[Numpy-discussion] Bus error for Debian / SPARC on current trunk

Mark Wiebe mwwiebe@gmail....
Sun Mar 4 22:32:35 CST 2012


On Sun, Mar 4, 2012 at 10:08 PM, Matthew Brett <matthew.brett@gmail.com>wrote:

> Hi,
>
> On Sun, Mar 4, 2012 at 11:41 AM, Mark Wiebe <mwwiebe@gmail.com> wrote:
> > On Sun, Mar 4, 2012 at 11:27 AM, Matthew Brett <matthew.brett@gmail.com>
> > wrote:
> >>
> >> Hi,
> >>
> >> On Sat, Mar 3, 2012 at 12:07 AM, Matthew Brett <matthew.brett@gmail.com
> >
> >> wrote:
> >> > Hi,
> >> >
> >> > On Fri, Mar 2, 2012 at 9:05 PM, Charles R Harris
> >> > <charlesr.harris@gmail.com> wrote:
> >> >>
> >> >>
> >> >> On Fri, Mar 2, 2012 at 4:36 PM, Matthew Brett <
> matthew.brett@gmail.com>
> >> >> wrote:
> >> >>>
> >> >>> Hi,
> >> >>>
> >> >>> Sorry that this report is not complete, I don't have full access to
> >> >>> this box but, on a Debian squeeze machine running linux
> >> >>> 2.6.32-5-sparc64-smp:
> >> >>>
> >> >>> nosetests
> >> >>>
> >> >>>
> ~/usr/local/lib/python2.6/site-packages/numpy/lib/tests/test_io.py:TestFromTxt.test_user_missing_values
> >> >>>
> >> >>> test_user_missing_values (test_io.TestFromTxt) ... Bus error
> >> >>>
> >> >>> This on current master : 1.7.0.dev-b9872b4
> >> >>>
> >> >>
> >> >> Hmm, some tests might have been recently enabled. Any chance of
> doing a
> >> >> bisection?
> >>
> >> Struggling because compilation is very slow and there are lots of
> >> untestable commits.  df907e6 is the first known bad.  Here's the
> >> output from a log:
> >>
> >> * df907e6 - (HEAD, refs/bisect/bad) BLD: Failure in single file build
> >> mode because of a static function in two separate files (6 months ago)
> >> [Mark Wiebe]
> >> * 01b200b - (refs/bisect/skip-01b200b10149312f51234448e44b230b1b548046)
> >> BUG: nditer: The nditer was reusing the reduce loop inappropriately
> >> (#1938) (6 months ago) [Mark Wiebe]
> >> * f45fd67 - (refs/bisect/skip-f45fd67fe8eefc8fd2e4b914ab4e376ab5226887)
> >> DOC: Small tweak to release notes (6 months ago) [Mark Wiebe]
> >> * 73be11d - (refs/bisect/skip-73be11db794d115a7d9bd2e822c0d8008bc14a28)
> >> BUG: Some bugs in squeeze and concatenate found by testing SciPy (6
> >> months ago) [Mark Wiebe]
> >> * c873295 - (refs/bisect/skip-c8732958c8e07f2306029dfde2178faf9c01d049)
> >> TST: missingdata: Finish up NA mask tests for np.std and np.var (6
> >> months ago) [Mark Wiebe]
> >> * e15712c - (refs/bisect/skip-e15712cf5df41806980f040606744040a433b331)
> >> BUG: nditer: NA masks in arrays with leading 1 dimensions had an issue
> >> (6 months ago) [Mark Wiebe]
> >> * ded81ae - (refs/bisect/skip-ded81ae7d529ac0fba641b7e5e3ecf52e120700f)
> >> ENH: missingdata: Implement tests for np.std, add skipna= and
> >> keepdims= parameters to more functions (6 months ago) [Mark Wiebe]
> >> * a112fc4 - (refs/bisect/skip-a112fc4a6b28fbb85e1b0c6d423095d13cf7b226)
> >> ENH: missingdata: Implement skipna= support for np.std and np.var (6
> >> months ago) [Mark Wiebe]
> >> * 0fa4f22 - (refs/bisect/skip-0fa4f22fec4b19e2a8c1d93e5a1f955167c9addd)
> >> ENH: missingdata: Support 'skipna=' parameter in np.mean (6 months
> >> ago) [Mark Wiebe]
> >> * bfda229 - (refs/bisect/skip-bfda229ec93d37b1ee2cdd8b9443ec4e34536bbf)
> >> ENH: missingdata: Create count_reduce_items function (6 months ago)
> >> [Mark Wiebe]
> >> * d9b3f90 - (refs/bisect/skip-d9b3f90de3213ece9a78b77088fdec17910e81d9)
> >> ENH: missingdata: Move the Reduce boilerplate into a function
> >> PyArray_ReduceWrapper (6 months ago) [Mark Wiebe]
> >> * 67ece6b - (refs/bisect/skip-67ece6bdd2b35d011893e78154dbff6ab51c7d35)
> >> ENH: missingdata: Finish count_nonzero as a full-fledged reduction
> >> operation (6 months ago) [Mark Wiebe]
> >> * 6bfd819 - (refs/bisect/skip-6bfd819a0897caf6e6db244930c40ed0d17b9e62)
> >> ENH: missingdata: Towards making count_nonzero a full-featured
> >> reduction operation (6 months ago) [Mark Wiebe]
> >> * a1faa1b - (refs/bisect/skip-a1faa1b6883c47333508a0476c1304b0a8a3f64e)
> >> ENH: missingdata: Move some of the refactored reduction code into the
> >> API (6 months ago) [Mark Wiebe]
> >> * f597374 - (refs/bisect/skip-f597374edc298810083799e8539c99fc0a93b319)
> >> ENH: missingdata: Change default to create NA-mask when NAs are in
> >> lists (6 months ago) [Mark Wiebe]
> >> * 965e4cf - (refs/bisect/skip-965e4cff5c4c50e8ff051a3363adc6cf6aa640cd)
> >> ENH: missingdata: trying some more functions to see how they treat NAs
> >> (6 months ago) [Mark Wiebe]
> >> * b1cb211 - (refs/bisect/skip-b1cb211d159c617ee4ebd16266d6f1042417ef75)
> >> ENH: missingdata: Add nastr= parameter to np.set_printoptions() (6
> >> months ago) [Mark Wiebe]
> >> * ba4d116 - (refs/bisect/skip-ba4d1161fe4943cb720f35c0abfd0581628255d6)
> >> BUG: missingdata: Fix mask usage in PyArray_TakeFrom, add tests for it
> >> (6 months ago) [Mark Wiebe]
> >> * a3a0ee8 - (refs/bisect/skip-a3a0ee8c72fdd55ffacb96bbb1fa9c3569cfb3e9)
> >> BUG: missingdata: The ndmin parameter to np.array wasn't respecting NA
> >> masks (6 months ago) [Mark Wiebe]
> >> * 9194b3a - (refs/bisect/skip-9194b3af704df71aa9b1ff2f53f169848d0f9dc7)
> >> ENH: missingdata: Rewrite PyArray_Concatenate to work with NA masks (6
> >> months ago) [Mark Wiebe]
> >> * 99a21ef - (refs/bisect/good-99a21efff4b1f2292dc370c7c9c7c58f10385f2a)
> >> ENH: missingdata: Add NA support to np.diagonal, change np.diagonal to
> >> always return a view (6 months ago) [Mark Wiebe]
> >>
> >> So - the problem arises somewhere between 99a21ef (good) and  df907e6
> >> (bad)
> >>
> >> There seems to be a compilation error for the skipped commits - here's
> >> the one I tested, 9194b3a:
> >
> >
> > If you enable separate compilation by setting an environment variable,
> these
> > commits should build as well.
> >
> > $ export ENABLE_SEPARATE_COMPILATION=1
> > <proceed with builds>
>
> I might be doing something wrong but:
>

I made a mistake, sorry! I even copy/pasted the variable name to make sure
I didn't misspell it, but I didn't notice that setup.py uses a different
but nearly identical name internally as the environment variable. That
should have been

$ export NPY_SEPARATE_COMPILATION=1

The place this is used inside of setup.py is here:

https://github.com/numpy/numpy/blob/master/numpy/core/setup.py#L14

I really dislike this build feature, it repeatedly trips me up. In my
opinion, the build should be changed to always do separate compilation, and
the single file mode should be eradicated.

Thanks ,
Mark


>
> In file included from numpy/core/src/multiarray/scalartypes.c.src:25,
>                 from
> numpy/core/src/multiarray/multiarraymodule_onefile.c:10:
> numpy/core/src/multiarray/_datetime.h:9: warning: function declaration
> isn't a prototype
> In file included from
> numpy/core/src/multiarray/multiarraymodule_onefile.c:13:
> numpy/core/src/multiarray/datetime.c:34: warning: function declaration
> isn't a prototype
> In file included from
> numpy/core/src/multiarray/multiarraymodule_onefile.c:41:
> numpy/core/src/multiarray/nditer_constr.c:2373: error: redefinition of
> 'intp_abs'
> numpy/core/src/multiarray/shape.c:927: note: previous definition of
> 'intp_abs' was here
> In file included from numpy/core/src/multiarray/scalartypes.c.src:25,
>                 from
> numpy/core/src/multiarray/multiarraymodule_onefile.c:10:
> numpy/core/src/multiarray/_datetime.h:9: warning: function declaration
> isn't a prototype
> In file included from
> numpy/core/src/multiarray/multiarraymodule_onefile.c:13:
> numpy/core/src/multiarray/datetime.c:34: warning: function declaration
> isn't a prototype
> In file included from
> numpy/core/src/multiarray/multiarraymodule_onefile.c:41:
> numpy/core/src/multiarray/nditer_constr.c:2373: error: redefinition of
> 'intp_abs'
> numpy/core/src/multiarray/shape.c:927: note: previous definition of
> 'intp_abs' was here
> error: Command "gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv
> -O2 -Wall -Wstrict-prototypes -fPIC -Inumpy/core/include
> -Ibuild/src.linux-sparc64-2.6/numpy/core/include/numpy
> -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core
> -Inumpy/core/src/npymath -Inumpy/core/src/multiarray
> -Inumpy/core/src/umath -Inumpy/core/src/npysort -Inumpy/core/include
> -I/usr/include/python2.6
> -Ibuild/src.linux-sparc64-2.6/numpy/core/src/multiarray
> -Ibuild/src.linux-sparc64-2.6/numpy/core/src/umath -c
> numpy/core/src/multiarray/multiarraymodule_onefile.c -o
>
> build/temp.linux-sparc64-2.6/numpy/core/src/multiarray/multiarraymodule_onefile.o"
> failed with exit status 1
>
> (bare-env)[matthew@vagus ~/dev_trees/numpy ((9194b3a...)|BISECTING)]$
> echo $ENABLE_SEPARATE_COMPILATION
> 1
>
> Best,
>
> Matthew
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