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Protobuf crashes Mex-file

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Torsten Knüppel
Torsten Knüppel on 2 Mar 2019
Edited: Martijn on 23 Dec 2019
Dear all,
I would like to write a Mex-function that uses protobuf. Unfortunately, my program crashes after calling clear all or recompiling.
In order to illustrate my problem I wrote a reduced version. It consists of three files:
  1. An empty MEX-file called protoTest.cpp
#include "mex.hpp"
#include "mexAdapter.hpp"
class MexFunction : public matlab::mex::Function {
void operator()(matlab::mex::ArgumentList outputs, matlab::mex::ArgumentList inputs) {
2. A very simple protobuf file called data3d.proto
syntax = "proto2";
package testproto;
message Data3d {
required float x = 1;
required float y = 2;
required float z = 3;
3. A Matlab script for compiling and running the whole thing
% Run protobuf compiler
system('protoc --cpp_out=./ ./*.proto');
% Compile mex file
mex('protoTest.cpp', '', '-lprotobuf');
% Run mex function
% Clear all
clear all
% Run mex function again -> Crash
disp('Run again..');
I have found similar error descriptions online, but in most cases memory leaks were the cause. I don't see this here.
Some things I have tried so far:
  • link the static version of libprotobuf -> didn't manage to get it working
  • compile the protobuf file into an object file first and afterwards link it to the mex-file -> no difference
  • play around with compiler/linker settings - no success, but I have too little experience with that and my attempts were mostly try-and-error based.
Any suggestions on how to make this work would be greatly appreciated.
Thanks in advance,
Torsten Knüppel
Torsten Knüppel on 8 Apr 2019
Hi Nishanth,
unfortunately not.
There is something mentioned about problems with clashing symbols on the CMake documentation page for their FindMatlab package ( - but I'm not sure that this is relevant here. Adding the given linker options didn't solve the problem for me.
Best regards
Sebastian Baur
Sebastian Baur on 12 Apr 2019
Edited: Sebastian Baur on 12 Apr 2019
I just saw a workaround to the clear all / clear mex problem. Using
in your mex file will make it unresponsive to clear commands. This way you can use Matlab normally after your first call to your mex function.
It reinforces the need for a restart of Matlab for recompiling though, as
will just bring you back to crashing after clear.

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Answers (1)

Martijn on 23 Dec 2019
Edited: Martijn on 23 Dec 2019
It appears that this a more generic limitation of protocol buffers, see for example:
If that is indeed true and protocol buffers simply has not been designed to be loaded multiple times in a single process by "loading, unloading and then again loading" a dynamic library which was linked against protocol buffers, then I do not think it is feasible you can somehow fix/resolve this limitation in a MEX-file (which is in fact a dynamic library; which is loaded on the first call, unloaded by clear mex and then loaded again on the next call). What you might be able to do however is:
1. Prevent your MEX-file from being unloaded by the call to clear mex which is indeed accomplished by a mexLock() as mentiond in Sebastian's comment.
2. Try running your MEX-file in an external mexhost such that you can completely terminate and restart this mexhost process whenever you need to reload your MEX-file.


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