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

Nils Wagner nwagner at mecha.uni-stuttgart.de
Tue Mar 21 01:37:16 CST 2006


Travis Oliphant wrote:
> Arnd Baecker wrote:
>   
>>   
>>     
>>>>> 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.
>>>>
>>>> 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
>>>>       
>>>>         
>
> Yes, this helps.
>
> But, it would be nice if you could post all the compilation warnings for 
> the ndimage package encountered during a scipy build.  It's an issue 
> with maybelong being used in the definition and then int* later.
>
> I've fixed what I found, but other issues may linger.  It looks like 
> ndimage was not 64-bit ready.
>
> -Travis
>
>
>
>
> _______________________________________________
> Scipy-dev mailing list
> Scipy-dev at scipy.net
> http://www.scipy.net/mailman/listinfo/scipy-dev
>   

>>> scipy.__version__
'0.4.9.1757'

scipy.test(1,10) (on a 64bit machine) results in
 geometric transform 1 ... FAIL
geometric transform 2 ... FAIL
geometric transform 3 ... FAIL
geometric transform 4 ... FAIL
geometric transform 5 ... FAIL
geometric transform 6 ... FAIL
geometric transform 7 ... FAIL
geometric transform 8 ... FAIL
geometric transform 10 ... FAIL
geometric transform 13 ... FAIL
geometric transform 14 ... FAIL
geometric transform 15 ... FAIL
geometric transform 16 ... FAIL
geometric transform 17 ... FAIL
geometric transform 18 ... FAIL
geometric transform 19 ... FAIL
geometric transform 20 ... FAIL
geometric transform 21 ... FAIL
geometric transform 22 ... FAIL
geometric transform 23 ... FAIL
geometric transform 24 ... FAIL

histogram 1
Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread 16384 (LWP 16492)]
0x00002aaaadf4c6d6 in NI_Histogram (input=0xd3d7d0, labels=0x0, min_label=-1, max_label=2, indices=0x0, n_results=1, histograms=0x9b35b0,
    min=0, max=10, nbins=46909632806922) at ni_measure.c:752
752           ph[jj][kk] = 0;
(gdb) bt
#0  0x00002aaaadf4c6d6 in NI_Histogram (input=0xd3d7d0, labels=0x0, min_label=-1, max_label=2, indices=0x0, n_results=1,
    histograms=0x9b35b0, min=0, max=10, nbins=46909632806922) at ni_measure.c:752
#1  0x00002aaaadf4224d in Py_Histogram (obj=<value optimized out>, args=<value optimized out>) at nd_image.c:1103
#2  0x00002aaaaac5496a in PyEval_EvalFrame (f=0x606030) at ceval.c:3547
#3  0x00002aaaaac55404 in PyEval_EvalCodeEx (co=0x2aaaae05c340, globals=<value optimized out>, locals=<value optimized out>, args=0x2,
    argcount=4, kws=0x980578, kwcount=0, defs=0x2aaaade17a88, defcount=2, closure=0x0) at ceval.c:2730
#4  0x00002aaaaac53aba in PyEval_EvalFrame (f=0x9803a0) at ceval.c:3640
#5  0x00002aaaaac53b97 in PyEval_EvalFrame (f=0x976960) at ceval.c:3629
#6  0x00002aaaaac55404 in PyEval_EvalCodeEx (co=0x2aaaabbeed50, globals=<value optimized out>, locals=<value optimized out>,
    args=0x2aaab6555de8, argcount=2, kws=0xb31d10, kwcount=0, defs=0x2aaaabc060e8, defcount=1, closure=0x0) at ceval.c:2730
#7  0x00002aaaaac0e9af in function_call (func=0x2aaaabc05758, arg=0x2aaab6555dd0, kw=<value optimized out>) at funcobject.c:548
#8  0x00002aaaaabfa760 in PyObject_Call (func=<value optimized out>, arg=<value optimized out>, kw=<value optimized out>)
    at abstract.c:1751
#9  0x00002aaaaac532e2 in PyEval_EvalFrame (f=0xc3d4a0) at ceval.c:3824
#10 0x00002aaaaac55404 in PyEval_EvalCodeEx (co=0x2aaaabbeedc0, globals=<value optimized out>, locals=<value optimized out>,
    args=0x2aaab5b43890, argcount=2, kws=0x0, kwcount=0, defs=0x0, defcount=0, closure=0x0) at ceval.c:2730
#11 0x00002aaaaac0e9af in function_call (func=0x2aaaabc057d0, arg=0x2aaab5b43878, kw=<value optimized out>) at funcobject.c:548
#12 0x00002aaaaabfa760 in PyObject_Call (func=<value optimized out>, arg=<value optimized out>, kw=<value optimized out>)
    at abstract.c:1751
#13 0x00002aaaaac02131 in instancemethod_call (func=<value optimized out>, arg=0x2aaab5b43878, kw=0x0) at classobject.c:2431
#14 0x00002aaaaabfa760 in PyObject_Call (func=<value optimized out>, arg=<value optimized out>, kw=<value optimized out>)
    at abstract.c:1751
#15 0x00002aaaaac5380d in PyEval_EvalFrame (f=0x6283e0) at ceval.c:3755
#16 0x00002aaaaac55404 in PyEval_EvalCodeEx (co=0x2aaaabbe4340, globals=<value optimized out>, locals=<value optimized out>,
    args=0x2aaab5b710b0, argcount=2, kws=0x0, kwcount=0, defs=0x2aaaabc06b68, defcount=1, closure=0x0) at ceval.c:2730
#17 0x00002aaaaac0e9af in function_call (func=0x2aaaabc09cf8, arg=0x2aaab5b71098, kw=<value optimized out>) at funcobject.c:548
#18 0x00002aaaaabfa760 in PyObject_Call (func=<value optimized out>, arg=<value optimized out>, kw=<value optimized out>)
    at abstract.c:1751

Nils






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