I am trying to install and use dolfin on Arch Linux, with Python 2.7.3.
What is the best way to find out what is causing segmentation faults such as these?
$ python2 -c "import dolfin; print dolfin.__version__"
[3] 6491 segmentation fault (core dumped) python2 -c "import dolfin; print
dolfin.__version__"
I have tried inspecting the core file through gdb:
$ sudo systemd-coredumpctl gdb 6491
but they are always truncated:
Reading symbols from /usr/bin/python2.7...(no debugging symbols
found)...done.
BFD: Warning: /var/tmp/coredump-wSi8DV is truncated: expected
core file size >= 39694336, found: 25165824.
warning: core file may not match specified executable file.
[New LWP 7056]
Cannot access memory at address 0x7fe70be0d148
Cannot access memory at address 0x7fe70be0d140
I have tried adding 'print' statements between commands and have tracked the problem down to this load_module line, which loads a module that has been built by swig:
fp, pathname, description = imp.find_module('_common', [dirname(__file__)])
print "_mod = imp.load_module('_common', \n\tfp=%s, \n\tpathname=%s, \n\tdescription=%s)" % ( fp, pathname, description)
_mod = imp.load_module('_common', fp, pathname, description)
and that 'print' line prints the following, which looks correct:
_mod = imp.load_module('_common',
fp=<open file '_common.so', mode 'rb' at 0x282d150>,
pathname=_common.so,
description=('.so', 'rb', 3))
[1] 9039 segmentation fault (core dumped) python2 -c "import dolfin; print dolfin.__version__"
I have tried adding sys.settrace at the start the module get more information but that doesn't happen.
So, I inspect the linkage of the shared library it is trying to load:
$ ldd _common.so
libexpat.so.1 => /lib64/libexpat.so.1 (0x00007f52fe960000)
libavformat.so.54 => /lib64/libavformat.so.54 (0x00007f52fe61d000)
libavcodec.so.54 => /lib64/libavcodec.so.54 (0x00007f52fd6bb000)
libavutil.so.51 => /lib64/libavutil.so.51 (0x00007f52fd48d000)
libswscale.so.2 => /lib64/libswscale.so.2 (0x00007f52fd240000)
libvtkImaging.so.5.10 => /usr/lib/vtk-5.10/libvtkImaging.so.5.10 (0x00007f52fcb6e000)
libvtkftgl.so.5.10 => /usr/lib/vtk-5.10/libvtkftgl.so.5.10 (0x00007f52fc960000)
libfreetype.so.6 => /lib64/libfreetype.so.6 (0x00007f52fc6c1000)
libQtGui.so.4 => /lib64/libQtGui.so.4 (0x00007f52fba1d000)
libQtCore.so.4 => /lib64/libQtCore.so.4 (0x00007f52fb546000)
libGL.so.1 => /lib64/libGL.so.1 (0x00007f52fb223000)
libXt.so.6 => /lib64/libXt.so.6 (0x00007f52fafbc000)
libvtkParallel.so.5.10 => /usr/lib/vtk-5.10/libvtkParallel.so.5.10 (0x00007f52faabd000)
libvtkexoIIc.so.5.10 => /usr/lib/vtk-5.10/libvtkexoIIc.so.5.10 (0x00007f52fa877000)
libvtkVolumeRendering.so.5.10 => /usr/lib/vtk-5.10/libvtkVolumeRendering.so.5.10 (0x00007f52f9fdf000)
libQtWebKit.so.4 => /lib64/libQtWebKit.so.4 (0x00007f52f81f9000)
libQtSql.so.4 => /lib64/libQtSql.so.4 (0x00007f52f7fb9000)
libQtNetwork.so.4 => /lib64/libQtNetwork.so.4 (0x00007f52f7c81000)
libvtkViews.so.5.10 => /usr/lib/vtk-5.10/libvtkViews.so.5.10 (0x00007f52f7993000)
libvtkInfovis.so.5.10 => /usr/lib/vtk-5.10/libvtkInfovis.so.5.10 (0x00007f52f7357000)
libpci.so.3 => /usr/lib/libpci.so.3 (0x00007f52f714b000)
libxcb.so.1 => /usr/lib/libxcb.so.1 (0x00007f52f6f2b000)
libcblas.so => /usr/lib/libcblas.so (0x00007f52f6d0a000)
libssl.so.1.0.0 => /lib64/libssl.so.1.0.0 (0x00007f52f6a9f000)
libcrypto.so.1.0.0 => /lib64/libcrypto.so.1.0.0 (0x00007f52f6696000)
libhdf5_hl.so.7.4.0 => /lib64/libhdf5_hl.so.7.4.0 (0x00007f52f6465000)
librtmp.so.0 => /lib64/librtmp.so.0 (0x00007f52f6249000)
libva.so.1 => /lib64/libva.so.1 (0x00007f52f6031000)
libxvidcore.so.4 => /lib64/libxvidcore.so.4 (0x00007f52f5d19000)
libx264.so.128 => /lib64/libx264.so.128 (0x00007f52f59ca000)
libvpx.so.1 => /lib64/libvpx.so.1 (0x00007f52f5729000)
libvorbisenc.so.2 => /lib64/libvorbisenc.so.2 (0x00007f52f525a000)
libvorbis.so.0 => /lib64/libvorbis.so.0 (0x00007f52f502d000)
libtheoraenc.so.1 => /lib64/libtheoraenc.so.1 (0x00007f52f4def000)
libtheoradec.so.1 => /lib64/libtheoradec.so.1 (0x00007f52f4bd4000)
libspeex.so.1 => /lib64/libspeex.so.1 (0x00007f52f49bb000)
libschroedinger-1.0.so.0 => /lib64/libschroedinger-1.0.so.0 (0x00007f52f46ef000)
libopenjpeg.so.1 => /lib64/libopenjpeg.so.1 (0x00007f52f44c7000)
libopencore-amrwb.so.0 => /lib64/libopencore-amrwb.so.0 (0x00007f52f42b3000)
libopencore-amrnb.so.0 => /lib64/libopencore-amrnb.so.0 (0x00007f52f4088000)
libmp3lame.so.0 => /lib64/libmp3lame.so.0 (0x00007f52f3e11000)
libgsm.so.1 => /lib64/libgsm.so.1 (0x00007f52f3c06000)
libglib-2.0.so.0 => /lib64/libglib-2.0.so.0 (0x00007f52f390f000)
libgobject-2.0.so.0 => /lib64/libgobject-2.0.so.0 (0x00007f52f36c1000)
libSM.so.6 => /lib64/libSM.so.6 (0x00007f52f34b9000)
libICE.so.6 => /lib64/libICE.so.6 (0x00007f52f329c000)
libXrender.so.1 => /lib64/libXrender.so.1 (0x00007f52f3091000)
libfontconfig.so.1 => /lib64/libfontconfig.so.1 (0x00007f52f2e57000)
libXext.so.6 => /lib64/libXext.so.6 (0x00007f52f2c43000)
libnvidia-tls.so.310.19 => /lib64/libnvidia-tls.so.310.19 (0x00007f52f2a40000)
libnvidia-glcore.so.310.19 => /lib64/libnvidia-glcore.so.310.19 (0x00007f52f054d000)
libVPIC.so.5.10 => /usr/lib/vtk-5.10/libVPIC.so.5.10 (0x00007f52f0328000)
libCosmo.so.5.10 => /usr/lib/vtk-5.10/libCosmo.so.5.10 (0x00007f52f00e0000)
libsqlite3.so.0 => /lib64/libsqlite3.so.0 (0x00007f52efe33000)
libgstapp-0.10.so.0 => /lib64/libgstapp-0.10.so.0 (0x00007f52efc27000)
libgstinterfaces-0.10.so.0 => /lib64/libgstinterfaces-0.10.so.0 (0x00007f52efa14000)
libgstpbutils-0.10.so.0 => /lib64/libgstpbutils-0.10.so.0 (0x00007f52ef7f0000)
libgstvideo-0.10.so.0 => /lib64/libgstvideo-0.10.so.0 (0x00007f52ef5d4000)
libgstbase-0.10.so.0 => /lib64/libgstbase-0.10.so.0 (0x00007f52ef37f000)
libgstreamer-0.10.so.0 => /lib64/libgstreamer-0.10.so.0 (0x00007f52ef096000)
libvtkalglib.so.5.10 => /usr/lib/vtk-5.10/libvtkalglib.so.5.10 (0x00007f52eee75000)
libresolv.so.2 => /usr/lib/libresolv.so.2 (0x00007f52eec5e000)
libXau.so.6 => /usr/lib/libXau.so.6 (0x00007f52eea5a000)
libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0x00007f52ee853000)
libogg.so.0 => /lib64/libogg.so.0 (0x00007f52ee64d000)
liborc-0.4.so.0 => /lib64/liborc-0.4.so.0 (0x00007f52ee3d1000)
libpcre.so.1 => /lib64/libpcre.so.1 (0x00007f52ee16e000)
libgthread-2.0.so.0 => /lib64/libgthread-2.0.so.0 (0x00007f52edf6b000)
libffi.so.6 => /lib64/libffi.so.6 (0x00007f52edd63000)
libuuid.so.1 => /lib64/libuuid.so.1 (0x00007f52edb5e000)
libgmodule-2.0.so.0 => /lib64/libgmodule-2.0.so.0 (0x00007f52ed959000)
I have read that the segfault may be caused by a shared library being linked with a library that was built with (or is linked with?) a different version of another library but how can I find out which one(s) cause the trouble? Thanks.
Update
If I start the Python interpreter with ltrace then it works (this would have previously caused the segfault as above):
$ ltrace python2
__libc_start_main(0x400710, 1, 0x7fff640c6f38, 0x400810 <unfinished ...>
Py_Main(1, 0x7fff640c6f38, 0x7fff640c6f48, 0x400710Python 2.7.3 (default, Dec 12 2012,07:12:24)
[GCC 4.7.2] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from dolfin import *
>>>
Why is there no segfault when run by ltrace?
Update 2
Turns out configuring via CMake with -DCMAKE_BUILD_TYPE=Debug still allows the optimisation flag '-O' to be passed to g++. I'll try rebuilding with debug symbols (flag '-g') and see how that goes.
Update 3
Compiling with the -g flag makes no difference.
Update 4
Running directly from gdb does not expose the segmentation fault (presumably it uses some form of ltrace, as above):
$ gdb --args python2 -c "import dolfin; print dolfin.__version__"
GNU gdb (GDB) 7.5.1
Copyright (C) 2012 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law. Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-unknown-linux-gnu".
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>...
Reading symbols from /usr/bin/python2...(no debugging symbols found)...done.
(gdb) run
Starting program: /usr/bin/python2 -c import\ dolfin\;\ print\ dolfin.__version__
warning: Could not load shared library symbols for linux-vdso.so.1.
Do you need "set solib-search-path" or "set sysroot"?
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/usr/lib/libthread_db.so.1".
Traceback (most recent call last):
File "/usr/share/gdb/auto-load/usr/lib/libgobject-2.0.so.0.3400.3-gdb.py", line 9, in <module>
from gobject import register
File "/usr/share/glib-2.0/gdb/gobject.py", line 3, in <module>
import gdb.backtrace
ImportError: No module named backtrace
1.0.0+
[Inferior 1 (process 8008) exited normally]
(gdb)
I have tried inspecting the core file through gdb ... but they are always truncated
Use GDB on the live process instead:
gdb --args python2 -c "import dolfin; print dolfin.__version__"
(gdb) run
I had a similar issue with dolfin. The culprit was the nvidia driver. I rolled it back from the latest and things worked again. I had to go through /var/log/messages to find the core dump, run it with gdb. somewhere towards the top were nvidia libraries.
来源：https://stackoverflow.com/questions/13962014/how-to-investigate-python2-segfault-on-imp-load-module