[FieldTrip] mexa64 files

[Dr. Burkhard Maess]

Dear Fieldtrip-Team,

since the upgrade to Linux 6.1.0-32-amd64 my copies of fieldtrip keeps 
rejecting to work due to this error message:

Invalid MEX-file 
'/software/fieldtrip-20201117/fileio/private/ft_getopt.mexa64':
/software/rothirsch2/fieldtrip-20201117/fileio/private/ft_getopt.mexa64: 
failed to map segment from shared object
Error in ft_read_header (line 182)
headerformat   = ft_getopt(varargin, 'headerformat');

I am using matlab R2024b currently, but have tested older version in 
respect to the above problem. None if the versions R2022a, R2024a or 
R2024b can use the mex-files anymore.  They were usuable with an older 
installation of the linux machine. However, after the system update it 
does not work. The version of fieldtrip does not matter either. So, I 
read on your website and considered recompiling the mex files a good idea.

However, this was not completed without errors. It stopped while 
compiling with g++ (see below). Do you have any hints how to get around 
this problem?

Thank you very much and best wishes,

Burkhard


in matlab (R2024b)

 >> ft_compile_mex(true)
Compiling MEX file compat/matlablt2010b/@uint64/abs ...
Building with 'gcc'.
MEX completed successfully.
Compiling MEX file compat/matlablt2010b/@uint64/min ...
Building with 'gcc'.
MEX completed successfully.
# .... lots of successes :)

Compiling MEX file src/read_24bit ...
Building with 'gcc'.
MEX completed successfully.
Compiling MEX file src/lmoutr ...
Building with 'gcc'.
/nobackup/rothirsch2/fieldtrip-20201117/src/geometry.c: In function 
‘ltrisect’:
/nobackup/rothirsch2/fieldtrip-20201117/src/geometry.c:176:15: warning: 
implicit declaration of function ‘mxGetNaN’ 
[-Wimplicit-function-declaration]
   176 |     proj[0] = mxGetNaN();
       |               ^~~~~~~~
MEX completed successfully.
Compiling MEX file src/ltrisect ...
Building with 'gcc'.
/nobackup/rothirsch2/fieldtrip-20201117/src/geometry.c: In function 
‘ltrisect’:
/nobackup/rothirsch2/fieldtrip-20201117/src/geometry.c:176:15: warning: 
implicit declaration of function ‘mxGetNaN’ 
[-Wimplicit-function-declaration]
   176 |     proj[0] = mxGetNaN();
       |               ^~~~~~~~

MEX completed successfully.
Compiling MEX file src/plinproj ...
Building with 'gcc'.
/nobackup/rothirsch2/fieldtrip-20201117/src/geometry.c: In function 
‘ltrisect’:
/nobackup/rothirsch2/fieldtrip-20201117/src/geometry.c:176:15: warning: 
implicit declaration of function ‘mxGetNaN’ 
[-Wimplicit-function-declaration]
   176 |     proj[0] = mxGetNaN();
       |               ^~~~~~~~

MEX completed successfully.
ompiling MEX file src/ptriproj ...
Building with 'gcc'.
/nobackup/rothirsch2/fieldtrip-20201117/src/geometry.c: In function 
‘ltrisect’:
/nobackup/rothirsch2/fieldtrip-20201117/src/geometry.c:176:15: warning: 
implicit declaration of function ‘mxGetNaN’ 
[-Wimplicit-function-declaration]
   176 |     proj[0] = mxGetNaN();
       |               ^~~~~~~~

MEX completed successfully.
Compiling MEX file src/routlm ...
Building with 'gcc'.
/nobackup/rothirsch2/fieldtrip-20201117/src/geometry.c: In function 
‘ltrisect’:
/nobackup/rothirsch2/fieldtrip-20201117/src/geometry.c:176:15: warning: 
implicit declaration of function ‘mxGetNaN’ 
[-Wimplicit-function-declaration]
   176 |     proj[0] = mxGetNaN();
       |               ^~~~~~~~

MEX completed successfully.
Compiling MEX file src/solid_angle ...
Building with 'gcc'.
/nobackup/rothirsch2/fieldtrip-20201117/src/geometry.c: In function 
‘ltrisect’:
/nobackup/rothirsch2/fieldtrip-20201117/src/geometry.c:176:15: warning: 
implicit declaration of function ‘mxGetNaN’ 
[-Wimplicit-function-declaration]
   176 |     proj[0] = mxGetNaN();
       |               ^~~~~~~~

MEX completed successfully.
Compiling MEX file src/rfbevent ...
Building with 'gcc'.
MEX completed successfully.
# ... lots of successes again

Compiling MEX file external/fileexchange/CalcMD5 ...
Building with 'gcc'.
MEX completed successfully.
Compiling MEX file src/mxSerialize_cpp ...
Building with 'g++'.
Error using ft_compile_mex>compile_mex_list (line 217)
Error using mex
/nobackup/rothirsch2/fieldtrip-20201117/src/mxSerialize_cpp.cpp:10:1: 
error: ‘EXTERN_C’ does not name a type
    10 | EXTERN_C mxArray* mxSerialize(mxArray const *);
       | ^~~~~~~~
/nobackup/rothirsch2/fieldtrip-20201117/src/mxSerialize_cpp.cpp:11:1: 
error: ‘EXTERN_C’ does not name a type
    11 | EXTERN_C mxArray* mxDeserialize(const void *, size_t);
       | ^~~~~~~~
/nobackup/rothirsch2/fieldtrip-20201117/src/mxSerialize_cpp.cpp: In 
function ‘void mexFunction(int, mxArray**, int, const
mxArray**)’:
/nobackup/rothirsch2/fieldtrip-20201117/src/mxSerialize_cpp.cpp:22:31: 
error: ‘mxSerialize’ was not declared in this scope
    22 |         plhs[0] = (mxArray *) mxSerialize(prhs[0]);
       |                               ^~~~~~~~~~~


Error in ft_compile_mex (line 114)
   compile_mex_list(L, ftpath, force);
   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

-- 
Dr. Burkhard Maess
Brain Networks (@brainnetleipzig)
Max Planck Institute for Human Cognitive and Brain Sciences
Stephanstr. 1a, D-04301 Leipzig, Germany
phone/fax: +49 341 9940-2526/-2511   https://www.cbs.mpg.de/~maess

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