Mailman 3 August 2012 - SciPy-User

gamma.pdf numerically unstable?
by Tom Furmston Aug. 6, 2012

Aug. 6, 2012

Hi, I'm trying to use the gamma distribution in the SciPy library, but it appears to be numerically unstable. First, I've imported the library with from scipy.stats import gamma I want to evaluate the gamma distribution are x = 1.6, where the gamma distribution has the parameters shape = 142, scale = 0.0098. When I type gamma.pdf(1.6, 142, loc=0, scale=0.0098) I get a value of inf. According to matlab the value should be around 0.7030. Am I using this distribution correctly? Is this distribution known to suffer from numerical issues? TAI

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Re: [SciPy-User] help speeding up a Runge-Kuta algorithm (cython, f2py, ...) (Sturla Molden) (Sturla Molden)
by Sergio Rojas Aug. 6, 2012

Aug. 6, 2012

> Which version of Cython do you have (use at least 0.16). > Sturla I missed that. Now the full stuff compiles and runs: >$ python -c "from Cython.Compiler.Version import version; print version" 0.16 >$ python runme.py numpy_only: 3.5 sec cythonized_numpy: 2.62 sec cythonized_numpy_2: 4.15 sec cythonized_numpy_2b: 3.35 sec cythonized_numpy_3: 1.48 sec cythonized_numpy_4: 1.18 sec pointer_arith: 1.19 sec memview: 1.22 sec Sergio ************************************************************ Here is an example code of how to use Cython as a Fortran killer: https://github.com/sturlamolden/memview_benchmarks/blob/master/memview.pyx In this case, the performance with -O2 was just 2.2% slower than "plain C" with pointer arithmetics. It is possible to write very fast array code with Cython, but you must do it right. For comparison, this is very slow: https://github.com/sturlamolden/memview_benchmarks/blob/master/cythonized_n… What this mean is this: For anything but trivial code, the NumPy syntax is just too slow and should be avoided! I breiefly looked at the Cython code posted in this thread, and it suffers form all these issues. Sturla **********************************************

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kmeans2 question/issue
by James Abel Aug. 6, 2012

Aug. 6, 2012

Hi, I'm trying to use scipy.cluster.vq.kmeans2() but I'm getting inconsistent output. With a simple test input that should have 3 clusters, I'm getting good results most of the time but every so often the output creates the wrong clustering. If anyone could point to what I'm doing wrong I'd appreciate it! Code and sample output below. Thanks! James Code: import sys import scipy from scipy.cluster.vq import * print sys.version vals = scipy.array((0.0,0.1,0.5,0.6,1.0,1.1)) print vals white_vals = whiten(vals) print white_vals.shape, white_vals # try it several times to see if we get similar answers count = 0 while count < 5: res, idx = kmeans2(white_vals, 3) # changing iter doesn't seem to matter print res, idx count += 1 Output: 2.7.3 (default, Apr 10 2012, 23:31:26) [MSC v.1500 32 bit (Intel)] [ 0. 0.1 0.5 0.6 1. 1.1] (6,) [ 0. 0.24313227 1.21566135 1.45879362 2.4313227 2.67445496] [ 0.12156613 2.55288883 1.33722748] [0 0 2 2 1 1] [ 0.12156613 2.55288883 1.33722748] [0 0 2 2 1 1] [ 1.33722748 2.55288883 0.12156613] [2 2 0 0 1 1] [ 2.18819043 0.48626454 -0.97292963] [1 1 1 0 0 0] <-- unexpected result [ 0.12156613 2.55288883 1.33722748] [0 0 2 2 1 1] C:\PYTHON27\lib\site-packages\scipy\cluster\vq.py:588: UserWarning: One of the clusters is empty. Re-run kmean with a different initialization. warnings.warn("One of the clusters is empty. "

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Re: [SciPy-User] help speeding up a Runge-Kuta algorithm (cython, f2py, ...) (Sturla Molden)
by Sergio Rojas Aug. 5, 2012

Aug. 5, 2012

************************************************************ Here is an example code of how to use Cython as a Fortran killer: https://github.com/sturlamolden/memview_benchmarks/blob/master/memview.pyx In this case, the performance with -O2 was just 2.2% slower than "plain C" with pointer arithmetics. It is possible to write very fast array code with Cython, but you must do it right. For comparison, this is very slow: https://github.com/sturlamolden/memview_benchmarks/blob/master/cythonized_n… What this mean is this: For anything but trivial code, the NumPy syntax is just too slow and should be avoided! I breiefly looked at the Cython code posted in this thread, and it suffers form all these issues. Sturla ********************************************** Hello Sturla, I am wondering whether there is a problem with my phyton installation or something is missing in your "memview.pyx" file as the following compiling error arises: cythoning memview.pyx to memview.c Error compiling Cython file: ------------------------------------------------------------ ... cimport numpy as np cimport cython @cython.boundscheck(False) @cython.wraparound(False) cdef np.float64_t slice_func(np.float64_t[::1] Xi, ^ ------------------------------------------------------------ memview.pyx:7:42: Expected an identifier or literal Sergio PD. Compilation works fine in the other files (cythonized_numpy_2b.pyx cythonized_numpy_4.pyx pointer_arith.pyx cythonized_numpy_2.pyx cythonized_numpy.pyx cythonized_numpy_3.pyx). Taking out that module in the "runme.py" file the output is: >$ python runme.py numpy_only: 3.13 sec cythonized_numpy: 2.38 sec cythonized_numpy_2: 3.8 sec cythonized_numpy_2b: 3.27 sec cythonized_numpy_3: 1.52 sec cythonized_numpy_4: 1.19 sec pointer_arith: 1.19 sec

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scipy installation error
by x.piter＠gmail.com Aug. 5, 2012

Aug. 5, 2012

Hi I try to install scpy 10.1 (or 11) on debian testing, but get the following error: error: Command "gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/include/python2.6 -I/usr/lib/pymodules/python2.6/numpy/core/include -I/usr/lib/pymodules/python2.6/numpy/core/include -c scipy/spatial/qhull/src/poly.c -o build/temp.linux-i686-2.6/scipy/spatial/qhull/src/poly.o" failed with exit status 1 Does anybody knows a solution for it? Thanks. Petro

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Re: [SciPy-User] help speeding up a Runge-Kuta algorithm (cython, f2py, ...)
by Jonathan Stickel Aug. 5, 2012

Aug. 5, 2012

I am sure properly coded Cython is great, but I really struggled when I tried to use it. I found that it allows you to write really slow code without errors or warnings. I found the profiling tools to be only marginally helpful. So many different ways to do the same thing... which is the best? All the documentation is nice, but very long and dense. I am having much more success with f2py (using F90 syntax). Either your code runs fast, or it simply will not compile (excepting segfault bugs that can sometimes be difficult to track down). Improved and updated documentation would be helpful, but otherwise f2py is now what I turn to when speed is crucial. My 2 cents. YMMV. Jonathan On 08/04/2012 02:45 AM, scipy-user-request(a)scipy.org wrote: > Date: Sat, 04 Aug 2012 03:03:38 +0200 > From: Sturla Molden > Subject: Re: [SciPy-User] help speeding up a Runge-Kuta algorithm > (cython, f2py, ...) > > Den 03.08.2012 21:05, skrev Pauli Virtanen: >> >It's Fortran 77. You need to declare >> > >> > double precision dzdt >> > >> >I'd suggest writing Fortran 90 --- no need to bring more F77 code into >> >existence;) >> > > With the new typed memoryviews in Cython, there is no need to bring more > Fortran of any sort into existance.;-)

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trouble installing scipy on os x 10.7.4
by carmel Aug. 4, 2012

Aug. 4, 2012

Hi, I'm on OS X 10.7.4 and am having trouble installing scipy. $ gcc --version: i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.9.00) $ gfortran --version: GNU Fortran (GCC) 4.2.3 I got gfortran from here: http://r.research.att.com/tools/ I already have numpy 1.6.1, am trying to install scipy-0.11.0rc1. The full output of $ python setup.py build is in this paste: http://pastebin.com/xs1fQ0fW All help welcome, I don't know anything about this stuff... I also downloaded and supposedly successfully installed the 10.7 specific add-on, from here: http://r.research.att.com/tools/gcc-42-5666.3-darwin11.pkg So I was surprised to see that the gcc version is the llvm-gcc-4.2 one that the installation guide warns about. Not sure how to change that or what I did wrong... Thanks, Carmel

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[ANN] SIAM Conference on Computational Science & Engineering Submission Deadlines Approaching!
by Fernando Perez Aug. 2, 2012

Aug. 2, 2012

Dear Colleagues, the SIAM CSE13 conference will be held next year in Boston, and this is a conference that is well suited for much of the type of work that goes on in the open source scientific Python development community (and Julia). The conference is co-chaired by Hans-Petter Langtangen, well known around these parts for his several books on scientific computing with Python and for having led a campus-wide adoption of Python as the core computational foundation across the University of Oslo. I am also on the program committee, as well as Randy LeVeque and other Python-friendly folks. An excellent way to participate is to organize a one- or two-part minisymposium on a specific topic with a group of related speakers (instructions at http://www.siam.org/meetings/cse13/submissions.php). Please note that the MS deadline is fast approaching: August 13, 2012. If you have any further questions, don't hesitate to contact me or one of the other organizers if you feel they can address your concerns more directly: "Fernando Perez" <Fernando.Perez(a)berkeley.edu> "Randy LeVeque" <rjl(a)amath.washington.edu> (Reproducible research track) "Hans Petter Langtangen" <hpl(a)simula.no> (Conference co-chair) "Karen Willcox" <kwillcox(a)mit.edu> (conference chair) ---------- Forwarded message ---------- From: Karen Willcox <kwillcox(a)mit.edu> Date: Tue, Jul 24, 2012 at 6:08 AM Subject: [SIAM-CSE] SIAM Conference on Computational Science & Engineering Submission Deadlines Approaching! To: SIAM-CSE(a)siam.org *SIAM Conference on Computational Science & Engineering (CSE13)* February 25-March 1, 2013 The Westin Boston Waterfront, Boston, Massachusetts, USA**** ** ** SUBMISSION DEADLINES ARE APPROACHING!**** August 13, 2012: Minisymposium proposals September 10, 2012: Abstracts for contributed and minisymposium speakers**** Visit http://www.siam.org/meetings/cse13/submissions.php to submit.**** ** ** Twitter hashtag: #SIAMcse13**** ** ** For more information about the conference, visit * http://www.siam.org/meetings/cse13/* or contact SIAM Conference Department at meetings(a)siam.org.**** -- Karen Willcox Professor and Associate Department Head Department of Aeronautics and Astronautics, MIT http://acdl.mit.edu/willcox.html _______________________________________________ SIAM-CSE mailing list To post messages to the list please send them to: SIAM-CSE(a)siam.org http://lists.siam.org/mailman/listinfo/siam-cse

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ANN: PySAL 1.4
by Serge Rey Aug. 2, 2012

Aug. 2, 2012

On behalf of the PySAL development team, I'm happy to announce the official release of PySAL 1.4. PySAL is a library of tools for spatial data analysis and geocomputation written in Python. PySAL 1.4, the fifth official release of PySAL brings the following key enhancements: - spatial regression (spreg): - Integration of scipy.sparse structures in all the regression classes - Probit - Probit with diagnostics for spatial effects - exploratory spatial data analysis (esda): - Generalized Gamma statistics for spatial autocorrelation - spatial dynamics (spatial_dynamics): - O(n log n) algorithm for spatial tau (spatial rank correlation) - LISA Markov transitions and tests for spatial dynamics - computational geometry (cg) and spatial networks - efficient point to nearest LineSegment search - generate network topology from shapefiles - utilities for interfacing with networkx - integration of network cluster code (beta) among the 155 commits and bug fixes since the last release, 6 months ago. PySAL modules ------------- - pysal.core — Core Data Structures and IO - pysal.cg — Computational Geometry - pysal.esda — Exploratory Spatial Data Analysis - pysal.inequality — Spatial Inequality Analysis - pysal.spatial_dynamics — Spatial Dynamics - pysal.spreg - Regression and Diagnostics - pysal.region — Spatially Constrained Clustering - pysal.weights — Spatial Weights - pysal.FileIO — PySAL FileIO: Module for reading and writing various file types in a Pythonic way Downloads -------------- Binary installers and source distributions are available for download at http://code.google.com/p/pysal/downloads/list Documentation ------------- The documentation site is here http://pysal.geodacenter.org/1.4 Web sites --------- PySAL's home is here http://pysal.org/ The developer's site is here http://code.google.com/p/pysal/ Mailing Lists ------------- Please see the developer's list here http://groups.google.com/group/pysal-dev Help for users is here http://groups.google.com/group/openspace-list Bug reports and feature requests -------------------------------- To search for or report bugs, as well as request enhancements, please see http://code.google.com/p/pysal/issues/list License information ------------------- See the file "LICENSE.txt" for information on the history of this software, terms & conditions for usage, and a DISCLAIMER OF ALL WARRANTIES. Many thanks to all who contributed! Serge, on behalf of the PySAL development team. -- Sergio (Serge) Rey Professor, School of Geographical Sciences and Urban Planning GeoDa Center for Geospatial Analysis and Computation Arizona State University http://geoplan.asu.edu/rey Editor, International Regional Science Review http://irx.sagepub.com

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[CONF] Call for papers AMS Jan 6-10 2013
by Jonathan Rocher Aug. 2, 2012

Aug. 2, 2012

Dear all, Sorry for the cross post. Abstract submission is open for the Third Symposium on Advances in Modeling and Analysis Using Python at the AMS Annual Meeting in Austin, TX, January 6-10, 2013. The call for papers and link to submit an abstract is located here: http://annual.ametsoc.org/2013/index.cfm/programs-and-events/conferences-an… The abstract submission deadline is extended to August 28, 2012. We are soliciting papers related to all areas of the use of Python in the atmospheric and oceanic sciences. Please pass along this announcement to your friends and colleagues! Thanks! Regards, Jonathan for the organizing committee -- Jonathan Rocher, PhD Scientific software developer Enthought, Inc. jrocher(a)enthought.com 1-512-536-1057 http://www.enthought.com

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