What has to be true of `a` so that eig(a) fails to converge? DG
Actual output:
>>> from numpy import linalg as LA
>>> LA.eig(np.diag((1,2,3)))
(array([ 1., 2., 3.]), array([[ 1., 0., 0.],
[ 0., 1., 0.],
[ 0., 0., 1.]]))
i.e., a line feed wasn't inserted between w and v.
Bug?
DG
Linear Algebra! (My favorite!) Let's get it to pink or better by next Wed! DG
Proposed Agenda
Old Business:
Timetable for approval of Ralf's patch for ticket #1146
New Business:
Clarification of how much and what should be in the docstrings of methods which are equivalent to some function
Please email me any additional items ASAP. (And your Skype ID if you haven't already and want to participate.)
Also, thanks to all who chipped in this past week to get Polynomials to the "Goal Met (almost)" state; there
are a few pending road blocks to completion, but generally, I'd say it was a success. Here are a few
proposals for "Category of the Week" for the coming week:
Financial Functions - Status: 50% done Leader: Skipper Seabold
Random Number Generation - Status: 57% done Leader: Alan Jackson
Linear Algebra - Status: 24% done Leader: None (yet)
Feel free to cast a vote via email if you won't be able to join the Skypecon.
Talk to you tomorrow, hopefully.
David Goldsmith
Technical Editor
Hi everyone,
I have stumbled on some interesting behavior of scipy.io.loadmat. The short of it - it looks like loadmat is gobbling up memory in some unjustified manner and releasing it under some strange circumstances.
Here's the long story. This is all happening on a Mac OS 10.5.7, running EPD 4.0.30001 (Python 2.5.2), but with a relatively new version of scipy (see below).
I start ipython -pylab in one terminal and run 'top' in another, in order to monitor the memory usage. Here's what I get initially:
PhysMem: 417M wired, 449M active, 183M inactive, 1055M used, 3041M free.
Then:
In [1]: import scipy
In [2]: scipy.__version__
Out[2]: '0.8.0.dev5606'
In [3]: import scipy.io as sio
Here's what it looks like now:
PhysMem: 418M wired, 450M active, 183M inactive, 1058M used, 3038M free.
So far, so good. I read in a large matfile with tons of data in it:
In [4]: a = sio.loadmat('/Users/arokem/Projects/SchizoSpread/Scans/SMR033109_MC/Gray/Original/TSeries/Scan1/tSeries1.mat')
PhysMem: 419M wired, 1024M active, 183M inactive, 1632M used, 2464M free.
So - about 600 MB of memory is taken up by this new variable.
Now to the wierdness:
In [5]: b
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
/Users/arokem/<ipython console> in <module>()
NameError: name 'b' is not defined
Of course - 'b' doesn't exist!
But now, the memory usage has dramatically gone down:
PhysMem: 420M wired, 740M active, 183M inactive, 1350M used, 2746M free.
So - just invoking an error in the ipython command line has freed up 300 MB. Where did they come from? I tried different things - assigning other variables doesn't seem to free up this memory. Neither do calls to other functions. Except "plot()", which does seem to do the trick for some reason. Interestingly, when I run all this in a python interactive session (and not ipython), I get a similar memory usage initially. Calling a non-existent variable does not free up the memory, but other things do. For example, import matplotlib.pylab into the namespace did the trick. Does anyone have any idea what is going on?
Thanks --
Ariel
--
Ariel Rokem
Helen Wills Neuroscience Institute
University of California, Berkeley
http://argentum.ucbso.berkeley.edu/ariel
_______________________________________________ Scipy-dev mailing list Scipy-dev <at> scipy.org http://mail.scipy.org/mailman/listinfo/scipy-dev
Hi, all. Below are the Minutes of last week's Summer Marathon Weekly Skypecon. Before that, you'll note in
them that the participants decided to fix the Skypecon time to Wednesday's, 19:00 UTC. Well, I already
need to request a "variance" for Wed. July 15 - anyone object strongly to Tuesday July 14, 18:00 UTC that
week? Thanks!
DG
PS: Note that that's three Weds. from now - the next two, July 1 and July 8, the Skypecon will be at the
designated time, 19:00 UTC; please email me any items you'd like to see on the agenda. And now, without
further ado, I give you... the Minutes!
Numpy Doc Summer '09 Marathon
June 24, 2009 Skypecon Minutes
Start: 19:00 UTC
End: 20:00 UTC
Present:
David Goldsmith, Secretary
Stefan van der Walt
Ralf Gommers
Pauli Virtanen
Discussions:
0) Clarifying the Doc Standard vis-à-vis classes and their constructors, attributes, instances
(created by numpy), and constants
Agreed that, for now at least, c-tors will be documented in the class docstring
Agreed that, because we might want to group attributes into meaningful categories within their class,
we’ll stick with manual generation and annotation of such lists of attributes
Instances: Pauli explained how things work “behind the scenes,” and it was decided that the way it's
currently done is okay. For what that way is, see patch attached to ticket #1146, http://projects.scipy.org/numpy/ticket/1146
Constants: At first, said it’s moot because we can’t easily modify constants’ docstrings, but then
Pauli pointed out that the development version of NumPy has the subpackage numpy.doc.constants,
wherein constants can be documented at module scope. Did not settle on exactly how it should look but were
in agreement that it should be a) kept short, and b) use the same sections as for functions where applicable.
1) Two "pre-proof" reviews: technical (“Is it correct?”) and presentation (“Is it clear and as
simple as possible, modulo being correct?”)
Note: the presentation issue is seen as distinct from whether or not the docstring is grammatically
correct and free of typos, these latter to be assured by the final proof
Discussed the “pros” (our labor pool, in general, consists of persons who are stronger in one area or
the other, but not both; dividing the review process in this way makes it more manageable and thus less
intimidating for prospective reviewers) and “cons” (compounding and complicating the overall
process in this way will just push back completion that much further); decided that the pros outweigh the
cons, and thus this division should be added to the review process, but, recognizing that these reviews
are beyond the stated goal of the Summer Marathon, decided that required changes to the Wiki can be
designated as “medium” priority.
It came up after the meeting that there is still confusion about the meaning of the proposal, and that if the
“non-technical” review is as described above, then at least one meeting participants opted to
change his “vote,” resulting in a “tie” regarding “endorsement” of the proposal; we await
clarification from the proposer regarding his intended meaning.
2) Adding a FAQ page to the Wiki
Discussed how recent questions/issues arising on the mailing list and in the Comments sections of the Wiki
demonstrate the need for the Wiki to have something like a FAQ page.
Pauli agreed to create a “mock-up” for dissemination and discussion, which he has already completed
and published at http://docs.scipy.org/numpy/Questions+Answers/
3) Meeting time
Decided that 19:00 UTC Wednesdays is a good time, and that, all else equal, it's probably better to fix the
time than have it "float." Consequently, next Summer Marathon Skypecon is scheduled for:
Wednesday, July 1, 19:00 UTC
Notes:
Ralf noted an inconsistency on the Milestones page between the Goal statement and the color scheme, which
the Secretary has corrected
Again, had periodic dropout problems all around.
_______________________________________________
Scipy-dev mailing list
Scipy-dev <at> scipy.org
http://mail.scipy.org/mailman/listinfo/scipy-dev
I am pleased to announce that the Python Software Foundation is sponsoring 10 students' travel, registration, and accommodation for the SciPy 2009 conference (Aug. 18-23). The focus of the conference is both on scientific libraries and tools developed with Python and on scientific or engineering achievements using Python. If you're in college or a graduate program, please check out the details here: http://conference.scipy.org/student-funding About the conference -------------------- SciPy 2009, the 8th Python in Science conference, will be held from August 18-23, 2009 at Caltech in Pasadena, CA, USA. The conference starts with two days of tutorials to the scientific Python tools. There will be two tracks, one for introduction of the basic tools to beginners, and one for more advanced tools. The tutorials will be followed by two days of talks. Both days of talks will begin with a keynote address. The first day’s keynote will be given by Peter Norvig, the Director of Research at Google; while, the second keynote will be delivered by Jon Guyer, a Materials Scientist in the Thermodynamics and Kinetics Group at NIST. The program committee will select the remaining talks from submissions to our call for papers. All selected talks will be included in our conference proceedings edited by the program committee. After the talks each day we will provide several rooms for impromptu birds of a feather discussions. Finally, the last two days of the conference will be used for a number of coding sprints on the major software projects in our community. For the 8th consecutive year, the conference will bring together the developers and users of the open source software stack for scientific computing with Python. Attendees have the opportunity to review the available tools and how they apply to specific problems. By providing a forum for developers to share their Python expertise with the wider commercial, academic, and research communities, this conference fosters collaboration and facilitates the sharing of software components, techniques, and a vision for high level language use in scientific computing. For further information, please visit the conference homepage: http://conference.scipy.org. Important Dates --------------- * Friday, July 3: Abstracts Due * Friday, July 10: Announce accepted talks, post schedule * Friday, July 10: Early Registration ends * Tuesday-Wednesday, August 18-19: Tutorials * Thursday-Friday, August 20-21: Conference * Saturday-Sunday, August 22-23: Sprints * Friday, September 4: Papers for proceedings due Executive Committee ------------------- * Jarrod Millman, UC Berkeley, USA (Conference Chair) * Gaël Varoquaux, INRIA Saclay, France (Program Co-Chair) * Stéfan van der Walt, University of Stellenbosch, South Africa (Program Co-Chair) * Fernando Pérez, UC Berkeley, USA (Tutorial Chair)
And the winner is...polynomials! I'll make a note on the Milestones page. Feel free to add yourself either as a leader or a helper if you like (though you don't need to do so, to participate, obviously). Again, the idea is that this will motivate us to "finish" this category by next Wednesday's Skypecon. Happy doc-ing!
All, How do we document a warning, a note that should be displayed differently as a note ? Don't we have a "Warnings" entry in the docstrings standard ? Thx
Hi. Where is class multiarray defined? Thanks! DG
Hi! For the purposes of meeting the documentation standard, are data attributes regarded has "returning" something, i.e., should ndarray.itemsize, for example, have a Returns section? DG
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