools.py", line 426, in compile_function verbose=verbose, **kw) File "/usr/local/lib/python2.2/site-packages/scipy/weave/ext_tools.py", line 321, in compile verbose = verbose, **kw) File "/usr/local/lib/python2.2/site-packages/scipy/weave/build_tools.py", line 203, in build_extension setup(name = module_name, ext_modules = [ext],verbose=verb) File "/usr/local/lib/python2.2/distutils/core.py", line 157, in setup raise SystemExit, "error: " + str(msg) CompileError: error: command 'gcc' failed with exit status 1 ---------------------------------------------------------------------- Ran 601 tests in 244.250s FAILED (errors=1) <unittest.TextTestRunner instance at 0x858556c> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Platform information: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> posix linux2 uname -a: Linux localhost.localdomain 2.4.18-3smp #1 SMP Thu Apr 18 07:27:31 EDT 2002 i686 OS: redhat 7.3 gcc -v: Reading specs from /usr/lib/gcc-lib/i386-redhat-linux/2.96/specs gcc version 2.96 20000731 (Red Hat Linux 7.3 2.96-110) g77 --version GNU Fortran 0.5.26 20000731 (Red Hat Linux 7.3 2.96-110) python22 -c 'import sys;print sys.version' 2.2.1 (#1, Jun 2 2002, 08:38:08) [GCC 2.96 20000731 (Red Hat Linux 7.3 2.96-110)] python22 -c 'import Numeric;print Numeric.__version__' 21.0 f2py: F2PY-2.13.175-1250 atlas: atlas3.4.0. the atlas libraries are located in /usr/local/lib/atals the lpack libraries are located in /usr/local/lib system_info.py: atlas_info: FOUND: libraries = ['lapack', 'f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/local/lib', '/usr/local/lib/atlas'] fftw_info: FOUND: libraries = ['dfftw', 'drfftw', 'dfftw_threads', 'drfftw_threads'] library_dirs = ['/usr/local/lib'] define_macros = [('SCIPY_DFFTW_H', 1)] include_dirs = ['/usr/local/include'] x11_info: FOUND: libraries = ['X11'] library_dirs = ['/usr/X11R6/lib'] include_dirs = ['/usr/X11R6/include'] ....................................................................................................... python22 build_flib.py command: f77 -V -c /tmp/__dummy.f -o /tmp/__dummy.o 256 f77: invalid version number format command: f77 -version 256 f77: unrecognized option `-version' /usr/bin/ld: cannot open output file a.out: Permission denied collect2: ld returned 1 exit status command: f90 -V 32512 sh: f90: command not found command: ifc -FI -V -c /tmp/__dummy.f -o /tmp/__dummy.o 32512 sh: ifc: command not found command: efc -FI -V -c /tmp/__dummy.f -o /tmp/__dummy.o 32512 sh: efc: command not found command: f95 -V 32512 sh: f95: command not found command: fort -V 32512 sh: fort: command not found command: DF /what 32512 sh: DF: command not found command: g77 --version 0 GNU Fortran 0.5.26 20000731 (Red Hat Linux 7.3 2.96-110) Copyright (C) 1997 Free Software Foundation, Inc. For more version information on components of the GNU Fortran compilation system, especially useful when reporting bugs, type the command `g77 --verbose'. 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'. command: vf90 -v 32512 sh: vf90: command not found command: f90 +version 32512 sh: f90: command not found command: g77 --version 0 GNU Fortran 0.5.26 20000731 (Red Hat Linux 7.3 2.96-110) Copyright (C) 1997 Free Software Foundation, Inc. For more version information on components of the GNU Fortran compilation system, especially useful when reporting bugs, type the command `g77 --verbose'. 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'. command: F -V 32512 sh: F: command not found command: g77 --version 0 GNU Fortran 0.5.26 20000731 (Red Hat Linux 7.3 2.96-110) Copyright (C) 1997 Free Software Foundation, Inc. For more version information on components of the GNU Fortran compilation system, especially useful when reporting bugs, type the command `g77 --verbose'. 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'. Gnu 0.5.26 Thanks, D. Bernard

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ATLAS and LAPACK libraries
by damian June 8, 2002

June 8, 2002

Hello, I am trying to build scipy from source, and I have installed LAPACK and ATLAS but I am a bit confussed on how to link them. More to the point, the directions state to do the following ... mkdir tmp cd tmp ar x ../liblapack.a cp <your LAPACK path & lib> ../liblapack.a ar r ../liblapack.a *.o cd .. rm -rf tmp .................................... I don't understand the line " cp <your LAPACK path & lib> ../liblapack.a " . What exactly do I copy? To me it looks like you extract the library then archive it again. My guess is that you are trying to add extra object files ito the liblapack.a archive, but I am not quite sure how the above commnads acomplish that. dbernard

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plot.plt speed
by Douglas Eck June 7, 2002

June 7, 2002

I need to plot 10 time series on the same plot window. But it's quite slow: plot.plt(rand(10,200)) takes 18 seconds. plot.plt(rand(1,2000)) takes less than one second There are some tricks for speeding up the first case in gnuplot by reshaping the array to be 1,2000 and adding a second array for the x values. [[1:200][1:200]....[1:200]]. But this has other problems. Any ideas? My timeseries are more on the order of (25,2500).... not pretty. Cheers, Doug -- Dr. Douglas Eck, http://www.idsia.ch/~doug Istituto Dalle Molle di Studi sull'Intelligenza Artificiale (IDSIA) Neural Networks, Rhythm Perception and Production, Dynamical Systems

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problems with scipy.io.read_array
by Remco.Strijbos＠jdsu.com June 7, 2002

June 7, 2002

The same error occurs on both Linux (mandrake 8,2 with binary rpm of scipy ) and Windows. There is nothing special with the text file, the same error occurs when you write and read back an array as in the code below: import Numeric import scipy.io x=Numeric.identity(3,Numeric.Float) scipy.io.write_array('test2.dat',x) y=scipy.io.read_array('test2.dat') Remco. This email contains information that may be confidential and privileged. Unless you are the addressee (or authorized to receive for the addressee), you may not use, copy or disclose this message to anybody or the information contained herein. If you have received this email in error, please notify the sender and delete this message. Thank you.

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