[SciPy-User] How to fix Aborted SciPy version 0.16.0b2 test ?

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[SciPy-User] How to fix Aborted SciPy version 0.16.0b2 test ?

Sergio Rojas
Hello all,
 
Runing on Ubuntu 14.04 LTS and under Python 3.5.0b3 and NumPy version 1.9.2, the
SciPy (version 0.16.0b2) test is aborting at 
 
#------------
test_interpolative.TestInterpolativeDecomposition.test_badcall ... ok
test_interpolative.TestInterpolativeDecomposition.test_id(<class 'numpy.float64'>,) ... *** Error in `python3': free(): invalid next size (normal): 0x00000000039e1f60 ***
Aborted
#------------
 
would it be possible to fix it?
 
Thanks in advance for your help,
 
Sergio
PD. Some extra info is as follows:
 
$ python3 Python 3.5.0b3 (default, Jul 21 2015, 12:33:54)
[GCC 4.8.4] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import scipy
>>> scipy.show_config()
blas_mkl_info:
  NOT AVAILABLE
atlas_3_10_threads_info:
    libraries = ['tatlas', 'tatlas', 'tatlas']
    define_macros = [('ATLAS_INFO', '"\\"3.11.34\\""')]
    include_dirs = ['/home/myProg/NumLibs64b/include']
    library_dirs = ['/home/myProg/NumLibs64b/lib']
    language = f77
openblas_lapack_info:
  NOT AVAILABLE
lapack_mkl_info:
  NOT AVAILABLE
openblas_info:
  NOT AVAILABLE
mkl_info:
  NOT AVAILABLE
lapack_opt_info:
    libraries = ['tatlas', 'tatlas', 'tatlas']
    define_macros = [('ATLAS_INFO', '"\\"3.11.34\\""')]
    include_dirs = ['/home/myProg/NumLibs64b/include']
    library_dirs = ['/home/myProg/NumLibs64b/lib']
    language = f77
atlas_3_10_blas_threads_info:
    libraries = ['tatlas']
    define_macros = [('HAVE_CBLAS', None), ('ATLAS_INFO', '"\\"3.11.34\\""')]
    include_dirs = ['/home/myProg/NumLibs64b/include']
    library_dirs = ['/home/myProg/NumLibs64b/lib']
    language = c
blas_opt_info:
    libraries = ['tatlas']
    define_macros = [('HAVE_CBLAS', None), ('ATLAS_INFO', '"\\"3.11.34\\""')]
    include_dirs = ['/home/myProg/NumLibs64b/include']
    library_dirs = ['/home/myProg/NumLibs64b/lib']
    language = c
>>> scipy.test('full', verbose=2)
Running unit tests for scipy
NumPy version 1.9.2
NumPy is installed in /home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-packages/numpy
SciPy version 0.16.0b2
SciPy is installed in /home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-packages/scipy
Python version 3.5.0b3 (default, Jul 21 2015, 12:33:54) [GCC 4.8.4]
nose version 1.3.7
/home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-packages/scipy/_lib/decorator.py:205: DeprecationWarning: inspect.getargspec() is deprecated, use inspect.signature() instead
...
...
test_y_bad_size (test_fblas.TestZswap) ... ok
test_y_stride (test_fblas.TestZswap) ... ok
test_interpolative.TestInterpolativeDecomposition.test_badcall ... ok
test_interpolative.TestInterpolativeDecomposition.test_id(<class 'numpy.float64'>,) ... *** Error in `python3': free(): invalid next size (normal): 0x00000000039e1f60 ***
Aborted
 
 

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Re: How to fix Aborted SciPy version 0.16.0b2 test ?

ralfgommers


On Tue, Jul 21, 2015 at 9:39 PM, Sergio Rojas <[hidden email]> wrote:
Hello all,
 
Runing on Ubuntu 14.04 LTS and under Python 3.5.0b3 and NumPy version 1.9.2, the
SciPy (version 0.16.0b2) test is aborting at 
 
#------------
test_interpolative.TestInterpolativeDecomposition.test_badcall ... ok
test_interpolative.TestInterpolativeDecomposition.test_id(<class 'numpy.float64'>,) ... *** Error in `python3': free(): invalid next size (normal): 0x00000000039e1f60 ***
Aborted
#------------
 
would it be possible to fix it?

Hi Sergio, thanks for the report. A few questions:
- did 0.15.1 work for you with the same install method
- does the problem still occur with the final 0.16.0 release?
- is the issue specific to Python 3.5 or not?


Opening an issue on Github and attaching a gdb traceback (see http://scipy.org/bug-report.html) would be helpful.

Cheers,
Ralf

 
 
Thanks in advance for your help,
 
Sergio
PD. Some extra info is as follows:
 
$ python3 Python 3.5.0b3 (default, Jul 21 2015, 12:33:54)
[GCC 4.8.4] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import scipy
>>> scipy.show_config()
blas_mkl_info:
  NOT AVAILABLE
atlas_3_10_threads_info:
    libraries = ['tatlas', 'tatlas', 'tatlas']
    define_macros = [('ATLAS_INFO', '"\\"3.11.34\\""')]
    include_dirs = ['/home/myProg/NumLibs64b/include']
    library_dirs = ['/home/myProg/NumLibs64b/lib']
    language = f77
openblas_lapack_info:
  NOT AVAILABLE
lapack_mkl_info:
  NOT AVAILABLE
openblas_info:
  NOT AVAILABLE
mkl_info:
  NOT AVAILABLE
lapack_opt_info:
    libraries = ['tatlas', 'tatlas', 'tatlas']
    define_macros = [('ATLAS_INFO', '"\\"3.11.34\\""')]
    include_dirs = ['/home/myProg/NumLibs64b/include']
    library_dirs = ['/home/myProg/NumLibs64b/lib']
    language = f77
atlas_3_10_blas_threads_info:
    libraries = ['tatlas']
    define_macros = [('HAVE_CBLAS', None), ('ATLAS_INFO', '"\\"3.11.34\\""')]
    include_dirs = ['/home/myProg/NumLibs64b/include']
    library_dirs = ['/home/myProg/NumLibs64b/lib']
    language = c
blas_opt_info:
    libraries = ['tatlas']
    define_macros = [('HAVE_CBLAS', None), ('ATLAS_INFO', '"\\"3.11.34\\""')]
    include_dirs = ['/home/myProg/NumLibs64b/include']
    library_dirs = ['/home/myProg/NumLibs64b/lib']
    language = c
>>> scipy.test('full', verbose=2)
Running unit tests for scipy
NumPy version 1.9.2
NumPy is installed in /home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-packages/numpy
SciPy version 0.16.0b2
SciPy is installed in /home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-packages/scipy
Python version 3.5.0b3 (default, Jul 21 2015, 12:33:54) [GCC 4.8.4]
nose version 1.3.7
/home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-packages/scipy/_lib/decorator.py:205: DeprecationWarning: inspect.getargspec() is deprecated, use inspect.signature() instead
...
...
test_y_bad_size (test_fblas.TestZswap) ... ok
test_y_stride (test_fblas.TestZswap) ... ok
test_interpolative.TestInterpolativeDecomposition.test_badcall ... ok
test_interpolative.TestInterpolativeDecomposition.test_id(<class 'numpy.float64'>,) ... *** Error in `python3': free(): invalid next size (normal): 0x00000000039e1f60 ***
Aborted
 
 

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Re: How to fix Aborted SciPy version 0.16.0b2 test ?

Sergio Rojas
In reply to this post by Sergio Rojas
For some reason I am not getting messages via the
mailing list. I am reading them at the web
[ http://mail.scipy.org/pipermail/scipy-user/2015-July/036660.html ]
 
>
>Hi Sergio, thanks for the report. A few questions:
>- did 0.15.1 work for you with the same install method
>- does the problem still occur with the final 0.16.0 release?
>- is the issue specific to Python 3.5 or not?
>
>Opening an issue on Github and attaching a gdb traceback (see
>http://scipy.org/bug-report.html) would be helpful.
>Cheers,
>Ralf
 
At this stage, Ralf, I have confirmed that the issue is NO
specific to Python 3.5 or to SciPy version 0.16.0b2 :
 
$ python
Python 2.7.10 (default, Jul 29 2015, 20:51:44)
[GCC 4.8.4] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import scipy
>>> scipy.test('full', verbose=2)
Running unit tests for scipy
NumPy version 1.9.2
NumPy is installed in /home/myProg/PythonGNU2710/Linux64b/lib/python2.7/site-pac
kages/numpy
SciPy version 0.16.0b2
SciPy is installed in /home/myProg/PythonGNU2710/Linux64b/lib/python2.7/site-pac
kages/scipy
Python version 2.7.10 (default, Jul 29 2015, 20:51:44) [GCC 4.8.4]
nose version 1.3.7
/home/myProg/PythonGNU2710/Linux64b/lib/python2.7/site-packages/numpy/lib/utils.
py:95: DeprecationWarning: `scipy.weave` is deprecated, use `weave` instead!
  warnings.warn(depdoc, DeprecationWarning)
test_hierarchy.TestCopheneticDistance.test_linkage_cophenet_tdist_Z ... ok
...
...
...
test_y_bad_size (test_fblas.TestZswap) ... ok
test_y_stride (test_fblas.TestZswap) ... ok
test_interpolative.TestInterpolativeDecomposition.test_badcall ... ok
test_interpolative.TestInterpolativeDecomposition.test_id(<type 'numpy.float64'>
,) ... *** Error in `/home/myProg/PythonGNU2710/Linux64b/bin/python': double fre
e or corruption (!prev): 0x0000000002d0d520 ***
Aborted
$

$ python3
Python 3.4.3 (default, Jul 29 2015, 16:07:32)
[GCC 4.8.4] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import scipy
>>> scipy.test('full', verbose=2)
Running unit tests for scipy
NumPy version 1.9.2
NumPy is installed in /home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-pack
ages/numpy
SciPy version 0.13.3
SciPy is installed in /home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-pack
ages/scipy
Python version 3.4.3 (default, Jul 29 2015, 16:07:32) [GCC 4.8.4]
nose version 1.3.7
/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/numpy/lib/utils.p
y:95: DeprecationWarning: `scipy.lib.blas` is deprecated, use `scipy.linalg.blas
` instead!
  warnings.warn(depdoc, DeprecationWarning)
...
...
...
test_interpolative.TestInterpolativeDecomposition.test_badcall ... ok
test_interpolative.TestInterpolativeDecomposition.test_id(<class 'numpy.float64'
>,) ... /home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/numpy/cor
e/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the
`ndim` attribute or function instead. To find the rank of a matrix see `numpy.li
nalg.matrix_rank`.
  VisibleDeprecationWarning)
*** Error in `python3': double free or corruption (!prev): 0x0000000001b1edb0 **
*
Aborted
$
 
 
Sent: Tuesday, July 21, 2015 at 3:39 PM
From: "Sergio Rojas" <[hidden email]>
To: [hidden email]
Subject: How to fix Aborted SciPy version 0.16.0b2 test ?
Hello all,
 
Runing on Ubuntu 14.04 LTS and under Python 3.5.0b3 and NumPy version 1.9.2, the
SciPy (version 0.16.0b2) test is aborting at 
 
#------------
test_interpolative.TestInterpolativeDecomposition.test_badcall ... ok
test_interpolative.TestInterpolativeDecomposition.test_id(<class 'numpy.float64'>,) ... *** Error in `python3': free(): invalid next size (normal): 0x00000000039e1f60 ***
Aborted
#------------
 
would it be possible to fix it?
 
Thanks in advance for your help,
 
Sergio
PD. Some extra info is as follows:
 
$ python3 Python 3.5.0b3 (default, Jul 21 2015, 12:33:54)
[GCC 4.8.4] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import scipy
>>> scipy.show_config()
blas_mkl_info:
  NOT AVAILABLE
atlas_3_10_threads_info:
    libraries = ['tatlas', 'tatlas', 'tatlas']
    define_macros = [('ATLAS_INFO', '"\\"3.11.34\\""')]
    include_dirs = ['/home/myProg/NumLibs64b/include']
    library_dirs = ['/home/myProg/NumLibs64b/lib']
    language = f77
openblas_lapack_info:
  NOT AVAILABLE
lapack_mkl_info:
  NOT AVAILABLE
openblas_info:
  NOT AVAILABLE
mkl_info:
  NOT AVAILABLE
lapack_opt_info:
    libraries = ['tatlas', 'tatlas', 'tatlas']
    define_macros = [('ATLAS_INFO', '"\\"3.11.34\\""')]
    include_dirs = ['/home/myProg/NumLibs64b/include']
    library_dirs = ['/home/myProg/NumLibs64b/lib']
    language = f77
atlas_3_10_blas_threads_info:
    libraries = ['tatlas']
    define_macros = [('HAVE_CBLAS', None), ('ATLAS_INFO', '"\\"3.11.34\\""')]
    include_dirs = ['/home/myProg/NumLibs64b/include']
    library_dirs = ['/home/myProg/NumLibs64b/lib']
    language = c
blas_opt_info:
    libraries = ['tatlas']
    define_macros = [('HAVE_CBLAS', None), ('ATLAS_INFO', '"\\"3.11.34\\""')]
    include_dirs = ['/home/myProg/NumLibs64b/include']
    library_dirs = ['/home/myProg/NumLibs64b/lib']
    language = c
>>> scipy.test('full', verbose=2)
Running unit tests for scipy
NumPy version 1.9.2
NumPy is installed in /home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-packages/numpy
SciPy version 0.16.0b2
SciPy is installed in /home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-packages/scipy
Python version 3.5.0b3 (default, Jul 21 2015, 12:33:54) [GCC 4.8.4]
nose version 1.3.7
/home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-packages/scipy/_lib/decorator.py:205: DeprecationWarning: inspect.getargspec() is deprecated, use inspect.signature() instead
...
...
test_y_bad_size (test_fblas.TestZswap) ... ok
test_y_stride (test_fblas.TestZswap) ... ok
test_interpolative.TestInterpolativeDecomposition.test_badcall ... ok
test_interpolative.TestInterpolativeDecomposition.test_id(<class 'numpy.float64'>,) ... *** Error in `python3': free(): invalid next size (normal): 0x00000000039e1f60 ***
Aborted
 
 

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Re: How to fix Aborted SciPy version 0.16.0b2 test ?

Sergio Rojas
 
This reported issue, Ralf, apparently has to do with the atlas library.
As shown in the following output, if instead using the mkl library
(from Intel) this time a scipy failure is obtained:
 
 
$ python3
Python 3.5.0b3 (default, Jul 21 2015, 12:33:54)
[GCC 4.8.4] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import scipy
>>> scipy.show_config()
blas_opt_info:
    library_dirs = ['/home/myPROG/IntelC/composer_xe_2013.0.079/mkl/lib/intel64'
]
    libraries = ['mkl_rt', 'pthread']
    define_macros = [('SCIPY_MKL_H', None)]
    include_dirs = ['/home/myPROG/IntelC/composer_xe_2013.0.079/mkl/include']
lapack_opt_info:
    library_dirs = ['/home/myPROG/IntelC/composer_xe_2013.0.079/mkl/lib/intel64'
]
    libraries = ['mkl_lapack95_lp64', 'mkl_rt', 'pthread']
    define_macros = [('SCIPY_MKL_H', None)]
    include_dirs = ['/home/myPROG/IntelC/composer_xe_2013.0.079/mkl/include']
lapack_mkl_info:
    library_dirs = ['/home/myPROG/IntelC/composer_xe_2013.0.079/mkl/lib/intel64'
]
    libraries = ['mkl_lapack95_lp64', 'mkl_rt', 'pthread']
    define_macros = [('SCIPY_MKL_H', None)]
    include_dirs = ['/home/myPROG/IntelC/composer_xe_2013.0.079/mkl/include']
blas_mkl_info:
    library_dirs = ['/home/myPROG/IntelC/composer_xe_2013.0.079/mkl/lib/intel64'
]
    libraries = ['mkl_rt', 'pthread']
    define_macros = [('SCIPY_MKL_H', None)]
    include_dirs = ['/home/myPROG/IntelC/composer_xe_2013.0.079/mkl/include']
openblas_lapack_info:
  NOT AVAILABLE
mkl_info:
    library_dirs = ['/home/myPROG/IntelC/composer_xe_2013.0.079/mkl/lib/intel64'
]
    libraries = ['mkl_rt', 'pthread']
    define_macros = [('SCIPY_MKL_H', None)]
    include_dirs = ['/home/myPROG/IntelC/composer_xe_2013.0.079/mkl/include']
>>> scipy.test('full', verbose=2)
Running unit tests for scipy
NumPy version 1.9.2
NumPy is installed in /home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-pack
ages/numpy
SciPy version 0.16.0b2
SciPy is installed in /home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-pack
ages/scipy
Python version 3.5.0b3 (default, Jul 21 2015, 12:33:54) [GCC 4.8.4]
nose version 1.3.7
/home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-packages/scipy/_lib/decora
tor.py:205: DeprecationWarning: inspect.getargspec() is deprecated, use inspect.
signature() instead
...
...
...
test_y_stride (test_fblas.TestZswap) ... ok
test_interpolative.TestInterpolativeDecomposition.test_badcall ... ok
test_interpolative.TestInterpolativeDecomposition.test_id(<class 'numpy.float64'
>,) ... ok
test_interpolative.TestInterpolativeDecomposition.test_id(<class 'numpy.complex1
28'>,) ... ok
test_interpolative.TestInterpolativeDecomposition.test_rand ... ok
test_sing_val_update (test_lapack.TestDlasd4) ... ok
...
...
...
Compare results with some values that were computed using mpmath. ... ok
Test values of lambda outside the domains of the functions. ... ok
======================================================================
FAIL: test_indeterminate_covariance (test_minpack.TestCurveFit)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-packages/scipy/opt
imize/tests/test_minpack.py", line 397, in test_indeterminate_covariance
    _assert_warns(OptimizeWarning, curve_fit, lambda x, a, b: a*x, xdata, ydata)
  File "/home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-packages/numpy/tes
ting/utils.py", line 1603, in assert_warns
    "%s( is %s)" % (func.__name__, warning_class, l[0]))
AssertionError: First warning for curve_fit is not a <class 'scipy.optimize.opti
mize.OptimizeWarning'>( is {message : DeprecationWarning('inspect.getargspec() i
s deprecated, use inspect.signature() instead',), category : 'DeprecationWarning
', filename : '/home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-packages/sc
ipy/optimize/minpack.py', lineno : 546, line : None})
----------------------------------------------------------------------
Ran 19371 tests in 441.458s
FAILED (KNOWNFAIL=129, SKIP=1319, failures=1)
<nose.result.TextTestResult run=19371 errors=0 failures=1>
>>>
 
For some reason I am not getting messages via the
mailing list. I am reading them at the web
[ http://mail.scipy.org/pipermail/scipy-user/2015-July/036660.html ]
 
>
>Hi Sergio, thanks for the report. A few questions:
>- did 0.15.1 work for you with the same install method
>- does the problem still occur with the final 0.16.0 release?
>- is the issue specific to Python 3.5 or not?
>
>Opening an issue on Github and attaching a gdb traceback (see
>http://scipy.org/bug-report.html) would be helpful.
>Cheers,
>Ralf
 
At this stage, Ralf, I have confirmed that the issue is NO
specific to Python 3.5 or to SciPy version 0.16.0b2 :
 
$ python
Python 2.7.10 (default, Jul 29 2015, 20:51:44)
[GCC 4.8.4] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import scipy
>>> scipy.test('full', verbose=2)
Running unit tests for scipy
NumPy version 1.9.2
NumPy is installed in /home/myProg/PythonGNU2710/Linux64b/lib/python2.7/site-pac
kages/numpy
SciPy version 0.16.0b2
SciPy is installed in /home/myProg/PythonGNU2710/Linux64b/lib/python2.7/site-pac
kages/scipy
Python version 2.7.10 (default, Jul 29 2015, 20:51:44) [GCC 4.8.4]
nose version 1.3.7
/home/myProg/PythonGNU2710/Linux64b/lib/python2.7/site-packages/numpy/lib/utils.
py:95: DeprecationWarning: `scipy.weave` is deprecated, use `weave` instead!
  warnings.warn(depdoc, DeprecationWarning)
test_hierarchy.TestCopheneticDistance.test_linkage_cophenet_tdist_Z ... ok
...
...
...
test_y_bad_size (test_fblas.TestZswap) ... ok
test_y_stride (test_fblas.TestZswap) ... ok
test_interpolative.TestInterpolativeDecomposition.test_badcall ... ok
test_interpolative.TestInterpolativeDecomposition.test_id(<type 'numpy.float64'>
,) ... *** Error in `/home/myProg/PythonGNU2710/Linux64b/bin/python': double fre
e or corruption (!prev): 0x0000000002d0d520 ***
Aborted
$

$ python3
Python 3.4.3 (default, Jul 29 2015, 16:07:32)
[GCC 4.8.4] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import scipy
>>> scipy.test('full', verbose=2)
Running unit tests for scipy
NumPy version 1.9.2
NumPy is installed in /home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-pack
ages/numpy
SciPy version 0.13.3
SciPy is installed in /home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-pack
ages/scipy
Python version 3.4.3 (default, Jul 29 2015, 16:07:32) [GCC 4.8.4]
nose version 1.3.7
/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/numpy/lib/utils.p
y:95: DeprecationWarning: `scipy.lib.blas` is deprecated, use `scipy.linalg.blas
` instead!
  warnings.warn(depdoc, DeprecationWarning)
...
...
...
test_interpolative.TestInterpolativeDecomposition.test_badcall ... ok
test_interpolative.TestInterpolativeDecomposition.test_id(<class 'numpy.float64'
>,) ... /home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/numpy/cor
e/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the
`ndim` attribute or function instead. To find the rank of a matrix see `numpy.li
nalg.matrix_rank`.
  VisibleDeprecationWarning)
*** Error in `python3': double free or corruption (!prev): 0x0000000001b1edb0 **
*
Aborted
$
 
 
Sent: Tuesday, July 21, 2015 at 3:39 PM
From: "Sergio Rojas" <[hidden email]>
To: [hidden email]
Subject: How to fix Aborted SciPy version 0.16.0b2 test ?
Hello all,
 
Runing on Ubuntu 14.04 LTS and under Python 3.5.0b3 and NumPy version 1.9.2, the
SciPy (version 0.16.0b2) test is aborting at 
 
#------------
test_interpolative.TestInterpolativeDecomposition.test_badcall ... ok
test_interpolative.TestInterpolativeDecomposition.test_id(<class 'numpy.float64'>,) ... *** Error in `python3': free(): invalid next size (normal): 0x00000000039e1f60 ***
Aborted
#------------
 
would it be possible to fix it?
 
Thanks in advance for your help,
 
Sergio
PD. Some extra info is as follows:
 
$ python3 Python 3.5.0b3 (default, Jul 21 2015, 12:33:54)
[GCC 4.8.4] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import scipy
>>> scipy.show_config()
blas_mkl_info:
  NOT AVAILABLE
atlas_3_10_threads_info:
    libraries = ['tatlas', 'tatlas', 'tatlas']
    define_macros = [('ATLAS_INFO', '"\\"3.11.34\\""')]
    include_dirs = ['/home/myProg/NumLibs64b/include']
    library_dirs = ['/home/myProg/NumLibs64b/lib']
    language = f77
openblas_lapack_info:
  NOT AVAILABLE
lapack_mkl_info:
  NOT AVAILABLE
openblas_info:
  NOT AVAILABLE
mkl_info:
  NOT AVAILABLE
lapack_opt_info:
    libraries = ['tatlas', 'tatlas', 'tatlas']
    define_macros = [('ATLAS_INFO', '"\\"3.11.34\\""')]
    include_dirs = ['/home/myProg/NumLibs64b/include']
    library_dirs = ['/home/myProg/NumLibs64b/lib']
    language = f77
atlas_3_10_blas_threads_info:
    libraries = ['tatlas']
    define_macros = [('HAVE_CBLAS', None), ('ATLAS_INFO', '"\\"3.11.34\\""')]
    include_dirs = ['/home/myProg/NumLibs64b/include']
    library_dirs = ['/home/myProg/NumLibs64b/lib']
    language = c
blas_opt_info:
    libraries = ['tatlas']
    define_macros = [('HAVE_CBLAS', None), ('ATLAS_INFO', '"\\"3.11.34\\""')]
    include_dirs = ['/home/myProg/NumLibs64b/include']
    library_dirs = ['/home/myProg/NumLibs64b/lib']
    language = c
>>> scipy.test('full', verbose=2)
Running unit tests for scipy
NumPy version 1.9.2
NumPy is installed in /home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-packages/numpy
SciPy version 0.16.0b2
SciPy is installed in /home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-packages/scipy
Python version 3.5.0b3 (default, Jul 21 2015, 12:33:54) [GCC 4.8.4]
nose version 1.3.7
/home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-packages/scipy/_lib/decorator.py:205: DeprecationWarning: inspect.getargspec() is deprecated, use inspect.signature() instead
...
...
test_y_bad_size (test_fblas.TestZswap) ... ok
test_y_stride (test_fblas.TestZswap) ... ok
test_interpolative.TestInterpolativeDecomposition.test_badcall ... ok
test_interpolative.TestInterpolativeDecomposition.test_id(<class 'numpy.float64'>,) ... *** Error in `python3': free(): invalid next size (normal): 0x00000000039e1f60 ***
Aborted
 
 

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Re: How to fix Aborted SciPy version 0.16.0b2 test ?

Sergio Rojas
In reply to this post by Sergio Rojas

  This is a followup of the question posed in the email subject.
The issue is about fixing the aborted test:
 
>----
> test_interpolative.TestInterpolativeDecomposition.test_id(<type 'numpy.float64
'> ,) ... *** Error in `/home/myProg/PythonGNU2710/Linux64b/bin/python': double
fre e or corruption (!prev): 0x0000000002d0d520 ***
> Aborted
>----

  After some extra work, the error seems to be associated with ATLAS 3.11.34
as it does not happen after changing to ATLAS 3.10.2

In summary,
Self tests of
SciPy version 0.16.0 using ATLAS 3.10.2 and NumPy version 1.9.2 under
Python 3.4.3 running on ubuntu 14.04 LTS, end outputing:

----------------------------------------------------------------------
Ran 19454 tests in 474.654s

OK (KNOWNFAIL=129, SKIP=1319)
<nose.result.TextTestResult run=19454 errors=0 failures=0>

    A failure, however, is found if using SciPy version 0.16.0
under Python 3.5.0b3:
FAIL: test_indeterminate_covariance (test_minpack.TestCurveFit)
----------------------------------------------------------------------
Ran 19454 tests in 457.759s

FAILED (KNOWNFAIL=129, SKIP=1319, failures=1)

    Three failures are obtained if using SciPy version 0.16.0b2:
under python 3.4.3

FAIL: test_decomp_update.TestQRinsert_F.test_fat_p_row_sqr
FAIL: test_decomp_update.TestQRinsert_F.test_fat_p_row_tall
test_decomp_update.TestQRinsert_f.test_fat_p_row_sqr

----------------------------------------------------------------------
Ran 19371 tests in 459.815s

FAILED (KNOWNFAIL=129, SKIP=1319, failures=3)

Regards,

Sergio

$ python3
Python 3.4.3 (default, Jul 29 2015, 16:07:32)
[GCC 4.8.4] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import scipy
>>> scipy.show_config()
lapack_mkl_info:
  NOT AVAILABLE
blas_mkl_info:
  NOT AVAILABLE
atlas_3_10_blas_threads_info:
    include_dirs = ['/home/myProg/NumLibsAtlas102/include']
    language = c
    library_dirs = ['/home/myProg/NumLibsAtlas102/lib']
    define_macros = [('HAVE_CBLAS', None), ('ATLAS_INFO', '"\\"3.10.2\\""')]
    libraries = ['tatlas']
openblas_lapack_info:
  NOT AVAILABLE
openblas_info:
  NOT AVAILABLE
atlas_3_10_threads_info:
    include_dirs = ['/home/myProg/NumLibsAtlas102/include']
    language = f77
    library_dirs = ['/home/myProg/NumLibsAtlas102/lib']
    define_macros = [('ATLAS_INFO', '"\\"3.10.2\\""')]
    libraries = ['tatlas', 'tatlas', 'tatlas']
blas_opt_info:
    include_dirs = ['/home/myProg/NumLibsAtlas102/include']
    language = c
    library_dirs = ['/home/myProg/NumLibsAtlas102/lib']
    define_macros = [('HAVE_CBLAS', None), ('ATLAS_INFO', '"\\"3.10.2\\""')]
    libraries = ['tatlas']
lapack_opt_info:
    include_dirs = ['/home/myProg/NumLibsAtlas102/include']
    language = f77
    library_dirs = ['/home/myProg/NumLibsAtlas102/lib']
    define_macros = [('ATLAS_INFO', '"\\"3.10.2\\""')]
    libraries = ['tatlas', 'tatlas', 'tatlas']
mkl_info:
  NOT AVAILABLE
>>> scipy.test('full', verbose=2)
Running unit tests for scipy
NumPy version 1.9.2
NumPy is installed in /home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-pack
ages/numpy
SciPy version 0.16.0
SciPy is installed in /home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-pack
ages/scipy
Python version 3.4.3 (default, Jul 29 2015, 16:07:32) [GCC 4.8.4]
nose version 1.3.7
...
...
...
----------------------------------------------------------------------
Ran 19454 tests in 474.654s

OK (KNOWNFAIL=129, SKIP=1319)
<nose.result.TextTestResult run=19454 errors=0 failures=0>
>>>
$
Script started on Thu 30 Jul 2015 04:57:34 PM EDT
$ python3
Python 3.4.3 (default, Jul 29 2015, 16:07:32)
[GCC 4.8.4] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import scipy
>>> scipy.show_config()
blas_mkl_info:
  NOT AVAILABLE
openblas_info:
  NOT AVAILABLE
blas_opt_info:
    libraries = ['tatlas']
    language = c
    library_dirs = ['/home/myProg/NumLibsAtlas102/lib']
    include_dirs = ['/home/myProg/NumLibsAtlas102/include']
    define_macros = [('HAVE_CBLAS', None), ('ATLAS_INFO', '"\\"3.10.2\\""')]
lapack_mkl_info:
  NOT AVAILABLE
lapack_opt_info:
    libraries = ['tatlas', 'tatlas', 'tatlas']
    language = f77
    library_dirs = ['/home/myProg/NumLibsAtlas102/lib']
    include_dirs = ['/home/myProg/NumLibsAtlas102/include']
    define_macros = [('ATLAS_INFO', '"\\"3.10.2\\""')]
openblas_lapack_info:
  NOT AVAILABLE
atlas_3_10_blas_threads_info:
    libraries = ['tatlas']
    language = c
    library_dirs = ['/home/myProg/NumLibsAtlas102/lib']
    include_dirs = ['/home/myProg/NumLibsAtlas102/include']
    define_macros = [('HAVE_CBLAS', None), ('ATLAS_INFO', '"\\"3.10.2\\""')]
atlas_3_10_threads_info:
    libraries = ['tatlas', 'tatlas', 'tatlas']
    language = f77
    library_dirs = ['/home/myProg/NumLibsAtlas102/lib']
    include_dirs = ['/home/myProg/NumLibsAtlas102/include']
    define_macros = [('ATLAS_INFO', '"\\"3.10.2\\""')]
mkl_info:
  NOT AVAILABLE
>>> scipy.test('full', verbose=2)
Running unit tests for scipy
NumPy version 1.9.2
NumPy is installed in /home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-pack
ages/numpy
SciPy version 0.16.0b2
SciPy is installed in /home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-pack
ages/scipy
Python version 3.4.3 (default, Jul 29 2015, 16:07:32) [GCC 4.8.4]
nose version 1.3.7
...
...
...
Test values of lambda outside the domains of the functions. ... ok

======================================================================
FAIL: test_decomp_update.TestQRinsert_F.test_fat_p_row_sqr
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/nose/case
.py", line 198, in runTest
    self.test(*self.arg)
  File "/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/scipy/lin
alg/tests/test_decomp_update.py", line 755, in test_fat_p_row_sqr
    self.base_fat_p_row_xxx(5)
  File "/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/scipy/lin
alg/tests/test_decomp_update.py", line 747, in base_fat_p_row_xxx
    check_qr(q1, r1, a1, self.rtol, self.atol)
  File "/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/scipy/lin
alg/tests/test_decomp_update.py", line 32, in check_qr
    assert_unitary(q, rtol, atol, assert_sqr)
  File "/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/scipy/lin
alg/tests/test_decomp_update.py", line 21, in assert_unitary
    assert_allclose(aTa, np.eye(a.shape[1]), rtol=rtol, atol=atol)
  File "/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/numpy/tes
ting/utils.py", line 1297, in assert_allclose
    verbose=verbose, header=header)
  File "/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/numpy/tes
ting/utils.py", line 665, in assert_array_compare
    raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=0.0001, atol=1.19209e-06

(mismatch 100.0%)
 x: array([[ 0.998973 +5.587935e-09j,  0.009882 +7.026103e-02j,
        -0.129242 -4.287320e-02j, -0.030052 -6.515425e-02j,
         0.005686 -9.261262e-02j,  0.031090 +1.492383e-02j,...
 y: array([[ 1.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.],
       [ 0.,  1.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.],
       [ 0.,  0.,  1.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.],...

======================================================================
FAIL: test_decomp_update.TestQRinsert_F.test_fat_p_row_tall
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/nose/case
.py", line 198, in runTest
    self.test(*self.arg)
  File "/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/scipy/lin
alg/tests/test_decomp_update.py", line 759, in test_fat_p_row_tall
    self.base_fat_p_row_xxx(7)
  File "/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/scipy/lin
alg/tests/test_decomp_update.py", line 747, in base_fat_p_row_xxx
    check_qr(q1, r1, a1, self.rtol, self.atol)
  File "/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/scipy/lin
alg/tests/test_decomp_update.py", line 32, in check_qr
    assert_unitary(q, rtol, atol, assert_sqr)
  File "/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/scipy/lin
alg/tests/test_decomp_update.py", line 21, in assert_unitary
    assert_allclose(aTa, np.eye(a.shape[1]), rtol=rtol, atol=atol)
  File "/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/numpy/tes
ting/utils.py", line 1297, in assert_allclose
    verbose=verbose, header=header)
  File "/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/numpy/tes
ting/utils.py", line 665, in assert_array_compare
    raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=0.0001, atol=1.19209e-06

(mismatch 100.0%)
 x: array([[ 1.006917 -6.984919e-09j,  0.009022 -8.255728e-02j,
         0.178461 -3.312873e-02j, -0.047311 +1.095396e-01j,
         0.059368 +8.496426e-02j,  0.031223 +1.194810e-02j,...
 y: array([[ 1.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,
         0.],
       [ 0.,  1.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,...

======================================================================
FAIL: test_decomp_update.TestQRinsert_f.test_fat_p_row_sqr
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/nose/case
.py", line 198, in runTest
    self.test(*self.arg)
  File "/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/scipy/lin
alg/tests/test_decomp_update.py", line 755, in test_fat_p_row_sqr
    self.base_fat_p_row_xxx(5)
  File "/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/scipy/lin
alg/tests/test_decomp_update.py", line 747, in base_fat_p_row_xxx
    check_qr(q1, r1, a1, self.rtol, self.atol)
  File "/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/scipy/lin
alg/tests/test_decomp_update.py", line 32, in check_qr
    assert_unitary(q, rtol, atol, assert_sqr)
  File "/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/scipy/lin
alg/tests/test_decomp_update.py", line 21, in assert_unitary
    assert_allclose(aTa, np.eye(a.shape[1]), rtol=rtol, atol=atol)
  File "/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/numpy/tes
ting/utils.py", line 1297, in assert_allclose
    verbose=verbose, header=header)
  File "/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/numpy/tes
ting/utils.py", line 665, in assert_array_compare
    raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=0.0001, atol=1.19209e-06

(mismatch 100.0%)
 x: array([[  8.658818e-01,   1.325921e-01,   2.875357e-01,   4.060289e-02,
          1.853821e-01,   2.545137e-02,  -2.103027e-01,   2.341471e-02,
          1.182279e-01,  -1.466596e-01,  -4.916818e-02,  -1.404783e-01],...
 y: array([[ 1.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.],
       [ 0.,  1.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.],
       [ 0.,  0.,  1.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.],...

----------------------------------------------------------------------
Ran 19371 tests in 459.815s

FAILED (KNOWNFAIL=129, SKIP=1319, failures=3)
<nose.result.TextTestResult run=19371 errors=0 failures=3>
>>>
$
$ python3
Python 3.5.0b3 (default, Jul 21 2015, 12:33:54)
[GCC 4.8.4] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import scipy
>>> scipy.show_config()
openblas_lapack_info:
  NOT AVAILABLE
atlas_3_10_threads_info:
    language = f77
    libraries = ['tatlas', 'tatlas', 'tatlas']
    define_macros = [('ATLAS_INFO', '"\\"3.10.2\\""')]
    library_dirs = ['/home/myProg/NumLibsAtlas102/lib']
    include_dirs = ['/home/myProg/NumLibsAtlas102/include']
blas_opt_info:
    language = c
    libraries = ['tatlas']
    define_macros = [('HAVE_CBLAS', None), ('ATLAS_INFO', '"\\"3.10.2\\""')]
    library_dirs = ['/home/myProg/NumLibsAtlas102/lib']
    include_dirs = ['/home/myProg/NumLibsAtlas102/include']
mkl_info:
  NOT AVAILABLE
lapack_opt_info:
    language = f77
    libraries = ['tatlas', 'tatlas', 'tatlas']
    define_macros = [('ATLAS_INFO', '"\\"3.10.2\\""')]
    library_dirs = ['/home/myProg/NumLibsAtlas102/lib']
    include_dirs = ['/home/myProg/NumLibsAtlas102/include']
lapack_mkl_info:
  NOT AVAILABLE
openblas_info:
  NOT AVAILABLE
blas_mkl_info:
  NOT AVAILABLE
atlas_3_10_blas_threads_info:
    language = c
    libraries = ['tatlas']
    define_macros = [('HAVE_CBLAS', None), ('ATLAS_INFO', '"\\"3.10.2\\""')]
    library_dirs = ['/home/myProg/NumLibsAtlas102/lib']
    include_dirs = ['/home/myProg/NumLibsAtlas102/include']
>>> scipy.test('full', verbose=2)
Running unit tests for scipy
NumPy version 1.9.2
NumPy is installed in /home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-pack
ages/numpy
SciPy version 0.16.0
SciPy is installed in /home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-pack
ages/scipy
Python version 3.5.0b3 (default, Jul 21 2015, 12:33:54) [GCC 4.8.4]
nose version 1.3.7
...
...
...
======================================================================
FAIL: test_indeterminate_covariance (test_minpack.TestCurveFit)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-packages/scipy/opt
imize/tests/test_minpack.py", line 397, in test_indeterminate_covariance
    _assert_warns(OptimizeWarning, curve_fit, lambda x, a, b: a*x, xdata, ydata)
  File "/home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-packages/numpy/tes
ting/utils.py", line 1603, in assert_warns
    "%s( is %s)" % (func.__name__, warning_class, l[0]))
AssertionError: First warning for curve_fit is not a <class 'scipy.optimize.opti
mize.OptimizeWarning'>( is {message : DeprecationWarning('inspect.getargspec() i
s deprecated, use inspect.signature() instead',), category : 'DeprecationWarning
', filename : '/home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-packages/sc
ipy/optimize/minpack.py', lineno : 546, line : None})

----------------------------------------------------------------------
Ran 19454 tests in 457.759s

FAILED (KNOWNFAIL=129, SKIP=1319, failures=1)
<nose.result.TextTestResult run=19454 errors=0 failures=1>
>>>


 

This reported issue, Ralf, apparently has to do with the atlas library.
As shown in the following output, if instead using the mkl library
(from Intel) this time a scipy failure is obtained:
 
 
$ python3
Python 3.5.0b3 (default, Jul 21 2015, 12:33:54)
[GCC 4.8.4] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import scipy
>>> scipy.show_config()
blas_opt_info:
    library_dirs = ['/home/myPROG/IntelC/composer_xe_2013.0.079/mkl/lib/intel64'
]
    libraries = ['mkl_rt', 'pthread']
    define_macros = [('SCIPY_MKL_H', None)]
    include_dirs = ['/home/myPROG/IntelC/composer_xe_2013.0.079/mkl/include']
lapack_opt_info:
    library_dirs = ['/home/myPROG/IntelC/composer_xe_2013.0.079/mkl/lib/intel64'
]
    libraries = ['mkl_lapack95_lp64', 'mkl_rt', 'pthread']
    define_macros = [('SCIPY_MKL_H', None)]
    include_dirs = ['/home/myPROG/IntelC/composer_xe_2013.0.079/mkl/include']
lapack_mkl_info:
    library_dirs = ['/home/myPROG/IntelC/composer_xe_2013.0.079/mkl/lib/intel64'
]
    libraries = ['mkl_lapack95_lp64', 'mkl_rt', 'pthread']
    define_macros = [('SCIPY_MKL_H', None)]
    include_dirs = ['/home/myPROG/IntelC/composer_xe_2013.0.079/mkl/include']
blas_mkl_info:
    library_dirs = ['/home/myPROG/IntelC/composer_xe_2013.0.079/mkl/lib/intel64'
]
    libraries = ['mkl_rt', 'pthread']
    define_macros = [('SCIPY_MKL_H', None)]
    include_dirs = ['/home/myPROG/IntelC/composer_xe_2013.0.079/mkl/include']
openblas_lapack_info:
  NOT AVAILABLE
mkl_info:
    library_dirs = ['/home/myPROG/IntelC/composer_xe_2013.0.079/mkl/lib/intel64'
]
    libraries = ['mkl_rt', 'pthread']
    define_macros = [('SCIPY_MKL_H', None)]
    include_dirs = ['/home/myPROG/IntelC/composer_xe_2013.0.079/mkl/include']
>>> scipy.test('full', verbose=2)
Running unit tests for scipy
NumPy version 1.9.2
NumPy is installed in /home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-pack
ages/numpy
SciPy version 0.16.0b2
SciPy is installed in /home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-pack
ages/scipy
Python version 3.5.0b3 (default, Jul 21 2015, 12:33:54) [GCC 4.8.4]
nose version 1.3.7
/home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-packages/scipy/_lib/decora
tor.py:205: DeprecationWarning: inspect.getargspec() is deprecated, use inspect.
signature() instead
...
...
...
test_y_stride (test_fblas.TestZswap) ... ok
test_interpolative.TestInterpolativeDecomposition.test_badcall ... ok
test_interpolative.TestInterpolativeDecomposition.test_id(<class 'numpy.float64'
>,) ... ok
test_interpolative.TestInterpolativeDecomposition.test_id(<class 'numpy.complex1
28'>,) ... ok
test_interpolative.TestInterpolativeDecomposition.test_rand ... ok
test_sing_val_update (test_lapack.TestDlasd4) ... ok
...
...
...
Compare results with some values that were computed using mpmath. ... ok
Test values of lambda outside the domains of the functions. ... ok
======================================================================
FAIL: test_indeterminate_covariance (test_minpack.TestCurveFit)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-packages/scipy/opt
imize/tests/test_minpack.py", line 397, in test_indeterminate_covariance
    _assert_warns(OptimizeWarning, curve_fit, lambda x, a, b: a*x, xdata, ydata)
  File "/home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-packages/numpy/tes
ting/utils.py", line 1603, in assert_warns
    "%s( is %s)" % (func.__name__, warning_class, l[0]))
AssertionError: First warning for curve_fit is not a <class 'scipy.optimize.opti
mize.OptimizeWarning'>( is {message : DeprecationWarning('inspect.getargspec() i
s deprecated, use inspect.signature() instead',), category : 'DeprecationWarning
', filename : '/home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-packages/sc
ipy/optimize/minpack.py', lineno : 546, line : None})
----------------------------------------------------------------------
Ran 19371 tests in 441.458s
FAILED (KNOWNFAIL=129, SKIP=1319, failures=1)
<nose.result.TextTestResult run=19371 errors=0 failures=1>
>>>
 
For some reason I am not getting messages via the
mailing list. I am reading them at the web
[ http://mail.scipy.org/pipermail/scipy-user/2015-July/036660.html ]
 

>
>Hi Sergio, thanks for the report. A few questions:
>- did 0.15.1 work for you with the same install method
>- does the problem still occur with the final 0.16.0 release?
>- is the issue specific to Python 3.5 or not?
>
>Opening an issue on Github and attaching a gdb traceback (see
>http://scipy.org/bug-report.html[http://scipy.org/bug-report.html]) would be helpful.
>Cheers,
>Ralf
 
At this stage, Ralf, I have confirmed that the issue is NO
specific to Python 3.5 or to SciPy version 0.16.0b2 :
 
$ python
Python 2.7.10 (default, Jul 29 2015, 20:51:44)
[GCC 4.8.4] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import scipy
>>> scipy.test('full', verbose=2)
Running unit tests for scipy
NumPy version 1.9.2
NumPy is installed in /home/myProg/PythonGNU2710/Linux64b/lib/python2.7/site-pac
kages/numpy
SciPy version 0.16.0b2
SciPy is installed in /home/myProg/PythonGNU2710/Linux64b/lib/python2.7/site-pac
kages/scipy
Python version 2.7.10 (default, Jul 29 2015, 20:51:44) [GCC 4.8.4]
nose version 1.3.7
/home/myProg/PythonGNU2710/Linux64b/lib/python2.7/site-packages/numpy/lib/utils.
py:95: DeprecationWarning: `scipy.weave` is deprecated, use `weave` instead!
  warnings.warn(depdoc, DeprecationWarning)
test_hierarchy.TestCopheneticDistance.test_linkage_cophenet_tdist_Z ... ok
...
...
...
test_y_bad_size (test_fblas.TestZswap) ... ok
test_y_stride (test_fblas.TestZswap) ... ok
test_interpolative.TestInterpolativeDecomposition.test_badcall ... ok
test_interpolative.TestInterpolativeDecomposition.test_id(<type 'numpy.float64'>
,) ... *** Error in `/home/myProg/PythonGNU2710/Linux64b/bin/python': double fre
e or corruption (!prev): 0x0000000002d0d520 ***
Aborted
$
$ python3
Python 3.4.3 (default, Jul 29 2015, 16:07:32)
[GCC 4.8.4] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import scipy
>>> scipy.test('full', verbose=2)
Running unit tests for scipy
NumPy version 1.9.2
NumPy is installed in /home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-pack
ages/numpy
SciPy version 0.13.3
SciPy is installed in /home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-pack
ages/scipy
Python version 3.4.3 (default, Jul 29 2015, 16:07:32) [GCC 4.8.4]
nose version 1.3.7
/home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/numpy/lib/utils.p
y:95: DeprecationWarning: `scipy.lib.blas` is deprecated, use `scipy.linalg.blas
` instead!
  warnings.warn(depdoc, DeprecationWarning)
...
...
...
test_interpolative.TestInterpolativeDecomposition.test_badcall ... ok
test_interpolative.TestInterpolativeDecomposition.test_id(<class 'numpy.float64'
>,) ... /home/myProg/PythonGnu343/Linux64b/lib/python3.4/site-packages/numpy/cor
e/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the
`ndim` attribute or function instead. To find the rank of a matrix see `numpy.li
nalg.matrix_rank`.
  VisibleDeprecationWarning)
*** Error in `python3': double free or corruption (!prev): 0x0000000001b1edb0 **
*
Aborted
$
 
 

Sent: Tuesday, July 21, 2015 at 3:39 PM
From: "Sergio Rojas" <[hidden email]>
To: [hidden email]
Subject: How to fix Aborted SciPy version 0.16.0b2 test ?

Hello all,
 
Runing on Ubuntu 14.04 LTS and under Python 3.5.0b3 and NumPy version 1.9.2, the
SciPy (version 0.16.0b2) test is aborting at 
 
#------------
test_interpolative.TestInterpolativeDecomposition.test_badcall ... ok
test_interpolative.TestInterpolativeDecomposition.test_id(<class 'numpy.float64'>,) ... *** Error in `python3': free(): invalid next size (normal): 0x00000000039e1f60 ***
Aborted

#------------
 
would it be possible to fix it?
 
Thanks in advance for your help,
 
Sergio
PD. Some extra info is as follows:
 

$ python3 Python 3.5.0b3 (default, Jul 21 2015, 12:33:54)
[GCC 4.8.4] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import scipy
>>> scipy.show_config()
blas_mkl_info:
  NOT AVAILABLE
atlas_3_10_threads_info:
    libraries = ['tatlas', 'tatlas', 'tatlas']
    define_macros = [('ATLAS_INFO', '"\\"3.11.34\\""')]
    include_dirs = ['/home/myProg/NumLibs64b/include']
    library_dirs = ['/home/myProg/NumLibs64b/lib']
    language = f77
openblas_lapack_info:
  NOT AVAILABLE
lapack_mkl_info:
  NOT AVAILABLE
openblas_info:
  NOT AVAILABLE
mkl_info:
  NOT AVAILABLE

lapack_opt_info:
    libraries = ['tatlas', 'tatlas', 'tatlas']
    define_macros = [('ATLAS_INFO', '"\\"3.11.34\\""')]
    include_dirs = ['/home/myProg/NumLibs64b/include']
    library_dirs = ['/home/myProg/NumLibs64b/lib']
    language = f77
atlas_3_10_blas_threads_info:
    libraries = ['tatlas']
    define_macros = [('HAVE_CBLAS', None), ('ATLAS_INFO', '"\\"3.11.34\\""')]
    include_dirs = ['/home/myProg/NumLibs64b/include']
    library_dirs = ['/home/myProg/NumLibs64b/lib']
    language = c
blas_opt_info:
    libraries = ['tatlas']
    define_macros = [('HAVE_CBLAS', None), ('ATLAS_INFO', '"\\"3.11.34\\""')]
    include_dirs = ['/home/myProg/NumLibs64b/include']
    library_dirs = ['/home/myProg/NumLibs64b/lib']
    language = c
>>> scipy.test('full', verbose=2)
Running unit tests for scipy
NumPy version 1.9.2

NumPy is installed in /home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-packages/numpy
SciPy version 0.16.0b2
SciPy is installed in /home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-packages/scipy
Python version 3.5.0b3 (default, Jul 21 2015, 12:33:54) [GCC 4.8.4]
nose version 1.3.7
/home/myProg/PythonGnu350/Linux64b/lib/python3.5/site-packages/scipy/_lib/decorator.py:205: DeprecationWarning: inspect.getargspec() is deprecated, use inspect.signature() instead
...
...
test_y_bad_size (test_fblas.TestZswap) ... ok
test_y_stride (test_fblas.TestZswap) ... ok
test_interpolative.TestInterpolativeDecomposition.test_badcall ... ok
test_interpolative.TestInterpolativeDecomposition.test_id(<class 'numpy.float64'>,) ... *** Error in `python3': free(): invalid next size (normal): 0x00000000039e1f60 ***
Aborted
 
 
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Re: How to fix Aborted SciPy version 0.16.0b2 test ?

Daπid
On 31 July 2015 at 15:21, Sergio Rojas <[hidden email]> wrote:
  After some extra work, the error seems to be associated with ATLAS 3.11.34
as it does not happen after changing to ATLAS 3.10.2

It must be noted that 3.11 is a developing branch, while the releases are 3.10, 3.12... So it is probably worth reporting the bug to ATLAS.

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