Mailman 3 August 2004 - SciPy-User

Further OS X (Jaguar) difficulties
by Tom Loredo Aug. 12, 2004

Aug. 12, 2004

Hello again- Well, building MacPy 2.3.4 from source didn't help me, either. I get the same regexp error. I'm beginning to wonder if there's something wrong with my system (though I don't have any problems with other software, and running DiskWarrior didn't turn up anything nor did it fix the problem). I also tried it on my G3 laptop running 10.2.8, but with MacPy 2.3, and I get the same error. The laptop and my G4 don't have identical software, so I'm not sure what that says about the nature of my problems. I've altered linalg/interface_gen.py to use pre rather than re, and the build goes fine until sparsetools, which causes another segfault: building extension "scipy.signal.sigtools" sources building extension "scipy.signal.spline" sources building extension "scipy.sparse._zsuperlu" sources building extension "scipy.sparse._dsuperlu" sources building extension "scipy.sparse._csuperlu" sources building extension "scipy.sparse._ssuperlu" sources building extension "scipy.sparse.sparsetools" sources creating build/src/Lib/sparse creating build/src/Lib/sparse/sparsetools Segmentation fault Rather than track that down, I omitted 'sparse' from the build and things went a lot further, until I reached fftpack (I do have fftw installed, so I'm not sure I need this). The ld fails; it appears it cannot find Python symbols (lines wrapped below): ------- gcc: build/src/fortranobject.c cc1: warning: changing search order for system directory "/usr/local/include" cc1: warning: as it has already been specified as a non-system directory /usr/local/bin/g77 -lcc_dynamic -bundle build/temp.darwin-6.8-Power_Macintosh-2.3/build/src/Lib/fftpack/ _fftpackmodule.o build/temp.darwin-6.8-Power_Macintosh-2.3/Lib/fftpack/src/zfft.o build/temp.darwin-6.8-Power_Macintosh-2.3/Lib/fftpack/src/drfft.o build/temp.darwin-6.8-Power_Macintosh-2.3/Lib/fftpack/src/zrfft.o build/temp.darwin-6.8-Power_Macintosh-2.3/Lib/fftpack/src/zfftnd.o build/temp.darwin-6.8-Power_Macintosh-2.3/build/src/fortranobject.o -L/usr/local/lib -L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.0 -Lbuild/temp.darwin-6.8-Power_Macintosh-2.3 -ldfftpack -lrfftw -lfftw -lg2c -o build/lib.darwin-6.8-Power_Macintosh-2.3/scipy/fftpack/_fftpack.so /usr/bin/ld: Undefined symbols: _PyArg_ParseTuple _PyArg_ParseTupleAndKeywords _PyCObject_AsVoidPtr _PyCObject_Type _PyComplex_Type _PyDict_GetItemString _PyDict_SetItemString _PyErr_Clear [snip] _Py_FindMethod __PyObject_New restFP saveFP collect2: ld returned 1 exit status error: Command "/usr/local/bin/g77 -lcc_dynamic -bundle build/temp.darwin-6.8-Power_Macintosh-2.3/build/src/Lib/fftpack/ _fftpackmodule.o build/temp.darwin-6.8-Power_Macintosh-2.3/Lib/fftpack/src/zfft.o build/temp.darwin-6.8-Power_Macintosh-2.3/Lib/fftpack/src/drfft.o build/temp.darwin-6.8-Power_Macintosh-2.3/Lib/fftpack/src/zrfft.o build/temp.darwin-6.8-Power_Macintosh-2.3/Lib/fftpack/src/zfftnd.o build/temp.darwin-6.8-Power_Macintosh-2.3/build/src/fortranobject.o -L/usr/local/lib -L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.0 -Lbuild/temp.darwin-6.8-Power_Macintosh-2.3 -ldfftpack -lrfftw -lfftw -lg2c -o build/lib.darwin-6.8-Power_Macintosh-2.3/scipy/fftpack/_fftpack.so" failed with exit status 1 -------- If anyone knows how I might fix this, please advise. Or perhaps it's another clue regarding my earlier problems. Thanks again, Tom

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core dump during import
by Skip Montanaro Aug. 12, 2004

Aug. 12, 2004

I'm the "python guy" at work which by default makes me the "scipy installation guy" as well, though I'm not using it for any of my own projects. Awhile ago I performed a very basic installation: install latest f2py install Numeric 23.1 install SciPy_complete-0.3 The platform is Solaris 9 on Intel. I'm using Python 2.3.4 (though originally installed using 2.3.3). GCC and G77 are both at 3.3.2. The installation goes fine with the one caveat that I needed to point LD_RUN_PATH at the g77 lib dir so libg2c.so.0 could be found at runtime. If I execute from scipy.stats import distribution at the interpreter prompt I get a segfault. Here's the beginning of the gdb traceback: #0 0x20ec8356 in ?? () #1 0xdd2d7e24 in Cephes_InitOperators (dictionary=0x8486dfc) at Lib/special/cephesmodule.c:413 #2 0xdd2d7a7a in initcephes () at Lib/special/cephesmodule.c:1105 #3 0x080d082e in _PyImport_LoadDynamicModule ( name=0x8040500 "scipy.special.cephes", pathname=0x8040070 "/opt/lang/python/lib/python2.3/site-packages/scipy/special/cephes.so", fp=0x8148780) at ../Python/importdl.c:53 #4 0x080cd637 in load_module (name=0x8040500 "scipy.special.cephes", fp=0x8148780, buf=0x8040070 "/opt/lang/python/lib/python2.3/site-packages/scipy/special/cephes.so", type=3, loader=0x0) at ../Python/import.c:1708 #5 0x080ce345 in import_submodule (mod=0x8149fa4, subname=0x804050e "cephes", fullname=0x8040500 "scipy.special.cephes") at ../Python/import.c:2291 #6 0x080cdea4 in load_next (mod=0x8149fa4, altmod=0x81265e0, p_name=0x8040930, buf=0x8040500 "scipy.special.cephes", p_buflen=0x80404fc) at ../Python/import.c:2111 #7 0x080cfbf1 in import_module_ex (name=0x0, globals=0x8486c64, locals=0x8486c64, fromlist=0x83e256c) at ../Python/import.c:1957 #8 0x080ced40 in PyImport_ImportModuleEx (name=0x8369c34 "cephes", globals=0x8486c64, locals=0x8486c64, fromlist=0x83e256c) at ../Python/import.c:1998 #9 0x080a1bde in builtin___import__ (self=0x0, args=0x8483d4c) at ../Python/bltinmodule.c:45 #10 0x080fac78 in PyCFunction_Call (func=0x8151bec, arg=0x8483d4c, kw=0x0) at ../Objects/methodobject.c:108 #11 0x08062e90 in PyObject_Call (func=0x8151bec, arg=0x8483d4c, kw=0x0) at ../Objects/abstract.c:1755 Since I don't use SciPy, Cephes or f2py outside of installing SciPy I don't really know where to start poking. Frame 1 is at this line: 413 f = PyUFunc_FromFuncAndData(cephes3a_functions, bdtr_data, cephes_4_types, 2, 3, 1, PyUFunc_None, "bdtr", bdtr_doc, 0); and cephes3a_functions looks suspicious: (gdb) p cephes3a_functions $2 = {0x5, 0x6} I presume considering the variable name those are supposed to be valid function pointers. Stepping through initcephes leads me to this: (gdb) n 393 cephes3a_functions[0] = PyUFunc_fff_f_As_iid_d; (gdb) n 391 cephes3_functions[2] = PyUFunc_ffF_F_As_ddD_D; (gdb) n 392 cephes3_functions[3] = PyUFunc_ddD_D; (gdb) n 394 cephes3a_functions[1] = PyUFunc_ddd_d_As_iid_d; (gdb) n 395 cephes3_2_functions[0] = PyUFunc_fff_ff_As_ddd_dd; (gdb) p cephes3a_functions $9 = {0x5, 0x6} (gdb) p PyUFunc_ddD_D $10 = {void (char **, int *, int *, void *)} 0xdd2e4720 <PyUFunc_ddD_D> (gdb) p PyUFunc_ddd_d_As_iid_d $11 = {void (char **, int *, int *, void *)} 0xdd2e4a20 <PyUFunc_ddd_d_As_iid_d> It seems there's something amiss with the cephes3a_functions initialization. In fact, other cephes*_functions variables appear bogus as well: (gdb) p cephes3_functions $12 = {0, 0, 0x3, 0x4} (gdb) p cephes1_functions $13 = {0x464c457f, 0x10101} (gdb) p cephes2_4_functions $14 = {0x7e34, 0x7} Does this ring a bell with anybody? Any clues about how to proceed would be appreciated. Thanks, -- Skip Montanaro Got spam? http://www.spambayes.org/ skip(a)pobox.com

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RE: [SciPy-user] Weave problems
by Bob.Cowdery＠CGI-Europe.com Aug. 12, 2004

Aug. 12, 2004

Thanks for the suggestions. I added a PYTHONCOMPILED env var and deleted all the intermediate and compiled files. Then compiled the two routines I have. It did put the compiled files in the right place, still using the temporary directory for intermediate files. It did however put an empty catalogue in PYTHONCOMPILED dir and the real catalogue in my temporary directory under python2_compiled which I don't understand. I think it helped slightly, I still have to keep compiling until it works. Even though I don't change anything it still rebuilds and then on other occations when I do change something it refuses to rebuild!! I also renamed the two plot files and they don't cause a problem now but I would still like to know what they were doing. In all other respects this is an excellent tool but this somewhat bizarre behaviour detracts from its usability. Bob -----Original Message----- From: scipy(a)zunzun.com [mailto:scipy@zunzun.com] Sent: 11 August 2004 07:26 To: scipy-user(a)scipy.net Subject: Re: [SciPy-user] Weave problems > When I try to run my application two things happen. I get a stream of > exceptions - I had odd problems on Windows that require me to occasionally delete all of weave's temporary files and then compile 'int a;' in a python script using weave to kind of restart it. I wrote a batch file to do this, and run it whenever I get problems like these; 90% of the time they clear up for me and the other 10% are my syntax errors. > ...I am left with wgnuplot.exe and gnuplot_helper.exe > between them taking 100% CPU and I have to kill those off > as well. Find and delete these two files, that was my solution. No answer from the mailing list on that one. Randy Phillips http://zunzun.com _______________________________________________ SciPy-user mailing list SciPy-user(a)scipy.net http://www.scipy.net/mailman/listinfo/scipy-user *** Confidentiality Notice *** Proprietary/Confidential Information belonging to CGI Group Inc. and its affiliates may be contained in this message. If you are not a recipient indicated or intended in this message (or responsible for delivery of this message to such person), or you think for any reason that this message may have been addressed to you in error, you may not use or copy or deliver this message to anyone else. In such case, you should destroy this message and are asked to notify the sender by reply email.

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Re: [SciPy-user] array2string
by Gary Ruben Aug. 12, 2004

Aug. 12, 2004

Hi Henk, > Wouldn't it be convenient when Numeric's ArrayPrinter.array2string would > allow for indentation and be defined as <snip> > BTW: Perhaps this is the wrong list --- I'm not aware however of a > dedicate Numeric mailing list. the dedicate Numeric mailing list is here: <http://lists.sourceforge.net/lists/listinfo/numpy-discussion> It would be worth reposting there although someone relevant has probably read your message on this list. Gary -- ___________________________________________________________ Sign-up for Ads Free at Mail.com http://promo.mail.com/adsfreejump.htm

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array2string
by H Jansen Aug. 12, 2004

Aug. 12, 2004

Wouldn't it be convenient when Numeric's ArrayPrinter.array2string would allow for indentation and be defined as def array2string(a, max_line_width = None, precision = None, suppress_small = None, separator=' ', array_output=0, base_indent=0, indent_first=1 # NEW ): rather than def array2string(a, max_line_width = None, precision = None, suppress_small = None, separator=' ', array_output=0 ): Internally, it calls _arrayToString anywith with default indentation arguments however, rather then letting them be user specified. --Henk BTW: Perhaps this is the wrong list --- I'm not aware however of a dedicate Numeric mailing list. -- ------------------------------------------------------------------------------ The disclaimer that applies to e-mail from TNO Physics and Electronics Laboratory can be found on: http://www.tno.nl/disclaimer/email.html ------------------------------------------------------------------------------

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Tensor methods?
by bulatov＠cs.orst.edu Aug. 12, 2004

Aug. 12, 2004

Is there any work on incorporating some optimization algorithm that uses 3rd or 4th degree information into scipy (ie Tenmin) ? Yaroslav

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Having trouble with scipy_distutils - specifying a fortran compiler
by Cory Davis Aug. 11, 2004

Aug. 11, 2004

Hi All, I have developed a Python package for atmospheric radiative transfer simulations in remote sensing applications (hhtp://www.met.ed.ac.uk/~cory/PyARTS). F2PY and scipy_distutils have been extremely helpful for creating and distributing this package. Until now I have installed the package using the command python setup.py install --home=~ ,which has been fine. But now because I have included some quad precision fortran code I need to use a different fortran compiler (instead of g77), for example the Lahey, or NAG compilers. According to the scipy_distutils section of the f2py user guide, to specify the compiler I now need to use the command 'build_ext' with the --fcompiler argument. The trouble is whenever I try to use this command on its own it complains about the f2py signature file included in the extension module sources. E.g. [cory@bruce PyARTS]$ python setup.py build_ext running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext customize GnuFCompiler customize GnuFCompiler customize GnuFCompiler using build_ext building 'scatsubs' extension compling C sources gcc options: '-pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -march=i386 -mcpu=i686 -D_GNU_SOURCE -fPIC -fPIC' error: unknown file type '.pyf' (from './src/scatsubs.pyf') I'm obviously doing something daft, but I have scoured the net for documentation to no avail. Can anyone offer me some advice? Thanks, Cory

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gplt.close()
by Steve Schmerler Aug. 11, 2004

Aug. 11, 2004

Hi all sorry for beeing so enthusiastic that I eventually sent an RE: twice :) here is my problem: I'm producing some gplt plots (windwos) in a script. When I call the script again I want to delete the old ones first. This works fine with xplt for i in range(n): winkill() [.. plot commands ...] When I try gplt instead: for i in range(n): close() only one window (the last one produced) is killed. Why is that ?? Thanx in advance for any hint. bye steve -- All those who believe in psychokinesis raise my hand. - Steven Wright -- NEU: WLAN-Router f�r 0,- EUR* - auch f�r DSL-Wechsler! GMX DSL = superg�nstig & kabellos http://www.gmx.net/de/go/dsl

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another gplt question
by matt Aug. 11, 2004

Aug. 11, 2004

I have code that plots several traces on several plots. I found hold and got that to work for plotting multiple traces on a plot. However, I seem to have frequent issues with data from a previous plot ending up on a subsequent plot in addition to the new data. Is there a way to explicitly tell gplt that a plot is done and all subsequent plot commands are for a new plot? It seems strange that there isn't an gplt instance for each plot or something of that nature. -Matt

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genetic algorithm examples
by Jeff Hodges Aug. 11, 2004

Aug. 11, 2004

Hey, Has anyone here used scipy.ga in a project? I'm trying to learn it but I'm running into walls. I've tried checking with the documentation, but all I can find is the api docs that are missing sorely needed explanations. I'm trying to learn it by reading the code as we speak, and I was hoping I might be able to look at someone else's code to really understand how it all ties together. Thanks!

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