Mailman 3 March 2008 - SciPy-Dev

Re: [SciPy-dev] scipy.optimize.nonlin.broyden2
by Ondrej Certik 20 Mar '08

20 Mar '08

On Wed, Mar 19, 2008 at 9:30 PM, argriffi <argriffi(a)ncsu.edu> wrote: > Hi Ondrej, > > Running the attached script should demonstrate the problem I mentioned. > I removed dependencies on other modules I had written, but let me know > if you want it reduced even further. Thanks, that is enough. I can reproduce the problem now: ------------------ test_solver_20 (__main__.TestCodonInversion) ... ok test_solver_40 (__main__.TestCodonInversion) ... ERROR ====================================================================== ERROR: test_solver_40 (__main__.TestCodonInversion) ---------------------------------------------------------------------- Traceback (most recent call last): File "CodonInversion.py", line 181, in test_solver_40 self._test_solver_helper(40) File "CodonInversion.py", line 173, in _test_solver_helper raise RuntimeError('failed on iteration %d of %d: %s' % (len(objective_function.guesses), iterations, str(e))) RuntimeError: failed on iteration 22 of 40: detected possibly invalid input to the objective function: (nan, nan, nan) ---------------------------------------------------------------------- Ran 2 tests in 0.029s FAILED (errors=1) ------------------------- And the reason is simple. If you look at this code: for n in range(iter): deltaxm=-Gm*Fxm xm=xm+deltaxm Fxm1=myF(F,xm) deltaFxm=Fxm1-Fxm Fxm=Fxm1 Gm=Gm+(deltaxm-Gm*deltaFxm)*deltaFxm.T/norm(deltaFxm)**2 And if you debug it, as I just did (for example using winpdb), you'll notice, that deltaFxm gets zero, after a lot of iterations, because you converged to a solution already. Then norm(deltaFxm) is 0 and after dividing by 0, you get a NaN in Gm, thus you get NaN in deltaxm and xm and you get NaN as an input into your function and here we are. The solution is to check that deltaFxm is near zero and stop iterating. Do you think you could please provide such a patch? :) Also with a test case. Thanks, Ondrej P.S. I CCed scipy-dev as I think you forgot to forward your email to it. I hope it's ok.

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openopt and algencan
by Nils Wagner 20 Mar '08

20 Mar '08

Hi all, I encountered a problem related to the python interface of algencan. See http://www.ime.usp.br/~egbirgin/tango/py.php The backtrace of my small test (comparison.py) is as follows: starting solver ALGENCAN (license: GPL) with problem unnamed *** glibc detected *** double free or corruption (out): 0x0000000000e17a40 *** PYTHON INTERFACE ERROR: in inip, PyEval_CallFunction returned NULL Program received signal SIGABRT, Aborted. [Switching to Thread 182894186368 (LWP 5735)] 0x0000003390e2e21d in raise () from /lib64/tls/libc.so.6 (gdb) bt #0 0x0000003390e2e21d in raise () from /lib64/tls/libc.so.6 #1 0x0000003390e2fa1e in abort () from /lib64/tls/libc.so.6 #2 0x0000003390e63291 in __libc_message () from /lib64/tls/libc.so.6 #3 0x0000003390e68eae in _int_free () from /lib64/tls/libc.so.6 #4 0x0000003390e691f6 in free () from /lib64/tls/libc.so.6 #5 0x0000002a9df3bd71 in memFree () from /data/home/nwagner/TANGO/pywrapper.so #6 0x0000002a9df3dc6b in pywrapper_solver () from /data/home/nwagner/TANGO/pywrapper.so #7 0x000000000048994b in PyEval_EvalFrameEx (f=0x1234c30, throwflag=Variable "throwflag" is not available. ) at Python/ceval.c:3564 #8 0x000000000048a205 in PyEval_EvalFrameEx (f=0x124f6b0, throwflag=Variable "throwflag" is not available. ) at Python/ceval.c:3650 #9 0x000000000048b791 in PyEval_EvalCodeEx (co=0x2a9d6ff288, globals=Variable "globals" is not available. ) at Python/ceval.c:2831 #10 0x00000000004894d1 in PyEval_EvalFrameEx (f=0x120f9e0, throwflag=Variable "throwflag" is not available. ) at Python/ceval.c:3659 #11 0x000000000048b791 in PyEval_EvalCodeEx (co=0x2a9c911918, globals=Variable "globals" is not available. ) at Python/ceval.c:2831 #12 0x00000000004d8ab8 in function_call (func=0x2a9c911aa0, arg=0x2a9cc91200, kw=0x12393f0) at Objects/funcobject.c:517 #13 0x00000000004194c3 in PyObject_Call (func=Variable "func" is not available. ) at Objects/abstract.c:1860 #14 0x0000000000487f3b in PyEval_EvalFrameEx (f=0x1210980, throwflag=Variable "throwflag" is not available. ) at Python/ceval.c:3844 #15 0x000000000048b791 in PyEval_EvalCodeEx (co=0x2a9b6b93f0, globals=Variable "globals" is not available. ) at Python/ceval.c:2831 #16 0x00000000004894d1 in PyEval_EvalFrameEx (f=0x6d2690, throwflag=Variable "throwflag" is not available. ) at Python/ceval.c:3659 #17 0x000000000048b791 in PyEval_EvalCodeEx (co=0x2a955fec60, globals=Variable "globals" is not available. ) at Python/ceval.c:2831 #18 0x000000000048b902 in PyEval_EvalCode (co=Variable "co" is not available. ) at Python/ceval.c:494 #19 0x00000000004adc9e in PyRun_FileExFlags (fp=0x65c010, filename=0x7fbffffa2c "comparison.py", start=Variable "start" is not available. ) at Python/pythonrun.c:1271 #20 0x00000000004aeb1f in PyRun_SimpleFileExFlags (fp=0x65c010, filename=0x7fbffffa2c "comparison.py", closeit=1, flags=0x7fbffff5dc) at Python/pythonrun.c:877 #21 0x0000000000411f77 in Py_Main (argc=-1073743316, argv=Variable "argv" is not available. ) at Modules/main.c:523 #22 0x0000003390e1c3fb in __libc_start_main () from /lib64/tls/libc.so.6 #23 0x000000000041163a in _start () How can I resolve the problem ? Any pointer would be appreciated. Thanks in advance Nils

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NumPy (1.0.5) DocDay (Fri, Mar. 21)
by Jarrod Millman 20 Mar '08

20 Mar '08

Hello, As I mentioned yesterday, I am holding a NumPy DocDay on Friday, March 21st. I am in Paris near the RER B or C Saint-Michel station (with Stefan van der Walt, Matthieu Brucher, and Gael Varoquaux). If you are in the area and want to join us just send me an email by the end of tonight and I will let you know where we are meeting. If you can't stop by, but are still willing to help out we will convene on IRC during the day on Friday (9:30am-?? GMT+1). Come join us at irc.freenode.net (channel scipy). We may update the list of priorities which is still located on the NumPy Trac Wiki: http://projects.scipy.org/scipy/numpy/wiki/DocDays While I am hoping to have everyone focus on NumPy, I would be happy if anyone wants to work on SciPy documentation as well: http://projects.scipy.org/scipy/scipy/wiki/DocDays Thanks, -- Jarrod Millman Computational Infrastructure for Research Labs 10 Giannini Hall, UC Berkeley phone: 510.643.4014 http://cirl.berkeley.edu/

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scikits learn
by Nils Wagner 20 Mar '08

20 Mar '08

Hi all, I found a syntax error in scikit learn. This is related to python version 2.4 Compiling /usr/lib/python2.4/site-packages/scikits/learn/utils/arffread.py ... File "/usr/lib/python2.4/site-packages/scikits/learn/utils/arffread.py", line 401 finally: SyntaxError: invalid syntax Nils

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Re: [SciPy-dev] bug in scipy.signal.wavelets.morlet()?
by Christoph T. Weidemann 20 Mar '08

20 Mar '08

> Thanks, Christoph. This is now fixed in SVN. Do you have a simple > test case we can use to ensure this doesn't happen again? I'll try to write a test case. Once I have the code, what's the best way for me to submit it? It would probably be easiest for me if I could get write access to the SVN repository (I'd be happy to make more contributions in the future ... I often notice small things that could be improved such as docstrings, but don't always take the time to submit a bug report), but I understand if you have more stringent criteria than a bug report and stated desire for granting people write access. On a slightly off-topic note, the following bug report (with fix!) seems to have been ignored since it was reported 2 months ago: http://scipy.org/scipy/scipy/ticket/595 Generally, what's the best way to report bugs? the wiki, this mailing list, both, ...? Best, Christoph

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unexpectedly slow norm()
by Nathan Bell 19 Mar '08

19 Mar '08

I use norm() frequently in my own codes and I was recently surprised to see it near the top of my profiling results. It seems that both SciPy and NumPy incur a large amount of overhead in this operation. Consider the following script ================================= from time import clock from numpy import inner, sqrt, ones import numpy.linalg import scipy.linalg from scipy.lib.blas import get_blas_funcs x = ones(5*1000*1000) scipy_norm = scipy.linalg.norm numpy_norm = numpy.linalg.norm def adhoc_norm(x): return sqrt(inner(x,x)) blas_norm = get_blas_funcs(('nrm2',),(x,))[0] for fn in [scipy_norm, numpy_norm, adhoc_norm, blas_norm ]: start = clock() for i in range(10): n = fn(x) end = clock() print "%f seconds per call" % ((end - start)/10.0) ================================= Which outputs the following on my laptop: 0.407000 seconds per call 0.089000 seconds per call 0.013000 seconds per call 0.012000 seconds per call -- Nathan Bell wnbell(a)gmail.com http://graphics.cs.uiuc.edu/~wnbell/

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scipy.optimize.nonlin.broyden2
by argriffi 19 Mar '08

19 Mar '08

This function solved my problem when I used 20 iterations, but when I used 40 iterations I got (nan, nan, nan). I logged the successive points for which my function was evaluated, and the process seemed to have converged to the correct answer before suddenly deciding to give nans. My current solution is to just use 20 iterations, but I would be interested to hear a safer solution. Alex

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bug in scipy.signal.wavelets.morlet()?
by Christoph T. Weidemann 19 Mar '08

19 Mar '08

Hi All! I came across what seems to me like an obvious bug in scipy.signal.wavelets.morlet(): If complete==True (the default setting) the output does not correspond to the formula in the docstring. I believe the bug would be fixed if the if statement were changed from: if complete: x -= exp(-0.5*(w**2)) to if complete: output -= exp(-0.5*(w**2)) Best, Christoph Weidemann

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DEFAULT section in site.cfg
by Stéfan van der Walt 18 Mar '08

18 Mar '08

Hi all, ConfigParser no longer allows a 'DEFAULT' section under Python 2.6, so I'd like to change that part of the site.cfg to something like 'general' or 'all'. Any suggestions, comments? Regards Stéfan

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Splitting sparsetools_wrap source file ?
by David Cournapeau 18 Mar '08

18 Mar '08

Hi, I think we already had a discussion about that a few months ago, and I would like to reiterate my wish of splitting the sparsetools_wrap source file. C++ compilers are already dead slow, and with such a big source file, compiling this file alone makes for a big part of the whole scipy build time. Is is possible to split source files ? Or having something smaller ? cheers, David

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