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C++ Mex file crashes matlab on 64bit linux, but not 32 bit windows, but program runs fine outside Matlab

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Richard Crozier
Richard Crozier on 24 Nov 2011
warning: the code I provide in this question may crash your machine
I have written a mex gateway function to a C++ class. If I compile this mex function on 32Bit windows using R2008a I have no problems. If I compile and run on Matlab R2011a running 64bit Scientific Linux (a version of Red Hat Enterprize Linux) matlab exits with a segfault when the mexfunction is called, although it appears to run about halfway through the program. The C++ class can be compiled and run (with a main function) outside of Matlab on both platforms with no errors. I am using Microsoft Visual C++ Express Edition on the windows machine, and gcc 4.4.5 on the Linux machine.
What is the cause of this and can I fix it?
A zip file containing the code and data files necessary to reproduce the problem can be downloaded from http://www.see.ed.ac.uk/~s0237326/downloads/mexcrash.zip. This zip file contains the .m and .cpp source code, and a text file for testing (Temp.fem). The file fmehsersetup.m shows the commands I am using to compile. The file Test_mexfmesher.m runs the mexfunction with an appropriate input for testing. The mex gateway function is mexfmesher.cpp, it calls the fmesher class which is made up of the files in the fmesher directory.
Below is a backtrace from the segfault:
Program received signal SIGSEGV, Segmentation fault.
0x00007ffff721be36 in ?? () from /opt/matlab-2011a/bin/glnxa64/../../bin/glnxa64/libmwservices.so
(gdb) backtrace
#0 0x00007ffff721be36 in ?? () from /opt/matlab-2011a/bin/glnxa64/../../bin/glnxa64/libmwservices.so
#1 0x00000034daa914f2 in std::basic_ostream<char, std::char_traits<char> >::flush() () from /opt/matlab-2011a/bin/glnxa64/../../bin/glnxa64/libstdc++.so.6
#2 0x00007ffff72302b0 in ioFlush () from /opt/matlab-2011a/bin/glnxa64/../../bin/glnxa64/libmwservices.so
#3 0x00007ffff61303f5 in ?? () from /opt/matlab-2011a/bin/glnxa64/../../bin/glnxa64/libmwm_interpreter.so
#4 0x00007ffff61330ec in ?? () from /opt/matlab-2011a/bin/glnxa64/../../bin/glnxa64/libmwm_interpreter.so
#5 0x00007ffff6130c7a in ?? () from /opt/matlab-2011a/bin/glnxa64/../../bin/glnxa64/libmwm_interpreter.so
#6 0x00007ffff6131741 in ?? () from /opt/matlab-2011a/bin/glnxa64/../../bin/glnxa64/libmwm_interpreter.so
#7 0x00007ffff618a7d9 in ?? () from /opt/matlab-2011a/bin/glnxa64/../../bin/glnxa64/libmwm_interpreter.so
#8 0x00007ffff686d7ef in Mfh_file::dispatch_fh(int, mxArray_tag**, int, mxArray_tag**) () from /opt/matlab-2011a/bin/glnxa64/../../bin/glnxa64/libmwm_dispatcher.so
#9 0x00007ffff61731f0 in ?? () from /opt/matlab-2011a/bin/glnxa64/../../bin/glnxa64/libmwm_interpreter.so
#10 0x00007ffff6114975 in ?? () from /opt/matlab-2011a/bin/glnxa64/../../bin/glnxa64/libmwm_interpreter.so
#11 0x00007ffff612e96e in ?? () from /opt/matlab-2011a/bin/glnxa64/../../bin/glnxa64/libmwm_interpreter.so
#12 0x00007ffff61330ec in ?? () from /opt/matlab-2011a/bin/glnxa64/../../bin/glnxa64/libmwm_interpreter.so
#13 0x00007ffff6130c7a in ?? () from /opt/matlab-2011a/bin/glnxa64/../../bin/glnxa64/libmwm_interpreter.so
#14 0x00007ffff6131741 in ?? () from /opt/matlab-2011a/bin/glnxa64/../../bin/glnxa64/libmwm_interpreter.so
#15 0x00007ffff618a7d9 in ?? () from /opt/matlab-2011a/bin/glnxa64/../../bin/glnxa64/libmwm_interpreter.so
#16 0x00007ffff686d7ef in Mfh_file::dispatch_fh(int, mxArray_tag**, int, mxArray_tag**) () from /opt/matlab-2011a/bin/glnxa64/../../bin/glnxa64/libmwm_dispatcher.so
#17 0x00007ffff61669b2 in ?? () from /opt/matlab-2011a/bin/glnxa64/../../bin/glnxa64/libmwm_interpreter.so
#18 0x00007ffff6128e13 in ?? () from /opt/matlab-2011a/bin/glnxa64/../../bin/glnxa64/libmwm_interpreter.so
#19 0x00007ffff6127eb7 in ?? () from /opt/matlab-2011a/bin/glnxa64/../../bin/glnxa64/libmwm_interpreter.so
#20 0x00007ffff6128397 in ?? () from /opt/matlab-2011a/bin/glnxa64/../../bin/glnxa64/libmwm_interpreter.so
#21 0x00007ffff6d378fe in ?? () from /opt/matlab-2011a/bin/glnxa64/../../bin/glnxa64/libmwbridge.so
#22 0x00007ffff6d384ae in mnParser () from /opt/matlab-2011a/bin/glnxa64/../../bin/glnxa64/libmwbridge.so
#23 0x00007ffff6ae0d39 in mcrInstance::mnParser_on_interpreter_thread() () from /opt/matlab-2011a/bin/glnxa64/../../bin/glnxa64/libmwmcr.so
#24 0x00007ffff6ac3db2 in ?? () from /opt/matlab-2011a/bin/glnxa64/../../bin/glnxa64/libmwmcr.so
#25 0x00007ffff6ac3ec0 in ?? () from /opt/matlab-2011a/bin/glnxa64/../../bin/glnxa64/libmwmcr.so
#26 0x00007fffee8badb6 in ?? () from /opt/matlab-2011a/bin/glnxa64/../../bin/glnxa64/../../bin/glnxa64/libmwuix.so
#27 0x00007fffee8c413d in ?? () from /opt/matlab-2011a/bin/glnxa64/../../bin/glnxa64/../../bin/glnxa64/libmwuix.so
#28 0x00007fffef3110bd in sysq::during_F<boost::weak_ptr<sysq::ws_ppeHook>, boost::shared_ptr<sysq::ws_ppeHook> > std::for_each<__gnu_cxx::__normal_iterator<boost::weak_ptr<sysq::ws_ppeHook>*, std::vector<boost::weak_ptr<sysq::ws_ppeHook>, std::allocator<boost::weak_ptr<sysq::ws_ppeHook> > > >, sysq::during_F<boost::weak_ptr<sysq::ws_ppeHook>, boost::shared_ptr<sysq::ws_ppeHook> > >(__gnu_cxx::__normal_iterator<boost::weak_ptr<sysq::ws_ppeHook>*, std::vector<boost::weak_ptr<sysq::ws_ppeHook>, std::allocator<boost::weak_ptr<sysq::ws_ppeHook> > > >, __gnu_cxx::__normal_iterator<boost::weak_ptr<sysq::ws_ppeHook>*, std::vector<boost::weak_ptr<sysq::ws_ppeHook>, std::allocator<boost::weak_ptr<sysq::ws_ppeHook> > > >, sysq::during_F<boost::weak_ptr<sysq::ws_ppeHook>, boost::shared_ptr<sysq::ws_ppeHook> >) ()
from /opt/matlab-2011a/bin/glnxa64/../../bin/glnxa64/../../bin/glnxa64/libuij.so
#29 0x00007fffef312989 in ?? () from /opt/matlab-2011a/bin/glnxa64/../../bin/glnxa64/../../bin/glnxa64/libuij.so
#30 0x00007fffef30f4ae in svWS_ProcessPendingEvents(int, int, bool) () from /opt/matlab-2011a/bin/glnxa64/../../bin/glnxa64/../../bin/glnxa64/libuij.so
#31 0x00007ffff6ac21c7 in ?? () from /opt/matlab-2011a/bin/glnxa64/../../bin/glnxa64/libmwmcr.so
#32 0x00007ffff6ac260a in ?? () from /opt/matlab-2011a/bin/glnxa64/../../bin/glnxa64/libmwmcr.so
#33 0x00007ffff6ac2d6f in ?? () from /opt/matlab-2011a/bin/glnxa64/../../bin/glnxa64/libmwmcr.so
#34 0x00000034d7a077e1 in start_thread () from /lib64/libpthread.so.0
#35 0x00000034d72e573d in clone () from /lib64/libc.so.6
(gdb) quit

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Accepted Answer

Jan
Jan on 24 Nov 2011
I try to run your fmeshersetup with MSVC 2008. I get these errors and warnings from the compiler:
FMESHER\fmesher.cpp(103) : warning C4800: 'int' : forcing value to bool 'true' or 'false' (performance warning)
FMESHER\fmesher.cpp(105) : warning C4800: 'int' : forcing value to bool 'true' or 'false' (performance warning)
FMESHER\fmesher.cpp(439) : error C2589: '(' : illegal token on right side of '::'
FMESHER\fmesher.cpp(439) : error C2059: syntax error : '::'
FMESHER\fmesher.cpp(626) : warning C4267: '=' : conversion from 'size_t' to 'int', possible loss of data
FMESHER\fmesher.cpp(646) : warning C4267: '=' : conversion from 'size_t' to 'int', possible loss of data
FMESHER\fmesher.cpp(678) : warning C4267: '=' : conversion from 'size_t' to 'int', possible loss of data
FMESHER\fmesher.cpp(883) : warning C4267: '=' : conversion from 'size_t' to 'int', possible loss of data
FMESHER\fmesher.cpp(895) : warning C4267: '=' : conversion from 'size_t' to 'int', possible loss of data
FMESHER\fmesher.cpp(935) : warning C4267: '=' : conversion from 'size_t' to 'int', possible loss of data
FMESHER\fmesher.cpp(941) : warning C4267: '=' : conversion from 'size_t' to 'int', possible loss of data
FMESHER\fmesher.cpp(998) : warning C4267: '=' : conversion from 'size_t' to 'int', possible loss of data
FMESHER\fmesher.cpp(1004) : warning C4267: '=' : conversion from 'size_t' to 'int', possible loss of data
FMESHER\fmesher.cpp(1110) : warning C4267: '=' : conversion from 'size_t' to 'int', possible loss of data
FMESHER\fmesher.cpp(1116) : warning C4267: '=' : conversion from 'size_t' to 'int', possible loss of data
FMESHER\fmesher.cpp(1251) : warning C4267: '=' : conversion from 'size_t' to 'int', possible loss of data
FMESHER\fmesher.cpp(1257) : warning C4267: '=' : conversion from 'size_t' to 'int', possible loss of data
FMESHER\fmesher.cpp(1337) : warning C4800: 'int' : forcing value to bool 'true' or 'false' (performance warning)
FMESHER\fmesher.cpp(1371) : warning C4800: 'int' : forcing value to bool 'true' or 'false' (performance warning)
FMESHER\fmesher.cpp(1447) : warning C4800: 'int' : forcing value to bool 'true' or 'false' (performance warning)
The error in line 439 concerns "std::min" and can be fixed easily. Afterwards the next run of the setup reveals, that there are a lot of size_t to int conversions in writepoly.cpp also.
I currently have the impression, that your function fails in writepoly. I do some further tests, but please do not wait for me.
EDITED: The function crashs in writepoly.cpp->Line 1025. You try to free memory which points to NULL, e.g. in.pointattributelist, out.pointattributelist, out.neighborlist, out.segmentlist, out.segmentmarkerlist.
On one hand this let my Matlab crash such, that it cannot be restarted without restarting the OS. On the other hand it is not smart to call free() without testing for NULL. If I see, that the success of malloc() is not checked also, I would not trust this software.

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Richard Crozier
Richard Crozier on 24 Nov 2011
Re: your edit, apologies if this has caused you any problems, having to restart your whole system! I have not experienced this on either windows or Linux, maybe I've just been lucky. I will look into the correct way to deal with this memory allocation.
Jan
Jan on 24 Nov 2011
@Richard: I do not test foreign C-code on a productive machine, therefore the crashs are ok.
Of course it would be smart, if free() checks for NULL itself. But a careful C-programmer would not rely of the library functions to catch this. Most likely other StdC libs include such a check.
The warnings do not appear under 32 bit systems, because the size_t to int causes troubles in 64 bit systems only.
Richard Crozier
Richard Crozier on 24 Nov 2011
@Jan, thanks again for the help, I have also added a warning to others who might download the code to the question.

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More Answers (1)

Jan
Jan on 24 Nov 2011
You've posted 1.7MB source code. You cannot expect, that somebody debugs this large code for you. The conversion fom 32 to 64 bit systems is critical, if the data model does not consider this and assumes that int and pointers are signed INT32 values.
If you have the impression, that the program appears to run about halfway, please explain, why you think so. Either use a debugger or insert some output until you find the line causing the crash.

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Richard Crozier
Richard Crozier on 24 Nov 2011
Actually, to correct myself the data file was not this big, but the source does make up just under a MB.
Jan
Jan on 24 Nov 2011
If I unzip the file, I get 1'796'481 bytes in C files inside \temp\fmesher, while the file "Temp.fem" has only 10kB.
Richard Crozier
Richard Crozier on 24 Nov 2011
There were a few other unnessessary c and cpp files now removed. On another forum some has suggested the problem may be due to the fact that matlab use its own libstdc++ (stored in /opt/matlab-2011a/bin/glnxa64/libstdc++.so.6) instead of the main one (stored in /usr/lib/x86_64-linux-gnu/). Unfortunately I am not a sudoer and cannot force matlab to use the main libstdc++ on my system.

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