Mailman 3 March 2008 - NumPy-Discussion

Trouble using f2py on successful numpy build from SVN (1.0.5 dev4951)
by Joshua Lippai 01 Apr '08

01 Apr '08

I am using Mac OS X 10.5.2, with Python 2.5.2. My build output for NumPy is clean and successful and my numpy.test produces no errors or failures, but when I type f2py from Terminal, I get the following: $ f2py Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/Current/bin/f2py", line 5, in <module> pkg_resources.run_script('numpy==1.0.5.dev4951', 'f2py') File "build/bdist.macosx-10.3-i386/egg/pkg_resources.py", line 448, in run_script File "build/bdist.macosx-10.3-i386/egg/pkg_resources.py", line 1160, in run_script pkg_resources.ResolutionError: No script named 'f2py' Any ideas what could be up here? Josh

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code using Numeric and LinearAlgebra
by gordon 01 Apr '08

01 Apr '08

i came across some code that uses calls like LinearAlgebra.eigenvectors(L) and Numeric.matrixmultiply(v, x) which gives compilation errors on my new numpy installation.Is it possible to get such code compiled while using new version of numpy? when evalues, evectors = LinearAlgebra.eigenvectors(L) is computed for a symmetric covariance matrix L ,how are eigenvectors arranged in evectors? are they in columns?can i simply replace the above call by linalg.eigh()? Similarly can i just replace Numeric.matrixmultiply(v, x) with numpy.dot() , or is there something i must watch for in the above two cases?

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Applying PIL patch
by izak marais 31 Mar '08

31 Mar '08

Hi all, Sorry for the beginner question. I want to apply the PIL-numpy patch from http://www.scipy.org/Cookbook/PIL?highlight=%28PIL%29 . I have the latest windows binaries of numpy, scipy and PIL installed. I searched python.org, but couldn't find info on applying patches. How do I apply the patch? Detailed instructions on the cookbook page would be appreciated... perhaps I should modify it to include any lucid responses to this email? Regards Izak ____________________________________________________________________________________ OMG, Sweet deal for Yahoo! users/friends:Get A Month of Blockbuster Total Access, No Cost. W00t http://tc.deals.yahoo.com/tc/blockbuster/text2.com

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Re: [Numpy-discussion] OSX 10.4 installation problems
by mhgreen＠uchicago.edu 31 Mar '08

31 Mar '08

I updated gcc and everything works fine now. Thanks! ---- Original message ---- >Date: Mon, 31 Mar 2008 09:56:48 -0700 >From: Christopher Barker <Chris.Barker(a)noaa.gov> >Subject: Re: [Numpy-discussion] OSX 10.4 installation problems >To: Discussion of Numerical Python <numpy-discussion(a)scipy.org> > >Robert Kern wrote: >> This is your main problem. Where did you get this gcc? I believe the >> one that comes with the Developer Tools is 4.0.1. > >yup: >$ gcc --version >powerpc-apple-darwin8-gcc-4.0.1 (GCC) 4.0.1 (Apple Computer, Inc. build >5367) > >$ which gcc >/usr/bin/gcc > >Otherwise, I've got the same setup as the OP, and numpy built fine the >las time I tried it. > >-Chris > > > >-- >Christopher Barker, Ph.D. >Oceanographer > >Emergency Response Division >NOAA/NOS/OR&R (206) 526-6959 voice >7600 Sand Point Way NE (206) 526-6329 fax >Seattle, WA 98115 (206) 526-6317 main reception > >Chris.Barker(a)noaa.gov >_______________________________________________ >Numpy-discussion mailing list >Numpy-discussion(a)scipy.org >http://projects.scipy.org/mailman/listinfo/numpy-discussion

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OSX 10.4 installation problems
by mhgreen＠uchicago.edu 31 Mar '08

31 Mar '08

Hi, I cannot seem to install numpy on my mac. Here is some relevant info: I have the following installed on my PPC G4 powerbook: MacOSX 10.4.10 gcc version 4.0.0 gfortran version 4.2.1 fftw version 3.1.2 MacPython version 2.5.2 Xcode version 2.0 I have the unzipped numpy directory placed in /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages I am using the following command in terminal to try to install: python setup.py install I am getting a ton of errors, but the first few include: Could not locate executable f95 Could not locate executable f90 Could not locate executable f77 Could not locate executable xlf90 Could not locate executable xlf Could not locate executable ifort Could not locate executable ifc Could not locate executable g77 gcc: installation problem, cannot exec 'i686-apple-darwin8-gcc-4.0.0': No such file or directory And after that an assortment of probably at least 100 errors. Any help would be appreciated! Thanks. Matt

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Re: [Numpy-discussion] How do I make numpy raise exceptions instead of print warnings?
by Roy H. Han 31 Mar '08

31 Mar '08

Thank you, Robert! numpy.seterr() is very helpful. It is just what I needed. numpy.seterr(all = 'raise') forces numpy to raise exceptions instead of printing warnings. [begin quote] numpy.seterr(all = None, divide = None, over = None, under = None, invalid = None) Valid values for each type of error are the strings "ignore", "warn", "raise", and "call". [end quote] Date: Sat, 29 Mar 2008 17:05:42 -0500 From: "Robert Kern" <robert.kern(a)gmail.com> On Sat, Mar 29, 2008 at 4:25 PM, Roy H. Han <rhh2109(a)columbia.edu> wrote: > Is there a way to have numpy raise exceptions instead of printing > warnings? The printed warnings make debugging hard. numpy.seterr() Read the docstring for the various options. -- Robert Kern

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f2py from numpy 1.0.5 on OSX 10.4.11/QuadPPC fails with undefined symbols
by Harry Mangalam 31 Mar '08

31 Mar '08

Also using g95, which is fairly new I guess, but is a downstream requirement for the application. installed python 2.5 from darwin ports, installed most of rest of the python stuff from ports as well, numpy 1.0.4 failed repeatedly with 'too many options' error when processing cmdline options so installed 1.0.5 from svn. got same 'too many errors'. guessed and removed '--debug' from commandline: f2py --opt="-O3" -c -m \ fd_rrt1d --fcompiler=g95 --debug --link-lapack_opt *.f and that cured THAT problem. same version and same commandline worked fine on Linux, but now get the "Undefined symbols:" problem that I've seen posted elsewhere but not resolved (or not in a way that fixes my problem). Here's the last few lines of the command that was kicked off by: f2py --opt="-O3" -c -m fd_rrt1d --fcompiler=g95 --link-lapack_opt *.f (incidentally, this is the same final error from both the ports version (1.0.4) and the self-built one (1.0.5). It's obviously a link error, but to what lib and where to insert the -l specification?) I originally ran this with the environment LDFLAGS set but then ran it also with LDFLAGS set to "" and then UNset ie: $unset LDFLAGS the result is the same in all cases (see below). There's obviously a link error, but what are the missing libs and where are they? Would this have been caused by running the port install with LDFLAGS set? Thanks in advance. hjm the last lines of the build are: g95:f77: CQZ.f g95:f77: Umatrix1D.f g95:f77: fd_rrt1d.f g95:f77: /tmp/tmp28SqLa/src.macosx-10.3-ppc-2.5/fd_rrt1d-f2pywrappers.f /usr/local/bin/g95 -L/Users/hjm/lib \ /tmp/tmp28SqLa/tmp/tmp28SqLa/src.macosx-10.3-ppc-2.5/fd_rrt1dmodule.o\ /tmp/tmp28SqLa/tmp/tmp28SqLa/src.macosx-10.3-ppc-2.5/fortranobject.o \ /tmp/tmp28SqLa/CQZ.o /tmp/tmp28SqLa/Umatrix1D.o \ /tmp/tmp28SqLa/fd_rrt1d.o \ /tmp/tmp28SqLa/tmp/tmp28SqLa/src.macosx-10.3-ppc-2.5/fd_rrt1d-f2pywrappers.o\ -o ./fd_rrt1d.so -Wl,-framework -Wl,Accelerate ld: Undefined symbols: _PyArg_ParseTupleAndKeywords _PyCObject_AsVoidPtr _PyCObject_FromVoidPtr _PyCObject_Type _PyComplex_Type _PyDict_GetItemString _PyDict_SetItemString _PyErr_Clear _PyErr_Format _PyErr_NewException _PyErr_Occurred _PyErr_Print _PyErr_SetString _PyExc_ImportError _PyExc_MemoryError _PyExc_RuntimeError _PyExc_ValueError _PyFloat_Type _PyImport_ImportModule _PyInt_Type _PyModule_GetDict _PyNumber_Float _PyNumber_Int _PyObject_GetAttrString _PyObject_IsTrue _PyObject_SetAttrString _PyObject_Str _PySequence_Check _PySequence_GetItem _PyString_FromString _PyString_Type _PyType_IsSubtype _PyType_Type _Py_BuildValue _Py_InitModule4 __Py_NoneStruct _fprintf$LDBLStub _PyDict_DelItemString _PyDict_New _PyExc_AttributeError _PyExc_TypeError _PyMem_Free _PyObject_Type _PyString_AsString _PyString_ConcatAndDel _Py_FindMethod __PyObject_New _sprintf$LDBLStub _MAIN_ -- Harry Mangalam - Research Computing, NACS, E2148, Engineering Gateway, UC Irvine 92697 949 824 0084(o), 949 285 4487(c) -- [A Nation of Sheep breeds a Government of Wolves. Edward R. Murrow]

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whitespace error in automatic generation of Numpy_Example_List_With_Doc/script
by josef pumuckl 31 Mar '08

31 Mar '08

Hi, I was trying to automatically doctest some of the examples in Numpy_Example_List_With_Doc and obtained a large number of whitespace errors. The tests, that I tried, passed after turning of whitespace checking in doctest. Later I saw that the original numpy example list has leading whitespace that, I think, gets removed by the script that generates the With_Doc page. I think on line 179 a right strip should be used instead of a strip(), so that any leading white space is kept: change `` line = line.strip()`` to ``line = line.rstrip()`` the new lines read: for i, line in enumerate(input_data): # look for optional anchor name line = line.rstrip() match = re_anchor.match(line) Looking briefly at the newly generated output, everything still seems to be correctly generated, but I haven't verified if everything is really correct. Josef PS: This is my second attempt to send to the mailing list; I guess my first message got spam filtered

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How do I make numpy raise exceptions instead of print warnings?
by Roy H. Han 29 Mar '08

29 Mar '08

Is there a way to have numpy raise exceptions instead of printing warnings? The printed warnings make debugging hard.

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Re: [Numpy-discussion] OSX 10.4 installation problems
by mhgreen＠uchicago.edu 29 Mar '08

29 Mar '08

I am not sure where my version of gcc is from or how it was installed. I installed Xcode from the CD I got with the computer (in 2005). I will try updating it and see if everything works better. Thanks. ---- Original message ---- >Date: Sat, 29 Mar 2008 16:01:59 -0500 >From: "Robert Kern" <robert.kern(a)gmail.com> >Subject: Re: [Numpy-discussion] OSX 10.4 installation problems >To: "Discussion of Numerical Python" <numpy-discussion(a)scipy.org> > >On Sat, Mar 29, 2008 at 1:04 PM, <mhgreen(a)uchicago.edu> wrote: >> Hi, >> >> I cannot seem to install numpy on my mac. Here is some >> relevant info: >> >> I have the following installed on my PPC G4 powerbook: >> >> MacOSX 10.4.10 >> gcc version 4.0.0 >> gfortran version 4.2.1 >> fftw version 3.1.2 >> MacPython version 2.5.2 >> Xcode version 2.0 >> >> I have the unzipped numpy directory placed in >> /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages > >No, don't do that. Unzip it somewhere else to build. > >> I am using the following command in terminal to try to install: >> >> python setup.py install >> >> I am getting a ton of errors, but the first few include: >> >> Could not locate executable f95 >> Could not locate executable f90 >> Could not locate executable f77 >> Could not locate executable xlf90 >> Could not locate executable xlf >> Could not locate executable ifort >> Could not locate executable ifc >> Could not locate executable g77 >> >> gcc: installation problem, cannot exec >> 'i686-apple-darwin8-gcc-4.0.0': No such file or directory > >This is your main problem. Where did you get this gcc? I believe the >one that comes with the Developer Tools is 4.0.1. > >-- >Robert Kern > >"I have come to believe that the whole world is an enigma, a harmless >enigma that is made terrible by our own mad attempt to interpret it as >though it had an underlying truth." > -- Umberto Eco >_______________________________________________ >Numpy-discussion mailing list >Numpy-discussion(a)scipy.org >http://projects.scipy.org/mailman/listinfo/numpy-discussion

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