Mailman 3 August 2012 - NumPy-Discussion

A sad day for our community. John Hunter: 1968-2012.
by Fernando Perez 29 Aug '12

29 Aug '12

Dear friends and colleagues, I am terribly saddened to report that yesterday, August 28 2012 at 10am, John D. Hunter died from complications arising from cancer treatment at the University of Chicago hospital, after a brief but intense battle with this terrible illness. John is survived by his wife Miriam, his three daughters Rahel, Ava and Clara, his sisters Layne and Mary, and his mother Sarah. Note: If you decide not to read any further (I know this is a long message), please go to this page for some important information about how you can thank John for everything he gave in a decade of generous contributions to the Python and scientific communities: http://numfocus.org/johnhunter. Just a few weeks ago, John delivered his keynote address at the SciPy 2012 conference in Austin centered around the evolution of matplotlib: http://www.youtube.com/watch?v=e3lTby5RI54 but tragically, shortly after his return home he was diagnosed with advanced colon cancer. This diagnosis was a terrible discovery to us all, but John took it with his usual combination of calm and resolve, and initiated treatment procedures. Unfortunately, the first round of chemotherapy treatments led to severe complications that sent him to the intensive care unit, and despite the best efforts of the University of Chicago medical center staff, he never fully recovered from these. Yesterday morning, he died peacefully at the hospital with his loved ones at his bedside. John fought with grace and courage, enduring every necessary procedure with a smile on his face and a kind word for all of his caretakers and becoming a loved patient of the many teams that ended up involved with his case. This was no surprise for those of us who knew him, but he clearly left a deep and lasting mark even amongst staff hardened by the rigors of oncology floors and intensive care units. I don't need to explain to this community the impact of John's work, but allow me to briefly recap, in case this is read by some who don't know the whole story. In 2002, John was a postdoc at the University of Chicago hospital working on the analysis of epilepsy seizure data in children. Frustrated with the state of the existing proprietary solutions for this class of problems, he started using Python for his work, back when the scientific Python ecosystem was much, much smaller than it is today and this could have been seen as a crazy risk. Furthermore, he found that there were many half-baked solutions for data visualization in Python at the time, but none that truly met his needs. Undeterred, he went on to create matplotlib (http://matplotlib.org) and thus overcome one of the key obstacles for Python to become the best solution for open source scientific and technical computing. Matplotlib is both an amazing technical achievement and a shining example of open source community building, as John not only created its backbone but also fostered the development of a very strong development team, ensuring that the talent of many others could also contribute to this project. The value and importance of this are now painfully clear: despite having lost John, matplotlib continues to thrive thanks to the leadership of Michael Droetboom, the support of Perry Greenfield at the Hubble Telescope Science Institute, and the daily work of the rest of the team. I want to thank Perry and Michael for putting their resources and talent once more behind matplotlib, securing the future of the project. It is difficult to overstate the value and importance of matplotlib, and therefore of John's contributions (which do not end in matplotlib, by the way; but a biography will have to wait for another day...). Python has become a major force in the technical and scientific computing world, leading the open source offers and challenging expensive proprietary platforms with large teams and millions of dollars of resources behind them. But this would be impossible without a solid data visualization tool that would allow both ad-hoc data exploration and the production of complex, fine-tuned figures for papers, reports or websites. John had the vision to make matplotlib easy to use, but powerful and flexible enough to work in graphical user interfaces and as a server-side library, enabling a myriad use cases beyond his personal needs. This means that now, matplotlib powers everything from plots in dissertations and journal articles to custom data analysis projects and websites. And despite having left his academic career a few years ago for a job in industry, he remained engaged enough that as of today, he is still the top committer to matplotlib; this is the git shortlog of those with more than 1000 commits to the project: 2145 John Hunter <jdh2358(a)gmail.com> 2130 Michael Droettboom <mdboom(a)gmail.com> 1060 Eric Firing <efiring(a)hawaii.edu> All of this was done by a man who had three children to raise and who still always found the time to help those on the mailing lists, solve difficult technical problems in matplotlib, teach courses and seminars about scientific Python, and more recently help create the NumFOCUS foundation project. Despite the challenges that raising three children in an expensive city like Chicago presented, he never once wavered from his commitment to open source. But unfortunately now he is not here anymore to continue providing for their well-being, and I hope that all those who have so far benefited from his generosity, will thank this wonderful man who always gave far more than he received. Thanks to the rapid action of Travis Oliphant, the NumFOCUS foundation is now acting as an escrow agent to accept donations that will go into a fund to support the education and care of his wonderful girls Rahel, Ava and Clara. If you have benefited from John's many contributions, please say thanks in the way that would matter most to him, by helping Miriam continue the task of caring for and educating Rahel, Ava and Clara. You will find all the information necessary to make a donation here: http://numfocus.org/johnhunter Remember that even a small donation helps! If all those who ever use matplotlib give just a little bit, in the long run I am sure that we can make a difference. If you are a company that benefits in a serious way from matplotlib, remember that John was a staunch advocate of keeping all scientific Python projects under the BSD license so that commercial users could benefit from them without worry. Please say thanks to John in a way commensurate with your resources (and check how much a yearly matlab license would cost you in case you have any doubts about the value you are getting...). John's family is planning a private burial in Tennessee, but (most likely in September) there will also be a memorial service in Chicago that friends and members of the community can attend. We don't have the final scheduling details at this point, but I will post them once we know. I would like to again express my gratitude to Travis Oliphant for moving quickly with the setup of the donation support, and to Eric Jones (the founder of Enthought and another one of the central figures in our community) who immediately upon learning of John's plight contributed resources to support the family with everyday logistics while John was facing treatment as well as my travel to Chicago to assist. This kind of immediate urge to come to the help of others that Eric and Travis displayed is a hallmark of our community. Before closing, I want to take a moment to publicly thank the incredible staff of the University of Chicago medical center. The last two weeks were an intense and brutal ordeal for John and his loved ones, but the hospital staff offered a sometimes hard to believe, unending supply of generosity, care and humanity in addition to their technical competence. The latter is something we expect from a first-rate hospital at a top university, where the attending physicians can be world-renowned specialists in their field. But the former is often forgotten in a world often ruled by a combination of science and concerns about regulations and liability. Instead, we found generous and tireless staff who did everything in their power to ease the pain, always putting our well being ahead of any mindless adherence to protocol, patiently tending to every need we had and working far beyond their stated responsibilities to support us. To name only one person (and many others are equally deserving), I want to thank Dr. Carla Moreira, chief surgical resident, who spent the last few hours of John's life with us despite having just completed a solid night shift of surgical work. Instead of resting she came to the ICU and worked to ensure that those last hours were as comfortable as possible for John; her generous actions helped us through a very difficult moment. It is now time to close this already too long message... John, thanks for everything you gave all of us, and for the privilege of knowing you. Fernando. ps - I have sent this with my 'mailing lists' email. If you need to contact me directly for anything regarding the above, please write to my regular address at Fernando.Perez(a)berkeley.edu, where I do my best to reply more promptly.

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distutils: compiler used by add_library
by Matyáš Novák 29 Aug '12

29 Aug '12

Hi, I wrote extension some numerical extension for python, that requires compiling and linking additional fortran sources. I find out, that these libraries can be easily added using config.add_library() function, but there is a problem. The --fcompiler command doesn't propagate to the stage where the libraries are compiled, so the default (and in my case wrong) compiler is used. (If I try compile the files using add_extension method, they are compiled by desired compiler, but I need combine more sources in one extension so I think that I can't use add_extension). Is there any way how to force python to use the right compiler, or at least hardcode the compiler in the setup.py? Thanks a lot for suggestions, Matyas

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Re: [Numpy-discussion] blaze lib announcement
by Michael Lehn 29 Aug '12

29 Aug '12

> This looks interesting: > > http://code.google.com/p/blaze-lib/ So maybe you also want to have a look at http://flens.sf.net Just to promote my own baby in this context too ;-) Cheers, Michael

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config.add_library()
by Chris Barker 29 Aug '12

29 Aug '12

Hi folks, I'm working on a package that will contain a bunch of cython extensions, all of which need to link against a pile of C++ code. What I think I need to do is build that C++ as a dynamic library, so I can link everything against it. It would be nice if I could leverage distutils to build that library for me. Particularly since Windows and OS-X and Linux all seem to need things a little (or q lot) different. It looks like numpy.distuitls' config.add_library might be what I need, but the docs are pretty sprarse: This page: http://docs.scipy.org/doc/numpy-1.5.x/reference/generated/numpy.distutils.m… confused me a bit: """ Parameters : name : str Name of the extension. """ Is this really building an extension, or is that some docs string brought over from the distutils Extension class? So -- is config.add_lirary() what I'm looking for? If so are there better docs and/or examples you canpoint me to? Thanks, -Chris Christopher Barker, Ph.D. Oceanographer Emergency Response Division NOAA/NOS/OR&R (206) 526-6959 voice 7600 Sand Point Way NE (206) 526-6329 fax Seattle, WA 98115 (206) 526-6317 main reception Chris.Barker(a)noaa.gov

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blaze lib announcement
by Neal Becker 29 Aug '12

29 Aug '12

This looks interesting: http://code.google.com/p/blaze-lib/

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Mark Florisson's GSoC, minivect, and NumPy
by Dag Sverre Seljebotn 27 Aug '12

27 Aug '12

I just wanted to draw the attention of NumPy devs to Mark Florisson's GSoC work. It is 'minivect', a tool to use for compiling array expressions (think (as a concept) a shared backend between Cython, Theano, numba, though it's only used in Cython currently). His M. Sc. thesis, "Techniques for Static and Dynamic Compilation of Array Expressions", is up here: https://github.com/markflorisson88/minivect/tree/master/thesis As you can see he even beats Intel Fortran for some array layouts, and in general have comparable performance with it. The benchmarks are mostly for two-operand operations, i.e. operations where NumPy semantics would be OK. IMO, if anybody ever wants to revamp NumPy's computation abilities and get that 2-3x speedup (e.g., make it multi-threaded), this is a very good place to start. Dag

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vectorized multi-matrix multiplication
by Alex Flint 26 Aug '12

26 Aug '12

I have two lists of 3x3 arrays and I would like to compute the matrix product of the i-th element in the first list with the i-th element in the second list. Of course, I could just loop over the lists: for i in range(n): out[i] = dot( matrices1[i], matrices2[i] ) However, the list is quite long, and each matrix is very small (3x3) so this turns out to be quite slow. Is there a way to do this with a single numpy call? I have looked at tensordot but it outputs an N x N x 3 x 3 array, whereas I want an N x 3 x 3 output. I've also looked at various broadcasting tricks but I haven't found anything that works yet. Alex

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[ANN] Call for abstracts: BigData minisymposium at CSE'13, February 2013, Boston
by Fernando Perez 23 Aug '12

23 Aug '12

Dear colleagues, next year's SIAM conference on Computational Science and Engineering, CSE'13, will take place in Boston, February 25-March 1 (http://www.siam.org/meetings/cse13), and for this version there will be a track focused on the topic of Big Data. This term has rapidly risen in recent discussions of science and even of mainstream business computing, and for good reasons. Today virtually all disciplines are facing a flood of quantitative information whose volumes have often grown faster than the quality of our tools for extracting insight from these data. SIAM hopes that CSE'13 will provide an excellent venue for discussing these problems, from the vantage point offered by a community whose expertise combines analytical insights, algorithmic development, software engineering and domain-specific applications. As part of this event, Titus Brown (http://ged.msu.edu) and I are organizing a minisymposium where we would like to have a group of presentations that address both novel algorithmic ideas and computational approaches as well as domain-specific problems. Data doesn't appear in a vacuum, and data from different domains presents a mix of common problems along with questions that may be specific to each; we hope that by engaging a dialog between those working on algorithmic and implementation questions and those with specific problems from the field, valuable insights can be obtained. If you would like to contribute to this minisymposium, please contact us directly at: "C. Titus Brown" <ctb(a)msu.edu>, "Fernando Perez" <Fernando.Perez(a)berkeley.edu> with your name and affiliation, the title of your proposed talk and a brief description (actual abstracts are due later so an informal description will suffice for now), by Wednesday August 29. For more details on the submission process, see: http://www.siam.org/meetings/cse13/submissions.php Please forward this to any interested colleagues. Regards, Titus and Fernando.

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unsubscribe
by Amit Nagal 23 Aug '12

23 Aug '12

Please unsubscribe me Visit us at Booth No. 5 at 2012 ChemOutsourcing Conference, 10-13 Sept 2012, Ocean Place Resort - Long Branch, NJ, United States Visit us at Booth No. 4 at World Conference on Pharmacometrics, 5-7 Sept 2012, Grand Hilton Hotel, Seoul, Korea ________________________________ Notice: The information contained in this electronic mail message is intended only for the use of the designated recipient. This message is privileged and confidential. and the property of GVK BIO or its affiliates and subsidiaries. If the reader of this message is not the intended recipient or an agent responsible for delivering it to the intended recipient, you are hereby notified that you have received this message in error and that any review, dissemination, distribution, or copying of this message is strictly prohibited. If you have received this communication in error, please notify us immediately by telephone +91-40-66929999<tel:%2B91-40-66929999> and destroy any and all copies of this message in your possession (whether hard copies or electronically stored copies).

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Re: [Numpy-discussion] 64bit infrastructure
by Sayth Renshaw 22 Aug '12

22 Aug '12

> Message: 4 > Date: Fri, 17 Aug 2012 15:25:21 -0700 > From: Matthew Brett <matthew.brett(a)gmail.com> > Subject: Re: [Numpy-discussion] 64bit infrastructure > To: Discussion of Numerical Python <numpy-discussion(a)scipy.org> > Message-ID: > <CAH6Pt5qa27Zb+UkOZB5EzsLK5UuoB-f8UcwFjdL2YcEBRZ=Wdw(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi, > > On Fri, Aug 17, 2012 at 2:25 PM, Sayth Renshaw <flebber.crue(a)gmail.com> wrote: >>> >>> Hi Sayth, >>> >>> On Thu, Aug 16, 2012 at 8:51 PM, Sayth Renshaw <flebber.crue(a)gmail.com> wrote: >>>> Hi >>>> >>>> I was just wondering if the current absence of 64bit builds was as a result >>>> of an infrastructure or funding concern. >>>> >>>> I like many now have only 64 bit systems and am using the unofficial builds. >>>> >>>> If it was something we could raise funds to resolve, how much? Or is it more >>>> complex than that? >>> >>> Which platform, windows? >>> >>> Ondrej >>> >>> >> >> Yes I have a Windows 7 64Bit install and a ubuntu 64 Bit install. > > Isn't the numpy ubuntu install 64 bit by default? > > You may have seen that there are numpy and scipy 64-bit windows installers here: > > http://www.lfd.uci.edu/~gohlke/pythonlibs/ > > Do they work for you? > > Best, > > Matthew > > > ------------------------------ > Thanks Matthew yeah that's the one I am currently using and it is working ok but just thought if there was a way to help 64bit builds become official then I would ask. Sayth

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