[SciPy-dev] crash with 'import scipy.linalg' and 'import scipy.io'

John Pye john@curioussymbols....
Wed Mar 7 22:31:16 CST 2007


Hi all,

I am getting a crash when I call "from scipy import io". Normally this
works fine, but when I make the call from an *embedded* python script,
it goes haywire. See below for some GDB output. You can see the C code
has done some stuff, then the embedded python frame starts up. But there
is a crash when it gets to "import scipy.linalg", although "import
scipy" works fine. "import scipy.io" also gives a crash.

Note that this is with standard Ubuntu packages for numpy and scipy, but
with a locally build newer package of matplotlib.

john@roadwork:~/ascend$ dpkg -l matplotlib python-scipy python-numpy
Desired=Unknown/Install/Remove/Purge/Hold
| Status=Not/Installed/Config-files/Unpacked/Failed-config/Half-installed
|/ Err?=(none)/Hold/Reinst-required/X=both-problems (Status,Err:
uppercase=bad)
||/ Name                       Version                    Description
+++-==========================-==========================-====================================================================
ii  matplotlib                 0.90.0-2                   Matlab(TM)
style python plotting package
ii  python-numpy               1.0rc1-0ubuntu1            Numerical
Python adds a fast array facility to the Python language
ii  python-scipy               0.5.1-3ubuntu2             scientific
tools for Python
john@roadwork:~/ascend$

Has anyone else seen this behaviour? Is there anything I can do to work
around this problem?

Cheers
JP

base/generic/integrator/ida.c:1707 (integrator_ida_write_matrix):
Calculating dg/dx...
base/generic/system/jacobian.c:78 (system_jacobian): nr = 0
base/generic/system/jacobian.c:79 (system_jacobian): nv = 2
base/generic/linear/mtx_basic.c:3234 (mtx_write_region_mmio): Wrote
matrix range (0 x 2) to file
WROTE MATRICES TO FILE. NOW PROCESSING...
IMPORTING scipy...
IMPORTING scipy.linang...

Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread -1209911104 (LWP 22996)]
0xb5a60b41 in PyArray_API () from
/usr/lib/python2.4/site-packages/numpy/core/multiarray.so
(gdb) where
#0  0xb5a60b41 in PyArray_API () from
/usr/lib/python2.4/site-packages/numpy/core/multiarray.so
#1  0xb3987fc7 in init_flinalg () at
/usr/lib/python2.4/site-packages/numpy/core/include/numpy/__multiarray_api.h:952
#2  0x080d6844 in _PyImport_LoadDynamicModule (name=0xbf8577d7
"scipy.linalg._flinalg",
    pathname=0xbf856767
"/usr/lib/python2.4/site-packages/scipy/linalg/_flinalg.so",
fp=0x869f8a8) at ../Python/importdl.c:53
#3  0x080d47d5 in load_module (name=0xbf8577d7 "scipy.linalg._flinalg",
fp=0xb5a60b40,
    buf=0xbf856767
"/usr/lib/python2.4/site-packages/scipy/linalg/_flinalg.so", type=3,
loader=0x8) at ../Python/import.c:1689
#4  0x080d4f8b in import_submodule (mod=0xb482550c, subname=0xbf8577e4
"_flinalg", fullname=0xbf8577d7 "scipy.linalg._flinalg")
    at ../Python/import.c:2276
#5  0x080d540a in load_next (mod=0xb482550c, altmod=0x8124c58,
p_name=<value optimized out>,
    buf=0xbf8577d7 "scipy.linalg._flinalg", p_buflen=0xbf8577cc) at
../Python/import.c:2096
#6  0x080d563e in PyImport_ImportModuleEx (name=0xb39b5f54 "_flinalg",
globals=0xb39a11c4, locals=0xb39a11c4, fromlist=0x8124c58)
    at ../Python/import.c:1931
#7  0x080af9e0 in builtin___import__ (self=0x0, args=0xb39b81bc) at
../Python/bltinmodule.c:45
#8  0x08058c27 in PyObject_Call (func=0x8, arg=0xb39b81bc, kw=0x0) at
../Objects/abstract.c:1795
#9  0x080b395c in PyEval_CallObjectWithKeywords (func=0xb7debd6c,
arg=0xb39b81bc, kw=0x0) at ../Python/ceval.c:3435
#10 0x080b77b3 in PyEval_EvalFrame (f=0x8424b1c) at ../Python/ceval.c:2020
#11 0x080ba4b9 in PyEval_EvalCodeEx (co=0xb39b6aa0, globals=0xb39a11c4,
locals=0xb39a11c4, args=0x0, argcount=0, kws=0x0,
    kwcount=0, defs=0x0, defcount=0, closure=0x0) at ../Python/ceval.c:2741
#12 0x080ba527 in PyEval_EvalCode (co=0xb39b6aa0, globals=0xb39a11c4,
locals=0xb39a11c4) at ../Python/ceval.c:484
#13 0x080d3d8c in PyImport_ExecCodeModuleEx (name=0xbf85abb7
"scipy.linalg.flinalg", co=0xb39b6aa0,
    pathname=0xbf858b07
"/usr/lib/python2.4/site-packages/scipy/linalg/flinalg.pyc") at
../Python/import.c:636
#14 0x080d4406 in load_source_module (name=0xbf85abb7
"scipy.linalg.flinalg",
    pathname=0xbf858b07
"/usr/lib/python2.4/site-packages/scipy/linalg/flinalg.pyc", fp=<value
optimized out>)
    at ../Python/import.c:915
#15 0x080d4f8b in import_submodule (mod=0xb482550c, subname=0xbf85abc4
"flinalg", fullname=0xbf85abb7 "scipy.linalg.flinalg")
    at ../Python/import.c:2276
#16 0x080d540a in load_next (mod=0xb482550c, altmod=0x8124c58,
p_name=<value optimized out>,
    buf=0xbf85abb7 "scipy.linalg.flinalg", p_buflen=0xbf85abac) at
../Python/import.c:2096
#17 0x080d563e in PyImport_ImportModuleEx (name=0xb39b5e54 "flinalg",
globals=0xb481ef0c, locals=0xb481ef0c, fromlist=0xb48215cc)
    at ../Python/import.c:1931
#18 0x080af9e0 in builtin___import__ (self=0x0, args=0xb39b80f4) at
../Python/bltinmodule.c:45
#19 0x08058c27 in PyObject_Call (func=0x8, arg=0xb39b80f4, kw=0x0) at
../Objects/abstract.c:1795
#20 0x080b395c in PyEval_CallObjectWithKeywords (func=0xb7debd6c,
arg=0xb39b80f4, kw=0x0) at ../Python/ceval.c:3435
#21 0x080b77b3 in PyEval_EvalFrame (f=0x81a7374) at ../Python/ceval.c:2020
#22 0x080ba4b9 in PyEval_EvalCodeEx (co=0xb39b6960, globals=0xb481ef0c,
locals=0xb481ef0c, args=0x0, argcount=0, kws=0x0,
    kwcount=0, defs=0x0, defcount=0, closure=0x0) at ../Python/ceval.c:2741
#23 0x080ba527 in PyEval_EvalCode (co=0xb39b6960, globals=0xb481ef0c,
locals=0xb481ef0c) at ../Python/ceval.c:484
#24 0x080d3d8c in PyImport_ExecCodeModuleEx (name=0xbf85df97
"scipy.linalg.basic", co=0xb39b6960,
    pathname=0xbf85bee7
"/usr/lib/python2.4/site-packages/scipy/linalg/basic.pyc") at
../Python/import.c:636
#25 0x080d4406 in load_source_module (name=0xbf85df97 "scipy.linalg.basic",
    pathname=0xbf85bee7
"/usr/lib/python2.4/site-packages/scipy/linalg/basic.pyc", fp=<value
optimized out>)
    at ../Python/import.c:915
#26 0x080d4f8b in import_submodule (mod=0xb482550c, subname=0xbf85dfa4
"basic", fullname=0xbf85df97 "scipy.linalg.basic")
    at ../Python/import.c:2276
#27 0x080d540a in load_next (mod=0xb482550c, altmod=0x8124c58,
p_name=<value optimized out>,
    buf=0xbf85df97 "scipy.linalg.basic", p_buflen=0xbf85df8c) at
../Python/import.c:2096
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