Mailman 3 June 2005 - SciPy-Dev

fftw3 support
by Matt Fishburn 23 Jul '05

23 Jul '05

Hello, I've attached patches against the current cvs source for fftw3 support in scipy. I've only tested these under x86 *nix (debian with various combinations of fftw-dev and fftw3-dev installed). Could a few people please try the patches and send build feedback? fft-c-source.diff is diff'ed against the c source/header files in Lib/fftpack/src and system_info.diff is diff'ed against the build detection code in scipy_core/scipy_distutils/system_info.py -Matt Fishburn

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ANN: SciPy 2005 Conference - Python for Scientific Computing
by Janet M. Swisher 30 Jun '05

30 Jun '05

Greetings, The 2nd annual *SciPy Conference* on Python for Scientific Computing will be held again this year at Caltech, September 22-23, 2005. History: -------- This event started as SciPy "Workshops" held in 2002 and 2003, with great participation by the ~70 people attending. In 2004, it became a "conference", with attendance jumping to 87 participants. Registration: ------------- Registration is now open. More information can be found here: http://www.scipy.org/wikis/scipy05 You may register early online for $100.00. Registration includes breakfast and lunch Thursday & Friday and a very nice dinner Thursday night. After July 29, registration will cost $150.00. Call for Presenters: -------------------- If you are interested in presenting at the conference, you can submit an abstract in Plain Text, PDF or MS Word formats to abstracts(a)scipy.org -- the deadline for abstract submission is July 29, 2005. Papers or presentation slides are acceptable and are due by August 26, 2005. Feedback: --------- If you have any feedback from last year's conference or suggestions for this year, please discuss via the scipy mailing list: list signup: http://www.scipy.org/mailinglists/ list address: scipy-user(a)scipy.org Please forward this announcement to anyone/list that might be interested. Best Regards, -- Janet Swisher --- Senior Technical Writer Enthought, Inc. http://www.enthought.com

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Compilation success with gfortran and gcc 4.0, but
by Ravikiran Rajagopal 29 Jun '05

29 Jun '05

Hi, I finally managed to compile SciPy CVS on Fedora Core 4 with gcc 4.0.0 and gfortran. I did not use the "old" g77 that is shipped with Fedora Core 4 for compatibility purposes. The following is the list of changes I needed: scipy_distutils/gnufcompiler.py 1. Add gfortran to the search list for fortran compilers. 2. Add libgfortran to the search list for g2c. 3. Remove the sse2 optimization flag. Lib 1. Replace Hollerith constants with quoted strings in odepack and quadpack; I used Fortran Tidy to do it. 2. In dqage.f, make sure 260 refers to the last line. 3. Hack the logic in the conjugate gradient methods so as not jump into the middle of a block. My changes should be viewed with extreme suspicion since I have never programmed seriously in Fortran and the last time I dabbled in it (for a few days) was in 1993 or 1994. While everything compiles, there are still runtime errors. The tests in scipy.special are a disaster. I recompiled everything with gcc 4.0.0 but with g77 from gcc 3.2.3 (which required none of the modifications above) and the same errors persist. Several of the tests (check_assoc_laguerre, chack_cheby*, check_gegenbauer, etc.) take 100% and do not return even after several hours. The numpyio todense() error is also found. Anyone have any ideas about fixing this? Regards, Ravi

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Current errors in scipy.test(1,verbosity=10)
by Nils Wagner 22 Jun '05

22 Jun '05

Hi all, I get two errors and 1 failure running scipy.test(1,verbosity=10) with latest cvs (scipy, Numerical and f2py) ====================================================================== ERROR: check_definition (scipy.fftpack.basic.test_basic.test_fftn) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib/python2.4/site-packages/scipy/fftpack/tests/test_basic.py", line 423, in check_definition assert_array_almost_equal(fftn(x),direct_dftn(x)) File "/usr/local/lib/python2.4/site-packages/scipy/fftpack/basic.py", line 283, in fftn return _raw_fftnd(tmp,shape,axes,1,overwrite_x,work_function) File "/usr/local/lib/python2.4/site-packages/scipy/fftpack/basic.py", line 219, in _raw_fftnd return work_function(x,s,direction,overwrite_x=overwrite_x) error: failed in converting 1st argument `x' of _fftpack.zfftnd to C/Fortran array ====================================================================== ERROR: check_definition (scipy.fftpack.basic.test_basic.test_ifftn) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib/python2.4/site-packages/scipy/fftpack/tests/test_basic.py", line 590, in check_definition assert_array_almost_equal(ifftn(x),direct_idftn(x)) File "/usr/local/lib/python2.4/site-packages/scipy/fftpack/basic.py", line 312, in ifftn return _raw_fftnd(tmp,shape,axes,-1,overwrite_x,work_function) File "/usr/local/lib/python2.4/site-packages/scipy/fftpack/basic.py", line 219, in _raw_fftnd return work_function(x,s,direction,overwrite_x=overwrite_x) error: failed in converting 1st argument `x' of _fftpack.zfftnd to C/Fortran array ====================================================================== FAIL: check_round (scipy.special.basic.test_basic.test_round) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib/python2.4/site-packages/scipy/special/tests/test_basic.py", line 1789, in check_round assert_array_equal(rnd,rndrl) File "/usr/local/lib/python2.4/site-packages/scipy_test/testing.py", line 715, in assert_array_equal assert cond,\ AssertionError: Arrays are not equal (mismatch 25.0%): Array 1: [10 10 11 11] Array 2: [10 10 10 11] ---------------------------------------------------------------------- Ran 1265 tests in 7.131s FAILED (failures=1, errors=2) <unittest.TextTestRunner object at 0x4195374c Nils

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Segmentation fault
by Nils Wagner 21 Jun '05

21 Jun '05

Hi all, Running the small test (see below) with latest f2py via cvs results in a segmentation fault. Since I was not sure whether this bug is related to f2py or scipy I downgraded f2py to the latest available tarball http://cens.ioc.ee/projects/f2py2e/#download Now the program works fine. So the bug must be added with the last changes in f2py. from scipy import * n = 20 m = 15 a = rand(n,m)+1j*rand(n,m) u,s,vt,info = linalg.flapack.zgesdd(a) Any pointer how to fix the problem in latest cvs would be appreciated. Thanks in advance Nils

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SciPy.org server migration tonight
by Joe Cooper 21 Jun '05

21 Jun '05

Hi all, I've been threatening a server migration of SciPy.org for a couple of weeks now, and tonight's the night on which at least some services will move (whether they like it or not). I will be shutting down CVS access in a few minutes, as the cvs2svn conversion takes a while to process and I will definitely move SciPy to Subversion tonight. Throughout the evening, other services will probably disappear for a bit, hopefully to reappear on the new server soon after. I'm certain there will be issues, as we're moving to much newer versions of all software, removing a bunch of old users, switching from CVS to Subversion, and a couple dozen other changes that don't come to mind right now. Please let me know if you see any such problems in the coming days. I'll notify the list when things are back to sanity as best as I can figure. Thanks!

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Bugfix for weave's catalog.
by Fernando Perez 18 Jun '05

18 Jun '05

Hi all, there has been a long-standing bug in weave.inline, where it recompiles stuff it shouldn't. I was finally able to track it down to a sys.path problem, where sys.path does not get the ~/.pythonXX_compiled directory added, and hence calls to pickle.load() fail when loading items from the shelved on-disk catalog. The patch here fixes that problem. In the process, I cleaned up catalog.py a bit, adding caching to the default_dir() call (which is used often) and adding a few catalog.close() calls for safety, since the semantics of shelved catalogs are undefined (implementation-dependent) if not explicitly closed. I can commit this, but I'd greatly appreciate it if someone else has a look at it first (Pearu, RKern?). I know that nobody likes to muck with the weave code, as it's a bit complex, but I'd feel safer if at least one more pair of eyeballs has a look at this before I commit. Regards, f

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RE: [SciPy-dev] Roadmap for scipy
by Charles Harris 18 Jun '05

18 Jun '05

I've done the Mersenne Twister using boost. With some work, this could probably be brought to a form that would work in SciPy. Suggestion on what you would like to see are welcome. -----Original Message----- From: scipy-dev-bounces(a)scipy.net on behalf of Robert Kern Sent: Fri 6/17/2005 2:13 PM To: SciPy Developers List Subject: Re: [SciPy-dev] Roadmap for scipy Nils Wagner wrote: > Dear Scipy-developers, > > The activity with respect to scipy-cvs is considerably lower than that > of other projects e.g. matplotlib > (at least for the last 4 months). > Is there any road map for further development of scipy right now ? Not an official one, I don't think. Personally, some day I'm going to get around to implementing the Mersenne Twister PRNG for Scipy. I have an implementation of Particle Swarm Optimization that needs some polishing, and I am working on a Differential Evolution code. Ideas for the units system I outlined a while ago keeps nagging me, but I don't know if I will ever get around to it. There is always the Accessible Scipy roadmap, but it needs volunteers. http://www.scipy.org/mailinglists/mailman?fn=scipy-dev/2004-October/002412.… -- Robert Kern rkern(a)ucsd.edu "In the fields of hell where the grass grows high Are the graves of dreams allowed to die." -- Richard Harter _______________________________________________ Scipy-dev mailing list Scipy-dev(a)scipy.net http://www.scipy.net/mailman/listinfo/scipy-dev

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Roadmap for scipy
by Nils Wagner 18 Jun '05

18 Jun '05

Dear Scipy-developers, The activity with respect to scipy-cvs is considerably lower than that of other projects e.g. matplotlib (at least for the last 4 months). Is there any road map for further development of scipy right now ? I would be glad to get some feedback to the point. Nils

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Status of LiveDocs?
by Tom Loredo 16 Jun '05

16 Jun '05

Hi folks- What is the status of LiveDocs? I have two summer students who I am introducing to Python & SciPy, and they are finding documentation to be an obstacle. I've been trying to access LiveDocs via the Documentation Home page for a few days now, with no luck. I was hoping they might find LiveDocs to be helpful.... Thanks, Tom

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