Mailman 3 September 2006 - SciPy-User

Usage of fmin_tnc and fmin_l_bfgs_b
by Nils Wagner 15 Sep '06

15 Sep '06

Hi all, I would like to solve a constrained optimization problem with scipy. As far as I understand it there exists two possible functions for my problem in scipy - fmin_tnc and fmin_l_bfgs_b. The problem is given by min f(x) subjected to \theta_1 \le theta \le theta_2 and r_1 \le r \le r_2 where x is a vector \in \mathds{R}^{2n+1}. theta is the last entry in x. r = \| x[:2*n] \| = linalg.norm(x[:2*n]) How do I specify the bounds for my problem ? I mean it's easy to define the bounds for the l a s t parameter (\theta) but I am at a loss how to formulate the bounds for x[0],...,x[2n-1] s e p a r a t e l y. bounds -- a list of (min, max) pairs for each element in x, defining the bounds on that parameter. Use None for one of min or max when there is no bound in that direction Any hint would be appreciated. Nils

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Scipy and fink
by Jerry 15 Sep '06

15 Sep '06

Can Scipy be installed from Fink? Is there any reason not to do this, assuming the usual "fink" search path /sw is in place? Jerry

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Trouble installing on OSX 10.4 Intel
by David Andrews 15 Sep '06

15 Sep '06

Hi, I'm a little lost here - i've d/led and installed everything in the scipy superpack, yet i am still unable to import certain components of scipy and matplotlib / pylab. The only thing that does appear to be fully installed is numpy, which i guess is a start. So here is what I get when i try 'from scipy import *': Traceback (most recent call last): File "<stdin>", line 1, in ? File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/linsolve/__init__.py", line 5, in ? from linsolve import * File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/linsolve/linsolve.py", line 1, in ? from scipy.sparse import isspmatrix_csc, isspmatrix_csr, isspmatrix, spdiags File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/sparse/__init__.py", line 5, in ? from sparse import * File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/sparse/sparse.py", line 12, in ? import sparsetools ImportError: Failure linking new module: /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/sparse/sparsetools.so: Library not loaded: /usr/local/lib/libgfortran.1.dylib Referenced from: /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/sparse/sparsetools.so Reason: image not found And with 'from pylab import *': Traceback (most recent call last): File "<stdin>", line 1, in ? File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/pylab.py", line 1, in ? from matplotlib.pylab import * ImportError: No module named matplotlib.pylab So any suggestions? I previously had a working install of matplotlib/pylab and numpy, if that suggest anything to you? I think sticking a readme file in the superpack might be a good idea. Cheers, Dave

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L-BFGS in scipy
by Nils Wagner 13 Sep '06

13 Sep '06

Hi all, Has someone implemented the limited memory BFGS method in scipy ? Nils http://citeseer.ist.psu.edu/liu89limited.html

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Compiling on a 64-bit Athlon Linux Machine
by Manbreaker Crag 13 Sep '06

13 Sep '06

I've successfully compiled and installed Numpy (latest SVN version), Scipy (latest SVN version), FFTW 3.1.2 and GotoBLAS 1.06 on a 64-bit dual-processor Athlon machine running Linux Fedora Core 3. Detailed directions on how this was done are available at: http://pong.tamu.edu/tiki/tiki-view_blog_post.php?blogId=6&postId=112 Corrections, suggestions, etc. are welcomed. Steve Baum

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Efficient submatrix of a sparse matrix
by Brendan Simons 13 Sep '06

13 Sep '06

Hi all, I have a neat little problem for which I think sparse matrices are the answer. I need to store a bunch of overlapping "intervals", (a, b pairs for which any a <= val < b crosses that interval) in a manner which makes "stabbing inquiries" (which intervals cross a specified value) easy. The canonical way to to this is with interval trees (a good summary here: http://w3.jouy.inra.fr/unites/miaj/public/vigneron/ cs4235/l5cs4235.pdf), however I think I can simplify things as follows: 1) perform an argsort on the interval a and b endpoints. This gives the position of each interval in an "order" matrix M, where each row and each column contains only one interval, and intervals are sorted in rows by start point, and in columns by endpoint 2) for a "stab" point x, do a binary search to find the row i and column j where x could be inserted into M and maintain its ordering. The submatrix of M[:i, j:] would contains all those intervals which start before x, and end after x. Since the order matrix M is mostly empty it would make sense to use a sparse matrix storage scheme, however the only one in scipy.sparse that allows 2d slicing is the dok_matrix, and the slicing algorithm is O(n), which is much too expensive for my purposes (I have to do thousands of stabbing inquiries on a space containing thousands of intervals). Is there no more efficient algorithm for 2d slicing of a sparse matrix? -Brendan -- Brendan Simons __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Scipy works on AMD now
by John Hassler 13 Sep '06

13 Sep '06

On an AMD AthlonXP (Model 6) 1600+ with: Python 2.4.3 numpy '1.0b5' scipy '0.5.1' numpy.test() runs without error. scipy.test() shows one error (see below). I'm not sure what this is, but all of my own numerical programs run without problems. Matplotlib didn't install properly, but when I added the missing files, it worked. All of my programs are now happily working. Many thanks to the people who put this all together. john ====================================================================== ERROR: check loadmat case cellnest ---------------------------------------------------------------------- Traceback (most recent call last): File "D:\program files\Python24\Lib\site-packages\scipy\io\tests\test_mio.py", line 80, in cc self._check_case(name, expected) File "D:\program files\Python24\Lib\site-packages\scipy\io\tests\test_mio.py", line 75, in _check_case self._check_level(k_label, expected, matdict[k]) File "D:\program files\Python24\Lib\site-packages\scipy\io\tests\test_mio.py", line 33, in _check_level self._check_level(level_label, ev, actual[i]) File "D:\program files\Python24\Lib\site-packages\scipy\io\tests\test_mio.py", line 30, in _check_level assert len(expected) == len(actual), "Different list lengths at %s" % label TypeError: len() of unsized object ---------------------------------------------------------------------- Ran 1569 tests in 23.143s FAILED (errors=1)

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ISP Changeover complete
by Jeff Strunk 12 Sep '06

12 Sep '06

Good evening, We have completed our internet service switchover. Thank you for your patience. If you have any trouble, please let me know. Thank you, Jeff Strunk IT Administrator Enthought, Inc.

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ISP changeover beginning in 30 minutes (7:00 PM Central)
by Jeff Strunk 12 Sep '06

12 Sep '06

Good evening, We will begin switching our internet service over in about 30 minutes. Please allow for up to two hours of downtime. I will send an email announcing the completion of this maintenance. This will effect all Enthought servers as well as the SciPy server which hosts many Open Source projects. We apologize for the inconvenience. Jeff Strunk Enthought, Inc.

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REMINDER: ISP changeover today 9/12 7:00 PM Central
by Jeff Strunk 12 Sep '06

12 Sep '06

Good morning, This is a reminder for this evening's network maintenance. Unfortunately, our recent change in internet service providers is not working out. We will be switching to a more reliable provider tonight at 7:00 PM Central. Please allow for up to two hours of downtime. I will send an email announcing the start and completion of this maintenance. This will effect all Enthought servers as well as the SciPy server which hosts many Open Source projects. Please pass this message along to people that I have missed. If you have any questions, please direct them to me. We apologize for the inconvenience. Jeff Strunk Enthought, Inc.

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