[SciPy-Dev] Errors in Scipy 0.13.3 & Python 3.3.5
Wim R. Cardoen
wcardoen at gmail.com
Tue Apr 22 21:41:02 EDT 2014
Hi Ralf,
Thanks for your reply.
I just submitted an issue on Github.
Please let me know if you want the output of the compilation and linking
process for scipy.
Best regards,
Wim
On Tue, Apr 22, 2014 at 3:39 PM, Ralf Gommers <ralf.gommers at gmail.com>wrote:
>
>
>
> On Tue, Apr 22, 2014 at 1:07 AM, Wim R. Cardoen <wcardoen at gmail.com>wrote:
>
>> Hello
>>
>> I compiled scipy 0.13.3 successfully
>> on a Centos 6 machine.
>> When I ran the test suite I obtained the following 5 errors
>> (I used OpenBlas (single threaded) for the BLAS/LAPACK library and
>> SuiteSparse for the AMD,UMFPACK libraries)
>>
>>
>> ======================================================================
>> FAIL: test_arpack.test_real_nonsymmetric_modes(False, <std-real-nonsym>,
>> 'f', 2, 'LM', None, 0.1, <function asarray at 0x7f989ca49b00>, 'r')
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>> File
>> "/software/pkg/python/3.3.5/lib/python3.3/site-packages/nose-1.3.1-py3.3.egg/nose/case.py",
>> line 198, in runTest
>> self.test(*self.arg)
>> File
>> "/software/pkg/python/3.3.5/lib/python3.3/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
>> line 259, in eval_evec
>> assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
>> File
>> "/software/pkg/python/3.3.5/lib/python3.3/site-packages/numpy/testing/utils.py",
>> line 1183, in assert_allclose
>> verbose=verbose, header=header)
>> File
>> "/software/pkg/python/3.3.5/lib/python3.3/site-packages/numpy/testing/utils.py",
>> line 644, in assert_array_compare
>> raise AssertionError(msg)
>> AssertionError:
>> Not equal to tolerance rtol=0.000357628, atol=0.000357628
>> error for eigs:standard, typ=f, which=LM, sigma=0.1, mattype=asarray,
>> OPpart=r, mode=normal
>> (mismatch 100.0%)
>> x: array([[-0.11649324+0.j, -0.05435310+0.j],
>> [ 0.13801208+0.j, -0.05894032+0.j],
>> [-0.21229853+0.j, -0.02815625+0.j],...
>> y: array([[-0.05698580+0.08018474j, -0.05435318+0.j ],
>> [ 0.06439485-0.09061003j, -0.05894023+0.j ],
>> [-0.12503998+0.17594382j, -0.02815617+0.j ],...
>>
>> ======================================================================
>> FAIL: test_arpack.test_real_nonsymmetric_modes(False, <std-real-nonsym>,
>> 'f', 2, 'LR', None, None, <function aslinearoperator at 0x7f988cd9fb90>,
>> None)
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>> File
>> "/software/pkg/python/3.3.5/lib/python3.3/site-packages/nose-1.3.1-py3.3.egg/nose/case.py",
>> line 198, in runTest
>> self.test(*self.arg)
>> File
>> "/software/pkg/python/3.3.5/lib/python3.3/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
>> line 259, in eval_evec
>> assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
>> File
>> "/software/pkg/python/3.3.5/lib/python3.3/site-packages/numpy/testing/utils.py",
>> line 1183, in assert_allclose
>> verbose=verbose, header=header)
>> File
>> "/software/pkg/python/3.3.5/lib/python3.3/site-packages/numpy/testing/utils.py",
>> line 644, in assert_array_compare
>> raise AssertionError(msg)
>> AssertionError:
>> Not equal to tolerance rtol=0.00178814, atol=0.000357628
>> error for eigs:standard, typ=f, which=LR, sigma=None,
>> mattype=aslinearoperator, OPpart=None, mode=normal
>> (mismatch 100.0%)
>> x: array([[ 0.13884316+0.j, -1.07112074+0.j],
>> [-0.08962911+0.j, -1.39801252+0.j],
>> [ 0.21701422+0.j, -0.93968379+0.j],...
>> y: array([[ 0.06020537+0.08471544j, -1.07112110+0.j ],
>> [-0.07497437-0.10549703j, -1.39801240+0.j ],
>> [ 0.13326693+0.18752094j, -0.93968397+0.j ],...
>>
>> ======================================================================
>> FAIL: test_basic.test_xlogy
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>> File
>> "/software/pkg/python/3.3.5/lib/python3.3/site-packages/nose-1.3.1-py3.3.egg/nose/case.py",
>> line 198, in runTest
>> self.test(*self.arg)
>> File
>> "/software/pkg/python/3.3.5/lib/python3.3/site-packages/scipy/special/tests/test_basic.py",
>> line 2736, in test_xlogy
>> assert_func_equal(special.xlogy, w2, z2, rtol=1e-13, atol=1e-13)
>> File
>> "/software/pkg/python/3.3.5/lib/python3.3/site-packages/scipy/special/_testutils.py",
>> line 87, in assert_func_equal
>> fdata.check()
>> File
>> "/software/pkg/python/3.3.5/lib/python3.3/site-packages/scipy/special/_testutils.py",
>> line 292, in check
>> assert_(False, "\n".join(msg))
>> File
>> "/software/pkg/python/3.3.5/lib/python3.3/site-packages/numpy/testing/utils.py",
>> line 44, in assert_
>> raise AssertionError(msg)
>> AssertionError:
>> Max |adiff|: 712.209
>> Max |rdiff|: 1027.5
>> Bad results (3 out of 6) for the following points (in output 0):
>> 0j (nan+0j)
>> => (-0+0j) != (nan+nanj)
>> (rdiff 0.0)
>> (1+0j) (2+0j) =>
>> (-711.5155851371305+0.7853981633976757j) != (0.6931471805599453+0j)
>> (rdiff 1027.5006309578175)
>> (1+0j) 1j =>
>> (-711.5155851371305+0.7853981633976757j) != 1.5707963267948966j
>> (rdiff 452.9651658054808)
>>
>> ======================================================================
>> FAIL: test_lambertw.test_values
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>> File
>> "/software/pkg/python/3.3.5/lib/python3.3/site-packages/nose-1.3.1-py3.3.egg/nose/case.py",
>> line 198, in runTest
>> self.test(*self.arg)
>> File
>> "/software/pkg/python/3.3.5/lib/python3.3/site-packages/scipy/special/tests/test_lambertw.py",
>> line 21, in test_values
>> assert_equal(lambertw(inf,1).real, inf)
>> File
>> "/software/pkg/python/3.3.5/lib/python3.3/site-packages/numpy/testing/utils.py",
>> line 304, in assert_equal
>> raise AssertionError(msg)
>> AssertionError:
>> Items are not equal:
>> ACTUAL: nan
>> DESIRED: inf
>>
>> ======================================================================
>> FAIL: test_lambertw.test_ufunc
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>> File
>> "/software/pkg/python/3.3.5/lib/python3.3/site-packages/numpy/testing/utils.py",
>> line 581, in chk_same_position
>> assert_array_equal(x_id, y_id)
>> File
>> "/software/pkg/python/3.3.5/lib/python3.3/site-packages/numpy/testing/utils.py",
>> line 718, in assert_array_equal
>> verbose=verbose, header='Arrays are not equal')
>> File
>> "/software/pkg/python/3.3.5/lib/python3.3/site-packages/numpy/testing/utils.py",
>> line 644, in assert_array_compare
>> raise AssertionError(msg)
>> AssertionError:
>> Arrays are not equal
>>
>> (mismatch 66.66666666666666%)
>> x: array([False, True, True], dtype=bool)
>> y: array([False, False, False], dtype=bool)
>>
>> During handling of the above exception, another exception occurred:
>>
>> Traceback (most recent call last):
>> File
>> "/software/pkg/python/3.3.5/lib/python3.3/site-packages/nose-1.3.1-py3.3.egg/nose/case.py",
>> line 198, in runTest
>> self.test(*self.arg)
>> File
>> "/software/pkg/python/3.3.5/lib/python3.3/site-packages/scipy/special/tests/test_lambertw.py",
>> line 93, in test_ufunc
>> lambertw(r_[0., e, 1.]), r_[0., 1., 0.567143290409783873])
>> File
>> "/software/pkg/python/3.3.5/lib/python3.3/site-packages/numpy/testing/utils.py",
>> line 811, in assert_array_almost_equal
>> header=('Arrays are not almost equal to %d decimals' % decimal))
>> File
>> "/software/pkg/python/3.3.5/lib/python3.3/site-packages/numpy/testing/utils.py",
>> line 607, in assert_array_compare
>> chk_same_position(x_isnan, y_isnan, hasval='nan')
>> File
>> "/software/pkg/python/3.3.5/lib/python3.3/site-packages/numpy/testing/utils.py",
>> line 587, in chk_same_position
>> raise AssertionError(msg)
>> AssertionError:
>> Arrays are not almost equal to 6 decimals
>>
>> x and y nan location mismatch:
>> x: array([ 0.+0.j, nan+0.j, nan+0.j])
>> y: array([ 0. , 1. , 0.567])
>>
>> ----------------------------------------------------------------------
>> Ran 8775 tests in 239.751s
>>
>> <scipy-dev at scipy.org>FAILED (KNOWNFAIL=114, SKIP=220, failures=5)
>> Running unit tests for scipy
>> NumPy version 1.8.1
>> NumPy is installed in
>> /software/pkg/python/3.3.5/lib/python3.3/site-packages/numpy
>> SciPy version 0.13.3
>> SciPy is installed in
>> /software/pkg/python/3.3.5/lib/python3.3/site-packages/scipy
>> Python version 3.3.5 (default, Apr 16 2014, 19:42:58) [GCC 4.4.7 20120313
>> (Red Hat 4.4.7-4)]
>> nose version 1.3.1
>>
>> Do you have any fix for these errors?
>>
>
> Hi Wim, thanks for the report. These all look new to me; I don't have an
> easy fix. The Arpack ones should have been fixed in 0.13.3 (they were a
> major issue on several platforms for 0.11.x/0.12.x), but apparently there's
> still something not 100% right.
>
> Could you open an issue on Github? Adding details about which compilers
> you used and about which processor may also be helpful.
>
> Ralf
>
>
>
>>
>> Thanks in advance.
>>
>> Wim
>>
>>
>> --
>> ---------------------------------------------------------------
>> Wim R. Cardoen, PhD
>> Staff Scientist,
>> Center for High Performance Computing
>> University of Utah
>> ---------------------------------------------------------------
>>
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>>
>
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