[SciPy-dev] scipy errors

Anne Archibald peridot.faceted@gmail....
Wed Nov 4 22:04:39 CST 2009


2009/11/4 Charles R Harris <charlesr.harris@gmail.com>:
>
>
> 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.

I don't know about SPARC, but I was able to trigger them on my
Pentium-M machine using the SSE2 version of ATLAS. (Which means, among
other things, that this problem is going to affect a reasonable number
of users.)

Part of the problem with using aligned matrices is that I'm not
confident I know which routines need aligned matrices: I found
segfaults using eig and svd, but many others were fine - on my
machine. svd was a particular problem because as I understand the
f2py, the matrix is already always copied on input (and adding the
aligned flag didn't help, though aligning the array before I called
svd made the problem go away).

Anne


> Chuck
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