scipy.test() segfault
Program received signal SIGSEGV, Segmentation fault. 0x00007ffff7ab2b26 in PyObject_RichCompare () from /usr/lib64/libpython2.7.so.1.0 (gdb) bt #0 0x00007ffff7ab2b26 in PyObject_RichCompare () from /usr/lib64/libpython2.7.so.1.0 #1 0x00007ffff7ab2def in PyObject_RichCompareBool () from /usr/lib64/libpython2.7.so.1.0 #2 0x00007fffe3ba8584 in OBJECT_compare (ip1=<optimized out>, ip2=<optimized out>) at scipy/signal/sigtoolsmodule.c:827 #3 0x00007ffff74b8b64 in msort_with_tmp.part.0 () from /lib64/libc.so.6 #4 0x00007ffff74b8e9b in qsort_r () from /lib64/libc.so.6 #5 0x00007fffe3ba90d6 in PyArray_OrderFilterND (op1=<optimized out>, op2=<optimized out>, order=54989472) at scipy/signal/sigtoolsmodule.c:969 #6 0x00007fffe3ba92a7 in sigtools_order_filterND (__NPY_UNUSED_TAGGEDdummy=<optimized out>, args=<optimized out>) at scipy/signal/sigtoolsmodule.c:1135 #7 0x00007ffff7affcaa in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0 #8 0x00007ffff7b059c3 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.7.so.1.0 #9 0x00007ffff7aff7ce in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0 #10 0x00007ffff7b0204f in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0 #11 0x00007ffff7b05727 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.7.so.1.0 #12 0x00007ffff7a9ddc8 in ?? () from /usr/lib64/libpython2.7.so.1.0 #13 0x00007ffff7a7d464 in PyObject_Call () from /usr/lib64/libpython2.7.so.1.0 #14 0x00007ffff7b00cae in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0 #15 0x00007ffff7b05727 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.7.so.1.0 #16 0x00007ffff7a9dba1 in ?? () from /usr/lib64/libpython2.7.so.1.0 #17 0x00007ffff7a7d464 in PyObject_Call () from /usr/lib64/libpython2.7.so.1.0 #18 0x00007ffff7a87c8e in ?? () from /usr/lib64/libpython2.7.so.1.0 #19 0x00007ffff7a7d464 in PyObject_Call () from /usr/lib64/libpython2.7.so.1.0 #20 0x00007ffff7acb84a in ?? () from /usr/lib64/libpython2.7.so.1.0 #21 0x00007ffff7a7d464 in PyObject_Call () from /usr/lib64/libpython2.7.so.1.0 #22 0x00007ffff7affe75 in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0 #23 0x00007ffff7b0204f in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0 #24 0x00007ffff7b05727 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.7.so.1.0 #25 0x00007ffff7a9ddc8 in ?? () from /usr/lib64/libpython2.7.so.1.0 #26 0x00007ffff7a7d464 in PyObject_Call () from /usr/lib64/libpython2.7.so.1.0 #27 0x00007ffff7b00cae in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0 #28 0x00007ffff7b05727 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.7.so.1.0 #29 0x00007ffff7a9dba1 in ?? () from /usr/lib64/libpython2.7.so.1.0 #30 0x00007ffff7a7d464 in PyObject_Call () from /usr/lib64/libpython2.7.so.1.0 #31 0x00007ffff7a87c8e in ?? () from /usr/lib64/libpython2.7.so.1.0 #32 0x00007ffff7a7d464 in PyObject_Call () from /usr/lib64/libpython2.7.so.1.0 #33 0x00007ffff7acb84a in ?? () from /usr/lib64/libpython2.7.so.1.0 #34 0x00007ffff7a7d464 in PyObject_Call () from /usr/lib64/libpython2.7.so.1.0 #35 0x00007ffff7affe75 in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0 #36 0x00007ffff7b05727 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.7.so.1.0
scipy.__version__ '0.12.0.dev-bb436fa' x86_64 GNU/Linux
Some context would be nice. How did you build (compilers, platform) and how do you make it crash? sigtoolsmodule.c hasn't been touched recently, so does it crash with 0.11.0 too? On Wed, Oct 31, 2012 at 8:03 PM, Nils Wagner <nils106@googlemail.com> wrote:
Program received signal SIGSEGV, Segmentation fault. 0x00007ffff7ab2b26 in PyObject_RichCompare () from /usr/lib64/libpython2.7.so.1.0 (gdb) bt #0 0x00007ffff7ab2b26 in PyObject_RichCompare () from /usr/lib64/libpython2.7.so.1.0 #1 0x00007ffff7ab2def in PyObject_RichCompareBool () from /usr/lib64/libpython2.7.so.1.0 #2 0x00007fffe3ba8584 in OBJECT_compare (ip1=<optimized out>, ip2=<optimized out>) at scipy/signal/sigtoolsmodule.c:827 #3 0x00007ffff74b8b64 in msort_with_tmp.part.0 () from /lib64/libc.so.6 #4 0x00007ffff74b8e9b in qsort_r () from /lib64/libc.so.6 #5 0x00007fffe3ba90d6 in PyArray_OrderFilterND (op1=<optimized out>, op2=<optimized out>, order=54989472) at scipy/signal/sigtoolsmodule.c:969 #6 0x00007fffe3ba92a7 in sigtools_order_filterND (__NPY_UNUSED_TAGGEDdummy=<optimized out>, args=<optimized out>) at scipy/signal/sigtoolsmodule.c:1135 #7 0x00007ffff7affcaa in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0 #8 0x00007ffff7b059c3 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.7.so.1.0 #9 0x00007ffff7aff7ce in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0 #10 0x00007ffff7b0204f in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0 #11 0x00007ffff7b05727 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.7.so.1.0 #12 0x00007ffff7a9ddc8 in ?? () from /usr/lib64/libpython2.7.so.1.0 #13 0x00007ffff7a7d464 in PyObject_Call () from /usr/lib64/libpython2.7.so.1.0 #14 0x00007ffff7b00cae in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0 #15 0x00007ffff7b05727 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.7.so.1.0 #16 0x00007ffff7a9dba1 in ?? () from /usr/lib64/libpython2.7.so.1.0 #17 0x00007ffff7a7d464 in PyObject_Call () from /usr/lib64/libpython2.7.so.1.0 #18 0x00007ffff7a87c8e in ?? () from /usr/lib64/libpython2.7.so.1.0 #19 0x00007ffff7a7d464 in PyObject_Call () from /usr/lib64/libpython2.7.so.1.0 #20 0x00007ffff7acb84a in ?? () from /usr/lib64/libpython2.7.so.1.0 #21 0x00007ffff7a7d464 in PyObject_Call () from /usr/lib64/libpython2.7.so.1.0 #22 0x00007ffff7affe75 in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0 #23 0x00007ffff7b0204f in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0 #24 0x00007ffff7b05727 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.7.so.1.0 #25 0x00007ffff7a9ddc8 in ?? () from /usr/lib64/libpython2.7.so.1.0 #26 0x00007ffff7a7d464 in PyObject_Call () from /usr/lib64/libpython2.7.so.1.0 #27 0x00007ffff7b00cae in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0 #28 0x00007ffff7b05727 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.7.so.1.0 #29 0x00007ffff7a9dba1 in ?? () from /usr/lib64/libpython2.7.so.1.0 #30 0x00007ffff7a7d464 in PyObject_Call () from /usr/lib64/libpython2.7.so.1.0 #31 0x00007ffff7a87c8e in ?? () from /usr/lib64/libpython2.7.so.1.0 #32 0x00007ffff7a7d464 in PyObject_Call () from /usr/lib64/libpython2.7.so.1.0 #33 0x00007ffff7acb84a in ?? () from /usr/lib64/libpython2.7.so.1.0 #34 0x00007ffff7a7d464 in PyObject_Call () from /usr/lib64/libpython2.7.so.1.0 #35 0x00007ffff7affe75 in PyEval_EvalFrameEx () from /usr/lib64/libpython2.7.so.1.0 #36 0x00007ffff7b05727 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.7.so.1.0
scipy.__version__ '0.12.0.dev-bb436fa' x86_64 GNU/Linux
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AFAIK the segfault was introduced recently. gcc (SUSE Linux) 4.6.2 GNU Fortran (SUSE Linux) 4.6.2 x86_64 GNU/Linux Python 2.7.2 (default, Aug 19 2011, 20:41:43) [GCC] on linux2
import scipy scipy.__version__ '0.12.0.dev-bb436fa' scipy.test(verbose=10) ... test_rank3 (test_signaltools.TestLinearFilterObject) ... ok test_basic (test_signaltools.TestMedFilt) ... ok Ticket #1124. Ensure this does not segfault. ... Segmentation fault
Nils
On Fri, Nov 2, 2012 at 7:14 PM, Nils Wagner <nils106@googlemail.com> wrote:
AFAIK the segfault was introduced recently. gcc (SUSE Linux) 4.6.2 GNU Fortran (SUSE Linux) 4.6.2 x86_64 GNU/Linux Python 2.7.2 (default, Aug 19 2011, 20:41:43) [GCC] on linux2
import scipy scipy.__version__ '0.12.0.dev-bb436fa' scipy.test(verbose=10) ... test_rank3 (test_signaltools.TestLinearFilterObject) ... ok test_basic (test_signaltools.TestMedFilt) ... ok Ticket #1124. Ensure this does not segfault. ... Segmentation fault
Are you running numpy master? If so, does this segfault with an older released version of numpy too? The relevant code in sigtoolsmodule.c hasn't been touched in a long time. Ralf
I am using NumPy version 1.8.0.dev-526b764 Nils On Sat, Nov 3, 2012 at 4:53 PM, Ralf Gommers <ralf.gommers@gmail.com> wrote:
On Fri, Nov 2, 2012 at 7:14 PM, Nils Wagner <nils106@googlemail.com>wrote:
AFAIK the segfault was introduced recently. gcc (SUSE Linux) 4.6.2 GNU Fortran (SUSE Linux) 4.6.2 x86_64 GNU/Linux Python 2.7.2 (default, Aug 19 2011, 20:41:43) [GCC] on linux2
import scipy scipy.__version__ '0.12.0.dev-bb436fa' scipy.test(verbose=10) ... test_rank3 (test_signaltools.TestLinearFilterObject) ... ok test_basic (test_signaltools.TestMedFilt) ... ok Ticket #1124. Ensure this does not segfault. ... Segmentation fault
Are you running numpy master? If so, does this segfault with an older released version of numpy too? The relevant code in sigtoolsmodule.c hasn't been touched in a long time.
Ralf
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On Sat, Nov 3, 2012 at 6:51 PM, Nils Wagner <nils106@googlemail.com> wrote:
I am using NumPy version 1.8.0.dev-526b764
So can you try with 1.6.2? Ralf
Nils
On Sat, Nov 3, 2012 at 4:53 PM, Ralf Gommers <ralf.gommers@gmail.com>wrote:
On Fri, Nov 2, 2012 at 7:14 PM, Nils Wagner <nils106@googlemail.com>wrote:
AFAIK the segfault was introduced recently. gcc (SUSE Linux) 4.6.2 GNU Fortran (SUSE Linux) 4.6.2 x86_64 GNU/Linux Python 2.7.2 (default, Aug 19 2011, 20:41:43) [GCC] on linux2
import scipy scipy.__version__ '0.12.0.dev-bb436fa' scipy.test(verbose=10) ... test_rank3 (test_signaltools.TestLinearFilterObject) ... ok test_basic (test_signaltools.TestMedFilt) ... ok Ticket #1124. Ensure this does not segfault. ... Segmentation fault
Are you running numpy master? If so, does this segfault with an older released version of numpy too? The relevant code in sigtoolsmodule.c hasn't been touched in a long time.
Ralf
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Sure. It works fine with numpy 1.6.2
scipy.__version__ '0.12.0.dev-2f17ff2' scipy.test() Running unit tests for scipy NumPy version 1.6.2 NumPy is installed in /home/nwagner/local/lib64/python2.7/site-packages/numpy SciPy version 0.12.0.dev-2f17ff2 SciPy is installed in /home/nwagner/local/lib64/python2.7/site-packages/scipy Python version 2.7.2 (default, Aug 19 2011, 20:41:43) [GCC] nose version 1.1.2 ...............
Ran 5592 tests in 179.134s OK (KNOWNFAIL=14, SKIP=28) <nose.result.TextTestResult run=5592 errors=0 failures=0> Nils On Sat, Nov 3, 2012 at 8:11 PM, Ralf Gommers <ralf.gommers@gmail.com> wrote:
On Sat, Nov 3, 2012 at 6:51 PM, Nils Wagner <nils106@googlemail.com>wrote:
I am using NumPy version 1.8.0.dev-526b764
So can you try with 1.6.2?
Ralf
Nils
On Sat, Nov 3, 2012 at 4:53 PM, Ralf Gommers <ralf.gommers@gmail.com>wrote:
On Fri, Nov 2, 2012 at 7:14 PM, Nils Wagner <nils106@googlemail.com>wrote:
AFAIK the segfault was introduced recently. gcc (SUSE Linux) 4.6.2 GNU Fortran (SUSE Linux) 4.6.2 x86_64 GNU/Linux Python 2.7.2 (default, Aug 19 2011, 20:41:43) [GCC] on linux2
>import scipy > scipy.__version__ '0.12.0.dev-bb436fa' >scipy.test(verbose=10) ... test_rank3 (test_signaltools.TestLinearFilterObject) ... ok test_basic (test_signaltools.TestMedFilt) ... ok Ticket #1124. Ensure this does not segfault. ... Segmentation fault
Are you running numpy master? If so, does this segfault with an older released version of numpy too? The relevant code in sigtoolsmodule.c hasn't been touched in a long time.
Ralf
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On Mon, Nov 5, 2012 at 8:37 PM, Nils Wagner <nils106@googlemail.com> wrote:
Sure. It works fine with numpy 1.6.2
Thanks Nils. I've been able to reproduce this now. It's caused by https://github.com/numpy/numpy/pull/2694. Will follow up on the numpy list. Ralf
scipy.__version__ '0.12.0.dev-2f17ff2' scipy.test() Running unit tests for scipy NumPy version 1.6.2 NumPy is installed in /home/nwagner/local/lib64/python2.7/site-packages/numpy SciPy version 0.12.0.dev-2f17ff2 SciPy is installed in /home/nwagner/local/lib64/python2.7/site-packages/scipy Python version 2.7.2 (default, Aug 19 2011, 20:41:43) [GCC] nose version 1.1.2 ...............
Ran 5592 tests in 179.134s
OK (KNOWNFAIL=14, SKIP=28) <nose.result.TextTestResult run=5592 errors=0 failures=0>
Nils
On Sat, Nov 3, 2012 at 8:11 PM, Ralf Gommers <ralf.gommers@gmail.com>wrote:
On Sat, Nov 3, 2012 at 6:51 PM, Nils Wagner <nils106@googlemail.com>wrote:
I am using NumPy version 1.8.0.dev-526b764
So can you try with 1.6.2?
Ralf
Nils
On Sat, Nov 3, 2012 at 4:53 PM, Ralf Gommers <ralf.gommers@gmail.com>wrote:
On Fri, Nov 2, 2012 at 7:14 PM, Nils Wagner <nils106@googlemail.com>wrote:
AFAIK the segfault was introduced recently. gcc (SUSE Linux) 4.6.2 GNU Fortran (SUSE Linux) 4.6.2 x86_64 GNU/Linux Python 2.7.2 (default, Aug 19 2011, 20:41:43) [GCC] on linux2
>>import scipy >> scipy.__version__ '0.12.0.dev-bb436fa' >>scipy.test(verbose=10) ... test_rank3 (test_signaltools.TestLinearFilterObject) ... ok test_basic (test_signaltools.TestMedFilt) ... ok Ticket #1124. Ensure this does not segfault. ... Segmentation fault
Are you running numpy master? If so, does this segfault with an older released version of numpy too? The relevant code in sigtoolsmodule.c hasn't been touched in a long time.
Ralf
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02.11.2012 20:14, Nils Wagner kirjoitti:
AFAIK the segfault was introduced recently. gcc (SUSE Linux) 4.6.2 GNU Fortran (SUSE Linux) 4.6.2 x86_64 GNU/Linux Python 2.7.2 (default, Aug 19 2011, 20:41:43) [GCC] on linux2 '0.12.0.dev-bb436fa' NumPy version 1.8.0.dev-526b764
Doesn't crash for me for this Numpy/Scipy version combination (Ubuntu 12.10). gcc-4.7 (Ubuntu/Linaro 4.7.2-2ubuntu1) 4.7.2 GNU Fortran (Ubuntu/Linaro 4.7.2-2ubuntu1) 4.7.2 x86_64 GNU/Linux Python 2.7.3 (default, Sep 26 2012, 21:51:14) [GCC 4.7.2] on linux2 However, Valgrind shows: ==31561== Invalid read of size 8 ==31561== at 0x4C2CD88: memcpy@@GLIBC_2.14 (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so) ==31561== by 0xE25A608: fill_buffer (sigtoolsmodule.c:796) ==31561== by 0xE25B344: PyArray_OrderFilterND (sigtoolsmodule.c:968) ==31561== by 0xE25C075: sigtools_order_filterND (sigtoolsmodule.c:1135) ==31561== by 0x45F911: PyEval_EvalFrameEx (in /usr/bin/python2.7) ==31561== by 0x467208: PyEval_EvalCodeEx (in /usr/bin/python2.7) ==31561== by 0x45FF76: PyEval_EvalFrameEx (in /usr/bin/python2.7) ==31561== by 0x467208: PyEval_EvalCodeEx (in /usr/bin/python2.7) ==31561== by 0x4D0241: PyEval_EvalCode (in /usr/bin/python2.7) ==31561== by 0x5102BA: ??? (in /usr/bin/python2.7) ==31561== by 0x4D01E3: PyRun_StringFlags (in /usr/bin/python2.7) ==31561== by 0x419F54: PyRun_SimpleStringFlags (in /usr/bin/python2.7) ==31561== Address 0x7f0e510 is 16 bytes before a block of size 8 alloc'd ==31561== at 0x4C2B3F8: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so) ==31561== by 0x68572A5: PyDataMem_NEW (multiarraymodule.c:3491) ==31561== by 0x67A81EE: PyArray_NewFromDescr (ctors.c:970) ==31561== by 0x67A9CA7: PyArray_FromAny (ctors.c:1649) ==31561== by 0x67AA069: PyArray_CheckFromAny (ctors.c:1757) ==31561== by 0x6851D58: _array_fromobject (multiarraymodule.c:1655) ==31561== by 0x464E18: PyEval_EvalFrameEx (in /usr/bin/python2.7) ==31561== by 0x467208: PyEval_EvalCodeEx (in /usr/bin/python2.7) ==31561== by 0x45FF76: PyEval_EvalFrameEx (in /usr/bin/python2.7) ==31561== by 0x467208: PyEval_EvalCodeEx (in /usr/bin/python2.7) ==31561== by 0x45FF76: PyEval_EvalFrameEx (in /usr/bin/python2.7) ==31561== by 0x467208: PyEval_EvalCodeEx (in /usr/bin/python2.7) -- Pauli Virtanen
participants (3)
-
Nils Wagner
-
Pauli Virtanen
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Ralf Gommers