[SciPy-User] SciPy 0.11.0 Failures in scipy.test()
Wim R. Cardoen
wcardoen at gmail.com
Tue Apr 2 16:09:12 EDT 2013
Hello,
This morning I installed numpy 1.7.0 and ran its test suite successfully.
After installing scipy 0.11.0 I ran the scipy test suite and obtained a
bunch of failures. (vide infra #2).
I compiled the code on the a RHEL6 box using gfortran (GNU Fortran (GCC)
4.4.6)
as well as gcc (gcc (GCC) 4.4.6)
I used the OS's blas and lapack library and compiled suitesparse myself.
Do you have any idea how can I resolve these failures?
Thanks,
Wim
#1: Configuration to compile scipy 0.11.0
------------------------------------------------------------------------------------------------------------------------------------
import scipy
>>> scipy.show_config()
blas_info:
libraries = ['blas', 'lapack']
library_dirs = ['/usr/lib64']
language = f77
amd_info:
libraries = ['amd']
library_dirs = ['/uufs/chpc.utah.edu/sys/pkg/suitesparse/4.0.2_rhel6/lib
']
define_macros = [('SCIPY_AMD_H', None)]
swig_opts = ['-I/uufs/
chpc.utah.edu/sys/pkg/suitesparse/4.0.2_rhel6/include']
include_dirs = ['/uufs/
chpc.utah.edu/sys/pkg/suitesparse/4.0.2_rhel6/include']
lapack_info:
libraries = ['lapack', 'lapack']
library_dirs = ['/usr/lib64']
language = f77
atlas_threads_info:
NOT AVAILABLE
blas_opt_info:
libraries = ['blas', 'lapack', 'lapack']
library_dirs = ['/usr/lib64']
language = f77
define_macros = [('NO_ATLAS_INFO', 1)]
atlas_blas_threads_info:
NOT AVAILABLE
umfpack_info:
libraries = ['umfpack', 'amd']
library_dirs = ['/uufs/chpc.utah.edu/sys/pkg/suitesparse/4.0.2_rhel6/lib
']
define_macros = [('SCIPY_UMFPACK_H', None), ('SCIPY_AMD_H', None)]
swig_opts = ['-I/uufs/
chpc.utah.edu/sys/pkg/suitesparse/4.0.2_rhel6/include', '-I/uufs/
chpc.utah.edu/sys/pkg/suitesparse/4.0.2_rhel6/include']
include_dirs = ['/uufs/
chpc.utah.edu/sys/pkg/suitesparse/4.0.2_rhel6/include']
lapack_opt_info:
libraries = ['lapack', 'lapack', 'blas', 'lapack', 'lapack']
library_dirs = ['/usr/lib64']
language = f77
define_macros = [('NO_ATLAS_INFO', 1)]
atlas_info:
NOT AVAILABLE
lapack_mkl_info:
NOT AVAILABLE
blas_mkl_info:
NOT AVAILABLE
atlas_blas_info:
NOT AVAILABLE
mkl_info:
NOT AVAILABLE
--------------------------------------------------------------------------------------------------------------------------------------
#2: Failures after executing the
command
import scipy
scipy.test()
-------------------------------------------------------------------------------------------------------------------------------------------
======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2, 'LM',
None, 0.5, <class 'scipy.sparse.csr.csr_matrix'>, None, 'normal')
----------------------------------------------------------------------
Traceback (most recent call last):
File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/nose-1.1.2-py2.7.egg/nose/case.py",
line 197, in runTest
self.test(*self.arg)
File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
line 257, in eval_evec
assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
line 1179, in assert_allclose
verbose=verbose, header=header)
File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
line 645, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=0.00178814, atol=0.000357628
error for eigsh:standard, typ=f, which=LM, sigma=0.5, mattype=csr_matrix,
OPpart=None, mode=normal
(mismatch 100.0%)
x: array([[ 2.38156418e-01, -6.75444982e+09],
[ -1.07853470e-01, -8.01245676e+09],
[ 1.24683023e-01, -5.19757686e+09],...
y: array([[ 2.38156418e-01, -5.70949789e+08],
[ -1.07853470e-01, -4.05829392e+08],
[ 1.24683023e-01, 6.25800146e+07],...
======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2, 'LM',
None, 0.5, <class 'scipy.sparse.csr.csr_matrix'>, None, 'buckling')
----------------------------------------------------------------------
Traceback (most recent call last):
File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/nose-1.1.2-py2.7.egg/nose/case.py",
line 197, in runTest
self.test(*self.arg)
File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
line 257, in eval_evec
assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
line 1179, in assert_allclose
verbose=verbose, header=header)
File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
line 645, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=0.00178814, atol=0.000357628
error for eigsh:standard, typ=f, which=LM, sigma=0.5, mattype=csr_matrix,
OPpart=None, mode=buckling
(mismatch 100.0%)
x: array([[ 3.53755447e-01, -2.29114355e+04],
[ -1.60204595e-01, -6.65625445e+04],
[ 1.85203065e-01, -2.69012500e+04],...
y: array([[ 3.53755447e-01, -8.88255444e+05],
[ -1.60204595e-01, -2.39343354e+06],
[ 1.85203065e-01, -3.96842525e+04],...
======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2, 'LM',
None, 0.5, <class 'scipy.sparse.csr.csr_matrix'>, None, 'cayley')
----------------------------------------------------------------------
Traceback (most recent call last):
File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/nose-1.1.2-py2.7.egg/nose/case.py",
line 197, in runTest
self.test(*self.arg)
File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
line 257, in eval_evec
assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
line 1179, in assert_allclose
verbose=verbose, header=header)
File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
line 645, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=0.00178814, atol=0.000357628
error for eigsh:standard, typ=f, which=LM, sigma=0.5, mattype=csr_matrix,
OPpart=None, mode=cayley
(mismatch 100.0%)
x: array([[ -2.38156418e-01, 1.04661597e+09],
[ 1.07853470e-01, 1.39930271e+09],
[ -1.24683023e-01, 9.56906461e+08],...
y: array([[ -2.38156418e-01, 7.63721281e+07],
[ 1.07853470e-01, 1.25169905e+08],
[ -1.24683023e-01, 2.91283130e+07],...
======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2, 'LM',
None, 0.5, <function asarray at 0xd19a28>, None, 'normal')
----------------------------------------------------------------------
Traceback (most recent call last):
File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/nose-1.1.2-py2.7.egg/nose/case.py",
line 197, in runTest
self.test(*self.arg)
File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
line 257, in eval_evec
assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
line 1179, in assert_allclose
verbose=verbose, header=header)
File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
line 645, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=0.000357628, atol=0.000357628
error for eigsh:standard, typ=f, which=LM, sigma=0.5, mattype=asarray,
OPpart=None, mode=normal
(mismatch 100.0%)
x: array([[ -2.38157020e-01, -9.38079485e+09],
[ 1.07853829e-01, -1.09927593e+10],
[ -1.24683096e-01, -7.26035649e+09],...
y: array([[ -2.38157028e-01, -1.14406333e+09],
[ 1.07853849e-01, -1.61444148e+09],
[ -1.24683097e-01, -9.66750843e+08],...
======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2, 'LM',
None, 0.5, <function asarray at 0xd19a28>, None, 'buckling')
----------------------------------------------------------------------
Traceback (most recent call last):
File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/nose-1.1.2-py2.7.egg/nose/case.py",
line 197, in runTest
self.test(*self.arg)
File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
line 257, in eval_evec
assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
line 1179, in assert_allclose
verbose=verbose, header=header)
File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
line 645, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=0.000357628, atol=0.000357628
error for eigsh:standard, typ=f, which=LM, sigma=0.5, mattype=asarray,
OPpart=None, mode=buckling
(mismatch 100.0%)
x: array([[ 3.53756177e-01, 3.54742236e+05],
[ -1.60205036e-01, 9.37802669e+05],
[ 1.85203150e-01, -6.91305082e+04],...
y: array([[ 3.53756197e-01, 1.19154973e+07],
[ -1.60205063e-01, 3.16087279e+07],
[ 1.85203158e-01, -2.15500940e+06],...
======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2, 'LM',
None, 0.5, <function asarray at 0xd19a28>, None, 'cayley')
----------------------------------------------------------------------
Traceback (most recent call last):
File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/nose-1.1.2-py2.7.egg/nose/case.py",
line 197, in runTest
self.test(*self.arg)
File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
line 257, in eval_evec
assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
line 1179, in assert_allclose
verbose=verbose, header=header)
File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
line 645, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=0.000357628, atol=0.000357628
error for eigsh:standard, typ=f, which=LM, sigma=0.5, mattype=asarray,
OPpart=None, mode=cayley
(mismatch 100.0%)
x: array([[ -2.38156244e-01, 3.27365597e+08],
[ 1.07853608e-01, 4.31395993e+08],
[ -1.24682902e-01, 2.93518385e+08],...
y: array([[ -2.38156393e-01, 2.20001033e+07],
[ 1.07853475e-01, 3.05206768e+07],
[ -1.24683015e-01, 8.50334431e+06],...
======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2, 'SM',
None, 0.5, <class 'scipy.sparse.csr.csr_matrix'>, None, 'buckling')
----------------------------------------------------------------------
Traceback (most recent call last):
File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/nose-1.1.2-py2.7.egg/nose/case.py",
line 197, in runTest
self.test(*self.arg)
File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
line 257, in eval_evec
assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
line 1179, in assert_allclose
verbose=verbose, header=header)
File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
line 645, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=0.00178814, atol=0.000357628
error for eigsh:standard, typ=f, which=SM, sigma=0.5, mattype=csr_matrix,
OPpart=None, mode=buckling
(mismatch 100.0%)
x: array([[ 3.32810915e-02, -1.39781114e+06],
[ 8.83144107e-02, 6.75649002e+05],
[ -5.86642416e-03, -6.19039713e+05],...
y: array([[ 3.32810915e-02, -2.24275052e+05],
[ 8.83144107e-02, 1.08299209e+05],
[ -5.86642416e-03, -9.86191556e+04],...
======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2, 'SM',
None, 0.5, <class 'scipy.sparse.csr.csr_matrix'>, None, 'cayley')
----------------------------------------------------------------------
Traceback (most recent call last):
File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/nose-1.1.2-py2.7.egg/nose/case.py",
line 197, in runTest
self.test(*self.arg)
File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
line 257, in eval_evec
assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
line 1179, in assert_allclose
verbose=verbose, header=header)
File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
line 645, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=0.00178814, atol=0.000357628
error for eigsh:standard, typ=f, which=SM, sigma=0.5, mattype=csr_matrix,
OPpart=None, mode=cayley
(mismatch 100.0%)
x: array([[ 3.87506792e-03, 4.25513135e+07],
[ 1.02828460e-02, -1.78393819e+07],
[ -6.83054282e-04, -3.54143274e+07],...
y: array([[ 3.87506792e-03, 2.90700178e+08],
[ 1.02828460e-02, -1.18728352e+08],
[ -6.83054282e-04, -2.87462041e+08],...
======================================================================
.......
======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <gen-symmetric>, 'd', 2, 'SA',
None, 0.5, <function asarray at 0xd19a28>, None, 'cayley')
----------------------------------------------------------------------
Traceback (most recent call last):
File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/nose-1.1.2-py2.7.egg/nose/case.py",
line 197, in runTest
self.test(*self.arg)
File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
line 257, in eval_evec
assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
line 1179, in assert_allclose
verbose=verbose, header=header)
File "/uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy/testing/utils.py",
line 645, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=4.44089e-13, atol=4.44089e-13
error for eigsh:general, typ=d, which=SA, sigma=0.5, mattype=asarray,
OPpart=None, mode=cayley
(mismatch 100.0%)
x: array([[-0.36892684, -0.01935691],
[-0.26850996, -0.11053158],
[-0.40976156, -0.13223572],...
y: array([[-0.43633077, -0.01935691],
[-0.25161386, -0.11053158],
[-0.36756684, -0.13223572],...
----------------------------------------------------------------------
Ran 5481 tests in 75.399s
FAILED (KNOWNFAIL=15, SKIP=41, failures=63)
Running unit tests for scipy
NumPy version 1.7.0
NumPy is installed in /uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/numpy
SciPy version 0.11.0
SciPy is installed in /uufs/
chpc.utah.edu/sys/pkg/python/2.7.3_rhel6/lib/python2.7/site-packages/scipy
Python version 2.7.3 (default, Mar 28 2013, 15:20:19) [GCC 4.4.6 20120305
(Red Hat 4.4.6-4)]
nose version 1.1.2
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