Mailman 3 February 2014 - NumPy-Discussion

Automatic issue triage.
by Charles R Harris Feb. 21, 2014

Feb. 21, 2014

After 6 days of trudging through the numpy issues and finally passing the half way point, I'm wondering if we can set up so that new defects get a small test that can be parsed out and run periodically to mark issues that might be fixed. I expect it can be done, but might be more trouble than it is worth to keep working. Thoughts? Chuck

3 4

Re: [Numpy-discussion] [JOB ANNOUNCEMENT] Software Developer permanent position
by David Goldsmith Feb. 21, 2014

Feb. 21, 2014

On Thu, Feb 20, 2014 at 10:37 PM, <numpy-discussion-request(a)scipy.org>wrote: > Date: Fri, 21 Feb 2014 07:43:17 +0100 > From: "V. Armando Sol?" <sole(a)esrf.fr> > *Ref. 8173* *- Deadline for returning application forms: * *01/04/2014* > I assume that's the European date format, i.e., the due date is April 1, 2014, not Jan. 4 2014, oui? DG

2 1

dot product by 1*n maxtrix multiply it's transform not equal to raw python dot product?
by Li Li Feb. 21, 2014

Feb. 21, 2014

hi all I am porting some python code to java but got different results. after long time debugging, I found the reason is numpy's result is not the same as java(even the result of raw python codes) one case is: vector:[0.446141, 0.10414999999999996](that's not accurate) it's binary representation of IEEE754 is: 0.446141:0011111111011100100011011001001011111011000110011110011100110010 0.10419..:0011111110111010101010011001001100001011111000001101111011010000 dot product by java(or raw python) of x1*x1+x2*x2 is: 0.20988901438..(0011111111001010110111011010010010101010010001110010110101000011) but the result of pynum: x*x.T is: 0011111111001010110111011010010010101010010001110010110101000010 the last bit of mantissa is one difference. I don't floating points always hard to make sure to get same result in different environment(not only hardware but also software such as compiler optimizing and reordering) But I still want to know why, thanks. My environment: Python 2.7.3 (default, Sep 26 2013, 20:03:06) [GCC 4.6.3] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import numpy >>> numpy.version.version '1.6.1'

1 0

[JOB ANNOUNCEMENT] Software Developer permanent position available at ESRF, France
by V. Armando Sole Feb. 21, 2014

Feb. 21, 2014

Dear colleagues, The ESRF is looking for a Software Developer: http://esrf.profilsearch.com/recrute/fo_annonce_voir.php?id=300 Our ideal candidate would be experienced on OpenGL, OpenCL and Python. Best regards, Armando

2 2

Re: [Numpy-discussion] [cython-users] Re: avoiding numpy temporaries via refcount
by jtaylor.debian＠googlemail.com Feb. 20, 2014

Feb. 20, 2014

On Wednesday, February 19, 2014 9:10:03 AM UTC+1, Stefan Behnel wrote: > > >> Nathaniel Smith wrote: > >>> Does anyone see any issue we might be overlooking in this refcount == > 1 > >>> optimization for the python api? I'll post a PR with the change > shortly. > >>> > >>> It occurs belatedly that Cython code like a = np.arange(10) > >>> b = np.arange(10) > >>> c = a + b might end up calling tp_add with refcnt 1 arrays. Ditto > for > >>> same with cdef np.ndarray or cdef object added. We should check... > > That can happen, yes. Cython only guarantees that the object it passes is > safely owned so that the reference cannot go away while it's being > processed by a function. If it's in a local (non-closure) variable (or > Cython temporary variable), that guarantee holds, so it's safe to pass > objects with only a single reference into a C function, and Cython will do > that. > > Stefan > thats unfortunate, it would be a quite significant improvement to numpy (~30% improvement to all operations involving temporaries). Is increasing the reference count before going into PyNumber functions really that expensive that its worth avoiding?

1 0

svd error checking vs. speed
by alex Feb. 20, 2014

Feb. 20, 2014

Hello list, Here's another idea resurrection from numpy github comments that I've been advised could be posted here for re-discussion. The proposal would be to make np.linalg.svd more like scipy.linalg.svd with respect to input checking. The argument against the change is raw speed; if you know that you will never feed non-finite input to svd, then np.linalg.svd is a bit faster than scipy.linalg.svd. An argument for the change could be to avoid issues reported on github like crashes, hangs, spurious non-convergence exceptions, etc. from the undefined behavior of svd of non-finite input. """ [...] the following numpy code hangs until I `kill -9` it. ``` $ python runtests.py --shell $ python Python 2.7.5+ [GCC 4.8.1] on linux2 >>> import numpy as np >>> np.__version__ '1.9.0.dev-e3f0f53' >>> A = np.array([[1e3, 0], [0, 1]]) >>> B = np.array([[1e300, 0], [0, 1]]) >>> C = np.array([[1e3000, 0], [0, 1]]) >>> np.linalg.svd(A) (array([[ 1., 0.], [ 0., 1.]]), array([ 1000., 1.]), array([[ 1., 0.], [ 0., 1.]])) >>> np.linalg.svd(B) (array([[ 1., 0.], [ 0., 1.]]), array([ 1.00000000e+300, 1.00000000e+000]), array([[ 1., 0.], [ 0., 1.]])) >>> np.linalg.svd(C) [hangs forever] ``` """ Alex

7 25

NumPy 1.8.0 ERRORS under INTEL MKL
by Sergio Rojas Feb. 20, 2014

Feb. 20, 2014

Below is the output of running numpy test installed using Intel MKL library. Alll 5001 Numpy tests pass if installed using either Atlas or OpenBlass Is there ny known way to fix them? Sergio $ python Python 2.7.3 (default, Feb 11 2014, 16:24:48) [GCC Intel(R) C++ gcc 4.6 mode] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import numpy >>> numpy.show_config() lapack_opt_info: libraries = ['mkl_rt', 'pthread'] library_dirs = ['/opt/intel/composer_xe_2013_sp1.1.106/mkl/lib/intel64'] define_macros = [('SCIPY_MKL_H', None)] include_dirs = ['/opt/intel/composer_xe_2013_sp1.1.106/mkl/include'] blas_opt_info: libraries = ['mkl_rt', 'pthread'] library_dirs = ['/opt/intel/composer_xe_2013_sp1.1.106/mkl/lib/intel64'] define_macros = [('SCIPY_MKL_H', None)] include_dirs = ['/opt/intel/composer_xe_2013_sp1.1.106/mkl/include'] openblas_info: NOT AVAILABLE lapack_mkl_info: libraries = ['mkl_rt', 'pthread'] library_dirs = ['/opt/intel/composer_xe_2013_sp1.1.106/mkl/lib/intel64'] define_macros = [('SCIPY_MKL_H', None)] include_dirs = ['/opt/intel/composer_xe_2013_sp1.1.106/mkl/include'] blas_mkl_info: libraries = ['mkl_rt', 'pthread'] library_dirs = ['/opt/intel/composer_xe_2013_sp1.1.106/mkl/lib/intel64'] define_macros = [('SCIPY_MKL_H', None)] include_dirs = ['/opt/intel/composer_xe_2013_sp1.1.106/mkl/include'] mkl_info: libraries = ['mkl_rt', 'pthread'] library_dirs = ['/opt/intel/composer_xe_2013_sp1.1.106/mkl/lib/intel64'] define_macros = [('SCIPY_MKL_H', None)] include_dirs = ['/opt/intel/composer_xe_2013_sp1.1.106/mkl/include'] >>> numpy.test('full', verbose=2) Running unit tests for numpy NumPy version 1.8.0 NumPy is installed in /opt/myProg/Python273intel/Linux64b/lib/python2.7/site-pac kages/numpy Python version 2.7.3 (default, Feb 11 2014, 16:24:48) [GCC Intel(R) C++ gcc 4.6 mode] nose version 1.3.0 test_api.test_array_array ... ok ... ... test_matlib.test_empty ... ok test_matlib.test_ones ... ok test_matlib.test_zeros ... ok test_matlib.test_identity ... ok test_matlib.test_eye ... ok test_matlib.test_rand ... ok test_matlib.test_randn ... ok test_matlib.test_repmat ... ok ====================================================================== ERROR: test_assumed_shape.TestAssumedShapeSumExample.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/case.py", line 381, in setUp try_run(self.inst, ('setup', 'setUp')) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/util.py", line 469, in try_run return func() File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 353, in setUp module_name=self.module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 144, in build_module __import__(module_name) ImportError: dynamic module does not define init function (init_test_ext_module_ 5403) ====================================================================== ERROR: test_callback.TestF77Callback.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/case.py", line 381, in setUp try_run(self.inst, ('setup', 'setUp')) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/util.py", line 469, in try_run return func() File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 348, in setUp module_name=self.module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 163, in build_code module_name=module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 144, in build_module __import__(module_name) ImportError: dynamic module does not define init function (init_test_ext_module_ 5403) ====================================================================== ERROR: test_callback.TestF77Callback.test_docstring ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/case.py", line 381, in setUp try_run(self.inst, ('setup', 'setUp')) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/util.py", line 469, in try_run return func() File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 348, in setUp module_name=self.module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 80, in wrapper raise ret ImportError: dynamic module does not define init function (init_test_ext_module_ 5403) ====================================================================== ERROR: test_kind.TestKind.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/case.py", line 381, in setUp try_run(self.inst, ('setup', 'setUp')) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/util.py", line 469, in try_run return func() File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 353, in setUp module_name=self.module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 144, in build_module __import__(module_name) ImportError: dynamic module does not define init function (init_test_ext_module_ 5403) ====================================================================== ERROR: test_mixed.TestMixed.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/case.py", line 381, in setUp try_run(self.inst, ('setup', 'setUp')) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/util.py", line 469, in try_run return func() File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 353, in setUp module_name=self.module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 144, in build_module __import__(module_name) ImportError: dynamic module does not define init function (init_test_ext_module_ 5403) ====================================================================== ERROR: test_mixed.TestMixed.test_docstring ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/case.py", line 381, in setUp try_run(self.inst, ('setup', 'setUp')) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/util.py", line 469, in try_run return func() File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 353, in setUp module_name=self.module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 80, in wrapper raise ret ImportError: dynamic module does not define init function (init_test_ext_module_ 5403) ====================================================================== ERROR: test_return_character.TestF77ReturnCharacter.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/case.py", line 381, in setUp try_run(self.inst, ('setup', 'setUp')) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/util.py", line 469, in try_run return func() File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 348, in setUp module_name=self.module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 163, in build_code module_name=module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 144, in build_module __import__(module_name) ImportError: dynamic module does not define init function (init_test_ext_module_ 5403) ====================================================================== ERROR: test_return_character.TestF90ReturnCharacter.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/case.py", line 381, in setUp try_run(self.inst, ('setup', 'setUp')) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/util.py", line 469, in try_run return func() File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 348, in setUp module_name=self.module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 163, in build_code module_name=module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 144, in build_module __import__(module_name) ImportError: dynamic module does not define init function (init_test_ext_module_ 5403) ====================================================================== ERROR: test_return_complex.TestF77ReturnComplex.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/case.py", line 381, in setUp try_run(self.inst, ('setup', 'setUp')) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/util.py", line 469, in try_run return func() File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 348, in setUp module_name=self.module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 163, in build_code module_name=module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 144, in build_module __import__(module_name) ImportError: dynamic module does not define init function (init_test_ext_module_ 5403) ====================================================================== ERROR: test_return_complex.TestF90ReturnComplex.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/case.py", line 381, in setUp try_run(self.inst, ('setup', 'setUp')) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/util.py", line 469, in try_run return func() File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 348, in setUp module_name=self.module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 163, in build_code module_name=module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 144, in build_module __import__(module_name) ImportError: dynamic module does not define init function (init_test_ext_module_ 5403) ====================================================================== ERROR: test_return_integer.TestF77ReturnInteger.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/case.py", line 381, in setUp try_run(self.inst, ('setup', 'setUp')) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/util.py", line 469, in try_run return func() File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 348, in setUp module_name=self.module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 163, in build_code module_name=module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 144, in build_module __import__(module_name) ImportError: dynamic module does not define init function (init_test_ext_module_ 5403) ====================================================================== ERROR: test_return_integer.TestF90ReturnInteger.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/case.py", line 381, in setUp try_run(self.inst, ('setup', 'setUp')) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/util.py", line 469, in try_run return func() File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 348, in setUp module_name=self.module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 163, in build_code module_name=module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 144, in build_module __import__(module_name) ImportError: dynamic module does not define init function (init_test_ext_module_ 5403) ====================================================================== ERROR: test_return_logical.TestF77ReturnLogical.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/case.py", line 381, in setUp try_run(self.inst, ('setup', 'setUp')) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/util.py", line 469, in try_run return func() File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 348, in setUp module_name=self.module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 163, in build_code module_name=module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 144, in build_module __import__(module_name) ImportError: dynamic module does not define init function (init_test_ext_module_ 5403) ====================================================================== ERROR: test_return_logical.TestF90ReturnLogical.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/case.py", line 381, in setUp try_run(self.inst, ('setup', 'setUp')) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/util.py", line 469, in try_run return func() File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 348, in setUp module_name=self.module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 163, in build_code module_name=module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 144, in build_module __import__(module_name) ImportError: dynamic module does not define init function (init_test_ext_module_ 5403) ====================================================================== ERROR: test_return_real.TestF77ReturnReal.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/case.py", line 381, in setUp try_run(self.inst, ('setup', 'setUp')) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/util.py", line 469, in try_run return func() File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 348, in setUp module_name=self.module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 163, in build_code module_name=module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 144, in build_module __import__(module_name) ImportError: dynamic module does not define init function (init_test_ext_module_ 5403) ====================================================================== ERROR: test_return_real.TestF90ReturnReal.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/case.py", line 381, in setUp try_run(self.inst, ('setup', 'setUp')) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/util.py", line 469, in try_run return func() File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 348, in setUp module_name=self.module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 163, in build_code module_name=module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 144, in build_module __import__(module_name) ImportError: dynamic module does not define init function (init_test_ext_module_ 5403) ====================================================================== ERROR: test_size.TestSizeSumExample.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/case.py", line 381, in setUp try_run(self.inst, ('setup', 'setUp')) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/util.py", line 469, in try_run return func() File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 353, in setUp module_name=self.module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 144, in build_module __import__(module_name) ImportError: dynamic module does not define init function (init_test_ext_module_ 5403) ====================================================================== ERROR: test_size.TestSizeSumExample.test_flatten ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/case.py", line 381, in setUp try_run(self.inst, ('setup', 'setUp')) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/util.py", line 469, in try_run return func() File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 353, in setUp module_name=self.module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 80, in wrapper raise ret ImportError: dynamic module does not define init function (init_test_ext_module_ 5403) ====================================================================== ERROR: test_size.TestSizeSumExample.test_transpose ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/case.py", line 381, in setUp try_run(self.inst, ('setup', 'setUp')) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/util.py", line 469, in try_run return func() File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 353, in setUp module_name=self.module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 80, in wrapper raise ret ImportError: dynamic module does not define init function (init_test_ext_module_ 5403) ---------------------------------------------------------------------- Ran 5001 tests in 161.433s FAILED (KNOWNFAIL=5, SKIP=7, errors=19) <nose.result.TextTestResult run=5001 errors=19 failures=0> >>> quit()

2 1

PyViennaCL
by Toby St Clere Smithe Feb. 20, 2014

Feb. 20, 2014

Hi all, Apologies for posting across lists; I thought that this might be of interest to both groups. I have just released PyViennaCL 1.0.0, which is a set of largely NumPy-compatible Python bindings to the ViennaCL linear algebra and numerical computation library for GPGPU and heterogeneous systems. PyViennaCL aims to make powerful GPGPU computing really transparently easy, especially for users already using NumPy for representing matrices. Please see my announcement below for links to source and packages and documentation, a list of features, and a list of missing pieces. I hope to iron out all those missing bits over the coming months, and work on closer integration, especially with PyOpenCL / PyCUDA, over the summer. Best wishes, Toby St Clere Smithe

1 0

NumPy 1.8.0 ERRORS under INTEL MKL
by Sergio Rojas Feb. 20, 2014

Feb. 20, 2014

Below is the output of running numpy test installed using Intel MKL library. Alll 5001 Numpy tests pass if installed using either Atlas or OpenBlass Is there ny known way to fix them? Sergio $ python Python 2.7.3 (default, Feb 11 2014, 16:24:48) [GCC Intel(R) C++ gcc 4.6 mode] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import numpy >>> numpy.show_config() lapack_opt_info: libraries = ['mkl_rt', 'pthread'] library_dirs = ['/opt/intel/composer_xe_2013_sp1.1.106/mkl/lib/intel64'] define_macros = [('SCIPY_MKL_H', None)] include_dirs = ['/opt/intel/composer_xe_2013_sp1.1.106/mkl/include'] blas_opt_info: libraries = ['mkl_rt', 'pthread'] library_dirs = ['/opt/intel/composer_xe_2013_sp1.1.106/mkl/lib/intel64'] define_macros = [('SCIPY_MKL_H', None)] include_dirs = ['/opt/intel/composer_xe_2013_sp1.1.106/mkl/include'] openblas_info: NOT AVAILABLE lapack_mkl_info: libraries = ['mkl_rt', 'pthread'] library_dirs = ['/opt/intel/composer_xe_2013_sp1.1.106/mkl/lib/intel64'] define_macros = [('SCIPY_MKL_H', None)] include_dirs = ['/opt/intel/composer_xe_2013_sp1.1.106/mkl/include'] blas_mkl_info: libraries = ['mkl_rt', 'pthread'] library_dirs = ['/opt/intel/composer_xe_2013_sp1.1.106/mkl/lib/intel64'] define_macros = [('SCIPY_MKL_H', None)] include_dirs = ['/opt/intel/composer_xe_2013_sp1.1.106/mkl/include'] mkl_info: libraries = ['mkl_rt', 'pthread'] library_dirs = ['/opt/intel/composer_xe_2013_sp1.1.106/mkl/lib/intel64'] define_macros = [('SCIPY_MKL_H', None)] include_dirs = ['/opt/intel/composer_xe_2013_sp1.1.106/mkl/include'] >>> numpy.test('full', verbose=2) Running unit tests for numpy NumPy version 1.8.0 NumPy is installed in /opt/myProg/Python273intel/Linux64b/lib/python2.7/site-pac kages/numpy Python version 2.7.3 (default, Feb 11 2014, 16:24:48) [GCC Intel(R) C++ gcc 4.6 mode] nose version 1.3.0 test_api.test_array_array ... ok ... ... test_matlib.test_empty ... ok test_matlib.test_ones ... ok test_matlib.test_zeros ... ok test_matlib.test_identity ... ok test_matlib.test_eye ... ok test_matlib.test_rand ... ok test_matlib.test_randn ... ok test_matlib.test_repmat ... ok ====================================================================== ERROR: test_assumed_shape.TestAssumedShapeSumExample.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/case.py", line 381, in setUp try_run(self.inst, ('setup', 'setUp')) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/util.py", line 469, in try_run return func() File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 353, in setUp module_name=self.module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 144, in build_module __import__(module_name) ImportError: dynamic module does not define init function (init_test_ext_module_ 5403) ====================================================================== ERROR: test_callback.TestF77Callback.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/case.py", line 381, in setUp try_run(self.inst, ('setup', 'setUp')) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/util.py", line 469, in try_run return func() File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 348, in setUp module_name=self.module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 163, in build_code module_name=module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 144, in build_module __import__(module_name) ImportError: dynamic module does not define init function (init_test_ext_module_ 5403) ====================================================================== ERROR: test_callback.TestF77Callback.test_docstring ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/case.py", line 381, in setUp try_run(self.inst, ('setup', 'setUp')) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/util.py", line 469, in try_run return func() File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 348, in setUp module_name=self.module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 80, in wrapper raise ret ImportError: dynamic module does not define init function (init_test_ext_module_ 5403) ====================================================================== ERROR: test_kind.TestKind.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/case.py", line 381, in setUp try_run(self.inst, ('setup', 'setUp')) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/util.py", line 469, in try_run return func() File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 353, in setUp module_name=self.module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 144, in build_module __import__(module_name) ImportError: dynamic module does not define init function (init_test_ext_module_ 5403) ====================================================================== ERROR: test_mixed.TestMixed.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/case.py", line 381, in setUp try_run(self.inst, ('setup', 'setUp')) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/util.py", line 469, in try_run return func() File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 353, in setUp module_name=self.module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 144, in build_module __import__(module_name) ImportError: dynamic module does not define init function (init_test_ext_module_ 5403) ====================================================================== ERROR: test_mixed.TestMixed.test_docstring ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/case.py", line 381, in setUp try_run(self.inst, ('setup', 'setUp')) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/util.py", line 469, in try_run return func() File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 353, in setUp module_name=self.module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 80, in wrapper raise ret ImportError: dynamic module does not define init function (init_test_ext_module_ 5403) ====================================================================== ERROR: test_return_character.TestF77ReturnCharacter.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/case.py", line 381, in setUp try_run(self.inst, ('setup', 'setUp')) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/util.py", line 469, in try_run return func() File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 348, in setUp module_name=self.module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 163, in build_code module_name=module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 144, in build_module __import__(module_name) ImportError: dynamic module does not define init function (init_test_ext_module_ 5403) ====================================================================== ERROR: test_return_character.TestF90ReturnCharacter.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/case.py", line 381, in setUp try_run(self.inst, ('setup', 'setUp')) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/util.py", line 469, in try_run return func() File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 348, in setUp module_name=self.module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 163, in build_code module_name=module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 144, in build_module __import__(module_name) ImportError: dynamic module does not define init function (init_test_ext_module_ 5403) ====================================================================== ERROR: test_return_complex.TestF77ReturnComplex.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/case.py", line 381, in setUp try_run(self.inst, ('setup', 'setUp')) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/util.py", line 469, in try_run return func() File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 348, in setUp module_name=self.module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 163, in build_code module_name=module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 144, in build_module __import__(module_name) ImportError: dynamic module does not define init function (init_test_ext_module_ 5403) ====================================================================== ERROR: test_return_complex.TestF90ReturnComplex.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/case.py", line 381, in setUp try_run(self.inst, ('setup', 'setUp')) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/util.py", line 469, in try_run return func() File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 348, in setUp module_name=self.module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 163, in build_code module_name=module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 144, in build_module __import__(module_name) ImportError: dynamic module does not define init function (init_test_ext_module_ 5403) ====================================================================== ERROR: test_return_integer.TestF77ReturnInteger.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/case.py", line 381, in setUp try_run(self.inst, ('setup', 'setUp')) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/util.py", line 469, in try_run return func() File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 348, in setUp module_name=self.module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 163, in build_code module_name=module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 144, in build_module __import__(module_name) ImportError: dynamic module does not define init function (init_test_ext_module_ 5403) ====================================================================== ERROR: test_return_integer.TestF90ReturnInteger.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/case.py", line 381, in setUp try_run(self.inst, ('setup', 'setUp')) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/util.py", line 469, in try_run return func() File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 348, in setUp module_name=self.module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 163, in build_code module_name=module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 144, in build_module __import__(module_name) ImportError: dynamic module does not define init function (init_test_ext_module_ 5403) ====================================================================== ERROR: test_return_logical.TestF77ReturnLogical.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/case.py", line 381, in setUp try_run(self.inst, ('setup', 'setUp')) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/util.py", line 469, in try_run return func() File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 348, in setUp module_name=self.module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 163, in build_code module_name=module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 144, in build_module __import__(module_name) ImportError: dynamic module does not define init function (init_test_ext_module_ 5403) ====================================================================== ERROR: test_return_logical.TestF90ReturnLogical.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/case.py", line 381, in setUp try_run(self.inst, ('setup', 'setUp')) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/util.py", line 469, in try_run return func() File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 348, in setUp module_name=self.module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 163, in build_code module_name=module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 144, in build_module __import__(module_name) ImportError: dynamic module does not define init function (init_test_ext_module_ 5403) ====================================================================== ERROR: test_return_real.TestF77ReturnReal.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/case.py", line 381, in setUp try_run(self.inst, ('setup', 'setUp')) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/util.py", line 469, in try_run return func() File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 348, in setUp module_name=self.module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 163, in build_code module_name=module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 144, in build_module __import__(module_name) ImportError: dynamic module does not define init function (init_test_ext_module_ 5403) ====================================================================== ERROR: test_return_real.TestF90ReturnReal.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/case.py", line 381, in setUp try_run(self.inst, ('setup', 'setUp')) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/util.py", line 469, in try_run return func() File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 348, in setUp module_name=self.module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 163, in build_code module_name=module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 144, in build_module __import__(module_name) ImportError: dynamic module does not define init function (init_test_ext_module_ 5403) ====================================================================== ERROR: test_size.TestSizeSumExample.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/case.py", line 381, in setUp try_run(self.inst, ('setup', 'setUp')) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/util.py", line 469, in try_run return func() File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 353, in setUp module_name=self.module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 74, in wrapper memo[key] = func(*a, **kw) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 144, in build_module __import__(module_name) ImportError: dynamic module does not define init function (init_test_ext_module_ 5403) ====================================================================== ERROR: test_size.TestSizeSumExample.test_flatten ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/case.py", line 381, in setUp try_run(self.inst, ('setup', 'setUp')) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/util.py", line 469, in try_run return func() File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 353, in setUp module_name=self.module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 80, in wrapper raise ret ImportError: dynamic module does not define init function (init_test_ext_module_ 5403) ====================================================================== ERROR: test_size.TestSizeSumExample.test_transpose ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/case.py", line 381, in setUp try_run(self.inst, ('setup', 'setUp')) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/nose-1.3 .0-py2.7.egg/nose/util.py", line 469, in try_run return func() File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 353, in setUp module_name=self.module_name) File "/opt/myProg/Python273intel/Linux64b/lib/python2.7/site-packages/numpy/f2 py/tests/util.py", line 80, in wrapper raise ret ImportError: dynamic module does not define init function (init_test_ext_module_ 5403) ---------------------------------------------------------------------- Ran 5001 tests in 161.433s FAILED (KNOWNFAIL=5, SKIP=7, errors=19) <nose.result.TextTestResult run=5001 errors=19 failures=0> >>> quit()

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PR adding an axis argument to np.bincount
by Jaime Fernández del Río Feb. 19, 2014

Feb. 19, 2014

I have just submitted a PR (https://github.com/numpy/numpy/pull/4330) adding an axis argument to bincount. It lets you do things that would have been hard before, but the UI when broadcasting arrays together and having an axis argument can get tricky, and there is no obvious example already in place to follow, so I'd like to get some feedback on my choices. *With no weights* When not using the 'weights' parameter, the counting is done over the axes passed in 'axis'. This defaults to all axes, i.e. the flattened array. The output will have the shape of the original array, with those axes removed, and an extra dimension of size 'n' added at the end, where 'n' is the larger of 'minlength' and the maximum value in the array plus one. This is pretty straightforward. I think the only design choices that warrant some discussion are: 1. Should the default value for 'axis' be all axes, just the last, just the first? 2. Having the extra dimension added at the end. It may seem more natural to have the new dimension replace a dimension that has been removed. But because 'axis' can hold multiple axes, this would require some guessing (the first? the last? first or last based in position in the array, or in position in the 'axis' tuple?), which is avoided by having a fixed position. The other option would be at the beginning, not the end of the shape. For counting I think the last dimensions is the right choice, but... As an example of how it works: >>> a = np.random.randint(5, size=(3, 400, 500)) >>> np.bincount(a, axis=(-1, -2)) array([[39763, 40086, 39832, 39970, 40349], [40006, 39892, 40226, 39938, 39938], [39990, 40082, 40184, 39818, 39926]]) So there were 40184 occurrences of 2 in a[2, :, :]. *With weights* This can get complicated, but the rules are simple: the two arrays are broadcasted together, and the axes removed refer to the axes in the input array before broadcasting. This is probably best illustrated with an example: >>> w = np.random.rand(100, 3, 2) >>> a = np.random.randint(4, size=(100,)) >>> np.bincount(a, w.T).T array([[[ 8.29654919, 9.65794721], [ 12.01620609, 10.06676672], [ 11.73217521, 10.42220345]], [[ 10.67034693, 11.7945728 ], [ 13.47044072, 11.45176676], [ 10.83104283, 12.00869285]], [[ 14.30506753, 8.18840995], [ 13.44466573, 13.18924624], [ 11.95200531, 12.92169698]], [[ 16.78580192, 16.96104034], [ 12.80863984, 15.04778831], [ 16.35114845, 14.63648771]]]) Here 'w' has shape '(100, 3, 2)', interpreted as a list of 100 arrays of shape '(3, 2)'. We want to add together the arrays into several groups, as indicated by another array 'a' of shape '(100,)', which is what is achieved above. Other options to consider are: >>> np.bincount(a[:, None, None], w).shape (4,) <-- WRONG: the axis of dimension 1 have not been added by broadcasting, so they get removed >>> np.bincount(a[:, None, None], w, axis=0).shape (3, 2, 4) <-- RIGHT, but this doesn't seem the ordering of the dimensions one would want. It seems to me that what anyone trying to do this would like to get back is an array of shape '(4, 3, 2)', so I think the construct bincount(x, w.T).T will be used often enough that it warrants some less convoluted way of getting that back. But unless someone can figure out a smart way of handling this, I'd rather wait to see how it gets used, and modify it later, rather than making up an uninformed UI which turns out to be useless. The obvious question for bincount with weights are: 1. Should axis refer to the axes **after** broadcasting? I don't think it makes sense to add over a dimension of size 1 in the input array, you can get the same result by summing over that dimension in `weights` before calling bincount, but I am open to other opinons. 2. Any ideas on how to better handle multidimensional weights? Thanks, Jaime -- (\__/) ( O.o) ( > <) Este es Conejo. Copia a Conejo en tu firma y ayúdale en sus planes de dominación mundial.I

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