Add old reST posts for archival.

old/090907-cse09-siam-news.rst

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+=============================
+ CSE'09 article in SIAM News
+=============================
+
+
+This isn't fresh-off-the-oven news, but it's still on the main SIAM News page,
+so I'll mention it as I am trying to do a better job of keeping up with this
+blog...
+
+As I mentioned on a `previous post`_, our three_ part_ minisymposium_ on Python
+at the SIAM `CSE09 conference`_ was fairly well received.  But even better,
+SIAM asked us to write up an article for publication in the `SIAM News
+bulletin`_.  I was really pleased with this, as SIAM News reaches a very broad
+international audience and is actually read by people.  I often find very
+interesting material in it, as the publication hits a very good balance of
+quality and not being overly specialized (as we all drown in work, we tend to
+focus only on very narrow publication lists for everyday reading,
+unfortunately).
+
+Randy, Hans-Petter and I drafted up an article, and we received great feedback
+from all of the presenters at the minisymposium, including figure contributions
+by `John Hunter`_ and `Hank Childs`_ (who was at LLNL at the time, and I'm
+delighted to see is just up the hill from me at LBL).
+
+Our article is now available in HTML `online at the SIAM site`_, and I also
+have a `PDF version`_ that is more suitable for printing in case you are
+interested (note that my version is missing the very last corrections from the
+SIAM editor, but the differences should be minor).
+
+.. Links
+
+.. _previous post: http://fdoperez.blogspot.com/2009/03/python-at-siam-cse09-meeting.html
+.. _three: http://meetings.siam.org/sess/dsp_programsess.cfm?SESSIONCODE=8044
+.. _part: http://meetings.siam.org/sess/dsp_programsess.cfm?SESSIONCODE=8045
+.. _minisymposium: http://meetings.siam.org/sess/dsp_programsess.cfm?SESSIONCODE=8046
+.. _CSE09 conference: http://www.siam.org/meetings/cse09/
+
+.. _SIAM News bulletin: http://www.siam.org/news/news.php
+.. _John Hunter: http://matplotlib.sf.net
+.. _Hank Childs: http://www.lbl.gov/cs/CSnews/CSnews073109c.html
+
+.. _online at the SIAM site: http://www.siam.org/news/news.php?id=1595
+.. _PDF version: https://cirl.berkeley.edu/fperez/papers/siam_news_py4science.pdf
+

old/091105-guido-visit.rst

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+==============================================
+ Guido van Rossum at UC Berkeley's Py4Science
+==============================================
+
+**Update:** Quick links
+
+   * Video_ of the entire session. The talks cover the first 50 minutes, and
+     Guido's part starts at the 54 minute mark.
+   * A `page with all the slides`_ on my site.
+   * Guido also blogged_ his impressions.
+   * Blog posts by `Jarrod Millman`_ and `Matthew Brett`_.
+
+.. _page with all the slides: http://fperez.org/py4science/2009_guido_ucb
+.. _blogged: http://neopythonic.blogspot.com/2009/11/python-in-scientific-world.html
+.. _Jarrod Millman: http://jarrodmillman.blogspot.com/2009/11/visit-from-guido-van-rossum.html
+.. _Matthew Brett: http://nipyworld.blogspot.com/2009/11/guido-van-rossum-talks-about-python-3.html
+
+On November 4 2009, we had a special session of our informal Py4Science_
+seminar where Guido van Rossum visited for an open discussion regarding the
+uses of the Python language in scientific research. Guido had expressed his
+interest in discussing the work that various scientists do with Python but
+mentioned that instead of a formal talk, he would prefer a format that allowed
+for more interaction with the audience.  We agreed that a good plan would be
+for us to present a rapid-fire sequence of very short talks highlighting
+multiple projects so that he could get a good "high altitude" view of the
+scientific python landscape, leaving then ample time for discussions with the
+audience.
+
+.. _Py4Science: https://cirl.berkeley.edu/view/Py4Science
+
+Guido has already posted `his impressions`_ of the visit, and so have my
+colleagues `Jarrod Millman`_ and `Matthew Brett`_, so I'll try to provide a
+complementary view here without too much repetition.
+
+.. _his impressions: http://neopythonic.blogspot.com/2009/11/python-in-scientific-world.html
+.. _Jarrod Millman: http://jarrodmillman.blogspot.com/2009/11/visit-from-guido-van-rossum.html
+.. _Matthew Brett: http://nipyworld.blogspot.com/2009/11/guido-van-rossum-talks-about-python-3.html
+
+We gathered for lunch first with a small group and had a very interesting
+discussion on various topics; we had a chance to talk in some detail about the
+transition to Python 3 for Numpy, something a number of people have started to
+think about seriously.  Numpy is pretty much a 'root dependency' for so many
+scientific projects, that until it makes the jump it will be very difficult for
+anyone else in science to seriously consider Python 3.  Understandably, Guido
+would like to see some movement from our community in this direction, and he
+offered useful guidance.  In particular, he said that in the core Python-dev
+team there might be enough interest that if we ask for help there, we might
+find developers willing to pitch in and provide some assistance.  He also
+expressed some disappointment that `PEP 3118`_, which was accepted with our
+interests in mind, still hadn't been fully implemented.  Limited manpower is
+the simple reason for this situation, but fortunately Jarrod mentioned that
+there's a good plan to address this in the near future.
+
+I had a chance to quiz Guido about something I've wondered for a while: Python
+has unusually good number types in its core (arbitrary length integers,
+extended precision decimals and complex numbers), but the integers divide
+either into the integers (the truncating behavior of Python 2.x) or into the
+floats (in 3.x).  While the 3.x division is an improvement, I would have really
+liked to see Python go to native rationals; for one thing, this would make the
+Sage 'language' (by which I mean the extensions Sage makes to pure Python)
+behave like Python in algorithms involving integers, eliminating a recurring
+source of confusion between the two.  I also happen to think it would be a
+'better' behavior, though there are valid reasons also for someone to expect a
+more 'calculator-like' answer to divisions like 1/2, who might be annoyed if
+they get 1/2 back instead of 0.5.  While obviously such changes will not be on
+the table for a long while (and I should say here that I am very happy with the
+planned moratorium to core language changes, as I hope that will allow a more
+focused effort on the needs of the standard library), it was interesting to
+hear Guido's approach to this question as one that could be handled via
+overloadable literals rather than a change of integer semantics.  I'd never
+thought of that, but it's an intriguing idea... Something to think about for
+when we start looking at Python 4000 :)
+
+.. _PEP 3118: http://www.python.org/dev/peps/pep-3118
+
+We then headed over to the official presentation, where we managed to cram 14
+talks in 50 minutes and then had a full hour of open conversation with Guido,
+where the audience asked him questions on a number of topics.  You can see a
+complete video_ of the entire session: after 50 minutes of talks we have a
+transition, and Guido's section starta at the 54 minute mark. On my website I
+have posted_ a page with all the slides for these mini-talks.
+
+I presented an overview_ introduction and material on behalf of 4 others who
+were not present locally, but coincidentally, `William Stein`_ of Sage_ fame
+was on campus to give a talk in the same building almost at the same time, and
+he could present the Sage slides directly. `Ondrej Certik`_ from SymPy_ was
+able to make the trip from Reno, completing our out-of-town speakers.  The
+other 7 presentations were from a number of local speakers (from various
+departments at UC Berkeley and Lawrence Berkeley National Laboratory, just up
+the hill from us).
+
+.. _overview: http://fperez.org/py4science/2009_guido_ucb/fperez_py4science_overview.pdf
+.. _video: http://www.archive.org/details/ucb_py4science_2009_11_04_Guido_van_Rossum
+.. _posted: http://fperez.org/py4science/2009_guido_ucb/index.html
+
+.. _William Stein: http://wstein.org
+.. _sage: http://sagemath.org
+.. _Ondrej Certik: http://ondrejcertik.blogspot.com/
+.. _sympy: http://code.google.com/p/sympy
+
+I have received very good feedback from several people, and I am really
+thankful to all the speakers for being so attentive to the time constraints,
+which let us pack a lot of material while leaving ample time for the discussion
+with Guido.  My intention with this was to really provide Guido with a broad
+understanding of how significant Python's penetration has been in scientific
+computing, where many different projects from disciplines ranging from computer
+science to astronomy are relying heavily on his creation.  I wanted both to
+thank him for creating and shepherding such a high-quality language for us
+scientists, and to establish a good line of communication with him (and
+indirectly the core python development group) so that he can understand better
+what are some of the use patterns, concerns and questions we may have regarding
+the language.
+
+I have the impression that in this we were successful, especially as we had
+time after the open presentations for a more detailed discussion of how we use
+and develop our tools.  Most of us in scientific computing end up spending an
+enormous amount of time with open interpreter sessions, typically IPython_ ones
+(I started the project in the first place because I wanted a *very good*
+interactive environment, beyond Python's default one), and in this work mode
+the key source of understanding for code are good docstrings.  This is an area
+where I've always been unhappy about the standard library, whose docstrings are
+typically not very good (and often they are non-existent).  We showed Guido the
+fabulous Numpy/Scipy `docstring editor`_ by Pauli Virtanen and Emmanuelle
+Gouillart, as well as the fact that Numpy has an actual `docstring standard`_
+that is easy to read yet fairly complete.  I hope that this may lead in the
+future to an increase in the quality of the Python docstrings, and perhaps even
+to the adoption of a more detailed docstring standard as part of `PEP 8`_,
+which I think would be very beneficial to the community at large.
+
+In the end, putting all this together took me a lot more time than I'd
+originally planned (I think I've had this same problem before...), but I am
+very pleased with the results.  Python has become a central tool for the work
+many of us do, and I am really happy to establish a good dialogue with Guido
+(and hopefully other core developers), which I'm sure will have benefits in
+both directions.
+
+.. _IPython: http://ipython.scipy.org
+.. _docstring editor: http://docs.scipy.org/numpy/Front%20Page/
+.. _docstring standard: http://projects.scipy.org/numpy/wiki/CodingStyleGuidelines#docstring-standard
+.. _pep 8: http://www.python.org/dev/peps/pep-0008
+

old/091215-claremont-py4science.rst

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+=====================
+ Py4science teaching
+=====================
+
+It's pretty clear to me that Python is rapidly growing in acceptance as a
+computational platform at universities everywhere.  I recently heard from `Josh
+Bloom`_ at UC Berkeley astronomy that his proposal for a short 'boot camp'
+course at the beginning of the Fall semester was approved.  This is excellent
+news, last year I taught `something similar`_ for neuroscience students and
+postdocs, and I'm glad to see the campus adopting python further as a key
+component of the computational training the science students receive.
+
+.. _Josh Bloom: http://astro.berkeley.edu/~jbloom/
+.. _something similar: http://fperez.org/py4science/workshop_berkeley_2008.html
+
+
+
+John Hunter and I just completed a few days ago teaching another such workshop
+at the Claremont Colleges, supported by an NSF grant that `John Milton`_,
+(J. Hunter's PhD advisor) has for exposing undergraduates to a number of
+research-related experiences.  This grant supports summer research internships
+where two undergrads visit together a research lab elsewhere to work
+independently on a project, which has already resulted in some really neat
+projects, as well as our teaching of scientific python tools (we were also
+there in 2008 and hopefully will continue next year).
+
+.. _John Milton: http://faculty.jsd.claremont.edu/jmilton/
+
+I have to say that I really enjoy teaching this type of workshop, especially
+now that the core tools are fairly mature, installation isn't the problem it
+used to be, and we have a chance of presenting interesting examples to the
+students from the very beginning.  John Hunter is a phenomenal lecturer, with a
+real knack for illustrating interesting concepts on the fly, in a very natural
+manner that is honestly similar to how exploratory work is *actually* done in
+real research, where you run a bit of code, plot some results, print a few
+things, code some more, etc.  In the picture above, he was working through some
+of the `matplotlib image tutorial
+<http://matplotlib.sourceforge.net/users/image_tutorial.html>`_, which gave us
+an opportunity to find and fix a small bug in how the luminance histogram was
+being computed (the current form is correct).  Every one of these students
+probably has a digital camera these days (if nothing else, in a cell phone), so
+an example like this is a great way to connect something they are used to with
+mathematical and programming concepts.
+
+
+This one is from a great illustration of random numbers and simple statistics.
+John built up interactively a simulation of random walks, working up from a
+single (one-dimensional) walker to a group of them, comparing the simulation
+results with the analytical predictions for various quantities (like mean and
+variance), and also explaining to the students how these squiggly lines could
+be considered a model of price fluctuations over time.  In this manner, he
+connected the somewhat abstract statistical concepts to something the students
+could relate to, namely the risk of an investment making a profit or a loss
+after a certain period.
+
+We also talked about FFTs, dynamical systems, error analysis, data formats, and
+a few other things.  It was very encouraging to have most of the students
+return on the second day, considering how this was a completely optional
+activity for them, covering an entire weekend (with morning lectures both days)
+right before they had to start diving into their finals.  But they were a smart
+and enthusiastic bunch, and I hope that the workshop gave them some useful
+starting points they can then develop on their own as they get involved in
+research projects.
+
+These are just two examples of how we are now seeing Python's acceptance in
+university computing growing.  We have a lot of work still ahead of us, but
+it's really encouraging to see how far we've come from the days when building
+scipy was a black art, IPython was little more than a different prompt for the
+python shell and matplotlib could only do basic line plots on top of libgd.  We
+now have tools that provide a complete computational environment for teaching
+and research, and things are only getting better...

old/091215-vision-hpc.rst

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+
+
+http://www.abhishek-tiwari.com/2009/08/visual-high-performance-computing-in.html
+
+From jose, re the python bof at SC 2009
+
+The BoF was very well attended -- standing room only. There were probably about
+100 people in the room. Spotz from Sandia Labs was there and it was a very
+interesting presentation regarding NVIDIA "copperhead" python-to-GPU
+programming. It's still very early in development, but looks very promising.
+
+No word on a corresponding workshop, though. The SC09 committee surveys the
+attendance of each of these BoF's and uses that as input for subsequent related
+events -- tutorials, workshops, etc. There is a lot of interest and some of the
+topics you brought up with your meeting with Guido surfaced -- especially GIL.
+
+Anyway, given the strength of the attendance, hopefully this will result in
+subsequent Python for HPC material at the next conference, which is in New
+Orleans.
+
+Just parenthetically, I also attended the high-level languages series, which
+included Matlab. Outside of the ability to distribute an array on multiple
+nodes, I really didn't see anything that was light years ahead of what you all
+have already implemented in IPython. In fact, during the question session, some
+professor brought up the fact that it was too expensive for his institution to
+continue to teach parallel programming using Matlab. Obviously, they weren't
+too happy to discuss that publicly.
+
+
+###
+http://www.paratools.com/ptoolsrte.php
+
+The Centos build (which includes associated binaries) has IPython in it.
+
+Hopefully, ptoolsrte will become part of the standard software installation for HPCMP and will thereby have IPython in it by default. That would be huge (~6000 DoD users ) at four major computational centers around the country would have this.
+