[SciPy-dev] scipy errors

Charles R Harris charlesr.harris@gmail....
Wed Nov 4 21:57:45 CST 2009


On Wed, Nov 4, 2009 at 8:39 PM, Anne Archibald <peridot.faceted@gmail.com>wrote:

> 2009/11/4 Charles R Harris <charlesr.harris@gmail.com>:
> > I see the following test errors on ubuntu_x86_64 9.10
> >
> > ERROR: Check linalg works with non-aligned memory
> > ----------------------------------------------------------------------
> > Traceback (most recent call last):
> >   File "/usr/lib/pymodules/python2.6/nose/case.py", line 183, in runTest
> >     self.test(*self.arg)
> >   File
> >
> "/usr/local/lib/python2.6/dist-packages/scipy/linalg/tests/test_decomp.py",
> > line 1067, in test_aligned_mem
> >     eig(z.T, overwrite_a=True)
> >   File "/usr/local/lib/python2.6/dist-packages/scipy/linalg/decomp.py",
> line
> > 158, in eig
> >     geev, = get_lapack_funcs(('geev',),(a1,))
> >   File "/usr/local/lib/python2.6/dist-packages/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
> [...]
> > I suspect the last failure is an mpmath version problem, and maybe the
> > second also. Is anyone else seeing the other error?
>
> This error is related to ticket 794:
> http://projects.scipy.org/scipy/ticket/794
> Under certain poorly-defined circumstances, passing non-aligned
> matrices to ATLAS can cause a segfault. I've posted a support request
> on the ATLAS tracker, hoping to find out whether it's supposed to be
> able to deal with non-aligned matrices, and in the meantime I have
> code to raise exceptions when non-aligned matrices are fed to LAPACK.
>
> I don't know whether the bug occurs at all on 64-bit systems, and I
> don't know whether it's the result of us abusing ATLAS or a bug in
> ATLAS. If it's a bug in ATLAS, I don't know for sure what triggers it
> - in particular, whether alignment actually solves the problem on all
> platforms.
>
>
> One solution would be to annotate all relevant f2py LAPACK wrappers
> with the new align8 keyword and hope that cures the problem (by
> forcing a copy of all not-sufficiently-aligned arrays on all LAPACK
> installations).
>
> Another "solution" would be to simply remove the failing test and tell
> people not to feed non-aligned matrices full of outrageous values into
> ATLAS on pain of segfaults. (The bug was filed by someone who'd had a
> segfault while working with an unpickled array, so it does bite some
> people.)
>
> A third option would be to raise ValueErrors any time non-aligned
> matrices are supposed to be passed to LAPACK. (This is what happens
> now, but the tests fail when this happens; if this were the permanent
> decision I would of course fix the tests to expect exceptions.)
>
> It might be possible, though I'm not sure how and it would be
> complicated, to trigger all this working-around only when using ATLAS.
>
>
> I'm not sure how best to deal with this. What do you think?
>
>
I haven't a clue as to what the best thing to do is. Using aligned matrices
might be the best workaround. Were the alignment problems on SPARC? I recall
a thread on the topic but don't remember what all was said.

Chuck
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