Mailman 3 October 2006 - NumPy-Discussion

Can' compile numpy 1.02rc3 on OSX 10.3.9
by Markus Rosenstihl 02 Nov '06

02 Nov '06

Hi! I try to compile numpy rc3 on Panther and get following errors. (I start build with "python2.3 setup.py build" to be sure to use the python shipped with OS X. I din't manage to compile Python2.5 either yet with similar errors) Does anynbody has an Idea? gcc-3.3 XCode 1.5 November gcc updater is installed regards Markus python2.3 setup.py build ... compile options: '-Ibuild/src.darwin-7.9.0-Power_Macintosh-2.3/numpy/core/src -Inumpy/core/include -Ibuild/src.darwin-7.9.0-Power_Macintosh-2.3/numpy/core -Inumpy/core/src -Inumpy/core/include -I/System/Library/Frameworks/Python.framework/Versions/2.3/include/ python2.3 -c' gcc: numpy/core/src/multiarraymodule.c In file included from numpy/core/src/arrayobject.c:511, from numpy/core/src/multiarraymodule.c:63: numpy/core/src/arraytypes.inc.src: In function `LONGDOUBLE_scan': numpy/core/src/arraytypes.inc.src:883: warning: long double format, npy_longdouble arg (arg 3) gcc -Wl,-F. -Wl,-F. -bundle -framework Python build/temp.darwin-7.9.0-Power_Macintosh-2.3/numpy/core/src/ multiarraymodule.o -o build/lib.darwin-7.9.0-Power_Macintosh-2.3/numpy/core/multiarray.so ld: Undefined symbols: _fstatvfs referenced from Python expected to be defined in libSystem _lchown referenced from Python expected to be defined in libSystem _statvfs referenced from Python expected to be defined in libSystem ld: Undefined symbols: _fstatvfs referenced from Python expected to be defined in libSystem _lchown referenced from Python expected to be defined in libSystem _statvfs referenced from Python expected to be defined in libSystem error: Command "gcc -Wl,-F. -Wl,-F. -bundle -framework Python build/temp.darwin-7.9.0-Power_Macintosh-2.3/numpy/core/src/ multiarraymodule.o -o build/lib.darwin-7.9.0-Power_Macintosh-2.3/numpy/core/multiarray.so" failed with exit status 1 ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642

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pyaudio 0.3, with docs !
by David Cournapeau 01 Nov '06

01 Nov '06

Hi, I improved pyaudio last WE using indications given by various people on the list or privately, and as I finally got the motivation to set-up something which looks like a webpage, there is a doc with examples which show how to use it. The API to open files for writing is much saner, and the setup.py should be smart enough to grab all informations necessary to the wrapper, including the location of the shared libsndfile: download: http://www.ar.media.kyoto-u.ac.jp/members/david/softwares/pyaudio/#installa… doc + examples: http://www.ar.media.kyoto-u.ac.jp/members/david/softwares/pyaudio/ I would appreciate to hear reports on platforms which are not linux (windows, mac os X) to see if my the setup.py works there, Cheers, David

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Re: [Numpy-discussion] Need more comments from scientific community on python-dev
by Travis Oliphant 01 Nov '06

01 Nov '06

Fernando Perez wrote: >On 10/31/06, Rich Shepard <rshepard(a)appl-ecosys.com> wrote: > > >>On Tue, 31 Oct 2006, Alan Isaac wrote: >> >> >> >>>The easiest access to this discussion for me was >>>http://news.gmane.org/group/gmane.comp.python.devel/ I cannot add to this >>>discussion, but I REALLY hope others will help Travis out here. (A few >>>have.) He is fielding a lot of questions, some of which look to me to be >>>from individuals who are ready to have fairly strong opinions without >>>really understanding the "why" of his proposals. >>> >>> >> All this is sufficiently far from my areas of expertise that I cannot >>contribute anything useful. Otherwise, I'd be happy to lend support. >> >> > >I actually worry about the same: I really would like to help, but >after reading the whole discussion, I realized that the low-level >details being asked and discussed are something I don't really know >enough to say anything. And I don't want to sound simply saying 'Hey, >Travis is great, listen to him!' to python-dev, since that (asides >from looking silly) can be somewhat counter-productive. > > >How does that sound, Travis? Is that something you think might help >you, esp. since so many of us are feeling woefully underqualified to >lend a useful hand in the actual discussion on python-dev? > > That would be great. I think a couple of things would also be useful. 1) Some way to indicate to python-dev that I'm actually speaking for more than just myself. So, while I agree that just supporting my PEP (which probably in reality needs work) without understanding it is counter-productive, a voice that says. "We really do need this kind of functionality" is at least one more voice. 2) Examples of sharing memory between two objects. PIL is the classic example and has some merit, but because the internal memory layout of the PIL is 'pointer-to-pointers' instead of 'big-chunk-of-memory' it's not a 1-1 match to NumPy and the array interface only can comunicate information about the "mode." But, I can see other examples. PyMedia, PyGame, PyVideo? CVXOPT, PyVoxel. All of these seem to define their own objects which are basically just interpretations of chunks of memory. At one time, we might have said "these should all be sub-classes of the ndarray". Now, we are thinking more along the lines of "these should all expose an array interface". The array interface is still more bulky then it needs to be (it has to go through the attribute-lookup process which can be slow). It would be much better if the extended buffer protocol were available as a function-pointer on the type object of the type. If you have an application where you've ever wanted NumPy in the core. See if the extended buffer protocol serves your purposes and if you agree, voice your approval for the PEP. In my mind, the data-format PEP does not need to go through if there really is a better way to pass data-format information through the buffer protocol. But, the extended buffer protocol we *do* need. -Travis >Regards, > >f >_______________________________________________ >SciPy-user mailing list >SciPy-user(a)scipy.org >http://projects.scipy.org/mailman/listinfo/scipy-user > >

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installing numpy on Tiger
by Alan Isaac 31 Oct '06

31 Oct '06

If other users will not profit from this question, please consider it OT and ignore it. But perhaps it will prove useful to some potential numpy users. I am a long time Windows user who has been happily using the Python and numpy installers. At work I need to use a Mac for a while. I installed Python 2.5 from python.org painlessly, but it looks like I'll have to compile numpy from source. Do I understand that right? I have used interpreted languages for pretty much all my computing needs, so I am hoping someone patient will point me to or lead me through the steps I need to take to successfully install numpy on this platform. Thank you, Alan Isaac ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642

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Haley Padgett
by Crystal Xiong 31 Oct '06

31 Oct '06

------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ Numpy-discussion mailing list Numpy-discussion(a)lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/numpy-discussion

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dtype.hasobject value
by Matthew Brett 31 Oct '06

31 Oct '06

Hi, I notice that the value for: zeros((1,), dtype=object).dtype.hasobject is now 63, whereas previously it had been 1. Is this intended? Thanks, Matthew ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642

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matrixdef.py
by Colin J. Williams 30 Oct '06

30 Oct '06

Line 71 has: data.view(subtype) This appears to involve a call to __array_finalize__. Is this an unconditional call? If not, what are the conditions? Why not use __init__ to handle these things, since it is always called after the __new__? Colin W. ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642

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Strange numpy.argmax behavior on object arrays in numpy 1.0.
by Tom Denniston 30 Oct '06

30 Oct '06

I recently upgraded to numpy 1.0 from 1.0b5. I noticed that numpy.argmaxbehavior is very strange on object arrays. See below: (Pdb) numpy.__version__ '1.0' (Pdb) numpy.argmax(numpy.array([2, 3], dtype=object)) 0 (Pdb) numpy.argmax(numpy.array([2, 3], dtype=int)) 1 (Pdb) numpy.argmax(numpy.array([2, 3], dtype=object), axis=0) 0 I would expect the argmax to behave the same on the dtype=int and dtype=object examples but it doesn't. Am I missing some subtelty or is this just a bug? 1.0 is the most recent version, right? --Tom ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ Numpy-discussion mailing list Numpy-discussion(a)lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/numpy-discussion

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Conversion about getting array interface into Python
by Travis Oliphant 30 Oct '06

30 Oct '06

If anybody has a desire to see the array interface into Python, please help by voicing an opinion on python-dev in the discussion about adding data-type objects to Python. There are a few prominent people who don't get why applications would need to share data-type information about memory areas. I need help giving reasons why. -Travis ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642

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glibc invalid pointer error
by David Huard 30 Oct '06

30 Oct '06

Hi, I have a script that crashes, but only if it runs over 9~10 hours, with the following backtrace from gdb. The script uses PyMC, and repeatedly calls (> 1000000) likelihood functions written in fortran and wrapped with f2py. Numpy: 1.0.dev3327 Python: 2.4.3 Does this backtrace give enough info to track the problem or do the gurus need more ? Thanks, David *** glibc detected *** free(): invalid pointer: 0x00002aaaac1257e0 *** Program received signal SIGABRT, Aborted. [Switching to Thread 46912504440528 (LWP 25269)] 0x00002aaaab09011d in raise () from /lib/libc.so.6 (gdb) backtrace #0 0x00002aaaab09011d in raise () from /lib/libc.so.6 #1 0x00002aaaab09184e in abort () from /lib/libc.so.6 #2 0x00002aaaab0c4e41 in __fsetlocking () from /lib/libc.so.6 #3 0x00002aaaab0ca90e in malloc_usable_size () from /lib/libc.so.6 #4 0x00002aaaab0cac56 in free () from /lib/libc.so.6 #5 0x00002aaaabff7770 in PyArray_FromArray (arr=0x1569500, newtype=0x2aaaac1257e0, flags=0) at arrayobject.c:7804 #6 0x00002aaaabfece56 in PyArray_FromAny (op=0x1569500, newtype=0x0, min_depth=0, max_depth=0, flags=0, context=0x0) at arrayobject.c:8257 #7 0x00002aaaabff40b1 in PyArray_MultiIterNew (n=2) at arrayobject.c:10253 #8 0x00002aaaabff44bc in _broadcast_cast (out=0x62b5, in=0x6, castfunc=0x2aaaabfbf5a0 <DOUBLE_to_FLOAT>, iswap=-1, oswap=6) at arrayobject.c:7445 #9 0x00002aaaabffe301 in PyArray_CastToType (mp=0x156dca0, at=<value optimized out>, fortran_=0) at arrayobject.c:7344 #10 0x00002aaaabffe785 in PyArray_FromScalar (scalar=0x1573b30, outcode=0x2aaaac1257e0) at scalartypes.inc.src:219 #11 0x00002aaaabfecff5 in PyArray_FromAny (op=0x1573b30, newtype=0x2aaaac1257e0, min_depth=0, max_depth=<value optimized out>, flags=0, context=0x0) at arrayobject.c:8260 #12 0x00002aaab6038b7b in array_from_pyobj (type_num=11, dims=0x7fffff8f6200, rank=1, intent=<value optimized out>, obj=0x1573b30) at build/src.linux-x86_64-2.4/fortranobject.c:653 #13 0x00002aaab6034aa9 in f2py_rout_flib_beta ( capi_self=<value optimized out>, capi_args=<value optimized out>, capi_keywds=<value optimized out>, f2py_func=0x2aaab603e830 <beta_>) at build/src.linux-x86_64-2.4/PyMC/flibmodule.c:2601 #14 0x0000000000414490 in PyObject_Call () #15 0x0000000000475de5 in PyEval_EvalFrame () #16 0x00000000004bdf69 in PyDescr_NewGetSet () #17 0x00000000004143eb in PyIter_Next () #18 0x000000000046ba53 in _PyUnicodeUCS4_IsNumeric () #19 0x0000000000477ab1 in PyEval_EvalFrame () #20 0x00000000004783ff in PyEval_EvalCodeEx () #21 0x000000000047699b in PyEval_EvalFrame () #22 0x0000000000476ab6 in PyEval_EvalFrame () #23 0x0000000000476ab6 in PyEval_EvalFrame () #24 0x00000000004783ff in PyEval_EvalCodeEx () #25 0x000000000047699b in PyEval_EvalFrame () #26 0x00000000004783ff in PyEval_EvalCodeEx () #27 0x000000000047699b in PyEval_EvalFrame () #28 0x00000000004783ff in PyEval_EvalCodeEx () #29 0x000000000047699b in PyEval_EvalFrame () #30 0x00000000004783ff in PyEval_EvalCodeEx () #31 0x0000000000478512 in PyEval_EvalCode () #32 0x000000000049c222 in PyRun_FileExFlags () #33 0x000000000049c4ae in PyRun_SimpleFileExFlags () #34 0x0000000000410a80 in Py_Main () #35 0x00002aaaab07d49b in __libc_start_main () from /lib/libc.so.6 #36 0x000000000040ffba in _start () ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ Numpy-discussion mailing list Numpy-discussion(a)lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/numpy-discussion

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