I am trying to create mex files for using some C++ code in Matlab, but running into an error with the compilation which, I guess, goes beyond Matlab. I am on Windows.
The example I'm struggling with is the Mex Interface example in the Armadillo library for linear algebra, available: here. The Matlab file is what I'm running and it looks like this:
% Compile the demo as a mex file
mex -lgfortran armaMex_demo.cpp -I/path/to/armadillo
The error I get is:
Error using mex
MEX cannot find library 'gfortran' specified with the -l option.
MEX looks for a file with one of the names:
libgfortran.lib
gfortran.lib
Please specify the path to this library with the -L option.
Trying some things I found online, I installed MinGW and cygwin64 and added the paths to their bin folders to my PATH variable. Before that I also installed MinGW via Matlab.
My question: How do I get it to link with gfortran?
If I search C:for libgfortran I find some files, but none of them have the file ending .lib (but e.g. .dll and .a) and if I search for gfortranI find some .exe files but again, no .lib file. If I run gfortran -dumpversion in the terminal, I get 4.9.3 back, so it is obviously there somewhere. I am obviously missing something, and this is really not my forte, to say the least.
Related
I had problems making mexmaci64 files using Mex from both jpeg_read.c and jpeg_write.c from jpeg toolbox. I asked my question here and the problem for jpeg_read solved.
but I still have a different error when I compile jpeg_write.c.
everything is the same and I didn't change any path or anything.
I don't understand why Matlab console returns this error.
Is this familiar to anybody? please let me know.
>> mex -compatibleArrayDims -I/usr/local/Cellar/jpeg/9d/include jpeg_write.c -L/usr/local/Cellar/jpeg/9d/lib -ljpeg
Building with 'Xcode with Clang'.
Error using mex
/Users/folder/jpeg_toolbox/jpeg_write.c:56:10: fatal error: 'jpegint.h' file not found
#include <jpegint.h>
^~~~~~~~~~~
1 error generated.
First off:
By pointing at the /usr/local/Cellar/jpeg/<version>/include location of the jpeg or other libraries, you're dependent on the specific version that is currently installed. You probably want to use /usr/local/opt/jpeg/include/ etc instead. /usr/local/opt is where Homebrew exposes its non-versioned presentations of its installed package contents.
So:
mex -compatibleArrayDims -I/usr/local/Cellar/jpeg/9d/include ...
This is pointing at the jpeg library. Does the jpeg library supply jpegint.h?
$ ls /usr/local/Cellar/jpeg/9d/include/
jconfig.h jerror.h jmorecfg.h jpeglib.h
Nope. So that's why it's not found. So you have to figure out where you can actually get jpegint.h from. Hit Google and consult your documentation to figure out what library you're actually trying to pull jpegint.h from, and pull that in, too, with the appropriate -I, -L, and -l flags.
If you think you have it already installed, you can use find /usr/local/Cellar -name jpegint.h to look for it. I found it in the gdcm package.
[~] $ find /usr/local/Cellar -name jpegint.h
/usr/local/Cellar/gdcm/3.0.8_1/include/gdcm-3.0/gdcmjpeg/jpegint.h
So you probably want something like:
mex -compatibleArrayDims -I/usr/local/opt/jpeg/include ...
-I/usr/local/opt/gdcm/include/gdcm-3.0/gdcmjpeg ...
jpeg_write.c ...
-L/usr/local/opt/jpeg/lib -L/usr/local/opt/gdcm/lib ...
-ljpeg -lgdcmjpeg16
(I don't know if you actually want -lgdcmjpeg8, -lgdcmjpeg12, or -lgdcmjpeg16, or maybe something else. I'm just guessing here. Consult the GDCM documentation.)
When I attempt to compile a .mex file on Windows, I get the following error. How can I fix this?
Error using mex
MEX cannot find library 'mwblas' specified with the -l option.
MEX looks for a file with one of the names:
libmwblas.lib
mwblas.lib
Please specify the path to this library with the -L option
As the error message states, you need to specify the directory in which the .lib file is located using the -L option or specify the full path to the .lib file as an input to mex. This library is located in matlabroot/extern/lib. So you could do something like
blas = fullfile(matlabroot,'extern','lib',computer('arch'),'microsoft', 'libmwblas.lib');
mex('-largeArrayDims', 'mymexfile.cpp', blas)
Or you can specify the folder with -L
libdir = fullfile(matlabroot,'extern','lib',computer('arch'),'microsoft');
mex('-largeArrayDims', ['-L', libdir], '-lmwblas', 'mymexfile.cpp', )
More info about compiling mex files to use LAPACK and BLAS is here
I have created a mex function (more specifically, using CUDA)
the compilation was successful, and I got a mex file zMul.mexmaci64
but on the execution, matlab reported an error:
Invalid MEX-file '/Users/zlw/Documents/MATLAB/lowComplexity/cbased/matMulGPU/zMul.mexmaci64':
dlopen(/Users/zlw/Documents/MATLAB/lowComplexity/cbased/matMulGPU/zMul.mexmaci64, 1):
Library not loaded: #rpath/libcublas.6.0.dylib
Referenced from: /Users/zlw/Documents/MATLAB/lowComplexity/cbased/matMulGPU/zMul.mexmaci64
Reason: image not found
What should I do do solve it?
additional info
setting the environment vars (PATH,LD_LIBRARY_PATH,DYLD_LIBRARY_PATH) in Matlab and in .bash_profile doesn't work for me
I'm pretty sure that the environment vars are set correctly because when I created an alias to the dylib file, Matlab detected it, tried to load it, but failed with message:no suitable image found
Thanks!
Use otool -L in both Matlab and UNIX console.
In Matlab:
!otool -L /path/to/zMul.mexmaci64
In UNIX console:
otool -L /path/to/zMul.mexmaci64
Try to find the difference between them. If there is a difference in dependency, that is probably breaking the MEX binary. You might need to apply the same technique for the dependent dylib objects recursively. Typically, enforcing the one appearing in UNIX console using DYLD_INSERT_LIBRARIES solves the problem.
Another possibility is the C++ runtime compatibility. If you're using OS X Mavericks, you should check that your MEX command is using libc++ but not libstdc++ in mexopts.sh. Below is my configuration example in mexopts.sh:
CC='clang'
CXX='clang++'
SDKROOT='/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/'
MACOSX_DEPLOYMENT_TARGET='10.9'
CFLAGS="$CFLAGS -Dchar16_t=uint16_t"
CXXFLAGS="$CXXFLAGS -std=c++11 -stdlib=libc++ -DCHAR16_T"
CXXLIBS="$MLIBS -lc++"
This post might help: http://www.seaandsailor.com/matlab-xcode6.html
It was easier than I thought. Just replace all 10.x with your OS X version and add -Dchar16_t=UINT16_T to CLIBS in mexopts.sh file.
I am having some issues in compiling using mex this software http://www.cmap.polytechnique.fr/~aspremon/ZIP/COVSEL.zip. When I use mex and give it the files to compile it shows the following error
error: 'CblasColMajor' undeclared (first use in this function)
I am compiling the mex file from matlab and in Mac LionOS. Any suggestions
I am using the following code to compile
mex BoxQP.c BoxQP_mex.c utils.c
Make sure the MACVERSION macro is defined, or define it yourself. It looks like the CblasColMajor enum is defined in the cblas.h file which is included on line 18 of BoxQP.h. So I'm guessing that you either need to install the cblas library or it's there by default on OSX. Here's what I had to use to compile it on Win32:
mex -v -g BoxQP_mex.c BoxQP.c utils.c -LC:\MATLAB\R2009bSP1\extern\lib\win32\microsoft -lmwblas
HTH, might want to include the line you're using to compile it if you can't figure it out.
EDIT
You'll need to find the library path for the Matlab install and then under that directory you'll need to look for extern\lib\ then look for your platform and library type like, extern\lib\linux\maxos I'm not sure what it will look like, but that's a guess. also, include the Mathworks BLAS library using, -lmwblas.
This is Subhash. I am having problem in linking fortran-matlab mex files.
I am running MATLAB R2010a. I am trying to mex fortran subroutines in MATLAB. I have installed MSYS, MinGW and gfortran. I have also downloaded and extracted gnumex in the c:\documents\MATLAB folder. I entered gnumex to run the installation settings.
At this point, I see a window pop-up and I entered the following:
MinGW's root directory ---> Pointed towards c:\mingw b) Cygwin's
root directory -----> left blank c)
Path to g95.exe ------> c:\mingw\bin
path to gfortran.exe ------> c:\program files\gfortran\bin e)
path to gnumex utilities ------> c:\users.....\matlab\gnumex
environment linking type ------> MinGW
generate mex dll or engine-----> mex
language for compilation -------> fortran 77
add stub ------> no
optimization level -----> -O3
path for libraries and .def files
c:\users...\Roaming\MathWorks\MATLAB\R2010a\gnumex
Mex options file to create:
c\users...\Roaming\MathWorks\MATLAB\R2010a\mexopts.bat
The above is my installation setup for mex with gnumex. When I hit make options file, an warning message pops out which says
" cannot corret mex.pl .....
"cannot open c:...\R2010a\bin\mex.pl for writing"
and when I hit ok, again it pops out saying to confirm overwrite of mexopts.bat .
I hit confirm and the opt file is created.
At this point I should have my mex setup ready. But, when I run the fortran mex examples xtimesy.f, etc.. ( I use mex filename.f at the command prompt) and I get the following error
g77: getValidInputLinkLibraries: No such file or directory
c:\prog~1\MATLAB\R2010A\BIN\MEX.PL: Error: Link of 'xtimesy.mexw32' failed.
Error using ---> mex at 222
unable to complete successfully.
I tried this uninstalling several times, but ended up with the same error.
Could anyone please let me know where am I going wrong. Is this not the correct procedure to link the g77? Please throw some light on this.
I appreciate your time..
Thanks.
I recently tried to mex some fortran routines and failed due to the poor support for fortran compilers by matlab in windows. I got around the problem by using f2c to convert the fortran to C code, then creating a gateway routine in C which calls the automatically generated C code functions and mexing the resul using the visual studio 2008 compiler which integrates nicely with matlab (the free express edition version is sufficient, you will also be able to use it for debugging).
You can get f2c from http://www.netlib.org/f2c/. You must link the produced C code to the f2c library, which you may also have to build from the sources.
I know this all sounds very complicated, but it was easiest solution I found.