Mailman 3 August 2006 - NumPy-Discussion

numpy1.04b4: undefined symbol: PyUnicodeUCS2_FromUnicode. error No _WIN32
by rex Aug. 28, 2006

Aug. 28, 2006

Numpy builds, but fails to run with the error message: > python Python 2.4.2 (#1, Apr 24 2006, 18:13:30) [GCC 4.1.0 (SUSE 10.1 Linux)] on linux2 >>> import numpy Traceback (most recent call last): File "<stdin>", line 1, in ? File "/usr/lib/python2.4/site-packages/numpy/__init__.py", line 35, in ? import core File "/usr/lib/python2.4/site-packages/numpy/core/__init__.py", line 5, in ? import multiarray ImportError: /usr/lib/python2.4/site-packages/numpy/core/multiarray.so: undefined symbol: PyUnicodeUCS2_FromUnicode Build was without BLAS or LAPACK. Results were the same when Intel MKL was used. python setup.py install >& inst.log Running from numpy source directory. non-existing path in 'numpy/distutils': 'site.cfg' F2PY Version 2_3078 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 [...] running install running build running config_fc running build_src building py_modules sources building extension "numpy.core.multiarray" sources adding 'build/src.linux-i686-2.4/numpy/core/config.h' to sources. executing numpy/core/code_generators/generate_array_api.py adding 'build/src.linux-i686-2.4/numpy/core/__multiarray_api.h' to sources. adding 'build/src.linux-i686-2.4/numpy/core/src' to include_dirs. numpy.core - nothing done with h_files= ['build/src.linux-i686-2.4/numpy/core/src/scalartypes .inc', 'build/src.linux-i686-2.4/numpy/core/src/arraytypes.inc', 'build/src.linux-i686-2.4/nu mpy/core/config.h', 'build/src.linux-i686-2.4/numpy/core/__multiarray_api.h'] building extension "numpy.core.umath" sources adding 'build/src.linux-i686-2.4/numpy/core/config.h' to sources. executing numpy/core/code_generators/generate_ufunc_api.py adding 'build/src.linux-i686-2.4/numpy/core/__ufunc_api.h' to sources. adding 'build/src.linux-i686-2.4/numpy/core/src' to include_dirs. numpy.core - nothing done with h_files= ['build/src.linux-i686-2.4/numpy/core/src/scalartypes .inc', 'build/src.linux-i686-2.4/numpy/core/src/arraytypes.inc', 'build/src.linux-i686-2.4/nu mpy/core/config.h', 'build/src.linux-i686-2.4/numpy/core/__ufunc_api.h'] building extension "numpy.core._sort" sources adding 'build/src.linux-i686-2.4/numpy/core/config.h' to sources. executing numpy/core/code_generators/generate_array_api.py adding 'build/src.linux-i686-2.4/numpy/core/__multiarray_api.h' to sources. numpy.core - nothing done with h_files= ['build/src.linux-i686-2.4/numpy/core/config.h', 'bui ld/src.linux-i686-2.4/numpy/core/__multiarray_api.h'] building extension "numpy.core.scalarmath" sources adding 'build/src.linux-i686-2.4/numpy/core/config.h' to sources. executing numpy/core/code_generators/generate_array_api.py adding 'build/src.linux-i686-2.4/numpy/core/__multiarray_api.h' to sources. executing numpy/core/code_generators/generate_ufunc_api.py adding 'build/src.linux-i686-2.4/numpy/core/__ufunc_api.h' to sources. numpy.core - nothing done with h_files= ['build/src.linux-i686-2.4/numpy/core/config.h', 'bui ld/src.linux-i686-2.4/numpy/core/__multiarray_api.h', 'build/src.linux-i686-2.4/numpy/core/__ ufunc_api.h'] building extension "numpy.core._dotblas" sources building extension "numpy.lib._compiled_base" sources building extension "numpy.numarray._capi" sources building extension "numpy.fft.fftpack_lite" sources building extension "numpy.linalg.lapack_lite" sources ### Warning: Using unoptimized lapack ### adding 'numpy/linalg/lapack_litemodule.c' to sources. adding 'numpy/linalg/zlapack_lite.c' to sources. adding 'numpy/linalg/dlapack_lite.c' to sources. adding 'numpy/linalg/blas_lite.c' to sources. adding 'numpy/linalg/dlamch.c' to sources. adding 'numpy/linalg/f2c_lite.c' to sources. building extension "numpy.random.mtrand" sources Could not locate executable f95 customize GnuFCompiler customize GnuFCompiler customize GnuFCompiler using config ******************************************************************************************* C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC compile options: '-Inumpy/core/src -Inumpy/core/include -I/usr/include/python2.4 -c' gcc: _configtest.c _configtest.c:7:2: error: #error No _WIN32 _configtest.c:7:2: error: #error No _WIN32 failure. removing: _configtest.c _configtest.o ******************************************************************************************* building data_files sources [...] changing mode of /usr/bin/f2py to 755 running install_data copying build/src.linux-i686-2.4/numpy/core/__multiarray_api.h -> /usr/lib/python2.4/site-pac kages/numpy/core/include/numpy copying build/src.linux-i686-2.4/numpy/core/multiarray_api.txt -> /usr/lib/python2.4/site-pac kages/numpy/core/include/numpy copying build/src.linux-i686-2.4/numpy/core/__ufunc_api.h -> /usr/lib/python2.4/site-packages /numpy/core/include/numpy copying build/src.linux-i686-2.4/numpy/core/ufunc_api.txt -> /usr/lib/python2.4/site-packages /numpy/core/include/numpy Any pointers would be much appreciated. This isn't the first time I've spent days trying to get SciPy built under SUSE... :( -rex

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Re: [Numpy-discussion] C Api newbie question
by Matt Knox Aug. 28, 2006

Aug. 28, 2006

>>Matt Knox wrote:>>> Hi there. I'm in the unfortunate situation of trying to track down a >> memory error in someone elses code, and to make matters worse I don't >> really know jack squat about C programming. The problem seems to arise >> when several numpy arrays are created from C arrays in the C api and >> returned to python, and then trying to print out or cast to a string >> the resulting array. I think the problem may be happening due to the >> following chunk of code:>> {>> PyObject* temp = PyArray_SimpleNewFromData(1, &numobjs, typeNum, >> dbValues);>> PyObject* temp2 = PyArray_FromArray((PyArrayObject*)temp, >> ((PyArrayObject*)temp)->descr, DEFAULT_FLAGS | ENSURECOPY);>> Py_DECREF(temp);>> PyDict_SetItemString(returnVal, "data", temp2);>> Py_DECREF(temp2);>> }>> >> Lets assume that all my other inputs up this point are fine and that >> numobjs, typeNum, and dbValues are fine. Is their anything obviously >> wrong with the above chunk of code? or does it appear ok? Ultimately >> the dictionary "returnVal" is returned by the function this code came >> from, and everything else is discarded. Any help is very greatly >> appreciated. Thanks in advance, > You didn't indicate what kind of trouble you are having.>> First of all, this is kind of odd style. Why is a new array created > from a data-pointer and then copied using PyArray_FromArray (the > ENSURECOPY flag will give you a copy)? Using>> temp2 = PyArray_Copy(temp)>> seems simpler. This will also avoid the reference-count problem that > is currently happening in the PyArray_FromArray call on the descr > structure. Any array-creation function that takes a descr structure > "steals" a reference to it, so you need to increment the reference count > if you are passing an unowned reference to a ->descr structure.>> -Travis Sorry. Yeah, the problem was the interpreter crashing on exit, which afteryour response definitely seems like it was a reference count issue. Ichanged the PyArray_FromArray call to be PyArray_Copy and it seems to workfine. Thank you very much! Love the numpy stuff (when I can stay in the python world and not mess withthe C stuff :) ). Keep up the great work! - Matt _________________________________________________________________ Be one of the first to try Windows Live Mail. http://ideas.live.com/programpage.aspx?versionId=5d21c51a-b161-4314-9b0e-49…

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memory corruption bug
by Sven Schreiber Aug. 28, 2006

Aug. 28, 2006

Hi, I experienced this strange bug which caused a totally unrelated variable to be overwritten (no exception or error was raised, so it took me while to rule out any errors of my own). The context where this is in is a method of a class (Vecm.getSW()), and the instance of Vecm is created within a different class (GG.__init__). Now, the affected variable is in the namespace of GG (it's GG.urate), and so I would think that anything local in Vecm.getSW() should not affect GG.urate, right? Originally I did: glx[lag:, :] -= temp But that caused the described problem. Then I tried: glx[lag:, :] = glx[lag:, :] - temp But the same problem remains. Then I worked around the slice assignment like this: temp4 = r_[zeros([lag, n_y]), temp] glx = glx - temp4 And everything is ok! However, when I alter the second line of this workaround to: glx -= temp4 The problem reappears! So I'm not even sure whether this is one or two bugs... This is with yesterday's numpy svn on windows, but the same thing happens with an earlier svn (~b2) as well. If you need further info, please tell me how to provide it. Thanks, Sven

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worthwhile carefree
by Beatrix Mcgrath Aug. 28, 2006

Aug. 28, 2006

The driver, a young man showily dressed, shoved down hishand-brake with an angry expression. Allevidences of the room having been used had been obliterated. Anyhow he wouldbe unable to penetrate to the truth. A little farther on hesecured a basket of Alpine strawberries. Its only effect was to make his pulsesthrob more wildly. He seizedher hand, pressing it hard, and fixed his eyes on hers. Allevidences of the room having been used had been obliterated. What else might happen he did not care, he must set himself free fromthis. Just once he looked back, then went into his room. Richard wanted to tell the man to drive to the hotel at once, but MrKurt would not let him. She was too statuesque to fall in love with. Thesethoughts flashed through his mind as he paused. Walking aimlessly through the Galleria Umberto, he ran into CesareSismondo. His father wassitting on a chair tugging at his shoes. Youll have to spend the night here, thats all. Was this a foundation uponwhich to rebuild his life? One or two people were moving about the hall on theirway to their rooms. We drove back again and I never even kissedher. He would leave the lake now and for ever. Richard managed to introduce other topics, and soonafterwards his father said he would go to bed. I must go and leave some cards, good-bye Katie, honey. I drove her to the racesin a hired drag with two horses. Atthe bridge over the Serpentine Ive got back to my marriage and UncleTheos cable to Dr Flössheim. Perhaps she wont even be there and if sheis I may not be able to speak to her. I often think of that wonderful stroke of luck of yours. Elinors affairs werevenial in comparison. He had not finished his cigarette when Virginia rushedinto the room, breathless. And by a strange irony it was he who at variousmoments of crisis in my life stood in the breach. They carried the parcels between them, and Richard took leave of heroutside the palazzo Peraldi. Itelephoned afterwards but I couldnt understand a word.

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Optimizing mean(axis=0) on a 3D array
by Martin Spacek Aug. 28, 2006

Aug. 28, 2006

Hello, I'm a bit ignorant of optimization in numpy. I have a movie with 65535 32x32 frames stored in a 3D array of uint8 with shape (65535, 32, 32). I load it from an open file f like this: >>> import numpy as np >>> data = np.fromfile(f, np.uint8, count=65535*32*32) >>> data = data.reshape(65535, 32, 32) I'm picking several thousand frames more or less randomly from throughout the movie and finding the mean frame over those frames: >>> meanframe = data[frameis].mean(axis=0) frameis is a 1D array of frame indices with no repeated values in it. If it has say 4000 indices in it, then the above line takes about 0.5 sec to complete on my system. I'm doing this for a large number of different frameis, some of which can have many more indices in them. All this takes many minutes to complete, so I'm looking for ways to speed it up. If I divide it into 2 steps: >>> temp = data[frameis] >>> meanframe = temp.mean(axis=0) and time it, I find the first step takes about 0.2 sec, and the second takes about 0.3 sec. So it's not just the mean() step, but also the indexing step that's taking some time. If I flatten with ravel: >>> temp = data[frameis].ravel() >>> meanframe = temp.mean(axis=0) then the first step still takes about 0.2 sec, but the mean() step drops to about 0.1 sec. But of course, this is taking a flat average across all pixels in the movie, which isn't what I want to do. I have a feeling that the culprit is the non contiguity of the movie frames being averaged, but I don't know how to proceed. Any ideas? Could reshaping the data somehow speed things up? Would weave.blitz or weave.inline or pyrex help? I'm running numpy 0.9.8 Thanks, Martin

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bad generator behaviour with sum
by listservs＠mac.com Aug. 28, 2006

Aug. 28, 2006

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 It seems like numpy.sum breaks generator expressions: In [1]: sum(i*i for i in range(10)) Out[1]: 285 In [2]: from numpy import sum In [3]: sum(i*i for i in range(10)) Out[3]: <generator object at 0x10eca58> Is this intentional? If so, how do I get the behaviour that I am after? Thanks, C. - -- Christopher Fonnesbeck + Atlanta, GA + fonnesbeck at mac.com + Contact me on AOL IM using email address -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.3 (Darwin) iD8DBQFE8fEKkeka2iCbE4wRAoi6AKCjqJHodGOme56nohrG3X/njjaHgACeIkyn PPB2+plZOyqV+HyLJgO+sSw= =Y0wt -----END PGP SIGNATURE-----

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odd import behavior
by Matthew Auger Aug. 28, 2006

Aug. 28, 2006

I recently installed python2.5c1, numpy-1.0b3, and matplotlib-0.87.4. I was getting an error when importing pylab that led me to this curious behavior: bash-2.05b$ python Python 2.5c1 (r25c1:51305, Aug 23 2006, 18:41:45) [GCC 4.0.2] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> from numpy.oldnumeric import * >>> M = matrix Traceback (most recent call last): File "<stdin>", line 1, in <module> NameError: name 'matrix' is not defined >>> from numpy.oldnumeric import matrix >>> M = matrix >>> Is there a reason matrix is not imported the first time?

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Constant array
by Carlos Pita Aug. 28, 2006

Aug. 28, 2006

Hi all! Is there a more efficient way of creating a constant K-valued array of size N than: zeros(N) + K ? Thank you in advance. Regards, Carlos --------------------------------- Preguntá. Respondé. Descubrí. Todo lo que querías saber, y lo que ni imaginabas, está en Yahoo! Respuestas (Beta). Probalo ya!

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Re: [Numpy-discussion] bad generator behaviour with sum
by listservs＠mac.com Aug. 28, 2006

Aug. 28, 2006

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Aug 27, 2006, at 4:19 PM, numpy-discussion- request(a)lists.sourceforge.net wrote: >> >> It seems like numpy.sum breaks generator expressions: >> >> In [1]: sum(i*i for i in range(10)) >> Out[1]: 285 >> >> In [2]: from numpy import sum >> >> In [3]: sum(i*i for i in range(10)) >> Out[3]: <generator object at 0x10eca58> >> >> Is this intentional? If so, how do I get the behaviour that I am >> after? >> > > > In [3]: sum([i*i for i in range(10)]) > Out[3]: 285 Well, thats a list comprehension, not a generator expression. I was after the latter because it is more efficient. Thanks, C. - -- Christopher Fonnesbeck + Atlanta, GA + fonnesbeck at mac.com + Contact me on AOL IM using email address -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.3 (Darwin) iD8DBQFE8hgdkeka2iCbE4wRAq8lAJ9dKPYQ35IE3qacf9K1KsBL59mdRACePn5S x0wHWs/PrVcJHCqf9tbQwRk= =0wFp -----END PGP SIGNATURE-----

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ticket system does not like me ! - seems broken ...
by Sebastian Haase Aug. 28, 2006

Aug. 28, 2006

Hi, I started submitting tickets over the numpy ticket system. But I never get email feedback when comments get added. Even though I put myself as CC. I then even subscribed to both scipy and numpy ticket mailing lists. I only got *some* numpy tickets emailed - very sporadically ! (I do get (lot's of) email from the svn mailing list.) Do others see similar problems ? -Sebastian Haase

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