Mailman 3 September 2008 - SciPy-User

Re: [SciPy-user] scipy.test fails: clapack module is empty (Bryan Keith)
by bernardo martins rocha Sept. 13, 2008

Sept. 13, 2008

Hi Bryan Keith, > 8. scipy.test fails: clapack module is empty (Bryan Keith) > I've got the same error with my installation (opensuse11 via yast --- science repository), please have a look at the message below. I also have a "Illegal Instruction" error in the end of the test, which is worse than your problem. I would like to get rid off this. Any suggestions? Thanks! -------------------------- In [1]: import scipy In [2]: scipy.test() Failed importing scipy.linsolve.umfpack: 'module' object has no attribute 'umfpack' Found 9/9 tests for scipy.cluster.tests.test_vq Found 20/20 tests for scipy.fftpack.tests.test_pseudo_diffs Found 4/4 tests for scipy.fftpack.tests.test_helper Found 18/18 tests for scipy.fftpack.tests.test_basic Found 1/1 tests for scipy.integrate.tests.test_integrate Found 3/3 tests for scipy.integrate.tests.test_quadrature Found 10/10 tests for scipy.integrate.tests.test_quadpack Found 6/6 tests for scipy.tests.test_fitpack Found 6/6 tests for scipy.tests.test_interpolate Found 28/28 tests for scipy.io.tests.test_mio Found 4/4 tests for scipy.io.tests.test_recaster Found 5/5 tests for scipy.io.tests.test_npfile Found 13/13 tests for scipy.io.tests.test_mmio Found 4/4 tests for scipy.io.tests.test_array_import Found 16/16 tests for scipy.lib.blas.tests.test_blas Found 128/128 tests for scipy.lib.blas.tests.test_fblas **************************************************************** WARNING: clapack module is empty ----------- See scipy/INSTALL.txt for troubleshooting. Notes: * If atlas library is not found by numpy/distutils/system_info.py, then scipy uses flapack instead of clapack. **************************************************************** Found 42/42 tests for scipy.lib.lapack.tests.test_lapack Found 4/4 tests for scipy.linalg.tests.test_lapack <module 'scipy.linalg.fblas' from '/usr/lib64/python2.5/site-packages/scipy/linalg/fblas.so'> Found 16/16 tests for scipy.linalg.tests.test_blas Found 6/6 tests for scipy.linalg.tests.test_iterative Found 41/41 tests for scipy.linalg.tests.test_basic Found 128/128 tests for scipy.linalg.tests.test_fblas Found 7/7 tests for scipy.linalg.tests.test_matfuncs Found 72/72 tests for scipy.linalg.tests.test_decomp Failed importing /usr/lib64/python2.5/site-packages/scipy/linsolve/umfpack/tests/test_umfpack.py: 'module' object has no attribute 'umfpack' Found 2/2 tests for scipy.maxentropy.tests.test_maxentropy Found 3/3 tests for scipy.misc.tests.test_pilutil Found 399/399 tests for scipy.ndimage.tests.test_ndimage Found 5/5 tests for scipy.odr.tests.test_odr Found 4/4 tests for scipy.optimize.tests.test_zeros Found 1/1 tests for scipy.optimize.tests.test_cobyla Found 8/8 tests for scipy.optimize.tests.test_optimize Found 10/10 tests for scipy.optimize.tests.test_nonlin Found 5/5 tests for scipy.signal.tests.test_signaltools Found 4/4 tests for scipy.signal.tests.test_wavelets Found 152/152 tests for scipy.sparse.tests.test_sparse Found 3/3 tests for scipy.special.tests.test_spfun_stats Found 342/342 tests for scipy.special.tests.test_basic Found 10/10 tests for scipy.stats.tests.test_morestats Found 107/107 tests for scipy.stats.tests.test_stats Found 73/73 tests for scipy.stats.tests.test_distributions Found 0/0 tests for scipy.weave.tests.test_c_spec Found 1/1 tests for scipy.weave.tests.test_ast_tools Found 9/9 tests for scipy.weave.tests.test_build_tools Found 2/2 tests for scipy.weave.tests.test_blitz_tools building extensions here: /home/rocha/.python25_compiled/m11 Found 1/1 tests for scipy.weave.tests.test_ext_tools Found 0/0 tests for scipy.weave.tests.test_inline_tools Found 26/26 tests for scipy.weave.tests.test_catalog Found 0/0 tests for scipy.weave.tests.test_scxx_sequence Found 74/74 tests for scipy.weave.tests.test_size_check Failed importing /usr/lib64/python2.5/site-packages/scipy/weave/tests/old_test_wx_spec.py: Could not locate wxPython base directory. Found 0/0 tests for scipy.weave.tests.test_scxx_dict Found 0/0 tests for scipy.weave.tests.test_scxx_object Found 3/3 tests for scipy.weave.tests.test_standard_array_spec Found 16/16 tests for scipy.weave.tests.test_slice_handler Failed importing /usr/lib64/python2.5/site-packages/scipy/weave/tests/test_wx_spec.py: Could not locate wxPython base directory. ../usr/lib64/python2.5/site-packages/scipy/cluster/vq.py:477: UserWarning: One of the clusters is empty. Re-run kmean with a different initialization. warnings.warn("One of the clusters is empty. " exception raised as expected: One of the clusters is empty. Re-run kmean with a different initialization. ..........Illegal instruction Bernardo M. Rocha

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**kwds in frozen distribution class
by joep Sept. 12, 2008

Sept. 12, 2008

I was trying to work on an example for the frozen distribution class, in response to the previous message by Michael. The change in method signature between frozen and not frozen class got me confused: I looked at the information in help(stats.norm.stats) and did not realize that the signature in help(stats.norm(loc = 10, scale = 10).stats) or help(stats.norm(loc = 10, scale = 10)) is different. Given the description it does what it says, but I think it would be easy to make the keyword arguments consistent between frozen and not frozen distribution The frozen distribution class does not take any additional keywords ------------------------------------------------------------------- e.g. >>> from scipy import stats >>> stats.norm.stats(loc = 10, scale = 10, moments='v') array(100.0) >>> stats.norm(loc = 10, scale = 10).stats(moments='v') Traceback (most recent call last): File "<pyshell#91>", line 1, in ? stats.norm(loc = 10, scale = 10).stats(moments='v') TypeError: stats() got an unexpected keyword argument 'moments' >>> stats.norm(loc = 10, scale = 10, moments='v').stats() array(100.0) line numbers from current trunk (http://projects.scipy.org/scipy/scipy/browser/trunk/scipy/stats/ distributions.py) 101 # Frozen RV class 102 class rv_frozen(object): 121 def stats(self): 122 return self.dist.stats(*self.args,**self.kwds) I think this change should work to accept additional keywords: 121 def stats(self,**kwds): kwds.update(self.kwds) 122 return self.dist.stats(*self.args,**kwds) Josef

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Why doesn't norm_gen have a 'dist' attribute?
by Michael Sept. 12, 2008

Sept. 12, 2008

> Message: 2 > Date: Wed, 10 Sep 2008 23:05:30 -0500 > From: "Robert Kern" <robert.kern(a)gmail.com> > Subject: Re: [SciPy-user] examples of using norm_gen > To: "SciPy Users List" <scipy-user(a)scipy.org> > Message-ID: > <3d375d730809102105v167195ceuf8c0cf9e725c5059(a)mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > On Wed, Sep 10, 2008 at 19:41, SimonPalmer <simon.palmer(a)gmail.com> wrote: > > can anyone point me in the direction of examples of how to use norm/ > > norm_gen from the scipy.stats.distributions module? > > The docstring gives a good overview of its capabilities. Is there > something specific you found confusing or inadequate about it? norm_gen doesn't appear to _generate_ anything, not directly anyway a=d.norm_gen(name='norm',longname='a normal') a is <class 'scipy.stats.distributions.norm_gen'> b=d.norm(x,size=n) b is <class 'scipy.stats.distributions.rv_frozen'> both a and b produce normal distributions that don't 'look' normal - see attached, though this is a bad test since the beta distribution looks totally mangled but is correc pdf1=a.pdf(x,size=n) pdf2=b.dist.pdf(x,size=n) Leaving norm_gen aside for a moment, c.f. the lack of the 'dist' attribute in 'a', one might also ask: what the dist attribute does? Where did it spring from? there's too much padding in the scipy sandwich, so to speak; e.g. the sheer number of ways of creating scipy distributions is slightly baffling; afaik norm_gen is a base class that is not to be used directly... but that's just a guess. That said, there is an 85-100 fold speed-up over using a np.random distribution + np.histogram Is there a guide somewhere explaining how scientific python api's are packaged/structured? import idioms? > -- > Robert Kern > > "I have come to believe that the whole world is an enigma, a harmless > enigma that is made terrible by our own mad attempt to interpret it as > though it had an underlying truth." > -- Umberto Eco

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Unexpected typecasting when adding sparse.lil_matrix
by Tony S Yu Sept. 11, 2008

Sept. 11, 2008

This may be expected behavior, but I found it surprising. Addition (or any other simple operation) of two lil sparse matrices returns a csc sparse matrix. The scipy website suggests that csc and csr matrices are more efficient than lil matrices for multiplication and inversion (and I guess for addition too), but this typecasting is still a little surprising. I was just curious if this is intentional. Thanks, -Tony #~~~~~~~~~ In [1]: import scipy.sparse as sparse In [2]: A = sparse.lil_eye([3, 3]) In [3]: A + A Out[3]: <3x3 sparse matrix of type '<type 'numpy.float64'>' with 3 stored elements (space for 3) in Compressed Sparse Column format>

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examples of using norm_gen
by SimonPalmer Sept. 10, 2008

Sept. 10, 2008

can anyone point me in the direction of examples of how to use norm/ norm_gen from the scipy.stats.distributions module? thanks Simon

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NumPy arrays that use memory allocated from other libraries or tools
by Travis E. Oliphant Sept. 9, 2008

Sept. 9, 2008

I wanted to point anybody interested to a blog post that describes a useful pattern for having a NumPy array that points to the memory created by a different memory manager than the standard one used by NumPy. The pattern shows how to create a NumPy array that points to previously allocated memory and then shows how to construct an object that allows the correct deallocator to be called when the NumPy array is freed. This may be useful if you are wrapping code that has it's own memory management scheme. Comments and feedback is welcome. The post is http://blog.enthought.com/?p=62 Best regards, -Travis Oliphant

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Pytrilinos on Windows
by Ish Aden Sept. 9, 2008

Sept. 9, 2008

Hello Could anyone who's successfully installed Pytrilinos on a Windows machine explain how they did it. Also, are there any mature/close to mature Python PDE solvers out there in addition to 'sfepy'. Thanks in advance. Ted

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need an IDL-like rebin function
by Ken Dere Sept. 9, 2008

Sept. 9, 2008

I have tried to use zoom as a rebin-like function but it's behavior at the edges of the array is not acceptable and I don't seem to be able to influence this behavior. Actually, I don't even want interpolation at this point. advice appreciated Ken Dere

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scipy.test fails: clapack module is empty
by Bryan Keith Sept. 9, 2008

Sept. 9, 2008

Hello, I'm trying to install scipy (0.6.0) on Ubuntu 8.04 64 bit with Python 2.5.2 and numpy 1.0.4 Installation (via apt-get) seems to go fine, but the test suite fails. I'm not sure how concerned I should be about this failure. I've searched for some of the errors that I'm getting but couldn't find anything to either resolve the tests and make me decide to ignore them. I'm pasting the test results below. Any help is appreciated. Thank you. Bryan >>> import scipy >>> scipy.test(level=1) Found 9/9 tests for scipy.cluster.vq Found 18/18 tests for scipy.fftpack.basic Found 4/4 tests for scipy.fftpack.helper Found 20/20 tests for scipy.fftpack.pseudo_diffs Found 1/1 tests for scipy.integrate Found 10/10 tests for scipy.integrate.quadpack Found 3/3 tests for scipy.integrate.quadrature Found 6/6 tests for scipy.interpolate Found 6/6 tests for scipy.interpolate.fitpack Found 4/4 tests for scipy.io.array_import Found 28/28 tests for scipy.io.mio Found 13/13 tests for scipy.io.mmio Found 5/5 tests for scipy.io.npfile Found 4/4 tests for scipy.io.recaster Found 16/16 tests for scipy.lib.blas Found 128/128 tests for scipy.lib.blas.fblas **************************************************************** WARNING: clapack module is empty ----------- See scipy/INSTALL.txt for troubleshooting. Notes: * If atlas library is not found by numpy/distutils/system_info.py, then scipy uses flapack instead of clapack. **************************************************************** Found 42/42 tests for scipy.lib.lapack Found 41/41 tests for scipy.linalg.basic <module 'scipy.linalg.fblas' from '/usr/lib/python2.5/site-packages/scipy/linalg/fblas.so'> Found 16/16 tests for scipy.linalg.blas Found 72/72 tests for scipy.linalg.decomp Found 128/128 tests for scipy.linalg.fblas Found 6/6 tests for scipy.linalg.iterative Found 4/4 tests for scipy.linalg.lapack Found 7/7 tests for scipy.linalg.matfuncs Found 9/9 tests for scipy.linsolve.umfpack Found 2/2 tests for scipy.maxentropy Found 3/3 tests for scipy.misc.pilutil Found 399/399 tests for scipy.ndimage Found 5/5 tests for scipy.odr Found 8/8 tests for scipy.optimize Found 1/1 tests for scipy.optimize.cobyla Found 10/10 tests for scipy.optimize.nonlin Found 4/4 tests for scipy.optimize.zeros Found 5/5 tests for scipy.signal.signaltools Found 4/4 tests for scipy.signal.wavelets Found 152/152 tests for scipy.sparse Found 342/342 tests for scipy.special.basic Found 3/3 tests for scipy.special.spfun_stats Found 107/107 tests for scipy.stats Found 73/73 tests for scipy.stats.distributions Found 10/10 tests for scipy.stats.morestats Found 0/0 tests for __main__ .../usr/lib/python2.5/site-packages/scipy/cluster/vq.py:477: UserWarning: One of the clusters is empty. Re-run kmean with a different initialization. warnings.warn("One of the clusters is empty. " exception raised as expected: One of the clusters is empty. Re-run kmean with a different initialization. ................................................Residual: 1.05006987327e-07 ..................../usr/lib/python2.5/site-packages/scipy/interpolate/fitpack2.py:458: UserWarning: The coefficients of the spline returned have been computed as the minimal norm least-squares solution of a (numerically) rank deficient system (deficiency=7). If deficiency is large, the results may be inaccurate. Deficiency may strongly depend on the value of eps. warnings.warn(message) ...... Don't worry about a warning regarding the number of bytes read. Warning: 1000000 bytes requested, 20 bytes read. .........................................................................caxpy:n=4 ..caxpy:n=3 ....ccopy:n=4 ..ccopy:n=3 .............cscal:n=4 ....cswap:n=4 ..cswap:n=3 .....daxpy:n=4 ..daxpy:n=3 ....dcopy:n=4 ..dcopy:n=3 .............dscal:n=4 ....dswap:n=4 ..dswap:n=3 .....saxpy:n=4 ..saxpy:n=3 ....scopy:n=4 ..scopy:n=3 .............sscal:n=4 ....sswap:n=4 ..sswap:n=3 .....zaxpy:n=4 ..zaxpy:n=3 ....zcopy:n=4 ..zcopy:n=3 .............zscal:n=4 ....zswap:n=4 ..zswap:n=3 ............................FF....................................................... **************************************************************** WARNING: cblas module is empty ----------- See scipy/INSTALL.txt for troubleshooting. Notes: * If atlas library is not found by numpy/distutils/system_info.py, then scipy uses fblas instead of cblas. **************************************************************** ...........................................................................................caxpy:n=4 ..caxpy:n=3 ....ccopy:n=4 ..ccopy:n=3 .............cscal:n=4 ....cswap:n=4 ..cswap:n=3 .....daxpy:n=4 ..daxpy:n=3 ....dcopy:n=4 ..dcopy:n=3 .............dscal:n=4 ....dswap:n=4 ..dswap:n=3 .....saxpy:n=4 ..saxpy:n=3 ....scopy:n=4 ..scopy:n=3 .............sscal:n=4 ....sswap:n=4 ..sswap:n=3 .....zaxpy:n=4 ..zaxpy:n=3 ....zcopy:n=4 ..zcopy:n=3 .............zscal:n=4 ....zswap:n=4 ..zswap:n=3 .......... **************************************************************** WARNING: clapack module is empty ----------- See scipy/INSTALL.txt for troubleshooting. Notes: * If atlas library is not found by numpy/distutils/system_info.py, then scipy uses flapack instead of clapack. **************************************************************** ...Result may be inaccurate, approximate err = 1.11929781998e-08 ...Result may be inaccurate, approximate err = 7.73070496507e-12 ......Use minimum degree ordering on A'+A. ..Use minimum degree ordering on A'+A. F..Use minimum degree ordering on A'+A. F............................................................................................................/usr/lib/python2.5/site-packages/scipy/ndimage/interpolation.py:41: UserWarning: Mode "reflect" may yield incorrect results on boundaries. Please use "mirror" instead. warnings.warn('Mode "reflect" may yield incorrect results on ' ........................................................................................................................................................................................................................................................................................................F..F.........................................................Use minimum degree ordering on A'+A. .....................................Use minimum degree ordering on A'+A. .....................................Use minimum degree ordering on A'+A. ................................Use minimum degree ordering on A'+A. ....................................................................................................................................................................................................................................................................................................................................................0.2 0.2 0.2 ......0.2 ..0.2 0.2 0.2 0.2 0.2 .........................................................................................................................................................................................................Ties preclude use of exact statistic. ..Ties preclude use of exact statistic. ...... ====================================================================== FAIL: check_syevr (scipy.lib.tests.test_lapack.test_flapack_float) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.5/site-packages/scipy/lib/lapack/tests/esv_tests.py", line 41, in check_syevr assert_array_almost_equal(w,exact_w) File "/usr/lib/python2.5/site-packages/numpy/testing/utils.py", line 232, in assert_array_almost_equal header='Arrays are not almost equal') File "/usr/lib/python2.5/site-packages/numpy/testing/utils.py", line 217, in assert_array_compare assert cond, msg AssertionError: Arrays are not almost equal (mismatch 33.3333333333%) x: array([-0.66992444, 0.48769474, 9.18222618], dtype=float32) y: array([-0.66992434, 0.48769389, 9.18223045]) ====================================================================== FAIL: check_syevr_irange (scipy.lib.tests.test_lapack.test_flapack_float) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.5/site-packages/scipy/lib/lapack/tests/esv_tests.py", line 66, in check_syevr_irange assert_array_almost_equal(w,exact_w[rslice]) File "/usr/lib/python2.5/site-packages/numpy/testing/utils.py", line 232, in assert_array_almost_equal header='Arrays are not almost equal') File "/usr/lib/python2.5/site-packages/numpy/testing/utils.py", line 217, in assert_array_compare assert cond, msg AssertionError: Arrays are not almost equal (mismatch 33.3333333333%) x: array([-0.66992444, 0.48769474, 9.18222618], dtype=float32) y: array([-0.66992434, 0.48769389, 9.18223045]) ====================================================================== FAIL: Solve: single precision complex ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.5/site-packages/scipy/linsolve/umfpack/tests/test_umfpack.py", line 32, in check_solve_complex_without_umfpack assert_array_almost_equal(a*x, b) File "/usr/lib/python2.5/site-packages/numpy/testing/utils.py", line 232, in assert_array_almost_equal header='Arrays are not almost equal') File "/usr/lib/python2.5/site-packages/numpy/testing/utils.py", line 217, in assert_array_compare assert cond, msg AssertionError: Arrays are not almost equal (mismatch 20.0%) x: array([ 1.00000000+0.j, 1.99999809+0.j, 3.00000000+0.j, 4.00000048+0.j, 5.00000000+0.j], dtype=complex64) y: array([1, 2, 3, 4, 5]) ====================================================================== FAIL: Solve: single precision ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.5/site-packages/scipy/linsolve/umfpack/tests/test_umfpack.py", line 43, in check_solve_without_umfpack assert_array_almost_equal(a*x, b) File "/usr/lib/python2.5/site-packages/numpy/testing/utils.py", line 232, in assert_array_almost_equal header='Arrays are not almost equal') File "/usr/lib/python2.5/site-packages/numpy/testing/utils.py", line 217, in assert_array_compare assert cond, msg AssertionError: Arrays are not almost equal (mismatch 20.0%) x: array([ 1. , 1.99999809, 3. , 4.00000048, 5. ], dtype=float32) y: array([1, 2, 3, 4, 5]) ====================================================================== FAIL: test_explicit (scipy.tests.test_odr.test_odr) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.5/site-packages/scipy/odr/tests/test_odr.py", line 50, in test_explicit -8.7849712165253724e-02]), File "/usr/lib/python2.5/site-packages/numpy/testing/utils.py", line 232, in assert_array_almost_equal header='Arrays are not almost equal') File "/usr/lib/python2.5/site-packages/numpy/testing/utils.py", line 217, in assert_array_compare assert cond, msg AssertionError: Arrays are not almost equal (mismatch 100.0%) x: array([ 1.26462971e+03, -5.42545890e+01, -8.64250389e-02]) y: array([ 1.26465481e+03, -5.40184100e+01, -8.78497122e-02]) ====================================================================== FAIL: test_multi (scipy.tests.test_odr.test_odr) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.5/site-packages/scipy/odr/tests/test_odr.py", line 191, in test_multi 0.5101147161764654, 0.5173902330489161]), File "/usr/lib/python2.5/site-packages/numpy/testing/utils.py", line 232, in assert_array_almost_equal header='Arrays are not almost equal') File "/usr/lib/python2.5/site-packages/numpy/testing/utils.py", line 217, in assert_array_compare assert cond, msg AssertionError: Arrays are not almost equal (mismatch 100.0%) x: array([ 4.31272063, 2.44289312, 7.76215871, 0.55995622, 0.46423343]) y: array([ 4.37998803, 2.43330576, 8.00288459, 0.51011472, 0.51739023]) ---------------------------------------------------------------------- Ran 1728 tests in 7.579s FAILED (failures=6) <unittest._TextTestResult run=1728 errors=0 failures=6> >>>

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maybe a bug in scipy.io.loadmat
by xiaojf Sept. 9, 2008

Sept. 9, 2008

Hi all, I found that scipy.io.loadmat(filename) doesn't work when filename contains '/' instead of '\\' as file path separater. """ Help on function loadmat in module scipy.io.mio: loadmat(file_name, mdict=None, appendmat=True, basename='raw', **kwargs) Load Matlab(tm) file file_name - Name of the mat file (do not need .mat extension if appendmat==True) If name not a full path name, search for the file on the sys.path list and use the first one found (the current directory is searched first). Can also pass open file-like object """ The problem is in function find_mat_file, which tries to find the file in directories listed in sys.path when there is no os.sep in file_name. I couldn't understand why the function find_mat_file() tries to find .mat file in directories listed in sys.path, since sys.path is module search path not data file search path. def find_mat_file(file_name, appendmat=True): ''' Try to find .mat file on system path file_name - file name string append_mat - If True, and file_name does not end in '.mat', appends it ''' if appendmat and file_name[-4:] == ".mat": file_name = file_name[:-4] if os.sep in file_name: full_name = file_name if appendmat: full_name = file_name + ".mat" else: full_name = None junk, file_name = os.path.split(file_name) for path in sys.path: test_name = os.path.join(path, file_name) if appendmat: test_name += ".mat" try: fid = open(test_name,'rb') fid.close() full_name = test_name break except IOError: pass return full_name

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