Mailman 3 February 2000 - NumPy-Discussion

RE: [Matrix-SIG] An Experiment in code-cleanup.
by Beausoleil, Raymond 07 Mar '00

07 Mar '00

I've been reading the posts on this topic with considerable interest. For a moment, I want to emphasize the "code-cleanup" angle more literally than the functionality mods suggested so far. Several months ago, I hacked my personal copy of the NumPy distribution so that I could use the Intel Math Kernel Library for Windows. The IMKL is (1) freely available from Intel at http://developer.intel.com/vtune/perflibst/mkl/index.htm; (2) basically BLAS and LAPACK, with an FFT or two thrown in for good measure; (3) optimized for the different x86 processors (e.g., generic x86, Pentium II & III); (4) configured to use 1, 2, or 4 processors; and (5) configured to use multithreading. It is an impressive, fast implementation. I'm sure there are similar native libraries available on other platforms. Probably due to my inexperience with both Python and NumPy, it took me a couple of days to successfully tear out the f2c'd stuff and get the IMKL linking correctly. The parts I've used work fine, but there are probably other features that I haven't tested yet that still aren't up to snuff. In any case, the resulting code wasn't very pretty. As long as the NumPy code is going to be commented and cleaned up, I'd be glad to help make sure that the process of using a native BLAS/LAPACK distribution (which was probably compiled using Fortran storage and naming conventions) is more straightforward. Among the more tedious issues to consider are: (1) The extent of the support for LAPACK. Do we want to stick with LAPACK Lite? (2) The storage format. If we've still got row-ordered matrices under the hood, and we want to use native LAPACK libraries that were compiled using column-major format, then we'll have to be careful to set all of the flags correctly. This isn't going to be a big deal, _unless_ NumPy will support more of LAPACK when a native library is available. Then, of course, there are the special cases: the IMKL has both a C and a Fortran interface to the BLAS. (3) Through the judicious use of header files with compiler-dependent flags, we could accommodate the various naming conventions used when the FORTRAN libraries were compiled (e.g., sgetrf_ or SGETRF). The primary output of this effort would be an expansion of the "Compilation Notes" subsection of Section 15 of the NumPy documentation, and some header files that made the recompilation easier than it is now. Regards, Ray ============================ Ray Beausoleil Hewlett-Packard Laboratories mailto:beausol@hpl.hp.com Vox: 425-883-6648 Fax: 425-883-2535 HP Telnet: 957-4951 ============================

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Matrix.py problem
by JEFFERY COLLINS 28 Feb '00

28 Feb '00

I installed the Numpy 15.2 and got the following error during the import of Matrix. Apparently, the version number is no longer embedded in the module doc string following the # sign. >>> import Matrix Traceback (innermost last): File "<stdin>", line 1, in ? File "/usr/local/lib/python1.5/site-packages/Numeric/Matrix.py", line 5, in ? __version__ = int(__id__[string.index(__id__, '#')+1:-1]) File "/usr/local/lib/python1.5/string.py", line 138, in index return _apply(s.index, args) ValueError: substring not found in string.index Jeff

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Casting problems with new version of NumPy.
by Travis Oliphant 25 Feb '00

25 Feb '00

The code sent by Herbert Roitblat pointed out some inconsistencies in the current NumPy, that I've fixed with two small changes: 1) Long's can no longer be safely cast to Int's (this is not safe on 64-bit machines anyway) -- this makes Numeric more consistent with how it interprets Python integers. 2) Automatic casting will be done when using rank-0 arrays to set elements of a Numeric array to be consistent with the behavior for Python scalars. The changes are in CVS right now, but are simple to change back if there is a problem. -Travis

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Array-casting problem.
by Travis Oliphant 25 Feb '00

25 Feb '00

Hi Herb, It has taken awhile for me to respond to this, but your problem's here illustrate exactly the kinds of difficulties one encounters with the current NumPy coercion rules: You do not have a bad version of Numeric. The behavior you describe is exactly what "should" happen though it needs to be fixed. I'll trace for you exactly what is going on as it could be illustrative to others: >>> a = zeros((5,5),'b') # You've just created a 5x5 byte array that follows "normal" coercion # rules filled with zeros. >>> a[3,3] = 8 # This line copies the rank-0 array of type 'b' created from the Python # Integer 8 (by a direct coercion in C) into element (3,3) of matrix a >>> temp = a[3,3] # This selects out the rank-0 array of typecode 'b' at position (3,3). As # of 15.2 this is nolonger changed to a scalar. Note that rank-0 arrays # act alot like scalars, but because there is not a one-to-one # correspondence between the Python Scalars and rank-0 arrays, this is not # automatically converted to a Python scalar (this is a change in 15.2) >>> temp = temp + 3 # This is the problem line for you right here. Something is wrong though, # since it should not be, a problem. # You are adding a rank-0 array of typecode 'b' to a Python Integer which # is interpreted by Numeric as a rank-0 array of typecode 'l'. The result # should be a Python Integer. For some reason this is returning an array # of typecode 'i' (which does not get automatically converted to a Python # scalar). >>> a[3,3] = temp # This would work fine if temp were the Python scalar it should be. # Right now, assignment doesn't let you assign an array of a "larger" type # to elements of a smaller type (except for Python scalars). Since temp # is (incorrectly I think) a type 'i' rank-0 array, it does not let you # make the assignment. At any rate it is inconsistent to let you assign # Python scalars but not rank-0 arrays of arbitrary precision, this should # be fixed. It is also a problem that temp + 3 returns an array of # typecode 'i'. I will look into fixing the above problems this example points out. Of course, it could also be fixed by having long integers lower in the coercion tree than byte arrays. Thanks for the feedback, Travis Oliphant

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Re: [Matrix-SIG] Numeric Array: adding a 0-D array to a cell in a 2-D array
by Konrad Hinsen 25 Feb '00

25 Feb '00

> We get the type error from trying to set the matrix element with a matrix > element (apparently). In the old version (1.9) on our NT box, > temp=a[kwd,kwd] results in temp being an int type. How can we either cast > the temp to an int or enable what we really want, which is to add an int to > a[kwd,kwd], as in a[kwd,kwd] = a[kwd,kwd] + jwd ? > > Do we have a bad version of Numeric? Maybe an experimental version. If you check the archives of this mailing list, you can find a recent discussion about proposed modifications. One of them was to eliminate the automatic conversion of rank-0 arrays to scalars, in order to prevent type promotion. Perhaps this proposal was implemented in the version you have. Note to the NumPy maintainers: please announce all new releases on this list, mentioning changes, especially those that affect backward compatibility. As a maintainer of code that makes heavy use of NumPy, I keep getting questions and bug reports caused by some new NumPy release that I haven't even heard of. A recent example is the change of location of the header files; C modules using arrays now have to include Numeric/arrayobject.h instead of simply arrayobject.h. I can understand this change (although I am not sure it's important enough to break compatibility), but I'd have preferred to learn about it directly and as early as possible. It's really no fun working through a 2 KB bug report sent by someone with zero knowledge of C. Konrad. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen(a)cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.55.69 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais -------------------------------------------------------------------------------

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Numeric Python under IRIX646
by Michel Sanner 21 Feb '00

21 Feb '00

Hi There, I just tried to add SGI running IRIX6.5 to the collection of Unix boxes I will support and I ran into the following problem: If I compile Python -O2 loading the Numeric extensions dumps the core, if I compile Python -g it works just fine and this regardless if Numeric is compile -g or -O2. After I re-compiled Objects/complexobject.o using -g (everything else being compiled -O2) I got it to work ... did anyone else out there see this kind of behavior ? I also post this to psa-members just in case this might be Python related -Michel -- ----------------------------------------------------------------------- >>>>>>>>>> AREA CODE CHANGE <<<<<<<<< we are now 858 !!!!!!! Michel F. Sanner Ph.D. The Scripps Research Institute Assistant Professor Department of Molecular Biology 10550 North Torrey Pines Road Tel. (858) 784-2341 La Jolla, CA 92037 Fax. (858) 784-2860 sanner(a)scripps.edu http://www.scripps.edu/sanner -----------------------------------------------------------------------

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Re: [Numpy-discussion] numpy documentation - alternative format?
by Herbert L. Roitblat 18 Feb '00

18 Feb '00

Adobe Acrobat has a shrink to fit option in their print menu. I'm not sure if it comes with their free-reader. Try printing as a 1up. It seems a small adaptation. HLR -----Original Message----- From: Peter Chang <peter(a)eexpc.eee.nott.ac.uk> To: Numpy-discussion(a)lists.sourceforge.net <Numpy-discussion(a)lists.sourceforge.net> Date: Friday, February 18, 2000 7:09 AM Subject: [Numpy-discussion] numpy documentation - alternative format? > >Hi there, > >I've just started to use python and numpy and want to print out the numpy >document but the PDF file has a strange aspect ratio which makes it hard >to print it as 2up on A4 paper. (I've tried hacking about with the >postscript generated by xpdf but it seems that there is no global setting >for page size!) > >Could the authors please provide alternative formats for the doc, eg. >as postscript files sized for A4 and letter so that people can print them >out easier? > >Thanks > Peter > > > >_______________________________________________ >Numpy-discussion mailing list >Numpy-discussion(a)lists.sourceforge.net >http://lists.sourceforge.net/mailman/listinfo/numpy-discussion >

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numpy documentation - alternative format?
by Peter Chang 18 Feb '00

18 Feb '00

Hi there, I've just started to use python and numpy and want to print out the numpy document but the PDF file has a strange aspect ratio which makes it hard to print it as 2up on A4 paper. (I've tried hacking about with the postscript generated by xpdf but it seems that there is no global setting for page size!) Could the authors please provide alternative formats for the doc, eg. as postscript files sized for A4 and letter so that people can print them out easier? Thanks Peter

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more speed?
by andrew x swan 17 Feb '00

17 Feb '00

This message was sent from Geocrawler.com by "andrew x swan" <a.swan(a)anprod.csiro.au> Be sure to reply to that address. hi - i've only just started using python and numpy... the program i wrote below runs much more slowly than a fortran equivalent. ie. on a dataset where the order of the matrix is (3325,3325), python took this long: 362.25user 0.74system 6:09.78elapsed 98%CPU and fortran took this long: 2.68user 1.12system 0:03.89elapsed 97%CPU is this because the element by element calculations involved are contained in python for loops? thanks #!/usr/bin/python from Numeric import * def nrm(pedigree): n_animals = len(pedigree) + 1 nrm = zeros((n_animals,n_animals),Float) for i in xrange(1,n_animals): isire = pedigree[i-1][1] idam = pedigree[i-1][2] nrm[i,i] = 1.0 + 0.5 * nrm[isire,idam] for j in xrange(i+1,n_animals): jsire = pedigree[j-1][1] jdam = pedigree[j-1][2] nrm[j,i] = 0.5 * (nrm[jsire,i] + nrm[jdam,i]) nrm[i,j] = nrm[j,i] return nrm if __name__ == '__main__': test_ped = [(1,0,0),(2,0,0),(3,1,0),(4,1,2), (5,3,4),(6,1,4),(7,5,6)] a = nrm(test_ped) print a Geocrawler.com - The Knowledge Archive

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re: scientific Python publishing venue
by gvwilson＠nevex.com 10 Feb '00

10 Feb '00

Hi, folks. A former colleague of mine is now editing a magazine devoted to scientific computing, and is looking for articles. If you're doing something scientific with Python, and want to tell the world about it, please give me a shout, and I'll forward more information. Greg Wilson http://www.software-carpentry.com

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