2009/11/4 Charles R Harris <charlesr.harris@[...].com> :
> 
> 
>  On Wed, Nov 4, 2009 at 8:39 PM, Anne Archibald <peridot.faceted@[...].com>
>  wrote:
> >
> > 2009/11/4 Charles R Harris <charlesr.harris@[...].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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