Mailman 3 November 2004 - SciPy-Dev

building lib.lapack without optimization
by Nils Wagner 03 Dec '04

03 Dec '04

Hi Pearu, It looks like an "optimization" problem With python setup_lapack.py build config_fc --noopt everything works fine. lib/lapack> python2.3 tests/test_lapack.py -v 10 Found 200 tests for __main__ check_gebal (__main__.test_clapack_complex) ... ok check_gehrd (__main__.test_clapack_complex) ... ok check_heev (__main__.test_clapack_complex) ... ok check_heev_complex (__main__.test_clapack_complex) ... ok check_heevd (__main__.test_clapack_complex) ... ok check_heevd_complex (__main__.test_clapack_complex) ... ok check_heevr (__main__.test_clapack_complex) ... ok check_heevr_complex (__main__.test_clapack_complex) ... ok check_heevr_irange (__main__.test_clapack_complex) ... ok check_heevr_irange_high (__main__.test_clapack_complex) ... ok check_heevr_irange_low (__main__.test_clapack_complex) ... ok check_heevr_vrange (__main__.test_clapack_complex) ... ok check_heevr_vrange_high (__main__.test_clapack_complex) ... ok check_heevr_vrange_low (__main__.test_clapack_complex) ... ok check_gebal (__main__.test_clapack_double) ... ok check_gehrd (__main__.test_clapack_double) ... ok check_syev (__main__.test_clapack_double) ... ok check_syevd (__main__.test_clapack_double) ... ok check_syevr (__main__.test_clapack_double) ... ok check_syevr_irange (__main__.test_clapack_double) ... ok check_syevr_irange_high (__main__.test_clapack_double) ... ok check_syevr_irange_low (__main__.test_clapack_double) ... ok check_syevr_irange_mid (__main__.test_clapack_double) ... ok check_syevr_vrange (__main__.test_clapack_double) ... ok check_syevr_vrange_high (__main__.test_clapack_double) ... ok check_syevr_vrange_low (__main__.test_clapack_double) ... ok check_syevr_vrange_mid (__main__.test_clapack_double) ... ok check_gebal (__main__.test_clapack_double_complex) ... ok check_gehrd (__main__.test_clapack_double_complex) ... ok check_heev (__main__.test_clapack_double_complex) ... ok check_heev_complex (__main__.test_clapack_double_complex) ... ok check_heevd (__main__.test_clapack_double_complex) ... ok check_heevd_complex (__main__.test_clapack_double_complex) ... ok check_heevr (__main__.test_clapack_double_complex) ... ok check_heevr_complex (__main__.test_clapack_double_complex) ... ok check_heevr_irange (__main__.test_clapack_double_complex) ... ok check_heevr_irange_high (__main__.test_clapack_double_complex) ... ok check_heevr_irange_low (__main__.test_clapack_double_complex) ... ok check_heevr_vrange (__main__.test_clapack_double_complex) ... ok check_heevr_vrange_high (__main__.test_clapack_double_complex) ... ok check_heevr_vrange_low (__main__.test_clapack_double_complex) ... ok check_gebal (__main__.test_clapack_float) ... ok check_gehrd (__main__.test_clapack_float) ... ok check_syev (__main__.test_clapack_float) ... ok check_syevd (__main__.test_clapack_float) ... ok check_syevr (__main__.test_clapack_float) ... ok check_syevr_irange (__main__.test_clapack_float) ... ok check_syevr_irange_high (__main__.test_clapack_float) ... ok check_syevr_irange_low (__main__.test_clapack_float) ... ok check_syevr_irange_mid (__main__.test_clapack_float) ... ok check_syevr_vrange (__main__.test_clapack_float) ... ok check_syevr_vrange_high (__main__.test_clapack_float) ... ok check_syevr_vrange_low (__main__.test_clapack_float) ... ok check_syevr_vrange_mid (__main__.test_clapack_float) ... ok check_gebal (__main__.test_flapack_complex) ... ok check_gehrd (__main__.test_flapack_complex) ... ok check_heev (__main__.test_flapack_complex) ... ok check_heev_complex (__main__.test_flapack_complex) ... ok check_heevd (__main__.test_flapack_complex) ... ok check_heevd_complex (__main__.test_flapack_complex) ... ok check_heevr (__main__.test_flapack_complex) ... ok check_heevr_complex (__main__.test_flapack_complex) ... ok check_heevr_irange (__main__.test_flapack_complex) ... ok check_heevr_irange_high (__main__.test_flapack_complex) ... ok check_heevr_irange_low (__main__.test_flapack_complex) ... ok check_heevr_vrange (__main__.test_flapack_complex) ... ok check_heevr_vrange_high (__main__.test_flapack_complex) ... ok check_heevr_vrange_low (__main__.test_flapack_complex) ... ok check_gebal (__main__.test_flapack_double) ... ok check_gehrd (__main__.test_flapack_double) ... ok check_syev (__main__.test_flapack_double) ... ok check_syevd (__main__.test_flapack_double) ... ok check_syevr (__main__.test_flapack_double) ... ok check_syevr_irange (__main__.test_flapack_double) ... ok check_syevr_irange_high (__main__.test_flapack_double) ... ok check_syevr_irange_low (__main__.test_flapack_double) ... ok check_syevr_irange_mid (__main__.test_flapack_double) ... ok check_syevr_vrange (__main__.test_flapack_double) ... ok check_syevr_vrange_high (__main__.test_flapack_double) ... ok check_syevr_vrange_low (__main__.test_flapack_double) ... ok check_syevr_vrange_mid (__main__.test_flapack_double) ... ok check_gebal (__main__.test_flapack_double_complex) ... ok check_gehrd (__main__.test_flapack_double_complex) ... ok check_heev (__main__.test_flapack_double_complex) ... ok check_heev_complex (__main__.test_flapack_double_complex) ... ok check_heevd (__main__.test_flapack_double_complex) ... ok check_heevd_complex (__main__.test_flapack_double_complex) ... ok check_heevr (__main__.test_flapack_double_complex) ... ok check_heevr_complex (__main__.test_flapack_double_complex) ... ok check_heevr_irange (__main__.test_flapack_double_complex) ... ok check_heevr_irange_high (__main__.test_flapack_double_complex) ... ok check_heevr_irange_low (__main__.test_flapack_double_complex) ... ok check_heevr_vrange (__main__.test_flapack_double_complex) ... ok check_heevr_vrange_high (__main__.test_flapack_double_complex) ... ok check_heevr_vrange_low (__main__.test_flapack_double_complex) ... ok check_gebal (__main__.test_flapack_float) ... ok check_gehrd (__main__.test_flapack_float) ... ok check_syev (__main__.test_flapack_float) ... ok check_syevd (__main__.test_flapack_float) ... ok check_syevr (__main__.test_flapack_float) ... ok check_syevr_irange (__main__.test_flapack_float) ... ok check_syevr_irange_high (__main__.test_flapack_float) ... ok check_syevr_irange_low (__main__.test_flapack_float) ... ok check_syevr_irange_mid (__main__.test_flapack_float) ... ok check_syevr_vrange (__main__.test_flapack_float) ... ok check_syevr_vrange_high (__main__.test_flapack_float) ... ok check_syevr_vrange_low (__main__.test_flapack_float) ... ok check_syevr_vrange_mid (__main__.test_flapack_float) ... ok ---------------------------------------------------------------------- Ran 108 tests in 0.245s OK lib/lapack>

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in-situ resizing array in C
by Pearu Peterson 01 Dec '04

01 Dec '04

Hi, I have a question to Numeric/Numarray experts: Let A be a contiguous one or two-dimensional array with shape (n,) or (m,n), respectively. Let k be a positive integer less than n. Reference count for A is 1. The objective is to execute A=A[:k] or A=A[:,:k], respctively, in C. Q: Is it safe to resize the array A by simply resetting its dimensions, that is, A->dimensions[0] = k; or A->dimensions[1] = k; if A->nd is 1 or 2, respectively, in C? This appears to work but may be there are some corner cases that I have overlooked. Would that work also when using Numarray? If not, how to resize (preferably in-situ) an array in C under the conditions given above? TIA, Pearu

3 5

segmentation fault in latest cvs using scipy.test()
by Nils Wagner 30 Nov '04

30 Nov '04

Hi all, I reveived a segmentation fault using latest scipy (cvs-version) '0.3.2_299.4503' Here is the output of gdb import scipy scipy.test() snip Program received signal SIGSEGV, Segmentation fault. [Switching to Thread 1077041376 (LWP 28627)] 0x47cc1560 in ATL_cdotc_xp0yp0aXbX () from /usr/lib/python2.3/site-packages/scipy/lib/lapack/flapack.so (gdb) Any pointer would be appreciated. It looks like my previous problem with symeig... Nils

2 7

cast documentation
by Alan G Isaac 27 Nov '04

27 Nov '04

i. The documentation for 'cast' at http://oliphant.ee.byu.edu:81/scipy_base/cast seems miscast. ii. Why isn't floor(A,Int) allowed (say, when A is a matrix of (small) floats)? It seems a lot clearer than A.astype(Int) which requires knowing the casting rules for a reader to understand it. Cheers, Alan Isaac

2 1

test matrix equality
by Alan G Isaac 27 Nov '04

27 Nov '04

Newbie question: What is the right/efficient way to test for equality between two matrices? While alltrue(ravel(A==B)) works, I am guessing alltrue(alltrue(A==B)) is better. If I import MA it seems I can use allequal, but this does not seem to be available otherwise. (Why??) Also, although this behaves like I want, it is oddly inconsistent with the other 'all' functions. I'd like to be able to just look at A.eq(B) for any matrices A and B. Thank you, Alan Isaac PS Suggestion: allow setting index=None for alltrue to test all individual elements.

2 2

using livedocs
by Pearu Peterson 26 Nov '04

26 Nov '04

Hi Travis, Could you explain how to you use livedocs? I can't get it work quite right. I have python-twisted and nevow installed. First, I had to execute twistd -oy livedocs.tac as a root. Otherwise I got a permission denied message in log. Is there a way to execute twistd as a normal user? Second, when the twistd server is up and I try to click some "Edit" link, I get a message: Sorry, but I couldn't find the object you requested. Is this expected? Thanks, Pearu

1 0

Small bug fix in l-bfgs-b solver
by Ed Schofield 25 Nov '04

25 Nov '04

The file lbfgsb.py in Lib/optimize/ has a bug that prevents it working with an argument list. Here's a patch: 179c179 < f[0], g = func_and_grad(x, *args) --- > f[0], g = func_and_grad(x) Cheers, Ed

2 1

FYI: math in wikis
by Fernando Perez 23 Nov '04

23 Nov '04

Hi all, just something I saw today on the Lyx mailing list. Since the topic of math, docs and wikis comes up regularly here, I figured it might be useful. Cheers, f ########################################################### LyX wiki now allows math using MimeTeX Von: chr-7XRkppT4KCs(a)public.gmane.org Datum: Montag 22 November 2004 02:37:33 nachmittags/abends Gruppen: gmane.editors.lyx.general Keine Referenzen FYI, the LyX wiki now lets you write math (and other LaTeX expressions) using a plugin called http://www.pmwiki.org/wiki/Cookbook/MimeTeX Simply put, writing {$x=y$} on a wiki page results in that equation being rendered as an image. So it's now possible to get rather complicated expressions displayed on the wiki. Now go and play in the sandbox :-) http://www.pmwiki.org/wiki/Main/WikiSandbox /Christian Christian Ridderström, +46-8-768 39 44 http://www.md.kth.se/~chr

5 7

wgnuplot.exe dependency in 0.3.2
by Joe Cooper 23 Nov '04

23 Nov '04

Hi all, I'm working on the next revision of Enthon today, and it looks like wgnuplot.exe has been introduced as a dependency of SciPy on Windows without being documented anywhere. Someone else ran into this last month, but there were no responses. Here's the error: running install_data error: can't copy 'Lib\gplt\wgnuplot.exe': doesn't exist or not a regular file A cursory glance at the setup code tells me that wgnuplot.exe doesn't have to be in Lib\ but it does have to exist in one of the other locations distutils is searching. Can I get a clarification on whether adding this dependency was intentional? I'd like to add it to the build instructions for Windows, if it will remain a dependency. I'm happy to add it to Enthon, if it provides additional functionality that people are using, but I don't want to unnecessarily complicate the package with dozens of competing tools (it's already 90MB in size in the last version, and there's at least 10MB worth of new packages going into the next version, and no significant removals). Thanks!

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Segmentation fault in symeig.test.test()
by Nils Wagner 20 Nov '04

20 Nov '04

Hi, I cannot resolve the problem with symeig.test.test() with respect to the symeig package. http://mdp-toolkit.sourceforge.net/symeig.html A back trace yields (no debugging symbols found)...>>> symeig.test.test() Random Seed: (1268049219, 2102953867) testComplex (symeig.test.test_symeig.SymeigTestCase) ... Program received signal SIGSEGV, Segmentation fault. [Switching to Thread 1077041376 (LWP 16623)] 0x411c1960 in ATL_cdotc_xp0yp0aXbX () from /usr/lib/python2.3/site-packages/symeig/froutines.so (gdb) bt #0 0x411c1960 in ATL_cdotc_xp0yp0aXbX () from /usr/lib/python2.3/site-packages/symeig/froutines.so #1 0x411b5463 in cdotc_ () from /usr/lib/python2.3/site-packages/symeig/froutines.so #2 0x41aac5fc in ?? () from /usr/lib/python2.3/site-packages/symeig/froutines.so #3 0x3eac8d56 in ?? () #4 0x41aac5fc in ?? () from /usr/lib/python2.3/site-packages/symeig/froutines.so #5 0x00000001 in ?? () #6 0xbfffca90 in ?? () #7 0xbfffcb48 in ?? () #8 0x41152f5c in chetd2_ () from /usr/lib/python2.3/site-packages/symeig/froutines.so #9 0x41130c69 in chetrd_ () from /usr/lib/python2.3/site-packages/symeig/froutines.so #10 0x4112f149 in cheevr_ () from /usr/lib/python2.3/site-packages/symeig/froutines.so #11 0x411256aa in f2py_rout_froutines_cheevr () from /usr/lib/python2.3/site-packages/symeig/froutines.so #12 0x411269e7 in fortran_call () from /usr/lib/python2.3/site-packages/symeig/froutines.so #13 0x4004b9e7 in PyObject_Call () from /usr/lib/libpython2.3.so.1.0 #14 0x400a4308 in eval_frame () from /usr/lib/libpython2.3.so.1.0 #15 0x400a68fe in PyEval_EvalCodeEx () from /usr/lib/libpython2.3.so.1.0 #16 0x400a501e in eval_frame () from /usr/lib/libpython2.3.so.1.0 #17 0x400a62a0 in eval_frame () from /usr/lib/libpython2.3.so.1.0 #18 0x400a62a0 in eval_frame () from /usr/lib/libpython2.3.so.1.0 #19 0x400a68fe in PyEval_EvalCodeEx () from /usr/lib/libpython2.3.so.1.0 #20 0x40061c2a in function_call () from /usr/lib/libpython2.3.so.1.0 #21 0x4004b9e7 in PyObject_Call () from /usr/lib/libpython2.3.so.1.0 #22 0x400547ab in instancemethod_call () from /usr/lib/libpython2.3.so.1.0 #23 0x4004b9e7 in PyObject_Call () from /usr/lib/libpython2.3.so.1.0 #24 0x400820ac in slot_tp_call () from /usr/lib/libpython2.3.so.1.0 ---Type <return> to continue, or q <return> to quit--- #25 0x4004b9e7 in PyObject_Call () from /usr/lib/libpython2.3.so.1.0 #26 0x400a4308 in eval_frame () from /usr/lib/libpython2.3.so.1.0 #27 0x400a68fe in PyEval_EvalCodeEx () from /usr/lib/libpython2.3.so.1.0 #28 0x40061c2a in function_call () from /usr/lib/libpython2.3.so.1.0 #29 0x4004b9e7 in PyObject_Call () from /usr/lib/libpython2.3.so.1.0 #30 0x400547ab in instancemethod_call () from /usr/lib/libpython2.3.so.1.0 #31 0x4004b9e7 in PyObject_Call () from /usr/lib/libpython2.3.so.1.0 #32 0x400820ac in slot_tp_call () from /usr/lib/libpython2.3.so.1.0 #33 0x4004b9e7 in PyObject_Call () from /usr/lib/libpython2.3.so.1.0 #34 0x400a4308 in eval_frame () from /usr/lib/libpython2.3.so.1.0 #35 0x400a68fe in PyEval_EvalCodeEx () from /usr/lib/libpython2.3.so.1.0 #36 0x40061c2a in function_call () from /usr/lib/libpython2.3.so.1.0 #37 0x4004b9e7 in PyObject_Call () from /usr/lib/libpython2.3.so.1.0 #38 0x400547ab in instancemethod_call () from /usr/lib/libpython2.3.so.1.0 #39 0x4004b9e7 in PyObject_Call () from /usr/lib/libpython2.3.so.1.0 #40 0x400820ac in slot_tp_call () from /usr/lib/libpython2.3.so.1.0 #41 0x4004b9e7 in PyObject_Call () from /usr/lib/libpython2.3.so.1.0 #42 0x400a4308 in eval_frame () from /usr/lib/libpython2.3.so.1.0 #43 0x400a62a0 in eval_frame () from /usr/lib/libpython2.3.so.1.0 #44 0x400a68fe in PyEval_EvalCodeEx () from /usr/lib/libpython2.3.so.1.0 #45 0x400a501e in eval_frame () from /usr/lib/libpython2.3.so.1.0 #46 0x400a68fe in PyEval_EvalCodeEx () from /usr/lib/libpython2.3.so.1.0 #47 0x400a6be5 in PyEval_EvalCode () from /usr/lib/libpython2.3.so.1.0 #48 0x400bfa98 in run_node () from /usr/lib/libpython2.3.so.1.0 #49 0x400c14e8 in PyRun_InteractiveOneFlags () from /usr/lib/libpython2.3.so.1.0 ---Type <return> to continue, or q <return> to quit--- #50 0x400c1656 in PyRun_InteractiveLoopFlags () from /usr/lib/libpython2.3.so.1.0 #51 0x400c1767 in PyRun_AnyFileExFlags () from /usr/lib/libpython2.3.so.1.0 #52 0x400c6ff3 in Py_Main () from /usr/lib/libpython2.3.so.1.0 #53 0x08048747 in main () Any idea what is erroneous here ? Can someone reproduce the segmentation fault ? Nils

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