Error when compiling c++11 code in a Matlab mex file - c++

Question

I have downloaded the following code:
CVPR 2014 intersection over union optimization code
cvpr2014-iou-code-1.0.zip
http://research.microsoft.com/en-us/downloads/e164fe21-ef2b-4e34-98c1-4868968abb06/
What I get is an archive with two folders, one called src/ and another one called matlab/. I am running Linux Fedora 19 and I can compile the code in src/ just fine. The problem arises when I try to compile the code in matlab/.
The README says:
Matlab compilation
------------------
From within Matlab, configure the compiler using "mex -setup", then adjust the
paths in matlab\compile_windows.m or matlab/compile_linux.m scripts and run
either "compile_linux.m" or "compile_windows.m" in the "matlab" directory.
More specifically for Linux:
Linux
=====
From within Matlab run "mex -setup", then edit the mexopts.sh file and modify
the settings
CXXFLAGS='-std=c++11 -fopenmp -march=native -D_GNU_SOURCE'
CXXLIBS="$RPATH $MLIBS -lm -lgomp"
CXXOPTIMFLAGS='-Ofast -DNDEBUG'
This will enable OpenMP and C++11 and should work from G++ 4.7 onwards.
From the matlab/ directory, call compile_linux to build all mex files.
So I open matlab and run mex -setup. I answer yes to the question:
>> mex -setup
Options files control which compiler to use, the compiler and link command
options, and the runtime libraries to link against.
Using the 'mex -setup' command selects an options file that is
placed in /user/wok/home/.matlab/R2012b and used by default for 'mex'. An options
file in the current working directory or specified on the command line
overrides the default options file in /user/wok/home/.matlab/R2012b.
To override the default options file, use the 'mex -f' command
(see 'mex -help' for more information).
The options files available for mex are:
1: /opt/matlab2012b/bin/mexopts.sh :
Template Options file for building gcc MEX-files
0: Exit with no changes
Enter the number of the compiler (0-1):
1
Overwrite /user/wok/home/.matlab/R2012b/mexopts.sh ([y]/n)?
y
/opt/matlab2012b/bin/mexopts.sh is being copied to
/user/wok/home/.matlab/R2012b/mexopts.sh
**************************************************************************
Warning: The MATLAB C and Fortran API has changed to support MATLAB
variables with more than 2^32-1 elements. In the near future
you will be required to update your code to utilize the new
API. You can find more information about this at:
http://www.mathworks.com/help/techdoc/matlab_external/bsflnue-1.html
Building with the -largeArrayDims option enables the new API.
**************************************************************************
Then I edit the file /user/wok/home/.matlab/R2012b/mexopts.sh and I follow the instructions from the README:
CXX='g++'
CXXFLAGS='-ansi -D_GNU_SOURCE'
CXXFLAGS="$CXXFLAGS -D_FILE_OFFSET_BITS=64"
CXXFLAGS="$CXXFLAGS -fPIC -pthread"
CXXLIBS="$RPATH $MLIBS -lm"
CXXOPTIMFLAGS='-O -DNDEBUG'
CXXDEBUGFLAGS='-g'
becomes:
CXX='g++'
CXXFLAGS='-std=c++11 -fopenmp -march=native -D_GNU_SOURCE'
CXXLIBS="$RPATH $MLIBS -lm -lgomp"
CXXOPTIMFLAGS='-Ofast -DNDEBUG'
CXXDEBUGFLAGS='-g'
After this step, I open matlab and edit compile_linux.m to add the path to Boost:
% You need to have boost 1.49 or higher installed (package libboost-dev on
% most distributions)
%
% Tested on Ubuntu 13.10, Matlab R2012b, gcc 4.8.1
% TODO: this assumes that boost headers are available in /usr/include, as on
% most systems. If you manually installed boost, please add -I/path/to/boost
mex -v -O ...
-output mex_voc_optimize -I../src ...
-I/user/wok/home/Softwares/Boost_1.54/include/boost ...
mex_voc_optimize.cpp matlab_helpers.cpp ...
-largeArrayDims
Edit: Following the first comment from Praetorian, I have added the -v flag.
Finally I run compile_linux, only to get a long list of errors, which I have shortened and pasted below:
>> compile_linux
-> mexopts.sh sourced from directory (DIR = $PREF_DIR)
FILE = /user/wok/home/.matlab/R2012b/mexopts.sh
----------------------------------------------------------------
-> MATLAB = /opt/matlab2012b
-> CC = gcc
-> CC flags:
CFLAGS = -ansi -D_GNU_SOURCE -fexceptions -fPIC -fno-omit-frame-pointer -pthread
CDEBUGFLAGS = -g
COPTIMFLAGS = -O -DNDEBUG
CLIBS = -Wl,-rpath-link,/opt/matlab2012b/bin/glnxa64 -L/opt/matlab2012b/bin/glnxa64 -lmx -lmex -lmat -lm -lstdc++
arguments =
-> CXX = g++
-> CXX flags:
CXXFLAGS = -ansi -D_GNU_SOURCE -fPIC -fno-omit-frame-pointer -pthread
CXXDEBUGFLAGS = -g
CXXOPTIMFLAGS = -O -DNDEBUG
CXXLIBS = -Wl,-rpath-link,/opt/matlab2012b/bin/glnxa64 -L/opt/matlab2012b/bin/glnxa64 -lmx -lmex -lmat -lm
arguments =
-> FC = gfortran
-> FC flags:
FFLAGS = -fexceptions -fbackslash -fPIC -fno-omit-frame-pointer
FDEBUGFLAGS = -g
FOPTIMFLAGS = -O
FLIBS = -Wl,-rpath-link,/opt/matlab2012b/bin/glnxa64 -L/opt/matlab2012b/bin/glnxa64 -lmx -lmex -lmat -lm
arguments =
-> LD = g++
-> Link flags:
LDFLAGS = -pthread -shared -Wl,--version-script,/opt/matlab2012b/extern/lib/glnxa64/mexFunction.map -Wl,--no-undefined
LDDEBUGFLAGS = -g
LDOPTIMFLAGS = -O
LDEXTENSION = .mexa64
arguments =
-> LDCXX =
-> Link flags:
LDCXXFLAGS =
LDCXXDEBUGFLAGS =
LDCXXOPTIMFLAGS =
LDCXXEXTENSION =
arguments =
----------------------------------------------------------------
Warning: You are using gcc version "4.8.2". The version
currently supported with MEX is "4.4.6".
For a list of currently supported compilers see:
http://www.mathworks.com/support/compilers/current_release/
-> g++ -c -I../src -I/user/wok/home/Softwares/Boost_1.54/include/boost -I/opt/matlab2012b/extern/include -I/opt/matlab2012b/simulink/include -DMATLAB_MEX_FILE -ansi -D_GNU_SOURCE -fPIC -fno-omit-frame-pointer -pthread -O -DNDEBUG "mex_voc_optimize.cpp"
In file included from /usr/include/c++/4.8.2/cstdint:35:0,
from mex_voc_optimize.cpp:8:
/usr/include/c++/4.8.2/bits/c++0x_warning.h:32:2: error: #error This file requires compiler and library support for the ISO C++ 2011 standard. This support is currently experimental, and must be enabled with the -std=c++11 or -std=gnu++11 compiler options.
#error This file requires compiler and library support for the \
^
In file included from ../src/lfp.h:18:0,
from ../src/voc.h:15,
from mex_voc_optimize.cpp:19:
../src/timing.h:15:2: error: ‘chrono’ in namespace ‘std’ does not name a type
std::chrono::time_point<std::chrono::high_resolution_clock> start_time;
^
../src/timing.h: In member function ‘double timer::elapsed_this_period() const’:
../src/timing.h:20:8: error: ‘std::chrono’ has not been declared
std::chrono::time_point<std::chrono::high_resolution_clock> end_time
^
../src/timing.h:20:32: error: ‘std::chrono’ has not been declared
std::chrono::time_point<std::chrono::high_resolution_clock> end_time
until
../src/voc.h:418:31: note: ‘P’ declared here, later in the translation unit
alpha[k_best] += P(j,k_best);
^
../src/voc.h: In instantiation of ‘std::pair<double, double> voc::prediction_function<TFloat>::compute_objective_c(int) const [with TFloat = double]’:
../src/voc.h:328:56: required from ‘double voc::prediction_function<TFloat>::compute_objective() const [with TFloat = double]’
mex_voc_optimize.cpp:250:39: required from here
../src/voc.h:315:17: error: ‘P’ was not declared in this scope
A_c += P(i,c);
^
../src/voc.h:318:17: error: ‘P’ was not declared in this scope
D_c += P(i,c);
^
mex: compile of ' "mex_voc_optimize.cpp"' failed.
Error using mex (line 206)
Unable to complete successfully.
Error in compile_linux (line 9)
mex -O ...
>>
I have tried editing the code to remove every call to chrono (for timers), then to replace unordered_map with map, etc., but it is a pain. I would like to be able to compile the mex file in matlab/ just like I can compile the c++ code in src/

Answer 1

Thanks to Praetorian's comment, I could pinpoint the problem. I had edited the wrong lines in mexopts.sh. Indeed, the CXXFLAGS appears at 3 different places, I had edited the flags at the first place, but it was necessary and sufficient to edit it at the second place (the first place was a decoy).
See for instance:
$ grep -n CXXLIBS /user/wok/home/.matlab/R2012b/mexopts.sh
74: CXXLIBS="$RPATH $MLIBS -lm"
129: CXXLIBS="$RPATH $MLIBS -lm"
199: CXXLIBS="$MLIBS -lstdc++"
So I edited the lines around line 129. The following lines
CXX='g++'
CXXFLAGS='-ansi -D_GNU_SOURCE'
CXXFLAGS="$CXXFLAGS -fPIC -fno-omit-frame-pointer -pthread"
CXXLIBS="$RPATH $MLIBS -lm"
CXXOPTIMFLAGS='-O -DNDEBUG'
CXXDEBUGFLAGS='-g'
become
CXX='g++'
CXXFLAGS='-std=c++11 -fopenmp -march=native -D_GNU_SOURCE'
CXXFLAGS="$CXXFLAGS -fPIC -fno-omit-frame-pointer -pthread"
CXXLIBS="$RPATH $MLIBS -lm -lgomp"
CXXOPTIMFLAGS='-Ofast -DNDEBUG'
CXXDEBUGFLAGS='-g'