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

Travis Oliphant oliphant.travis at ieee.org
Mon Mar 20 23:37:37 CST 2006


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







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