[SciPy-User] [SciPy-user] Scipy Superpack Errors and Failures

MDenno mgdenno@gmail....
Thu Oct 28 15:13:14 CDT 2010


Hello:

I have been trying to get numpy/scipy installed on my Mac (OSX 10.6.4) for a
few weeks now and just can't seem to make it all work.  I have tried 2
general approaches, building from source and using Chris Fonnesbeck's Scipy
Superpack, both of which have been giving me problems.  After much
installing and uninstalling of various programs/libraries I just did a fresh
install of OSX and gave the Superpack  (10-22-2010 version) another try, but
I am still having problems.  I don't think it is working correctly based on
running the tests.

First, some information about my setup:

$ gcc --version
i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5659)

$ gfortran --version
GNU Fortran (GCC) 4.2.1 (Apple Inc. build 5659) + GF 4.2.4

$ python
Python 2.6.1 (r261:67515, Feb 11 2010, 00:51:29) 
[GCC 4.2.1 (Apple Inc. build 5646)]

FFTW 3.2.2 built as follows:
	./configure CC="gcc -arch x86_64" CXX="g++ -arch x86_64" CPP="gcc -E"
CXXCPP="g++ -E"
	make
	sudo make install
	
XCode installed from xcode322_2148_developerdvd.dmg
	
Are there any other dependencies? UMFPACK?  ARPACK?

After installing and running the tests is it normal to have lots of warnings
and some errors and failures for scipy?  I ran the following:

>>> import scipy
>>> scipy.test()
Running unit tests for scipy
NumPy version 2.0.0.dev
NumPy is installed in
/Library/Python/2.6/site-packages/numpy-2.0.0.dev_20101022-py2.6-macosx-10.6-universal.egg/numpy
SciPy version 0.9.0.dev
SciPy is installed in
/Library/Python/2.6/site-packages/scipy-0.9.0.dev_20101022-py2.6-macosx-10.6-universal.egg/scipy
Python version 2.6.1 (r261:67515, Feb 11 2010, 00:51:29) [GCC 4.2.1 (Apple
Inc. build 5646)]
nose version 0.11.0

[lots of warnings omitted - I would be happy to provide them if they are
needed, but they are quite long]

======================================================================
ERROR: test_complex_nonsymmetric_modes
(test_arpack.TestEigenComplexNonSymmetric)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/Library/Python/2.6/site-packages/scipy-0.9.0.dev_20101022-py2.6-macosx-10.6-universal.egg/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
line 269, in test_complex_nonsymmetric_modes
    self.eval_evec(m,typ,k,which)
  File
"/Library/Python/2.6/site-packages/scipy-0.9.0.dev_20101022-py2.6-macosx-10.6-universal.egg/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
line 250, in eval_evec
    eval,evec=eigen(a,k,which=which)
  File
"/Library/Python/2.6/site-packages/scipy-0.9.0.dev_20101022-py2.6-macosx-10.6-universal.egg/scipy/sparse/linalg/eigen/arpack/arpack.py",
line 397, in eigen
    params.iterate()
  File
"/Library/Python/2.6/site-packages/scipy-0.9.0.dev_20101022-py2.6-macosx-10.6-universal.egg/scipy/sparse/linalg/eigen/arpack/arpack.py",
line 222, in iterate
    raise RuntimeError("Error info=%d in arpack" % self.info)
RuntimeError: Error info=-8 in arpack

======================================================================
ERROR: test_nonsymmetric_modes (test_arpack.TestEigenNonSymmetric)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/Library/Python/2.6/site-packages/scipy-0.9.0.dev_20101022-py2.6-macosx-10.6-universal.egg/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
line 206, in test_nonsymmetric_modes
    self.eval_evec(m,typ,k,which)
  File
"/Library/Python/2.6/site-packages/scipy-0.9.0.dev_20101022-py2.6-macosx-10.6-universal.egg/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
line 188, in eval_evec
    eval,evec=eigen(a,k,which=which,**kwds)
  File
"/Library/Python/2.6/site-packages/scipy-0.9.0.dev_20101022-py2.6-macosx-10.6-universal.egg/scipy/sparse/linalg/eigen/arpack/arpack.py",
line 397, in eigen
    params.iterate()
  File
"/Library/Python/2.6/site-packages/scipy-0.9.0.dev_20101022-py2.6-macosx-10.6-universal.egg/scipy/sparse/linalg/eigen/arpack/arpack.py",
line 222, in iterate
    raise RuntimeError("Error info=%d in arpack" % self.info)
RuntimeError: Error info=-8 in arpack

======================================================================
ERROR: test_starting_vector (test_arpack.TestEigenNonSymmetric)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/Library/Python/2.6/site-packages/scipy-0.9.0.dev_20101022-py2.6-macosx-10.6-universal.egg/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
line 216, in test_starting_vector
    self.eval_evec(self.symmetric[0],typ,k,which='LM',v0=v0)
  File
"/Library/Python/2.6/site-packages/scipy-0.9.0.dev_20101022-py2.6-macosx-10.6-universal.egg/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
line 188, in eval_evec
    eval,evec=eigen(a,k,which=which,**kwds)
  File
"/Library/Python/2.6/site-packages/scipy-0.9.0.dev_20101022-py2.6-macosx-10.6-universal.egg/scipy/sparse/linalg/eigen/arpack/arpack.py",
line 397, in eigen
    params.iterate()
  File
"/Library/Python/2.6/site-packages/scipy-0.9.0.dev_20101022-py2.6-macosx-10.6-universal.egg/scipy/sparse/linalg/eigen/arpack/arpack.py",
line 222, in iterate
    raise RuntimeError("Error info=%d in arpack" % self.info)
RuntimeError: Error info=-8 in arpack

======================================================================
FAIL: gaussian filter 3
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/Library/Python/2.6/site-packages/nose-0.11.0-py2.6.egg/nose/case.py", line
183, in runTest
    self.test(*self.arg)
  File
"/Library/Python/2.6/site-packages/scipy-0.9.0.dev_20101022-py2.6-macosx-10.6-universal.egg/scipy/ndimage/tests/test_ndimage.py",
line 468, in test_gauss03
    assert_almost_equal(output.sum(), input.sum())
  File
"/Library/Python/2.6/site-packages/numpy-2.0.0.dev_20101022-py2.6-macosx-10.6-universal.egg/numpy/testing/utils.py",
line 463, in assert_almost_equal
    raise AssertionError(msg)
AssertionError: 
Arrays are not almost equal
 ACTUAL: 49993304.0
 DESIRED: 49992896.0

======================================================================
FAIL: line-search Newton conjugate gradient optimization routine
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/Library/Python/2.6/site-packages/scipy-0.9.0.dev_20101022-py2.6-macosx-10.6-universal.egg/scipy/optimize/tests/test_optimize.py",
line 177, in test_ncg
    assert_(self.gradcalls == 18, self.gradcalls) # 0.8.0
  File
"/Library/Python/2.6/site-packages/numpy-2.0.0.dev_20101022-py2.6-macosx-10.6-universal.egg/numpy/testing/utils.py",
line 34, in assert_
    raise AssertionError(msg)
AssertionError: 16

======================================================================
FAIL: test_complex_symmetric_modes (test_arpack.TestEigenComplexSymmetric)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/Library/Python/2.6/site-packages/scipy-0.9.0.dev_20101022-py2.6-macosx-10.6-universal.egg/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
line 159, in test_complex_symmetric_modes
    self.eval_evec(self.symmetric[0],typ,k,which)
  File
"/Library/Python/2.6/site-packages/scipy-0.9.0.dev_20101022-py2.6-macosx-10.6-universal.egg/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
line 148, in eval_evec
    assert_array_almost_equal(eval,exact_eval,decimal=_ndigits[typ])
  File
"/Library/Python/2.6/site-packages/numpy-2.0.0.dev_20101022-py2.6-macosx-10.6-universal.egg/numpy/testing/utils.py",
line 774, in assert_array_almost_equal
    header='Arrays are not almost equal')
  File
"/Library/Python/2.6/site-packages/numpy-2.0.0.dev_20101022-py2.6-macosx-10.6-universal.egg/numpy/testing/utils.py",
line 618, in assert_array_compare
    raise AssertionError(msg)
AssertionError: 
Arrays are not almost equal

(mismatch 100.0%)
 x: array([ 1.07188725 +6.23436023e-08j,  4.91291142 -3.25412906e-08j],
dtype=complex64)
 y: array([ 5.+0.j,  6.+0.j], dtype=complex64)

----------------------------------------------------------------------
Ran 4771 tests in 78.922s

FAILED (KNOWNFAIL=13, SKIP=41, errors=3, failures=3)
<nose.result.TextTestResult run=4771 errors=3 failures=3>

Thank you in advance for your help.

Matt

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