[SciPy-User] scipy trunk build / segfault problem

Ralf Gommers ralf.gommers@googlemail....
Wed Oct 28 05:35:19 CDT 2009


On Tue, Oct 27, 2009 at 6:13 PM, Pierre GM <pgmdevlist@gmail.com> wrote:

>
> On Oct 27, 2009, at 6:52 AM, Ralf Gommers wrote:
>
> ...
> > Before each build I remove old files with:
> > $ rm -rf build/
> > $  sudo rm /Library/Python/2.6/site-packages/numpy.egg-link
> > (and same for SciPy)
> >
> >
> > Then I build NumPy (r7593) in-place with:
>
> Ralf,
> When you build in-place, you should try to remove old *.so from your
> numpy directory before rebuilding. That way, you're sure that the
> latest libraries are recompiled and you're not mixing old and new.
> Not sure whether it's appropriate in your case, though...
>

Thanks Pierre and Stefan. I did not realize removing the build dir was not
enough. Removing, as Stefan suggested, with
$ git clean -xdf
helped in that I can now build both NumPy and SciPy with numscons, with:
$ export LDFLAGS="-lgfortran -arch x86_64"
$ export FFLAGS="-arch x86_64"
$ NPY_SEPARATE_COMPILATION=1 python setupscons.py scons -i


There is still a segfault occurring, but I can import and test modules
separately. The only module that segfaults is "cluster". All other modules
are fine, with the exception of 5 unit tests failing. I pasted those below.

This does look like an actual problem with cluster. And David was seeing
this as well, so I will reopen the ticket.

Cheers,
Ralf




In addition there are a few test failures:
SCIPY.SPARSE

======================================================================
ERROR: test_complex_nonsymmetric_modes
(test_arpack.TestEigenComplexNonSymmetric)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/Users/rgommers/Code/scipy/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
line 264, in test_complex_nonsymmetric_modes
    self.eval_evec(m,typ,k,which)
  File
"/Users/rgommers/Code/scipy/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
line 245, in eval_evec
    eval,evec=eigen(a,k,which=which)
  File
"/Users/rgommers/Code/scipy/scipy/sparse/linalg/eigen/arpack/arpack.py",
line 220, in eigen
    raise RuntimeError("Error info=%d in arpack"%info)
RuntimeError: Error info=-8 in arpack

======================================================================
ERROR: test_nonsymmetric_modes (test_arpack.TestEigenNonSymmetric)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/Users/rgommers/Code/scipy/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
line 201, in test_nonsymmetric_modes
    self.eval_evec(m,typ,k,which)
  File
"/Users/rgommers/Code/scipy/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
line 183, in eval_evec
    eval,evec=eigen(a,k,which=which,**kwds)
  File
"/Users/rgommers/Code/scipy/scipy/sparse/linalg/eigen/arpack/arpack.py",
line 220, in eigen
    raise RuntimeError("Error info=%d in arpack"%info)
RuntimeError: Error info=-8 in arpack

======================================================================
ERROR: test_starting_vector (test_arpack.TestEigenNonSymmetric)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/Users/rgommers/Code/scipy/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
line 211, in test_starting_vector
    self.eval_evec(self.symmetric[0],typ,k,which='LM',v0=v0)
  File
"/Users/rgommers/Code/scipy/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
line 183, in eval_evec
    eval,evec=eigen(a,k,which=which,**kwds)
  File
"/Users/rgommers/Code/scipy/scipy/sparse/linalg/eigen/arpack/arpack.py",
line 220, in eigen
    raise RuntimeError("Error info=%d in arpack"%info)
RuntimeError: Error info=-8 in arpack

======================================================================
FAIL: test_complex_symmetric_modes (test_arpack.TestEigenComplexSymmetric)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/Users/rgommers/Code/scipy/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
line 153, in test_complex_symmetric_modes
    self.eval_evec(self.symmetric[0],typ,k,which)
  File
"/Users/rgommers/Code/scipy/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py",
line 142, in eval_evec
    assert_array_almost_equal(eval,exact_eval,decimal=_ndigits[typ])
  File "/Users/rgommers/Code/numpy/numpy/testing/utils.py", line 763, in
assert_array_almost_equal
    header='Arrays are not almost equal')
  File "/Users/rgommers/Code/numpy/numpy/testing/utils.py", line 607, 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 435 tests in 13.371s

FAILED (SKIP=11, errors=3, failures=2)



SCIPY.LINALG

======================================================================
ERROR: Check linalg works with non-aligned memory
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/Library/Python/2.6/site-packages/nose-0.11.1-py2.6.egg/nose/case.py", line
183, in runTest
    self.test(*self.arg)
  File "/Users/rgommers/Code/scipy/scipy/linalg/tests/test_decomp.py", line
1067, in test_aligned_mem
    eig(z.T, overwrite_a=True)
  File "/Users/rgommers/Code/scipy/scipy/linalg/decomp.py", line 158, in eig
    geev, = get_lapack_funcs(('geev',),(a1,))
  File "/Users/rgommers/Code/scipy/scipy/linalg/lapack.py", line 82, in
get_lapack_funcs
    raise ValueError("Non-aligned array cannot be passed to LAPACK without
copying")
ValueError: Non-aligned array cannot be passed to LAPACK without copying

----------------------------------------------------------------------
Ran 404 tests in 1.226s

FAILED (SKIP=1, errors=1)



SCIPY.FFTPACK

======================================================================
FAIL: test_random_real (test_basic.TestSingleIFFT)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rgommers/Code/scipy/scipy/fftpack/tests/test_basic.py", line
205, in test_random_real
    assert_array_almost_equal (y1, x)
  File "/Users/rgommers/Code/numpy/numpy/testing/utils.py", line 763, in
assert_array_almost_equal
    header='Arrays are not almost equal')
  File "/Users/rgommers/Code/numpy/numpy/testing/utils.py", line 607, in
assert_array_compare
    raise AssertionError(msg)
AssertionError:
Arrays are not almost equal

(mismatch 0.900900900901%)
 x: array([ 0.610 -2.416e-09j,  0.644 +2.148e-09j,  0.982 +6.927e-08j,
0.394 -2.470e-09j,
        0.453 -1.328e-08j,  0.555 +1.817e-08j,  0.928 +7.155e-10j,  0.277
-9.148e-09j,
        0.047 -4.693e-08j,  0.677 -4.837e-09j,  0.922 +1.798e-08j,  0.128
-4.354e-08j,...
 y: array([ 0.61 ,  0.644,  0.982,  0.394,  0.453,  0.555,  0.928,  0.277,
0.047,  0.677,
        0.922,  0.128,  0.785,  0.218,  0.747,  0.68 ,  0.792,  0.428,
0.986,  0.314,
        0.341,  0.901,  0.244,  0.714,  0.817,  0.27 ,  0.758,  0.788,
0.587,  0.937,...

----------------------------------------------------------------------
Ran 81 tests in 1.436s

FAILED (failures=1)
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