Segmentation Fault on OS X #23

peterswang · 2015-08-04T23:01:30Z

On 10.10.3, with Python 2.7.10 and boost and boost-python 1.58.0. Built using:

cmake .. -DCMAKE_BUILD_TYPE=Release -DDATA_DIR=~/test_images/coco-master/images/val2014 -DUSE_PYTHON=2
make -j9

Saw some warnings only, such as:
In file included from /Users/peterwang/CPP_Resources/lpo-release/lib/crf/crf.cpp:31:
/Users/peterwang/CPP_Resources/lpo-release/external/ibfs/ibfs.h:161:2: warning: 'Node' defined as a class here but previously declared as a struct
[-Wmismatched-tags]
class Node
^
/Users/peterwang/CPP_Resources/lpo-release/external/ibfs/ibfs.h:150:2: note: did you mean class here?
struct Node;
^~~~~~
class

Tried:

python train_lpo.py -f0 0.2 ../models/lpo_VOC_0.2.dat
and got: Segmentation fault: 11
This appears to have crashed on "from python.lpo import *" in lpo.py.

Crash report contained:
...
Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0 ??? 000000000000000000 0 + 0
1 org.python.python 0x0000000103d150dd PyEval_GetGlobals + 23
2 org.python.python 0x0000000103d2462b PyImport_Import + 137
3 org.python.python 0x0000000103d22d27 PyImport_ImportModule + 31
4 lpo.so 0x00000001033f45a3 init_numpy() + 19
5 lpo.so 0x00000001033f4779 defineUtil() + 25
6 lpo.so 0x00000001033f4499 init_module_lpo() + 9
7 libboost_python-mt.dylib 0x0000000103c36391 boost::python::handle_exception_impl(boost::function0) + 81
8 libboost_python-mt.dylib 0x0000000103c373b9 boost::python::detail::init_module(char const_, void (_)()) + 121
9 org.python.python 0x0000000101836327 _PyImport_LoadDynamicModule + 140
...

Saw the note in external/boost/readme.txt:
"In order to use a non-system boost library copy the "boost" and "libs" directory of a recent boost release (eg 1.57) here."

And in build/lib/python/CMakeFiles/lpo.dir/depend.make:
...
lib/python/CMakeFiles/lpo.dir/boost.cpp.o: /usr/local/include/boost/array.hpp
lib/python/CMakeFiles/lpo.dir/boost.cpp.o: /usr/local/include/boost/assert.hpp
lib/python/CMakeFiles/lpo.dir/boost.cpp.o: /usr/local/include/boost/bind.hpp
...

These seem to suggest the seg fault was due to boost version mismatch?

Is it sufficient to just do:

ln -s /usr/local/Cellar/boost/1.58.0 external/boost/
ln -s /usr/local/Cellar/boost/1.58.0/lib external/boost/libs

Or something else?

BTW, boost and boost-python were installed as part of setting up Caffe. The Caffe ImageNet model ran successfully when invoked from a Python test app.

Thanks for any light you could help shed.

philkr · 2015-08-07T04:06:51Z

I don't think that the struct / class thing causes the segfault. Can you try to build it using cmake -DCMAKE_BUILD_TYPE=Debug, and then run either gdb or lldm on it?

peterswang · 2015-08-09T07:28:25Z

Rebuilt with cmake -DCMAKE_BUILD_TYPE=Debug and run under lldb:

lldb -- python train_lpo.py -f0 0.2 ../models/lpo_VOC_0.2.dat
(lldb) target create "python"
Current executable set to 'python' (x86_64).
(lldb) settings set -- target.run-args "train_lpo.py" "-f0" "0.2" "../models/lpo_VOC_0.2.dat"
(lldb) breakpoint set -f boost.cpp -l 27
Breakpoint 1: no locations (pending).
WARNING: Unable to resolve breakpoint to any actual locations.
(lldb) r
Process 91895 launched: '/usr/local/bin/python' (x86_64)
Process 91895 stopped

thread matlab cmakelists GOP is included #1: tid = 0x67a797, 0x00007fff5fc01000 dyld_dyld_start, stop reason = exec frame #0: 0x00007fff5fc01000 dyld_dyld_start
dyld`_dyld_start:
-> 0x7fff5fc01000 <+0>: popq %rdi
0x7fff5fc01001 <+1>: pushq $0x0
0x7fff5fc01003 <+3>: movq %rsp, %rbp
0x7fff5fc01006 <+6>: andq $-0x10, %rsp
(lldb) br list
Current breakpoints:
1: file = 'boost.cpp', line = 27, locations = 0 (pending)

(lldb) br set -f contour.cpp -l 27
Breakpoint 2: no locations (pending).
WARNING: Unable to resolve breakpoint to any actual locations.
(lldb) br set -n BOOST_PYTHON_MODULE
Breakpoint 3: no locations (pending).
WARNING: Unable to resolve breakpoint to any actual locations.
(lldb) c
Process 91895 resuming
1 location added to breakpoint 2
Process 91895 stopped

thread matlab cmakelists GOP is included #1: tid = 0x67a797, 0x0000000000000000, queue = 'com.apple.main-thread', stop reason = EXC_BAD_ACCESS (code=1, address=0x0)
frame #0: 0x0000000000000000
error: memory read failed for 0x0

I've not debugged Python wrapper using lldb, nor gdb, before. Trying to set breakpoints directly in C++ files while running a Python wrapper didn't work.

Could you advise on how to track this down in lldb?

philkr · 2015-08-09T14:38:52Z

I think it added the breakpoints once lpo was loaded in python. See 1 location added to breakpoint 2.I think you're almost there, what is the backtrace for the EXC_BAD_ACCESS?

peterswang · 2015-08-11T07:13:40Z

Thanks for pointing lldb msg. Here's the debug log & backtrace:

$ lldb -- python train_lpo.py -f0 0.2 ../models/lpo_VOC_0.2.dat
(lldb) target create "python"
Current executable set to 'python' (x86_64).
(lldb) settings set -- target.run-args "train_lpo.py" "-f0" "0.2" "../models/lpo_VOC_0.2.dat"
(lldb) br set -f lpo.cpp -l 38
Breakpoint 1: no locations (pending).
WARNING: Unable to resolve breakpoint to any actual locations.
(lldb) r
Process 7734 launched: '/usr/local/bin/python' (x86_64)
Process 7734 stopped

thread matlab cmakelists GOP is included #1: tid = 0x2ab3c, 0x00007fff5fc01000 dyld_dyld_start, stop reason = exec frame #0: 0x00007fff5fc01000 dyld_dyld_start
dyld`_dyld_start:
-> 0x7fff5fc01000 <+0>: popq %rdi
0x7fff5fc01001 <+1>: pushq $0x0
0x7fff5fc01003 <+3>: movq %rsp, %rbp
0x7fff5fc01006 <+6>: andq $-0x10, %rsp
(lldb) c
Process 7734 resuming
3 locations added to breakpoint 1
Process 7734 stopped
thread matlab cmakelists GOP is included #1: tid = 0x2ab3c, 0x0000000103165a14 lpo.soinit_module_lpo() + 4 at lpo.cpp:38, queue = 'com.apple.main-thread', stop reason = breakpoint 1.1 frame #0: 0x0000000103165a14 lpo.soinit_module_lpo() + 4 at lpo.cpp:38
35
36 BOOST_PYTHON_MODULE(lpo) {
37 /************ Util **_/
-> 38 defineUtil();
39 #ifdef USE_DATASET
40 /_* Dataset *************/
41 defineDataset();
(lldb) s
Process 7734 stopped
thread matlab cmakelists GOP is included #1: tid = 0x2ab3c, 0x0000000103166524 lpo.sodefineUtil() + 4 at util.cpp:258, queue = 'com.apple.main-thread', stop reason = step in frame #0: 0x0000000103166524 lpo.sodefineUtil() + 4 at util.cpp:258
255 BOOST_PYTHON_FUNCTION_OVERLOADS(rasterize2,rasterize,1,2)
256 void defineUtil() {
257 // NOTE: This file has a ton of macros and templates, so it's going to take a while to compile ...
-> 258 init_numpy();
259 boost::python::numeric::array::set_module_and_type("numpy", "ndarray");
260
261 register_exception_translator(&translateAssertException);
(lldb) s
Process 7734 stopped
thread matlab cmakelists GOP is included #1: tid = 0x2ab3c, 0x00000001031661e4 lpo.soinit_numpy() + 4 at util.cpp:250, queue = 'com.apple.main-thread', stop reason = step in frame #0: 0x00000001031661e4 lpo.soinit_numpy() + 4 at util.cpp:250
247 }
248 #else
249 void init_numpy() {
-> 250 import_array();
251 }
252 #endif
253
(lldb) s
Process 7734 stopped
thread matlab cmakelists GOP is included #1: tid = 0x2ab3c, 0x000000010316622f lpo.so_import_array() + 15 at __multiarray_api.h:1632, queue = 'com.apple.main-thread', stop reason = step in frame #0: 0x000000010316622f lpo.so_import_array() + 15 at __multiarray_api.h:1632
1629 _import_array(void)
1630 {
1631 int st;
-> 1632 PyObject *numpy = PyImport_ImportModule("numpy.core.multiarray");
1633 PyObject *c_api = NULL;
1634
1635 if (numpy == NULL) {
(lldb) s
Process 7734 stopped
thread matlab cmakelists GOP is included #1: tid = 0x2ab3c, 0x0000000000000000, queue = 'com.apple.main-thread', stop reason = EXC_BAD_ACCESS (code=1, address=0x0)
frame #0: 0x0000000000000000
error: memory read failed for 0x0
(lldb) bt
thread matlab cmakelists GOP is included #1: tid = 0x1d5d9, 0x0000000000000000, queue = 'com.apple.main-thread', stop reason = EXC_BAD_ACCESS (code=1, address=0x0)
- frame #0: 0x0000000000000000
  frame matlab cmakelists GOP is included #1: 0x00000001033780dd PythonPyEval_GetGlobals + 23 frame #2: 0x000000010338762b PythonPyImport_Import + 137
  frame ImportError: No module named python.lpo #3: 0x0000000103385d27 PythonPyImport_ImportModule + 31 frame #4: 0x0000000104003234 lpo.so_import_array() + 20 at __multiarray_api.h:1632
  frame How to solve 'global name 'FileNotFoundError' is not defined" ? #5: 0x00000001040031e9 lpo.soinit_numpy() + 9 at util.cpp:250 frame #6: 0x0000000104003530 lpo.sodefineUtil() + 16 at util.cpp:258
  frame eval_box raises exception with demonstration models #7: 0x0000000104002a19 lpo.soinit_module_lpo() + 9 at lpo.cpp:38 frame #8: 0x0000000103299391 libboost_python-mt.dylibboost::python::handle_exception_impl(boost::function0) + 81
  frame More feedback to the user during load & computing #9: 0x000000010329a3b9 libboost_python-mt.dylibboost::python::detail::init_module(char const*, void (*)()) + 121 frame #10: 0x00000001040029fb lpo.soinitlpo + 27 at lpo.cpp:36
  ....

So, it crashed when executing:
PyObject *numpy = PyImport_ImportModule("numpy.core.multiarray");

The Python 2.7.10 reference shows:
PyObject* PyImport_ImportModule(const char *name)

Does this mean there's a bug in the numpy/core/include/numpy/__multiarray_api.h?

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Segmentation Fault on OS X #23

Segmentation Fault on OS X #23

peterswang commented Aug 4, 2015

philkr commented Aug 7, 2015

peterswang commented Aug 9, 2015

philkr commented Aug 9, 2015

peterswang commented Aug 11, 2015

Segmentation Fault on OS X #23

Segmentation Fault on OS X #23

Comments

peterswang commented Aug 4, 2015

philkr commented Aug 7, 2015

peterswang commented Aug 9, 2015

philkr commented Aug 9, 2015

peterswang commented Aug 11, 2015