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