[SciPy-dev] Scipy 0.4.8 segfaults on 64bit Linux (Ubuntu).

Arnd Baecker arnd.baecker at web.de
Mon Mar 20 02:59:10 CST 2006



On Mon, 20 Mar 2006, Arnd Baecker wrote:

> On Mon, 20 Mar 2006, Ed Schofield wrote:
>
> > On 20/03/2006, at 8:19 AM, Rudolph van der Merwe wrote:
> >
> > > scipy.test(10,10) definitely spits out A LOT MORE info. Here is the
> > > relevant part:
> > >
> > > check_y_stride (scipy.linalg.tests.test_fblas.test_zswap) ... ok
> > > affine_transform 1 ... FAIL
> > > affine transform 2 ... FAIL
> > > affine transform 3 ... FAIL
> > > affine transform 4 ... FAIL
> > > affine transform 5Segmentation fault
> >
> > This is occurring in the tests of the new ndimage package.  Try
> > deleting the file test_ndimage.py in /usr/lib/python2.4/site-packages/
> > scipy/ndimage/tests/ and re-running the tests.
> >
> > Meanwhile we need some developer with a 64-bit machine to track this
> > down :)
>
> I just tried it out, but don't see this segfault.

Hmm, maybe because it did not run at all:

import scipy.ndimage

---------------------------------------------------------------------------
exceptions.ImportError                               Traceback (most
recent call last)

/home/abaecker/<console>

/home/abaecker/BUILDS3/BuildDir/inst_numpy/lib/python2.4/site-packages/scipy/ndimage/__init__.py
     35 from morphology import *
     36
---> 37 from info import __doc__
     38 from numpy.testing import ScipyTest
     39 test = ScipyTest().test

ImportError: No module named info


Commenting out ``from info import __doc__`` I get:
In [1]: import scipy.ndimage
In [2]: scipy.ndimage.test(10, 10)
  Found 397 tests for scipy.ndimage
[...]
  Found 0 tests for __main__
affine_transform 1 ... FAIL
affine transform 2 ... FAIL
affine transform 3 ... FAIL
affine transform 4 ... FAIL
affine transform 5*** glibc detected *** free(): invalid next size (fast):
0x00000000009dd5b0 ***
Aborted

gdb backtrace:

Program received signal SIGABRT, Aborted.
[Switching to Thread 46912507335168 (LWP 13552)]
0x00002aaaab35f43a in raise () from /lib64/tls/libc.so.6
(gdb) bt
#0  0x00002aaaab35f43a in raise () from /lib64/tls/libc.so.6
#1  0x00002aaaab360870 in abort () from /lib64/tls/libc.so.6
#2  0x00002aaaab39506e in __libc_message () from /lib64/tls/libc.so.6
#3  0x00002aaaab39a40c in malloc_printerr () from /lib64/tls/libc.so.6
#4  0x00002aaaab39ae9c in free () from /lib64/tls/libc.so.6
#5  0x00002aaaae513e66 in NI_GeometricTransform (input=0x930d40, map=0,
map_data=0x0, matrix_ar=0xffffffffffffffff,
    shift_ar=0x0, coordinates=0x0, output=0x81b420, order=1, mode=4,
cval=0) at ni_interpolation.c:644
#6  0x00002aaaae50b7bc in Py_GeometricTransform (obj=0x34f0, args=0x34f0)
at nd_image.c:566
#7  0x0000000000478cfb in PyEval_EvalFrame (f=0x717bf0) at ceval.c:3558
#8  0x000000000047ad2f in PyEval_EvalCodeEx (co=0x2aaaae4e73b0,
globals=0x34f0, locals=0x6, args=0x717bf0, argcount=3,
    kws=0x6d5f10, kwcount=1, defs=0x2aaaae4ec068, defcount=8, closure=0x0)
at ceval.c:2736
#9  0x00000000004788f7 in PyEval_EvalFrame (f=0x6d5d40) at ceval.c:3650
#10 0x0000000000479fb1 in PyEval_EvalFrame (f=0x89ad70) at ceval.c:3640
#11 0x000000000047ad2f in PyEval_EvalCodeEx (co=0x2aaaab948ea0,
globals=0x34f0, locals=0x6, args=0x89ad70, argcount=2,
    kws=0x91d590, kwcount=0, defs=0x2aaaab950ee8, defcount=1, closure=0x0)
at ceval.c:2736
#12 0x00000000004c6099 in function_call (func=0x2aaaab95f7d0,
arg=0x2aaaae4f9ef0, kw=0x9564b0) at funcobject.c:548
#13 0x0000000000417700 in PyObject_Call (func=0x34f0, arg=0x34f0, kw=0x6)
at abstract.c:1756
#14 0x00000000004772ea in PyEval_EvalFrame (f=0x739540) at ceval.c:3835
#15 0x000000000047ad2f in PyEval_EvalCodeEx (co=0x2aaaab948f10,
globals=0x34f0, locals=0x6, args=0x739540, argcount=2, kws=0x0,
    kwcount=0, defs=0x0, defcount=0, closure=0x0) at ceval.c:2736
#16 0x00000000004c6099 in function_call (func=0x2aaaab95f848,
arg=0x2aaaae4f9ea8, kw=0x0) at funcobject.c:548
#17 0x0000000000417700 in PyObject_Call (func=0x34f0, arg=0x34f0, kw=0x6)
at abstract.c:1756
#18 0x0000000000420ee0 in instancemethod_call (func=0x34f0,
arg=0x2aaaae4f9ea8, kw=0x0) at classobject.c:2447
#19 0x0000000000417700 in PyObject_Call (func=0x34f0, arg=0x34f0, kw=0x6)
at abstract.c:1756
#20 0x00000000004777d9 in PyEval_EvalFrame (f=0x730390) at ceval.c:3766
#21 0x000000000047ad2f in PyEval_EvalCodeEx (co=0x2aaaab93a490,
globals=0x34f0, locals=0x6, args=0x730390, argcount=2, kws=0x0,
    kwcount=0, defs=0x2aaaab9609a8, defcount=1, closure=0x0) at
ceval.c:2736
#22 0x00000000004c6099 in function_call (func=0x2aaaab962d70,
arg=0x2aaaae4f9e60, kw=0x0) at funcobject.c:548
#23 0x0000000000417700 in PyObject_Call (func=0x34f0, arg=0x34f0, kw=0x6)
at abstract.c:1756
#24 0x0000000000420ee0 in instancemethod_call (func=0x34f0,
arg=0x2aaaae4f9e60, kw=0x0) at classobject.c:2447
#25 0x0000000000417700 in PyObject_Call (func=0x34f0, arg=0x34f0, kw=0x6)
at abstract.c:1756
#26 0x000000000044fd80 in slot_tp_call (self=0x2aaaae6ad0d0,
args=0x2aaaae6b3510, kwds=0x0) at typeobject.c:4536
#27 0x0000000000417700 in PyObject_Call (func=0x34f0, arg=0x34f0, kw=0x6)
at abstract.c:1756
#28 0x00000000004777d9 in PyEval_EvalFrame (f=0x7acb10) at ceval.c:3766
#29 0x000000000047ad2f in PyEval_EvalCodeEx (co=0x2aaaab94d960,
globals=0x34f0, locals=0x6, args=0x7acb10, argcount=2,
    kws=0x924cf0, kwcount=0, defs=0x0, defcount=0, closure=0x0) at
ceval.c:2736
#30 0x00000000004c6099 in function_call (func=0x2aaaab9610c8,
arg=0x2aaaae4f9e18, kw=0x956270) at funcobject.c:548
#31 0x0000000000417700 in PyObject_Call (func=0x34f0, arg=0x34f0, kw=0x6)
at abstract.c:1756
#32 0x00000000004772ea in PyEval_EvalFrame (f=0x6e9ec0) at ceval.c:3835
#33 0x000000000047ad2f in PyEval_EvalCodeEx (co=0x2aaaab94d9d0,
globals=0x34f0, locals=0x6, args=0x6e9ec0, argcount=2, kws=0x0,
    kwcount=0, defs=0x0, defcount=0, closure=0x0) at ceval.c:2736
#34 0x00000000004c6099 in function_call (func=0x2aaaab961140,
arg=0x2aaaae4f9dd0, kw=0x0) at funcobject.c:548
#35 0x0000000000417700 in PyObject_Call (func=0x34f0, arg=0x34f0, kw=0x6)
at abstract.c:1756
#36 0x0000000000420ee0 in instancemethod_call (func=0x34f0,
arg=0x2aaaae4f9dd0, kw=0x0) at classobject.c:2447
#37 0x0000000000417700 in PyObject_Call (func=0x34f0, arg=0x34f0, kw=0x6)
at abstract.c:1756
#38 0x000000000044fd80 in slot_tp_call (self=0x2aaaae4f7150,
args=0x2aaaae69bf90, kwds=0x0) at typeobject.c:4536
#39 0x0000000000417700 in PyObject_Call (func=0x34f0, arg=0x34f0, kw=0x6)
at abstract.c:1756
#40 0x00000000004777d9 in PyEval_EvalFrame (f=0x80a600) at ceval.c:3766
#41 0x0000000000479fb1 in PyEval_EvalFrame (f=0x6e8bd0) at ceval.c:3640
#42 0x000000000047ad2f in PyEval_EvalCodeEx (co=0x2aaaab93af10,
globals=0x34f0, locals=0x6, args=0x6e8bd0, argcount=3,
    kws=0x6e8ae0, kwcount=0, defs=0x2aaaab964728, defcount=2, closure=0x0)
at ceval.c:2736
#43 0x00000000004788f7 in PyEval_EvalFrame (f=0x6e8940) at ceval.c:3650
#44 0x000000000047ad2f in PyEval_EvalCodeEx (co=0x2aaaadb37340,
globals=0x34f0, locals=0x6, args=0x6e8940, argcount=0, kws=0x0,
    kwcount=0, defs=0x0, defcount=0, closure=0x0) at ceval.c:2736
#45 0x000000000047af72 in PyEval_EvalCode (co=0x34f0, globals=0x34f0,
locals=0x6) at ceval.c:484
#46 0x00000000004a1c72 in PyRun_InteractiveOneFlags (fp=0x2aaaaab132d0,
filename=0x4cbf24 "<stdin>", flags=0x7fffffe053ac)
    at pythonrun.c:1265

Does this already help?

Best, Arnd




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