Segmentation Fault running MEX on Linux

When starting simulation with a MEX file in Linux Matlab crashes with a segmentation fault. Tested with Matlab 2012b and 2015b (64bit). With Windows it works without problems.

System: CentOS 6.7

My expectation is that there are problems with conflicting libraries. The MEX uses multiple libraries including boost and libstdc++ with newer versions than the libs shipped with Matlab.

I get the following backtrace from gdb from core dump of matlab.

#0  0x00007fd3c8ad4b67 in access_mem ()
 from /opt/matlab/bin/glnxa64/libunwind.so.8
#1  0x00007fd3c8ad5abc in is_plt_entry ()
 from /opt/matlab/bin/glnxa64/libunwind.so.8
#2  0x00007fd3c8ad5c68 in _ULx86_64_step ()
 from /opt/matlab/bin/glnxa64/libunwind.so.8
#3  0x00007fd3ca6e4cf8 in ?? () from /opt/matlab/bin/glnxa64/libmwfl.so
#4  0x00007fd3ca6e4ed4 in fl::diag::stacktrace_base::capture(fl::diag::thread_context const&, unsigned long) () from /opt/matlab/bin/glnxa64/libmwfl.so
#5  0x00007fd3ca6e6fe4 in ?? () from /opt/matlab/bin/glnxa64/libmwfl.so
#6  0x00007fd3c0cb4845 in ?? () from /opt/matlab/bin/glnxa64/libmwmcr.so
#7  0x00007fd3c0cb6740 in ?? () from /opt/matlab/bin/glnxa64/libmwmcr.so
#8  0x00007fd3c0cb6831 in ?? () from /opt/matlab/bin/glnxa64/libmwmcr.so
#9  0x00007fd3c0cb6d64 in ?? () from /opt/matlab/bin/glnxa64/libmwmcr.so
#10 <signal handler called>
#11 0x000000000016ef8e in ?? ()
#12 0x00007fd32e036fdc in _ProcessMexSfunctionCmdLineCall ()
 from /home/user/software/linux64/tools/Matlab/link.mexa64
#13 0x00007fd32e037eb3 in mexFunction ()
 from /home/user/software/linux64/tools/Matlab/link.mexa64
#14 0x00007fd3bc639c4a in mexRunMexFile ()
 from /opt/matlab/bin/glnxa64/libmex.so
#15 0x00007fd3bc636244 in ?? () from /opt/matlab/bin/glnxa64/libmex.so
---Type <return> to continue, or q <return> to quit---
#16 0x00007fd3bc636de4 in ?? () from /opt/matlab/bin/glnxa64/libmex.so
#17 0x00007fd3c09b5dbd in Mfh_file::dispatch_fh_impl(void (Mfh_file::*)(int, mxArray_tag**, int, mxArray_tag**), int, mxArray_tag**, int, mxArray_tag**) ()
 from /opt/matlab/bin/glnxa64/libmwm_dispatcher.so
#18 0x00007fd3c09b6250 in Mfh_file::dispatch_fh(int, mxArray_tag**, int, mxArray_tag**) () from /opt/matlab/bin/glnxa64/libmwm_dispatcher.so
#19 0x00007fd3c09893c5 in mdDoMatlabFcnCall(int, mxArray_tag**, int, mxArray_tag const**, Mfh_MATLAB_fn*, mpLmgrUse) ()
 from /opt/matlab/bin/glnxa64/libmwm_dispatcher.so
#20 0x00007fd35989a701 in CMatlabCommandNoWatermark::execute(bool, mxErrorMode)
  () from /opt/matlab/bin/glnxa64/libmwsl_services.so
#21 0x00007fd35b007b0d in ?? () from /opt/matlab/bin/glnxa64/libmwsimulink.so
#22 0x00007fd35b6ff379 in ?? () from /opt/matlab/bin/glnxa64/libmwsimulink.so
#23 0x00007fd35b70044a in ?? () from /opt/matlab/bin/glnxa64/libmwsimulink.so
#24 0x00007fd35b6ecf01 in ?? () from /opt/matlab/bin/glnxa64/libmwsimulink.so
#25 0x00007fd35b6f18b2 in ?? () from /opt/matlab/bin/glnxa64/libmwsimulink.so
#26 0x00007fd35b6a5b1b in ?? () from /opt/matlab/bin/glnxa64/libmwsimulink.so
#27 0x00007fd35b43d187 in ?? () from /opt/matlab/bin/glnxa64/libmwsimulink.so
#28 0x00007fd35b48918d in ?? () from /opt/matlab/bin/glnxa64/libmwsimulink.so
#29 0x00007fd35b48b215 in ?? () from /opt/matlab/bin/glnxa64/libmwsimulink.so
#30 0x00007fd35ad362c0 in ?? () from /opt/matlab/bin/glnxa64/libmwsimulink.so
#31 0x00007fd35ad36533 in ?? () from /opt/matlab/bin/glnxa64/libmwsimulink.so
#32 0x00007fd35ad3820a in ?? () from /opt/matlab/bin/glnxa64/libmwsimulink.so
---Type <return> to continue, or q <return> to quit---
#33 0x00007fd35acdc4dc in ?? () from /opt/matlab/bin/glnxa64/libmwsimulink.so
#34 0x00007fd35add4d30 in ?? () from /opt/matlab/bin/glnxa64/libmwsimulink.so
#35 0x00007fd35add610b in ?? () from /opt/matlab/bin/glnxa64/libmwsimulink.so
#36 0x00007fd35b7220c3 in ?? () from /opt/matlab/bin/glnxa64/libmwsimulink.so
#37 0x00007fd35b72603b in ?? () from /opt/matlab/bin/glnxa64/libmwsimulink.so
#38 0x00007fd35b727791 in ?? () from /opt/matlab/bin/glnxa64/libmwsimulink.so
#39 0x00007fd35b75d6bc in ?? () from /opt/matlab/bin/glnxa64/libmwsimulink.so
#40 0x00007fd35acbe03b in ?? () from /opt/matlab/bin/glnxa64/libmwsimulink.so
#41 0x00007fd35aabc1c9 in ?? () from /opt/matlab/bin/glnxa64/libmwsimulink.so
#42 0x00007fd3c0973f35 in ?? ()
 from /opt/matlab/bin/glnxa64/libmwm_dispatcher.so
#43 0x00007fd3c095bc57 in Mfh_MATLAB_fn::dispatch_fh(int, mxArray_tag**, int, mxArray_tag**) () from /opt/matlab/bin/glnxa64/libmwm_dispatcher.so
#44 0x00007fd3bb2538af in ?? () from /opt/matlab/bin/glnxa64/libmwm_lxe.so
#45 0x00007fd3bb3777ff in ?? () from /opt/matlab/bin/glnxa64/libmwm_lxe.so
#46 0x00007fd3bb36d47f in ?? () from /opt/matlab/bin/glnxa64/libmwm_lxe.so
#47 0x00007fd3bb33a981 in ?? () from /opt/matlab/bin/glnxa64/libmwm_lxe.so
#48 0x00007fd3baf9cd6c in ?? () from /opt/matlab/bin/glnxa64/libmwm_lxe.so
#49 0x00007fd3baf874c1 in ?? () from /opt/matlab/bin/glnxa64/libmwm_lxe.so
#50 0x00007fd3baf96075 in ?? () from /opt/matlab/bin/glnxa64/libmwm_lxe.so
#51 0x00007fd3bb167033 in ?? () from /opt/matlab/bin/glnxa64/libmwm_lxe.so
#52 0x00007fd3bb12ec40 in ?? () from /opt/matlab/bin/glnxa64/libmwm_lxe.so
#53 0x00007fd3bb131078 in ?? () from /opt/matlab/bin/glnxa64/libmwm_lxe.so
---Type <return> to continue, or q <return> to quit---
#54 0x00007fd3bb131140 in ?? () from /opt/matlab/bin/glnxa64/libmwm_lxe.so
#55 0x00007fd3bb1a86bc in ?? () from /opt/matlab/bin/glnxa64/libmwm_lxe.so
#56 0x00007fd3bb1a8b42 in ?? () from /opt/matlab/bin/glnxa64/libmwm_lxe.so
#57 0x00007fd3bc86d2bc in ?? () from /opt/matlab/bin/glnxa64/libmwbridge.so
#58 0x00007fd3bc86def7 in mnParser() ()
 from /opt/matlab/bin/glnxa64/libmwbridge.so
#59 0x00007fd3c0c9cb4f in mcrInstance::mnParser_on_interpreter_thread() ()
 from /opt/matlab/bin/glnxa64/libmwmcr.so
#60 0x00007fd3c0c89443 in ?? () from /opt/matlab/bin/glnxa64/libmwmcr.so
#61 0x00007fd3c0c89a39 in boost::detail::task_object<void, boost::_bi::bind_t<void, void (*)(boost::function<void ()()> const&), boost::_bi::list1<boost::_bi::value<boost::function<void ()()> > > > >::do_run() ()
 from /opt/matlab/bin/glnxa64/libmwmcr.so
#62 0x00007fd3c0c8af47 in boost::detail::task_base<void>::run() ()
 from /opt/matlab/bin/glnxa64/libmwmcr.so
#63 0x00007fd3c0c8afa7 in ?? () from /opt/matlab/bin/glnxa64/libmwmcr.so
#64 0x00007fd3c0c862fa in ?? () from /opt/matlab/bin/glnxa64/libmwmcr.so
#65 0x00007fd3b51566b6 in ?? () from /opt/matlab/bin/glnxa64/libmwuix.so
#66 0x00007fd3b513c862 in ?? () from /opt/matlab/bin/glnxa64/libmwuix.so
#67 0x00007fd3c161c0df in ?? () from /opt/matlab/bin/glnxa64/libmwservices.so
#68 0x00007fd3c161c24c in ?? () from /opt/matlab/bin/glnxa64/libmwservices.so
#69 0x00007fd3c161dd9f in ?? () from /opt/matlab/bin/glnxa64/libmwservices.so
#70 0x00007fd3c161e84c in svWS_ProcessPendingEvents(int, int, bool) ()
---Type <return> to continue, or q <return> to quit---
 from /opt/matlab/bin/glnxa64/libmwservices.so
#71 0x00007fd3c0c869b8 in ?? () from /opt/matlab/bin/glnxa64/libmwmcr.so
#72 0x00007fd3c0c86cd4 in ?? () from /opt/matlab/bin/glnxa64/libmwmcr.so
#73 0x00007fd3c0c72fed in ?? () from /opt/matlab/bin/glnxa64/libmwmcr.so
#74 0x0000003e5f207aa1 in start_thread () from /lib64/libpthread.so.0
#75 0x0000003e5eae893d in clone () from /lib64/libc.so.6