Mailman 3 April 2006 - SciPy-User

GiNaC / Scipy ?
by Jelle Feringa / EZCT Architecture & Design Research April 25, 2006

April 25, 2006

Dear group, I've been really impressed by some recent efforts in bringing FEM to python: especially SyFi caught my eye, Symbolic Finite Element, and effort of Kent-Andre Mardal. The interesting thing here is that its built on top of the symbolic math lib GiNaC, http://www.ginac.de/ which has swig wrappers for python, Swigniac, http://swiginac.berlios.de/ I'm wondering how relevant Swigniac could be for Scipy? Cheers, -jelle //We get quite a bit of Matlab references on this list, //let's just not overlook Mathematica ;)

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which parallel programming package?
by Robert Cimrman April 25, 2006

April 25, 2006

Hi, I have checked the homepages of various parallel programing packages (based on MPI) listed at http://scipy.org/Topical_Software, and none of them seems to be recently updated. Which of them do/would you use and recommend? I do not need anything fancy, just pass a bunch of data (numpy arrays, scalars) over a cluster, and quickly. r.

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Re: [SciPy-user] [SciPy-dev] Google Summer of Code
by Robert Kern April 25, 2006

April 25, 2006

[Cross-posted because this is partially an announcement. Continuing discussion should go to only one list, please.] Antonio Arauzo Azofra wrote: > Google Summer of Code > http://code.google.com/soc/ > > Have you considered participating as a Mentoring organization? Offering > any project about Scipy? I'm not sure which "you" you are referring to here, but yes! Unfortunately, it was a bit late in the process to be applying as a mentoring organization. Google started consolidating mentoring organizations. However, I and several others at Enthought are volunteering to mentor through the PSF. I encourage others on these lists to do the same or to apply as students, whichever is appropriate. We'll be happy to provide SVN workspace for numpy and scipy SoC projects. I've added one fairly general scipy entry to the python.org Wiki page listing project ideas: http://wiki.python.org/moin/SummerOfCode If you have more specific ideas, please add them to the Wiki. Potential mentors: Neal Norwitz is coordinating PSF mentors this year and has asked that those he or Guido does not know personally to give personal references. If you've been active on this list, I'm sure we can play the "Two Degrees of Separation From Guido Game" and get you a reference from someone else here. -- Robert Kern robert.kern(a)gmail.com "I have come to believe that the whole world is an enigma, a harmless enigma that is made terrible by our own mad attempt to interpret it as though it had an underlying truth." -- Umberto Eco

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OSX Issue -- Symbol not found: _fprintf$LDBLStub
by Tony Mannucci April 25, 2006

April 25, 2006

I used to have a very similar problem until I used g77 with gcc 3.3 (sudo gcc_select 3.3) rather than gcc 4.0. Then the proper libraries were searched and the symbol found. The library you are having problems with appears to be written in C, so I don't if this applies. Make sure you are using the correct gcc by typing gcc_select without arguments. I think scipy needs f77 for some modules, so you must have a fortran compiler somewhere? I downloaded the binary from Khanna's HPC on OS X site, and followed the installation instructions carefully. Be sure to remove any old SciPy installations before retrying (e.g. /usr/lib/python2.4/site-packages/scipy or $HOME/lib/python2.4/ site-packages/scipy). -Tony > >Message: 5 >Date: Mon, 24 Apr 2006 18:03:09 -0700 >From: Gregory Crosswhite <gcross(a)u.washington.edu> >Subject: [SciPy-user] OSX Issue -- Symbol not found: _fprintf$LDBLStub >To: scipy-user(a)scipy.net >Message-ID: <19DA9FD8-3927-4FDD-8206-BA72A0D81E0A(a)u.washington.edu> >Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > >Hey! I'm attempting to get SciPy to run on OSX 10.4 (Tiger), with >the latest version of Xcode (2.2.1, I believe) installed. When I run >python and import scipy.fftpack, I get the following error: > >Python 2.4.3 (#1, Mar 30 2006, 11:02:15) >[GCC 4.0.1 (Apple Computer, Inc. build 5250)] on darwin >Type "help", "copyright", "credits" or "license" for more information. > >>> import scipy.fftpack >Traceback (most recent call last): > File "<stdin>", line 1, in ? > File "/Library/Frameworks/Python.framework/Versions/2.4/lib/ >python2.4/site-packages/scipy/fftpack/__init__.py", line 10, in ? > from basic import * > File "/Library/Frameworks/Python.framework/Versions/2.4/lib/ >python2.4/site-packages/scipy/fftpack/basic.py", line 13, in ? > import _fftpack as fftpack >ImportError: Failure linking new module: /Library/Frameworks/ >Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/ >fftpack/_fftpack.so: Symbol not found: _fprintf$LDBLStub > Referenced from: /Library/Frameworks/Python.framework/Versions/2.4/ >lib/python2.4/site-packages/scipy/fftpack/_fftpack.so > Expected in: dynamic lookup > > >I've tried both the MacPython binaries distributed at python.org, and >the ActiveState distribution. I've tried both downloading and >installing SciPy binaries (the latest version, 0.4.8, and an older >version, 0.4.4), and compiling them from source. The problem does >not go away whether I use GCC 3.3 or 4.0. > >Now, at one point in the past I had installed and gotten working >SciPy 0.3 from sources, so there might be a library sitting around >from that which is screwing things up, but I don't know where to >look! Under the belief that maybe the problem was an old version of >FFTW (or one compiled with GCC version 4.0 instead of 3.3) I >downloaded, compiled, and installed BOTH FFTW 2.1.5 and 3.1.1 using >GCC 3.3. Again, no change in the error message. > >There is exactly one thing that does seem to work, and that is using >the binary of version 0.4.9 built by Christopher Fonnesbeck, >downloadable from http://trichech.us/. I am using that for now, so >this isn't a terribly urgent issue, but it really bothers me that I >can't get any other binary or source distribution of SciPy working; >I wish I could figure out why his build works when even builds >performed on my own computer won't work. > >Does anyone have thoughts on what could be going wrong? > >Thanks a lot! :-) > >- Greg > > > -- Tony Mannucci Supervisor, Ionospheric and Atmospheric Remote Sensing Group Mail-Stop 138-308, Tel > (818) 354-1699 Jet Propulsion Laboratory, Fax > (818) 393-5115 California Institute of Technology, Email > Tony.Mannucci(a)jpl.nasa.gov 4800 Oak Grove Drive, http://genesis.jpl.nasa.gov Pasadena, CA 91109

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Changing the Trac authentication, for real this time!
by Robert Kern April 25, 2006

April 25, 2006

If you encounter errors accessing the Trac sites for NumPy and SciPy over the next hour or so, please wait until I have announced that I have finished. If things are still broken after that, please let me know and I will try to fix it immediately. The details of the changes were posted to the previous thread "Changing the Trac authentication". Apologies for any disruption and for the noise. -- Robert Kern robert.kern(a)gmail.com "I have come to believe that the whole world is an enigma, a harmless enigma that is made terrible by our own mad attempt to interpret it as though it had an underlying truth." -- Umberto Eco

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OSX Issue -- Symbol not found: _fprintf$LDBLStub
by Gregory Crosswhite April 25, 2006

April 25, 2006

Hey! I'm attempting to get SciPy to run on OSX 10.4 (Tiger), with the latest version of Xcode (2.2.1, I believe) installed. When I run python and import scipy.fftpack, I get the following error: Python 2.4.3 (#1, Mar 30 2006, 11:02:15) [GCC 4.0.1 (Apple Computer, Inc. build 5250)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import scipy.fftpack Traceback (most recent call last): File "<stdin>", line 1, in ? File "/Library/Frameworks/Python.framework/Versions/2.4/lib/ python2.4/site-packages/scipy/fftpack/__init__.py", line 10, in ? from basic import * File "/Library/Frameworks/Python.framework/Versions/2.4/lib/ python2.4/site-packages/scipy/fftpack/basic.py", line 13, in ? import _fftpack as fftpack ImportError: Failure linking new module: /Library/Frameworks/ Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/ fftpack/_fftpack.so: Symbol not found: _fprintf$LDBLStub Referenced from: /Library/Frameworks/Python.framework/Versions/2.4/ lib/python2.4/site-packages/scipy/fftpack/_fftpack.so Expected in: dynamic lookup I've tried both the MacPython binaries distributed at python.org, and the ActiveState distribution. I've tried both downloading and installing SciPy binaries (the latest version, 0.4.8, and an older version, 0.4.4), and compiling them from source. The problem does not go away whether I use GCC 3.3 or 4.0. Now, at one point in the past I had installed and gotten working SciPy 0.3 from sources, so there might be a library sitting around from that which is screwing things up, but I don't know where to look! Under the belief that maybe the problem was an old version of FFTW (or one compiled with GCC version 4.0 instead of 3.3) I downloaded, compiled, and installed BOTH FFTW 2.1.5 and 3.1.1 using GCC 3.3. Again, no change in the error message. There is exactly one thing that does seem to work, and that is using the binary of version 0.4.9 built by Christopher Fonnesbeck, downloadable from http://trichech.us/. I am using that for now, so this isn't a terribly urgent issue, but it really bothers me that I can't get any other binary or source distribution of SciPy working; I wish I could figure out why his build works when even builds performed on my own computer won't work. Does anyone have thoughts on what could be going wrong? Thanks a lot! :-) - Greg

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port C/C++ matlab mexing code to numpy
by Gennan Chen April 24, 2006

April 24, 2006

Hi! All, We have a a lot of C/C++ code written for interacting with Matlab (i.,e mexing code). I was wondering what's the best approach to port them into python/numpy/scipy? How about using SWIG? Any recommendation will be welcomed.... Gen-Nan Chen, PhD Chief Scientist Research and Development Group CorTechs Labs Inc (www.cortechs.net) 1020 Prospect St., #304, La Jolla, CA, 92037 Tel: 1-858-459-9700 ext 16 Fax: 1-858-459-9705 Email: gnchen(a)cortechs.net

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ask help for the userwanring
by imcs ee April 24, 2006

April 24, 2006

debian - sarge. when i use the scipy package. it prints the words below. but the python2.4-profiler in not in the source ...and i am not have the privilege to install. could i just ignore it .and will the result be reliable ? --- /usr/lib/python2.4/site-packages/scipy_base/ppimport.py:273: UserWarning: The pstats module is not available. Install the python2.4-profiler Debian package if you need it module = __import__(name,None,None,['*'])

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Changing the Trac authentication
by Robert Kern April 24, 2006

April 24, 2006

I will be changing the Trac authentication over the next hour or so. I will be installing the AccountManagerPlugin to allow users to create accounts for themselves without needing to have SVN write access. Anonymous users will not be able to edit the Wikis or tickets. Non-developer, but registered users will be able to do so with some restrictions, notably not being able to resolve tickets. Developers who currently have accounts will have the same username/password as before. If you have problems using the Trac sites before I announce that I am done, please wait until I am finished. If there are still problems, please let me know and I will try to fix them as soon as possible. Thank you for your patience. Hopefully, this change will resolve the spam problem. -- Robert Kern robert.kern(a)gmail.com "I have come to believe that the whole world is an enigma, a harmless enigma that is made terrible by our own mad attempt to interpret it as though it had an underlying truth." -- Umberto Eco

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scipy.test() crashes under win2k
by weg werp April 23, 2006

April 23, 2006

Hi group, I finally tried to install scipy. Everything appears to work, but scipy.test() crashes. I installed the prebuilt versions: first numpy-0.9.6r1.win32-py2.4.exe, then scipy-0.4.8.win32-py2.4-pentium3.exe (I assume that Pentium 4/SSE2 does not work on my Athlon). import numpy;numpy.test() works fine, but import scipy;scipy.test() first gives some warnings about overwriting fft, then runs all the tests ok, then shows a lot of dots (file test?) and crashes (drwatson log available). Any ideas? System: win2k sp4, Athlon XP 1700+, 768 MB Python 2.4 (#60, Nov 30 2004, 09:34:21) [MSC v.1310 32 bit (Intel)] on win32 Other point, slight nitpick for the website: it took my a few minutes to figure out the difference between the download and the install sections on the scipy website. In the download section I see some executables for windows, which is what I want as a newby. I then went to 'install' and expected some installation guidelines, but this seems more like an instruction for compiling from source (instant newby panic). Could the difference be made a little bit more clear? A few words are probably ok: -download section: 'these are prebuilt versions, for the latest version you have to compile yourself, see install'. -install section: 'installing from source, to download a prebuilt stable version see download' Thanks, Bas p.s.: I tried to send this message without subscribing to the list, but it got probably stuck in moderator approval. Is the policy to allow no posts from non-subscribers? If so, this should be stated on the web-page....

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