mxGPUArray.h file not found

Hello everyone,

I am running Maverick MAC OS X 64bits and Matlab 2013a/CUDA Toolkit 5.5 and GeForce650M card. I am sure that the CUDA installation was successful by trying several CUDA-C examples included in the toolkit installation.

Now I'm trying to perform mex compilation by following the procedure in http://www.mathworks.com.au/help/distcomp/run-mex-functions-containing-cuda-code.html#btrgje7.

with CUDA .cu file as provided in http://www.mathworks.com.au/help/distcomp/rmvd_matlablink__1da2f7c6e005a9643f6a92a0546e436a.html

And this command failed with an error:

>> mex mexGPUExample.cu  
mexGPUExample.cu:10:10: fatal error: 'gpu/mxGPUArray.h' file not found  
#include "gpu/mxGPUArray.h"  
         ^  
1 error generated.  
mex: compile of ' "mexGPUExample.cu"' failed.
Error using mex (line 206)
Unable to complete successfully.

Where can I find the mxGPUArray.h file? Why is it not on my search path?

[Jill Reese]

Did you follow the instructions to set up the gpu mex options file? The instructions are right above the text pointed to by your first link.

[Joss Knight]

Also, please try

>> mex -v mexGPUExample.cu

and post the resulting text - this will print out verbose text which will help us see why the compiler isn't finding that header file.

Note that if you don't have a mexopts.bat or mex_CUDA_maci64.xml file in the same directory as your .cu file, this will be the source of the problem.

[Khoa Tran]

Thank you so much! Just to provide more information. I compiled a few CUDA C files just to be sure that nvcc is properly installed and was successful. I also follow the instruction in the links very closely.

I tried the new mex -v option and saw this:

    >> setenv('MW_NVCC_PATH','/usr/local/CUDA/bin/nvcc')
    >> mex mexGPUExample.cu
    mexGPUExample.cu:10:10: fatal error: 'gpu/mxGPUArray.h' file not found
    #include "gpu/mxGPUArray.h"
             ^
    1 error generated.

        mex: compile of ' "mexGPUExample.cu"' failed.

    Error using mex (line 206)
    Unable to complete successfully.

    >> mex -v mexGPUExample.cu

    **************************************************************************
      Warning: Neither -compatibleArrayDims nor -largeArrayDims is selected. 
               Using -compatibleArrayDims. In the future, MATLAB will require
               the use of -largeArrayDims and remove the -compatibleArrayDims
               option. For more information, see:
               http://www.mathworks.com/help/matlab/matlab_external/upgrading-mex-files-to-use-64-bit-api.html
    **************************************************************************

    -> mexopts.sh sourced from directory (DIR = .)
       FILE = /Users/erictran/Dropbox/PhD/Codes/Paper_01/CUDA/mexopts.sh
    ----------------------------------------------------------------
    ->    MATLAB                = /Applications/MATLAB_R2013a.app
    ->    CC                    = xcrun  -sdk macosx10.8  clang
    ->    CC flags:
             CFLAGS             = -fno-common -arch x86_64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.8.sdk -mmacosx-version-min=10.8  -fexceptions
             CDEBUGFLAGS        = -g
             COPTIMFLAGS        = -O2 -DNDEBUG
             CLIBS              = -L/Applications/MATLAB_R2013a.app/bin/maci64 -lmx -lmex -lmat -lstdc++
             arguments          =  -DMX_COMPAT_32
    ->    CXX                   = xcrun  -sdk macosx10.8  clang++
    ->    CXX flags:
             CXXFLAGS           = -fno-common -fexceptions -arch x86_64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.8.sdk -mmacosx-version-min=10.8
             CXXDEBUGFLAGS      = -g
             CXXOPTIMFLAGS      = -O2 -DNDEBUG
             CXXLIBS            = -L/Applications/MATLAB_R2013a.app/bin/maci64 -lmx -lmex -lmat -lstdc++
             arguments          =  -DMX_COMPAT_32
    ->    FC                    = gfortran
    ->    FC flags:
             FFLAGS             = -fexceptions -m64 -fbackslash
             FDEBUGFLAGS        = -g
             FOPTIMFLAGS        = -O
             FLIBS              = -L/Applications/MATLAB_R2013a.app/bin/maci64 -lmx -lmex -lmat -L -lgfortran -L -lgfortranbegin
             arguments          =  -DMX_COMPAT_32
    ->    LD                    = xcrun -sdk macosx10.8 clang
    ->    Link flags:
             LDFLAGS            = -arch x86_64 -Wl,-syslibroot,/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.8.sdk -mmacosx-version-min=10.8 -bundle -Wl,-exported_symbols_list,/Applications/MATLAB_R2013a.app/extern/lib/maci64/mexFunction.map
             LDDEBUGFLAGS       = -g
             LDOPTIMFLAGS       = -O
             LDEXTENSION        = .mexmaci64
             arguments          = 
    ->    LDCXX                 = 
    ->    Link flags:
             LDCXXFLAGS         = 
             LDCXXDEBUGFLAGS    = 
             LDCXXOPTIMFLAGS    = 
             LDCXXEXTENSION     = 
             arguments          = 
    ----------------------------------------------------------------

    -> xcrun  -sdk macosx10.8  clang++ -c  -I/Applications/MATLAB_R2013a.app/extern/include -I/Applications/MATLAB_R2013a.app/simulink/include -DMATLAB_MEX_FILE -fno-common -fexceptions -arch x86_64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.8.sdk -mmacosx-version-min=10.8  -DMX_COMPAT_32 -O2 -DNDEBUG  "mexGPUExample.cu"

    mexGPUExample.cu:10:10: fatal error: 'gpu/mxGPUArray.h' file
          not found
    #include "gpu/mxGPUArray.h"
             ^
    1 error generated.

        mex: compile of ' "mexGPUExample.cu"' failed.

    Error using mex (line 206)
    Unable to complete successfully.

[Priyanka Bharadwaj]

Was this issue resolved. I have the similar error. Please let me the way around for this.

/matconvnet-1.0-beta24/matlab/src/bits/datamex.hpp:19:28: fatal error: gpu/mxGPUArray.h: No such file or directory

#include "gpu/mxGPUArray.h"

However I found that file under /usr/local/MATLAB/R2019b/toolbox/parallel/gpu/extern/include/gpu

Can you please let me know how to redirect to the right path while compiling?