Mailman 3 November 2012 - SciPy-Dev

Faster expm
by Alex Leach Nov. 15, 2012

Nov. 15, 2012

Dear List, I did some work a while back, which needed to calculate matrix exponentials, for which I used the EXPOKIT toolkit: http://www.maths.uq.edu.au/expokit/download.html EXPOKIT is written in Fortran, and I found that f2py did a pretty good job of creating a Python interface. More recently, I separated out the code and did some speed comparisons against scipy.linalg.expm. If I could direct your attention to the scipy-user mailing list, you'll find the build method and benchmark comparisons up there: http://mail.scipy.org/pipermail/scipy-user/2012-November/033588.html Wrapping EXPOKIT for Python has been done before, by a colleague of the original author, so I can't take all the credit. A presentation he gave, with some usage and build instructions can be found here (Pg 16-22): http://sf.anu.edu.au/~mhk900/Python_Workshop/short.pdf After some feedback from others on the SciPy-user mailing list, I obtained permission from the original author, Roger B. Sidje, to distribute EXPOKIT with SciPy under the BSD license. So, I've done a little more work over the last couple of days, in an attempt to merge EXPOKIT into SciPy, but of course there's still more work to be done. Unfortunately, I've run out of time to do this myself, (I've got to write my PhD thesis, which has nothing to do with this) so I'd like to pass over what I've done and forget about it, at least for the next 6 months or so. If you'd be interested in taking this off my hands, please let me know. I've had the small dense routines for Padé approximation working for ages, but the routines for Krylov projection of general sparse matrices are still giving some problems. Specifically, there's some STOP statements in the Fortran code that quit the program without raising exceptions. I haven't been able to get past these, so either the signature file I've edited is incorrect,the sparse matrix I've been testing with is wrong or too small, or something else is wrong. I've just made a fork of scipy on github, to which I've just pushed the files I've been working on: NEW: scipy/linalg/src/expokit.f scipy/linalg/expokit.pyf.src scipy/linalg/time_expm.py scipy/linalg/expowrap.py MODIFIED: scipy/linalg/setup.py expokit.f - EXPOKIT source code, with some very minor changes (Cf2py comments and changed matvec function call, as per above presentation) expokit.pyf.src - f2py signature file I've been editing from auto-generated version. time_expm.py - script I was testing everything with, before adding to expowrap.py.. Should not be included in distribution. expowrap.py - where I was going to put the python wrapper function. Was attempting to write a drop-in replacement for scipy.linalg.expm, but the sparse routines were giving problems... If you have any questions, please don't hesitate to ask. Kind regards, Alex

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Building docs from current master
by Andreas Hilboll Nov. 13, 2012

Nov. 13, 2012

Hi, trying to build the docs from current master, I run into this problem:: IOError: [Errno 2] No such file or directory: u'/home2/hilboll/src/scipy/doc/source/examples/normdiscr_plot1.py' Indeed, there's no folder ``doc/source/examples`` in master. Is this intended? What am I doing wrong? Cheers, Andreas.

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Review request: interp2d with partial redgrid backend
by John Travers Nov. 13, 2012

Nov. 13, 2012

Hi All, It has been a long time since I submitted any scipy hacks, but I got hit by an old issue of mine so decided to do something about it. The current interp2d backend uses the surfit routine from dierkx's fitpack, which is not meant for interpolation (which we choose when we set s=0.0). From the surfit.f code: c to choose s very small is strongly discouraged. this considerably c increases computation time and memory requirements. it may also c cause rank-deficiency (ier<-2) and endager numerical stability. I originally raised this a long time ago with ticket #286 which proposed replacing surfit with regrid which does not suffer from this problem. However as is rightly stated in the comments to that ticket, it changed interp2d to only work on rectangular grids rather than scattered data which is not acceptable (and an API breakage). So I propose to find a step by step solution to this. First the following code uses regrid whenever possible: https://github.com/jtravs/scipy/compare/master...interp2d_rectangular_fixes This fixes #286, #776, #898 and parts of #1364, #1072, and #703. Following this I hope to improve the docs a little and find a better solution to the scattered data problem rather than using surfit (which is great for smoothing BTW). Please note that this is my first attempt at the whole git workflow thing for scipy, so I hope this code review request is the right way to go. I hope to submit quite a few more changes, so please correct me where I go wrong! Cheers, John

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scipy.test() segfault
by Nils Wagner Nov. 5, 2012

Nov. 5, 2012

Program received signal SIGSEGV, Segmentation fault. 0x00007ffff7ab2b26 in PyObject_RichCompare () from /usr/lib64/libpython2.7.so.1.0 (gdb) bt #0 0x00007ffff7ab2b26 in PyObject_RichCompare () from /usr/lib64/libpython2.7.so.1.0 #1 0x00007ffff7ab2def in PyObject_RichCompareBool () from /usr/lib64/libpython2.7.so.1.0 #2 0x00007fffe3ba8584 in OBJECT_compare (ip1=<optimized out>, ip2=<optimized out>) at scipy/signal/sigtoolsmodule.c:827 #3 0x00007ffff74b8b64 in msort_with_tmp.part.0 () from /lib64/libc.so.6 #4 0x00007ffff74b8e9b in qsort_r () from /lib64/libc.so.6 #5 0x00007fffe3ba90d6 in PyArray_OrderFilterND (op1=<optimized out>, op2=<optimized out>, order=54989472) at scipy/signal/sigtoolsmodule.c:969 #6 0x00007fffe3ba92a7 in sigtools_order_filterND (__NPY_UNUSED_TAGGEDdummy=<optimized out>, args=<optimized out>) at scipy/signal/sigtoolsmodule.c:1135 #7 0x00007ffff7affcaa in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0 #8 0x00007ffff7b059c3 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.7.so.1.0 #9 0x00007ffff7aff7ce in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0 #10 0x00007ffff7b0204f in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0 #11 0x00007ffff7b05727 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.7.so.1.0 #12 0x00007ffff7a9ddc8 in ?? () from /usr/lib64/libpython2.7.so.1.0 #13 0x00007ffff7a7d464 in PyObject_Call () from /usr/lib64/libpython2.7.so.1.0 #14 0x00007ffff7b00cae in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0 #15 0x00007ffff7b05727 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.7.so.1.0 #16 0x00007ffff7a9dba1 in ?? () from /usr/lib64/libpython2.7.so.1.0 #17 0x00007ffff7a7d464 in PyObject_Call () from /usr/lib64/libpython2.7.so.1.0 #18 0x00007ffff7a87c8e in ?? () from /usr/lib64/libpython2.7.so.1.0 #19 0x00007ffff7a7d464 in PyObject_Call () from /usr/lib64/libpython2.7.so.1.0 #20 0x00007ffff7acb84a in ?? () from /usr/lib64/libpython2.7.so.1.0 #21 0x00007ffff7a7d464 in PyObject_Call () from /usr/lib64/libpython2.7.so.1.0 #22 0x00007ffff7affe75 in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0 #23 0x00007ffff7b0204f in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0 #24 0x00007ffff7b05727 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.7.so.1.0 #25 0x00007ffff7a9ddc8 in ?? () from /usr/lib64/libpython2.7.so.1.0 #26 0x00007ffff7a7d464 in PyObject_Call () from /usr/lib64/libpython2.7.so.1.0 #27 0x00007ffff7b00cae in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0 #28 0x00007ffff7b05727 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.7.so.1.0 #29 0x00007ffff7a9dba1 in ?? () from /usr/lib64/libpython2.7.so.1.0 #30 0x00007ffff7a7d464 in PyObject_Call () from /usr/lib64/libpython2.7.so.1.0 #31 0x00007ffff7a87c8e in ?? () from /usr/lib64/libpython2.7.so.1.0 #32 0x00007ffff7a7d464 in PyObject_Call () from /usr/lib64/libpython2.7.so.1.0 #33 0x00007ffff7acb84a in ?? () from /usr/lib64/libpython2.7.so.1.0 #34 0x00007ffff7a7d464 in PyObject_Call () from /usr/lib64/libpython2.7.so.1.0 #35 0x00007ffff7affe75 in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0 #36 0x00007ffff7b05727 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.7.so.1.0 >> scipy.__version__ '0.12.0.dev-bb436fa' x86_64 GNU/Linux

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