Mex can't find compiler after Xcode 7 update (R2015b)

Asked by Austin Blanton on 18 Sep 2015

Latest activity Commented on by Walter Roberson on 24 Jul 2019

258 views (last 30 days)

I recently updated Xcode to version 7. I was able to use mex before, and now it thinks I don't have a valid compiler. I clearly have several valid C compilers:

$ which gcc
/usr/bin/gcc
$ which clang
/usr/bin/clang

Before I get waaay in the weeds with details, is there a way to point mex to a clearly installed compiler, or a mex config file to update?

Here is the verbose output:

$ mex -v Dependencies/anigaussm/anigauss_mex.c Dependencies/anigaussm/anigauss.c -output anigauss
Verbose mode is on.
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:
   http://www.mathworks.com/help/matlab/matlab_external/upgrading-mex-files-to-use-64-bit-api.html.
No MEX options file identified; looking for an implicit selection.
... Looking for compiler 'Xcode with Clang' ...
... Looking for environment variable 'DEVELOPER_DIR' ...No.
... Executing command 'xcode-select -print-path' ...Yes ('/Applications/Xcode.app/Contents/Developer').
... Looking for folder '/Applications/Xcode.app/Contents/Developer' ...Yes.
... Executing command 'which xcrun' ...Yes ('/usr/bin/xcrun').
... Looking for folder '/usr/bin' ...Yes.
... Executing command 'defaults read com.apple.dt.Xcode IDEXcodeVersionForAgreedToGMLicense' ...No.
... Executing command 'defaults read /Library/Preferences/com.apple.dt.Xcode IDEXcodeVersionForAgreedToGMLicense' ...Yes ('7.0').
... Executing command '
agreed=7.0 
if echo $agreed | grep -E '[\.\"]' >/dev/null; then 
lhs=`expr "$agreed" : '\([0-9]*\)[\.].*'` 
rhs=`expr "$agreed" : '[0-9]*[\.]\(.*\)$'` 
if echo $rhs | grep -E '[\."]' >/dev/null; then 
rhs=`expr "$rhs" : '\([0-9]*\)[\.].*'` 
fi 
if [ $lhs -gt 4 ] || ( [ $lhs -eq 4 ] && [ $rhs -ge 3 ] ); then 
echo $agreed 
else 
exit 1
fi 
fi' ...Yes ('7.0').
... Executing command 'xcode-select -print-path' ...Yes ('/Applications/Xcode.app/Contents/Developer').
... Looking for folder '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk' ...No.
... Looking for folder '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk' ...No.
... Executing command 'find /Applications/Xcode.app/Contents/Developer -name MacOSX10.9.sdk' ...No.
... Executing command 'find $$ -name MacOSX10.10.sdk' ...No.
Did not find installed compiler 'Xcode with Clang'.
No supported compiler or SDK was found. For options, visit http://www.mathworks.com/support/compilers/R2015b/maci64.html.c

Looks like the Xcode SDK version has incremented, despite OSX still being 10.10:

$ ls /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs
MacOSX10.11.sdk

I tried creating a symlink there that points to MacOSX10.11.sdk, to no avail:

[...up to the fail point above...]
... Looking for folder '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk' ...Yes.
... Executing command 'echo /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk | rev | cut -c1-10 | rev | egrep -oh '[0-9]+\.[0-9]+'' ...Yes ('10.10').
Found installed compiler 'Xcode with Clang'.
Options file details
-------------------------------------------------------------------
  Compiler location: /Applications/Xcode.app/Contents/Developer
  Options file: /Applications/MATLAB_R2015b.app/bin/maci64/mexopts/clang_maci64.xml
  CMDLINE200 : /usr/bin/xcrun -sdk macosx10.10 clang -Wl,-twolevel_namespace -undefined error -arch x86_64 -mmacosx-version-min=10.10 -Wl,-syslibroot,/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -bundle  -Wl,-exported_symbols_list,"/Applications/MATLAB_R2015b.app/extern/lib/maci64/mexFunction.map" /var/folders/bt/bct7b52x0sb25z0pd5ky23xsg9dl8x/T//mex_32352732774360_62273/anigauss_mex.o /var/folders/bt/bct7b52x0sb25z0pd5ky23xsg9dl8x/T//mex_32352732774360_62273/anigauss.o  -O -Wl,-exported_symbols_list,"/Applications/MATLAB_R2015b.app/extern/lib/maci64/mexFunction.map"  -L"/Applications/MATLAB_R2015b.app/bin/maci64" -lmx -lmex -lmat -lc++ -o /Users/m29474/Desktop/code/selective_search_ijcv_with_python/anigauss.mexmaci64
  CC : /usr/bin/xcrun -sdk macosx10.10 clang
  DEFINES : -DMX_COMPAT_32   -DMATLAB_MEX_FILE
  MATLABMEX : -DMATLAB_MEX_FILE
  CFLAGS : -fno-common -arch x86_64 -mmacosx-version-min=10.10 -fexceptions -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk
  INCLUDE : -I"/Applications/MATLAB_R2015b.app/extern/include" -I"/Applications/MATLAB_R2015b.app/simulink/include"
  COPTIMFLAGS : -O2 -DNDEBUG
  CDEBUGFLAGS : -g
  LD : /usr/bin/xcrun -sdk macosx10.10 clang
  LDFLAGS : -Wl,-twolevel_namespace -undefined error -arch x86_64 -mmacosx-version-min=10.10 -Wl,-syslibroot,/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -bundle  -Wl,-exported_symbols_list,"/Applications/MATLAB_R2015b.app/extern/lib/maci64/mexFunction.map"
  LDBUNDLE : -bundle 
  LINKEXPORT : -Wl,-exported_symbols_list,"/Applications/MATLAB_R2015b.app/extern/lib/maci64/mexFunction.map"
  LINKLIBS : -L"/Applications/MATLAB_R2015b.app/bin/maci64" -lmx -lmex -lmat -lc++
  LDOPTIMFLAGS : -O
  LDDEBUGFLAGS : -g
  OBJEXT : .o
  LDEXT : .mexmaci64
  SETENV : CC="/usr/bin/xcrun -sdk macosx10.10 clang"
CXX="/usr/bin/xcrun -sdk macosx10.10 clang"
CFLAGS="-fno-common -arch x86_64 -mmacosx-version-min=10.10 -fexceptions -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -DMX_COMPAT_32   -DMATLAB_MEX_FILE"
CXXFLAGS="-fno-common -arch x86_64 -mmacosx-version-min=10.10 -fexceptions -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -DMX_COMPAT_32   -DMATLAB_MEX_FILE"
COPTIMFLAGS="-O2 -DNDEBUG"
CXXOPTIMFLAGS="-O2 -DNDEBUG"
CDEBUGFLAGS="-g"
CXXDEBUGFLAGS="-g"
LD="/usr/bin/xcrun -sdk macosx10.10 clang"
LDXX="/usr/bin/xcrun -sdk macosx10.10 clang"
LDFLAGS="-Wl,-twolevel_namespace -undefined error -arch x86_64 -mmacosx-version-min=10.10 -Wl,-syslibroot,/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -bundle  -Wl,-exported_symbols_list,"/Applications/MATLAB_R2015b.app/extern/lib/maci64/mexFunction.map" -L"/Applications/MATLAB_R2015b.app/bin/maci64" -lmx -lmex -lmat -lc++ -Wl,-exported_symbols_list,"/Applications/MATLAB_R2015b.app/extern/lib/maci64/mexFunction.map""
LDDEBUGFLAGS="-g"
  DEVELOPER_DIR_CHECK : 
  XCODE_DIR : /Applications/Xcode.app/Contents/Developer
  XCRUN_DIR : /usr/bin
  XCODE_AGREED_VERSION : 7.0
  ISYSROOT : /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk
  SDKVER : 10.10
  MATLABROOT : /Applications/MATLAB_R2015b.app
  ARCH : maci64
  SRC : /Users/m29474/Desktop/code/selective_search_ijcv_with_python/Dependencies/anigaussm/anigauss_mex.c;/Users/m29474/Desktop/code/selective_search_ijcv_with_python/Dependencies/anigaussm/anigauss.c
  OBJ : /var/folders/bt/bct7b52x0sb25z0pd5ky23xsg9dl8x/T//mex_32352732774360_62273/anigauss_mex.o;/var/folders/bt/bct7b52x0sb25z0pd5ky23xsg9dl8x/T//mex_32352732774360_62273/anigauss.o
  OBJS : /var/folders/bt/bct7b52x0sb25z0pd5ky23xsg9dl8x/T//mex_32352732774360_62273/anigauss_mex.o /var/folders/bt/bct7b52x0sb25z0pd5ky23xsg9dl8x/T//mex_32352732774360_62273/anigauss.o 
  SRCROOT : /Users/m29474/Desktop/code/selective_search_ijcv_with_python/Dependencies/anigaussm/anigauss_mex
  DEF : /var/folders/bt/bct7b52x0sb25z0pd5ky23xsg9dl8x/T//mex_32352732774360_62273/anigauss.def
  EXP : /Users/m29474/Desktop/code/selective_search_ijcv_with_python/anigauss.exp
  LIB : /Users/m29474/Desktop/code/selective_search_ijcv_with_python/anigauss.lib
  EXE : /Users/m29474/Desktop/code/selective_search_ijcv_with_python/anigauss.mexmaci64
  ILK : /Users/m29474/Desktop/code/selective_search_ijcv_with_python/anigauss.ilk
  MANIFEST : /Users/m29474/Desktop/code/selective_search_ijcv_with_python/anigauss.mexmaci64.manifest
  TEMPNAME : /Users/m29474/Desktop/code/selective_search_ijcv_with_python/anigauss
  EXEDIR : /Users/m29474/Desktop/code/selective_search_ijcv_with_python/
  EXENAME : anigauss
  OPTIM : -O2 -DNDEBUG
  LINKOPTIM : -O
  CMDLINE100_0 : /usr/bin/xcrun -sdk macosx10.10 clang -c -DMX_COMPAT_32   -DMATLAB_MEX_FILE -I"/Applications/MATLAB_R2015b.app/extern/include" -I"/Applications/MATLAB_R2015b.app/simulink/include" -fno-common -arch x86_64 -mmacosx-version-min=10.10 -fexceptions -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -O2 -DNDEBUG /Users/m29474/Desktop/code/selective_search_ijcv_with_python/Dependencies/anigaussm/anigauss_mex.c -o /var/folders/bt/bct7b52x0sb25z0pd5ky23xsg9dl8x/T//mex_32352732774360_62273/anigauss_mex.o
  CMDLINE100_1 : /usr/bin/xcrun -sdk macosx10.10 clang -c -DMX_COMPAT_32   -DMATLAB_MEX_FILE -I"/Applications/MATLAB_R2015b.app/extern/include" -I"/Applications/MATLAB_R2015b.app/simulink/include" -fno-common -arch x86_64 -mmacosx-version-min=10.10 -fexceptions -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -O2 -DNDEBUG /Users/m29474/Desktop/code/selective_search_ijcv_with_python/Dependencies/anigaussm/anigauss.c -o /var/folders/bt/bct7b52x0sb25z0pd5ky23xsg9dl8x/T//mex_32352732774360_62273/anigauss.o
  CMDLINE300_0 : rm -f /var/folders/bt/bct7b52x0sb25z0pd5ky23xsg9dl8x/T//mex_32352732774360_62273/anigauss_mex.o
  CMDLINE300_1 : rm -f /var/folders/bt/bct7b52x0sb25z0pd5ky23xsg9dl8x/T//mex_32352732774360_62273/anigauss.o
-------------------------------------------------------------------
Building with 'Xcode with Clang'.
/usr/bin/xcrun -sdk macosx10.10 clang -c -DMX_COMPAT_32   -DMATLAB_MEX_FILE -I"/Applications/MATLAB_R2015b.app/extern/include" -I"/Applications/MATLAB_R2015b.app/simulink/include" -fno-common -arch x86_64 -mmacosx-version-min=10.10 -fexceptions -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -O2 -DNDEBUG /Users/m29474/Desktop/code/selective_search_ijcv_with_python/Dependencies/anigaussm/anigauss_mex.c -o /var/folders/bt/bct7b52x0sb25z0pd5ky23xsg9dl8x/T//mex_32352732774360_62273/anigauss_mex.o
xcodebuild: error: SDK "macosx10.10" cannot be located.
xcrun: error: unable to find utility "clang", not a developer tool or in PATH

Help!

-Austin

0 Comments

5 Answers

Link

Answer by Ken Atwell on 18 Sep 2015

Edited by Ken Atwell on 20 Oct 2015

Accepted Answer

EDIT MathWorks has produced a patch for this issue. If at all possible, use the procedure outlined at http://www.mathworks.com/matlabcentral/answers/246507-why-can-t-mex-find-a-supported-compiler-in-matlab-r2015b-after-i-upgraded-to-xcode-7

Original Answer

This is an advanced maneuver, but get rid of that symlink and try doctoring this file:

>> edit ([matlabroot '/bin/maci64/mexopts/clang_maci64.xml'])

Toward the bottom, you will see a line that look like this, referencing "10.10":

 <dirExists name="$$/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk" />

Copy and paste this line (immediately after the first) and change the second one to "10.11", like this:

 <dirExists name="$$/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk" />
 <dirExists name="$$/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk" />

Do this against for another instance in this file -- both must be modified.

This should allow you to link against the OS X 10.11 SDK, but please be aware that this is configuration that has not been validated by MathWorks.

12 Comments

Show 9 older comments

Fabian Bernhard on 27 Oct 2015

Hi, What would be the directory if only the command line tools are installed without the full Xcode.app ? I have no .sdk folder.

xcode-select -print-path
/Library/Developer/CommandLineTools

Below full output of my mex -setup -v:

    >> mex -setup -v
Verbose mode is on.
... Looking for compiler 'Xcode with Clang' ...
... Looking for environment variable 'DEVELOPER_DIR' ...No.
... Executing command 'xcode-select -print-path' ...Yes ('/Library/Developer/CommandLineTools').
... Looking for folder '/Library/Developer/CommandLineTools' ...Yes.
... Executing command 'which xcrun' ...Yes ('/usr/bin/xcrun').
... Looking for folder '/usr/bin' ...Yes.
... Executing command 'defaults read com.apple.dt.Xcode IDEXcodeVersionForAgreedToGMLicense' ...Yes ('4.6.3').
... Executing command '
agreed=4.6.3 
 if echo $agreed | grep -E '[\.\"]' >/dev/null; then 
 lhs=`expr "$agreed" : '\([0-9]*\)[\.].*'` 
  rhs=`expr "$agreed" : '[0-9]*[\.]\(.*\)$'` 
 if echo $rhs | grep -E '[\."]' >/dev/null; then 
 rhs=`expr "$rhs" : '\([0-9]*\)[\.].*'` 
 fi 
 if [ $lhs -gt 4 ] || ( [ $lhs -eq 4 ] && [ $rhs -ge 3 ] ); then 
 echo $agreed 
 else 
 exit 1
 fi 
 fi' ...Yes ('4.6.3').
... Executing command 'xcode-select -print-path' ...Yes ('/Library/Developer/CommandLineTools').
... Looking for folder '/Library/Developer/CommandLineTools/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk' ...No.
... Looking for folder '/Library/Developer/CommandLineTools/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk' ...No.
... Looking for folder '/Library/Developer/CommandLineTools/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk' ...No.
... Executing command 'find /Library/Developer/CommandLineTools -name MacOSX10.9.sdk' ...No.
... Executing command 'find $$ -name MacOSX10.10.sdk' ...No.
... Executing command 'find $$ -name MacOSX10.11.sdk' ...No.
Did not find installed compiler 'Xcode with Clang'.
Error using mex
No supported compiler or SDK was found. For options, visit  http://www.mathworks.com/support/compilers/R2014b/maci64.html.

Sanat Kumar Tiwari on 19 Sep 2016

I was facing similar problem after upgrading to Xcode 8.0. Tried this solution which worked. But one need to add following line at the places Ken suggested:

name="$$/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk" /

Amod Agrawal on 12 Oct 2016

Hey! I have been trying to get this to work with Xcode 8.0 (after macOS Sierra upgrade). Just changing this line didn't work for me. Did you change anything besides this as well?

Walter Roberson on 12 Oct 2016

http://www.mathworks.com/matlabcentral/answers/303369-mex-cannot-find-a-supported-compiler-in-matlab-r2015b-after-i-upgraded-to-xcode-8-0#answer_235135

Link

Answer by Kaipeng on 19 Jun 2017

mex_clang.zip

if you use macOS 10.12.5 Sierra with Xcode 8.3.3，this file will work for Matlab 2016a:

0 Comments

Link

Answer by Chen on 13 Jan 2016

Hi Ken,

I am using 2014b, OSX 10.10.5 and installed Xcode 7. just tried to simply run 'mex fengdemo.F'. The fortran file is matlab example file. I made the change as you described above. 'mex -setup' seems ok;

I got this:

Building with 'gfortran'. f951: Warning: Nonexistent include directory '/Applications/MATLAB_R2014b.app/simulink/include' [-Wmissing-include-dirs]

Error using mex clang: error: no such file or directory: '1/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk'

Error in chentry (line 4) mex fengdemo.F;

Can you help?!

5 Comments

Show 2 older comments

Chen on 13 Jan 2016

Xcode.app is in Applications fold of my laptop;but why it shows '/Volumes/Xcode 1/Xcode.app/Contents/Developer' by 'xcode-select -p' command. By the way, I am using company computer, which might be set by our IT support, I guess.

Chen on 13 Jan 2016

god! when i run 'sudo xcode-select -switch /Applications/Xcode.app/ ' It needs password.

Is there any way to modify matlab files instead of asking IT guys?

Walter Roberson on 13 Jan 2016

No, you will need the sudo unless you install MATLAB in your own directory instead of available across the machine... but you would need authorization from your IT people for that.

Link

Answer by Jiefei Wang on 17 Nov 2016

Edited by Walter Roberson on 17 Nov 2016

Hi all,

mine is like as follows but still can't use mex files.

<cmdReturns name="xcode-select -print-path"/>
                    <or>
                        <dirExists name="$$/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk" />
                        <dirExists name="$$/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk" />
            <dirExists name="$$/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk" /> 
                        <cmdReturns name="find $$ -name MacOSX10.9.sdk" />
                        <cmdReturns name="find $$ -name MacOSX10.10.sdk" />
            <cmdReturns name="find $$ -name MacOSX10.11.sdk" />
                    </or>

Any suggestions?

Thanks

4 Comments

Show 1 older comment

Walter Roberson on 11 May 2017

R2016a has some aspects in different locations than R2016b or R2017a. Although the editing techniques and the files to change are the same for all three versions, the final files for R2016a are different than for R2016b / R2017a. I have attached the modified R2016a versions here. Unzip and put the two files into /Applications/MATLAB_R2016a.app/bin/maci64/mexopts

Amanda Baia Campos on 15 May 2017

Hi, it says

Error using mex /Applications/MATLAB_R2016a.app/bin/maci64/mexopts/clang++_maci64 2.xml is not a valid XML file.

Walter Roberson on 15 May 2017

clang-R2016a.zip

I might have accidentally uploaded aliases instead of the actual files. For R2016a try with the enclosed:

Link

Answer by Lin Yuan on 9 Feb 2017

Edited by Lin Yuan on 9 Feb 2017

Another answer, but I think it's basically the same as the previous answers.

First, you need to locate to the c++ compiler in your Matlab. Mine is /Applications/MATLAB_R2016a.app/bin/maci64/mexopts

And open the clang++_maci64.xml file with any editor, check/add the following line of codes(as the attached image highlighted)

I think, if your Matlab version are older than the system version being released(e.g OS 10.12 Sierra), it shouldn't add them in the file, so just add them manually could probably solve this kind of problem.

3 Comments

Eric Elharer on 26 Mar 2018

having the sane errors of invalid mex file Iread most of the comments regarding that issue withe no success.

if possible, ill need instructions step by step

Mac OS high Sierra & Score 9.2

Invalid MEX-file '/Users/ericelharar/Documents/MATLAB/Eric_Pedro/BM3D/bm3d_thr.mexmaci64':
dlopen(/Users/ericelharar/Documents/MATLAB/Eric_Pedro/BM3D/bm3d_thr.mexmaci64, 6): Library not loaded: @loader_path/libmat.dylib
  Referenced from: /Users/ericelharar/Documents/MATLAB/Eric_Pedro/BM3D/bm3d_thr.mexmaci64
  Reason: image not found.

Eric

Andy Zhang on 24 Jul 2019

Hi Eric,

Do you find the reasons of the error? I have the same issue.

Walter Roberson on 24 Jul 2019

In Sierra and later, Apple started enforcing a System Integrity feature.

The documented effect is that for some Apple provided apps that the app would ignore LD_LIBRARY_PATH and DYLD_LIBRARY_PATH and only link libraries in some places such /usr/lib.

The actual effect appears to be that it is doing that security for all or most applications in /Applications including matlab since it is installed there.

The work around is to copy the appropriate libraries into /usr/lib or to at least have a symbolic link there pointing to the actual location.

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