MEX file error under Ubuntu 20.04 starting from commit 6346ecd

[andreafarina]

Dear @fangq,
I experience the following error under Matlab2024a when I create mex or cudamex binaries starting from commit 6346ecd:

Invalid MEX-file
'/home/andreafarina/Documents/MCXStudio/MATLAB/mmclab/mmc.mexa64':
/usr/local/MATLAB/R2024a/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.6:
version `GLIBCXX_3.4.29' not found (required by
/home/andreafarina/Documents/MCXStudio/MATLAB/mmclab/mmc.mexa64)

Error in mmclab (line 430)
    [varargout{1:mmcout}] = mmc(cfg);

Error in demo_example_replay (line 44)
[cube, detp, ncfg, seeds] = mmclab(newcfg); % initial simulation

Do you have any hint to solve this?
Thanks a lot
Regards
Andrea

[andreafarina]

An update: the problem seems happening only if compiling with make cudamex. If I use cmake ..-DBUILD_CUDA=on the binary works smmohly.
Regards!

[fangq]

@andreafarina, can you do a make clean before running make cudamex? if the binary was compiled on your own machine, I don't see why the glibc symbol could not be found.

it is possible that those build on my nightly build server maybe have issues like this, but I don't expect locally build binary to see this error.

[andreafarina]

Absolutely, I typically do

make cudamex
make clean
make

to have both the binary and the mexfile. When I run mmclab from matlab with the new binary I get there error...
I've checked if the libstddc++.so.6 that matlab uses is compatible with GLIBCX_3.4.29. Here is the output:
strings /usr/local/MATLAB/R2024a/sys/os/glnxa64/libstdc++.so.6 | grep GLIBCXX
GLIBCXX
GLIBCXX_3.4
GLIBCXX_3.4.1
GLIBCXX_3.4.2
GLIBCXX_3.4.3
GLIBCXX_3.4.4
GLIBCXX_3.4.5
GLIBCXX_3.4.6
GLIBCXX_3.4.7
GLIBCXX_3.4.8
GLIBCXX_3.4.9
GLIBCXX_3.4.10
GLIBCXX_3.4.11
GLIBCXX_3.4.12
GLIBCXX_3.4.13
GLIBCXX_3.4.14
GLIBCXX_3.4.15
GLIBCXX_3.4.16
GLIBCXX_3.4.17
GLIBCXX_3.4.18
GLIBCXX_3.4.19
GLIBCXX_3.4.20
GLIBCXX_3.4.21
GLIBCXX_3.4.22
GLIBCXX_3.4.23
GLIBCXX_3.4.24
GLIBCXX_3.4.25
GLIBCXX_3.4.26
GLIBCXX_3.4.27
GLIBCXX_3.4.28

So I guess that, probably, if I update to MATLAB2024b I can solve the error, or I have to override the use of the matlab library with the one in my linux system. What dou you think?

[fangq]

@andreafarina, does this glibc symbol error also happens to make mex output?

if it only happens on cuda output, then it is possible that the cudart library (libcudart_static) was build using a different version of libstdc++ (compared to matlab or system's version).

if you want to see the detailed linking command, you can manually run the mex command, printed by make cudamex and replace mex by mex -v, it should print out the g++ command used to link the .mex file. you can see where the libstdc++ library is used.

[andreafarina]

@fangq I've tried also with make mex and the same error happens.
By using your suggestion running mex -v followed by the long line I see that a certain point is used (at least I guess) the options:
MWCPPLIB : "/usr/local/MATLAB/R2024a/sys/os/glnxa64/orig/libstdc++.so.6"
I guess the MATLAB version of libstdc++ is used, and in this case, only up to the 3.4.28 version of GLIBCXX is supported. As a workaround, before running matlab, I run the command:
export LD_PRELOAD=/usr/lib/x86_64-linux-gnu
so to force matlab to use the system libstdc++.so.6 library. In this case mmclab runs smoothly both if compiled under cudamex or mex. On my Ubuntu version I've gcc 11 version installed.
Thanks a lot! Anyway using cmake all goes smoothly! :)