I'm trying to invoke Parsido function in mex file using gfortran compiler on Linux system. I use following instruction to compile:
mex '-I ${EBROOTIMKL}/mkl/include'...,
'-L ${EBROOTIMKL}/mkl/lib'...,
-lmkl_rt...,
pardiso_sym_f90.f90 ero_dep_fortran.F -output ero_dep_fortran
I can successfully compile the mex file, but when I excute, Matlab crashes without any error information. I know it might be due to the use of -lmkl_rt, which might conflict with the Intel iomp5 implementation of OpenMP which MATLAB uses.
Any suggestions will be appreciated.
Related
Using Matlab 2013b, I ran the command mex -setup and I get the result:
>> mex -setup
Welcome to mex -setup. This utility will help you set up
a default compiler. For a list of supported compilers, see
http://www.mathworks.com/support/compilers/R2013b/win64.html
Please choose your compiler for building MEX-files:
Would you like mex to locate installed compilers [y]/n? n
My problem is, that under Matlab2016a I can't see this message - I only get the following result:
>> mex -setup
MEX configured to use 'Microsoft Visual C++ 2012 (C)' for C language compilation.
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/matlab/matlab_external/upgrading-mex-files-to-use-64-bit-api.html.
To choose a different language, select one from the following:
mex -setup C++
mex -setup FORTRAN
Please, how I could see the message
"Welcome to mex -setup. This utility will help you set up etc"
Thank you very much.
From the MATLAB documentation:
To change the default C++ compiler, type:
mex -setup cpp
This way you can change to different compilers if you have them. Calling mex -setup sets the C compiler, which may be different.
I have a script in matlab that calls other libraries. I use matlab version 2012a on linux . I get below error and I don't know how to fix it.
The error is :
Invalid MEX-file '/home/XXX/nearest_neighbors.mexa64':
libflann.so.1.8: cannot open shared object file: No such file or
directory
Error in flann_search (line 82)
[indices,dists] = nearest_neighbors('find_nn', data, testset, n, params);
Error in MyScript (line 73)
[nresult, ndists] = flann_search(Ntraindata', Ntraindata', resu.KNN, struct('algorithm','composite',...
That library you are referring to - https://github.com/mariusmuja/flann/ - has the nearest_neighbors function written in MEX code. MEX code is C code that is used to interface with MATLAB. People usually write heavily computationally burdening code over in MEX as it is known to handle loops and other things faster. The inputs come from MATLAB and are sent to this MEX function, and the outputs come from the MEX function and are piped back to MATLAB. It's basically a nice black box where you can use it just like any other MATLAB function. In fact, a lot of the functions that come shipped with MATLAB have MEX wrappers written to promote acceleration.
You are getting that error because you need to compile the nearest_neighbors function so that there is a MEX wrapper that can be called in MATLAB. That wrapper is missing because you haven't compiled the code.
First, you need to set up MEX. Make sure you have a compiler that is compatible with your version of MATLAB. You can do that by visiting this link:
http://www.mathworks.com/support/compilers/R20xxy/index.html
xx is the version number that belongs to your MATLAB and y is the character code that comes after it. For example, if you are using R2013a, you would visit:
http://www.mathworks.com/support/compilers/R2013a/index.html
Once you're there, go to your Operating System and ensure you have one of those supported compilers installed. Once you have that installed, go into MATLAB, and in the command prompt, type in:
mex -setup
This will allow you to set up MEX and choose the compiler you want. Given your error, you're using Linux 64-bit, so it should be very easy for you to get GCC. Just make sure that you choose a version of GCC that is compatible with your version of MATLAB. Once you choose the compiler, you can compile the code by doing this in the command prompt:
>> mex -v -O nearest_neighbors.cpp
This should generate the nearest_neighbors MEX file for you. Once that's done, you can now run the code.
For more detailed instructions, check out FLANN's user manual - http://people.cs.ubc.ca/~mariusm/uploads/FLANN/flann_manual-1.8.4.pdf - It tells you how to build and compile it for MATLAB use.
Good luck!
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.
The -f command-line argument to mex allows to specify the location of the mexopts.sh that we wish to use. But is there a way to tell Matlab to ignore mexopts.sh? In order to compile a specific MEX file I need to specify CC, CFLAGS, etc., directly on the command line when invoking mex. Values already given in mexopts.sh cause a conflict and cause mex to fail.
Thanks!