[SciPy-Dev] suitesparse vs scipy

Jack Howarth howarth@bromo.med.uc....
Tue Aug 30 07:55:15 CDT 2011


On Mon, Aug 29, 2011 at 08:36:42AM +0000, Pauli Virtanen wrote:
> Sun, 28 Aug 2011 19:26:04 -0400, Jack Howarth wrote:
> 
> > I've asked this question before without any responses. What are the
> > supported versions of suitesparse for use with scipy? The current scipy
> > 0.9.0 release doesn't appear to be fully compatible with suitesparse
> > 3.6.1 and causes testsuite failures in scipy.
> 
> Can you paste the test failures you see? 
> 
> Scipy does not use suitesparse except for the optional UMFPACK wrapper,
> which many people do not use. Suitesparse is still at 3.4.0 in
> Debian/Ubuntu, and I suppose newer ones have not been tested.
> 
> -- 
> Pauli Virtanen

Pauli,
    On x86_64-apple-darwin11, building scypy 0.9.0 against python2.7 using
the clang compilers and gfortran from FSF gcc 4.6.1, I get the following testsuite
results...

[MacPro:~] howarth% /sw/bin/python2.7
Python 2.7.2 (default, Jul 21 2011, 22:39:54) 
[GCC 4.2.1 Compatible Apple Clang 2.1 (tags/Apple/clang-163.7.1)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import scipy
>>> scipy.test()
Running unit tests for scipy
NumPy version 1.6.0
NumPy is installed in /sw/lib/python2.7/site-packages/numpy
SciPy version 0.9.0
SciPy is installed in /sw/lib/python2.7/site-packages/scipy
Python version 2.7.2 (default, Jul 21 2011, 22:39:54) [GCC 4.2.1 Compatible Apple Clang 2.1 (tags/Apple/clang-163.7.1)]
nose version 1.1.2
.............................................................................................................................................................................................................K......................................................................................................................K..K.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................F..FF......................................................................................................................................SSSSSS......SSSSSS......SSSS.....................................................F....FF.....S................................................................................................................................................................................................................K...........................................................................................................................................................................................SSSSS.........S.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................../sw/lib/python2.7/site-packages/scipy/sparse/linalg/dsolve/linsolve.py:259: DeprecationWarning: scipy.sparse.linalg.dsolve.umfpack will be removed, install scikits.umfpack instead
  ' install scikits.umfpack instead', DeprecationWarning )
../sw/lib/python2.7/site-packages/scipy/sparse/linalg/dsolve/linsolve.py:75: DeprecationWarning: scipy.sparse.linalg.dsolve.umfpack will be removed, install scikits.umfpack instead
  ' install scikits.umfpack instead', DeprecationWarning )
................K.K..KK.KK...........................................................................................................................................K...............................................................K...........................................................................................................................................................KK...............................................................................................................................................................................................................................................................................................................................................................................................................................K.K........................................................................................................................................................................................................................................................................................................................................................................................K........K.........SSSSSSS................................................................................................................................................................................................................................................................................................................................................................................................../sw/lib/python2.7/site-packages/scipy/stats/distributions.py:3546: RuntimeWarning: overflow encountered in exp
  return exp(c*x-exp(x)-gamln(c))
................................./sw/lib/python2.7/site-packages/scipy/stats/distributions.py:3955: RuntimeWarning: invalid value encountered in sqrt
  vals = 2*(bt+1.0)*sqrt(b-2.0)/((b-3.0)*sqrt(b))
.........................................................................................................................................................................................................................................................................................................S..............................................................................................................................................................................................F.............................................................................................................................................................................................................................................................................................................................................................................................................
======================================================================
FAIL: test_asum (test_blas.TestFBLAS1Simple)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/sw/lib/python2.7/site-packages/scipy/lib/blas/tests/test_blas.py", line 58, in test_asum
    assert_almost_equal(f([3,-4,5]),12)
  File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 468, in assert_almost_equal
    raise AssertionError(msg)
AssertionError: 
Arrays are not almost equal to 7 decimals
 ACTUAL: 0.0
 DESIRED: 12

======================================================================
FAIL: test_dot (test_blas.TestFBLAS1Simple)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/sw/lib/python2.7/site-packages/scipy/lib/blas/tests/test_blas.py", line 67, in test_dot
    assert_almost_equal(f([3,-4,5],[2,5,1]),-9)
  File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 468, in assert_almost_equal
    raise AssertionError(msg)
AssertionError: 
Arrays are not almost equal to 7 decimals
 ACTUAL: 0.0
 DESIRED: -9

======================================================================
FAIL: test_nrm2 (test_blas.TestFBLAS1Simple)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/sw/lib/python2.7/site-packages/scipy/lib/blas/tests/test_blas.py", line 78, in test_nrm2
    assert_almost_equal(f([3,-4,5]),math.sqrt(50))
  File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 468, in assert_almost_equal
    raise AssertionError(msg)
AssertionError: 
Arrays are not almost equal to 7 decimals
 ACTUAL: 0.0
 DESIRED: 7.0710678118654755

======================================================================
FAIL: test_asum (test_blas.TestFBLAS1Simple)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/sw/lib/python2.7/site-packages/scipy/linalg/tests/test_blas.py", line 57, in test_asum
    assert_almost_equal(f([3,-4,5]),12)
  File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 468, in assert_almost_equal
    raise AssertionError(msg)
AssertionError: 
Arrays are not almost equal to 7 decimals
 ACTUAL: 0.0
 DESIRED: 12

======================================================================
FAIL: test_dot (test_blas.TestFBLAS1Simple)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/sw/lib/python2.7/site-packages/scipy/linalg/tests/test_blas.py", line 66, in test_dot
    assert_almost_equal(f([3,-4,5],[2,5,1]),-9)
  File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 468, in assert_almost_equal
    raise AssertionError(msg)
AssertionError: 
Arrays are not almost equal to 7 decimals
 ACTUAL: 0.0
 DESIRED: -9

======================================================================
FAIL: test_nrm2 (test_blas.TestFBLAS1Simple)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/sw/lib/python2.7/site-packages/scipy/linalg/tests/test_blas.py", line 83, in test_nrm2
    assert_almost_equal(f([3,-4,5]),math.sqrt(50))
  File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 468, in assert_almost_equal
    raise AssertionError(msg)
AssertionError: 
Arrays are not almost equal to 7 decimals
 ACTUAL: 0.0
 DESIRED: 7.0710678118654755

======================================================================
FAIL: test_expon (test_morestats.TestAnderson)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/sw/lib/python2.7/site-packages/scipy/stats/tests/test_morestats.py", line 72, in test_expon
    assert_array_less(crit[:-1], A)
  File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 869, in assert_array_less
    header='Arrays are not less-ordered')
  File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 613, in assert_array_compare
    chk_same_position(x_id, y_id, hasval='inf')
  File "/sw/lib/python2.7/site-packages/numpy/testing/utils.py", line 588, in chk_same_position
    raise AssertionError(msg)
AssertionError: 
Arrays are not less-ordered

x and y inf location mismatch:
 x: array([ 0.911,  1.065,  1.325,  1.587])
 y: array(inf)

----------------------------------------------------------------------
Ran 4722 tests in 63.364s

FAILED (KNOWNFAIL=18, SKIP=31, failures=7)
<nose.result.TextTestResult run=4722 errors=0 failures=7>
>>> 

FYI, I see the same seven failures if I use Apple's gcc-4.2 compilers instead of the clang compilers.
          Jack

> 
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev@scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev


More information about the SciPy-Dev mailing list