Here is my ldconfig
$ ldconfig -p | grep blas
libptf77blas.so.3 (libc6,x86-64) => /usr/lib64/atlas/libptf77blas.so.3
libptcblas.so.3 (libc6,x86-64) => /usr/lib64/atlas/libptcblas.so.3
libf77blas.so.3 (libc6,x86-64) => /usr/lib64/atlas/libf77blas.so.3
libcblas.so.3 (libc6,x86-64) => /usr/lib64/atlas/libcblas.so.3
libblas.so.3 (libc6,x86-64) => /usr/lib64/libblas.so.3
libblas.so (libc6,x86-64) => /usr/lib64/libblas.so
When I try to compile with cblas, here is the error:
gcc -std=c99 -g -Wall -O0 -I../include -L../bin -I../externals/CXSparse/Include example_als_mcmc.c -lfastfm -L../externals/CXSparse/Lib -lcxsparse -lblas -lm -lcblas -o example_als_mcmc
/usr/bin/ld: cannot find -lcblas
collect2: ld returned 1 exit status
make: *** [example_als_mcmc] Error 1
I have cblas in ldconfig, why make cannot find it?
Thank you for your help.
Related
My question is about linking errors I get when compiling with external libraries using mex. I'm trying to compile C++ code using the external library fftw3 using Matlab's mex on MacOS using clang++. Here is an example
main.cpp
#include "fftw3.h"
int main(){
double * test = (double *) fftw_malloc(10*sizeof(double));
}
compiling this works
$ clang++ main.cpp -L/usr/local/lib -lfftw3
Now I try something similar with mex
mex.cpp
#include "math.h"
#include "matrix.h"
#include "mex.h"
#include "fftw3.h"
void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
{
double * test = (double *) fftw_malloc(10*sizeof(double));
}
in MATLAB
>> mex -setup C++;
>> mex -L/usr/local/lib -lfftw3 CXXFLAGS='-L/usr/local/lib -lfftw3' mex.cpp
Building with 'Xcode Clang++'.
Error using mex
clang: warning: -lfftw3: 'linker' input unused
clang: warning: argument unused during compilation: '-L/usr/local/lib'
/path/to/file/mex.cpp:4:10:
fatal error: 'fftw3.h' file not found
#include "fftw3.h"
^
1 error generated.
using the -v flag I get more detailed errors
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.
... Looking for compiler 'Xcode 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 ('7.1.1').
... Executing command '
agreed=7.1.1
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 ('7.1.1').
... 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/MacOSX10.7.sdk' ...No.
... Looking for folder '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.8.sdk' ...No.
... Looking for folder '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk' ...Yes.
... 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/MacOSX10.7.sdk' ...No.
... Looking for folder '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.8.sdk' ...No.
... Looking for folder '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk' ...Yes.
... Executing command 'echo /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk | rev | cut -c1-10 | rev | egrep -oh '[0-9]+\.[0-9]+'' ...Yes ('10.11').
Found installed compiler 'Xcode Clang++'.
Options file details
-------------------------------------------------------------------
Compiler location: /Applications/Xcode.app/Contents/Developer
Options file: ~/.matlab/R2014b/mex_C++_maci64.xml
CMDLINE100 : /usr/bin/xcrun -sdk macosx10.11 clang++ -c -DMX_COMPAT_32 -DMATLAB_MEX_FILE -I"/Applications/MATLAB_R2014b.app/extern/include" -I"/Applications/MATLAB_R2014b.app/simulink/include" -L/usr/local/lib -lfftw3 -O2 -DNDEBUG /path/to/file/mex.cpp -o /var/folders/09/dysbhb1d5zn98sq8lzkwpn5r0000gn/T//mex_291104578803706_45753/mex.o
CMDLINE200 : /usr/bin/xcrun -sdk macosx10.11 clang++ -Wl,-twolevel_namespace -undefined error -arch x86_64 -mmacosx-version-min=10.11 -Wl,-syslibroot,/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk -framework Cocoa -bundle -Wl,-exported_symbols_list,"/Applications/MATLAB_R2014b.app/extern/lib/maci64/mexFunction.map" -O -Wl,-exported_symbols_list,"/Applications/MATLAB_R2014b.app/extern/lib/maci64/mexFunction.map" /var/folders/09/dysbhb1d5zn98sq8lzkwpn5r0000gn/T//mex_291104578803706_45753/mex.o -lfftw3 -L/usr/local/lib -L"/Applications/MATLAB_R2014b.app/bin/maci64" -lmx -lmex -lmat -o mex.mexmaci64
CMDLINE300 : rm -f /var/folders/09/dysbhb1d5zn98sq8lzkwpn5r0000gn/T//mex_291104578803706_45753/mex.o
CXX : /usr/bin/xcrun -sdk macosx10.11 clang++
DEFINES : -DMX_COMPAT_32 -DMATLAB_MEX_FILE
MATLABMEX : -DMATLAB_MEX_FILE
CXXFLAGS : -L/usr/local/lib -lfftw3
INCLUDE : -I"/Applications/MATLAB_R2014b.app/extern/include" -I"/Applications/MATLAB_R2014b.app/simulink/include"
CXXOPTIMFLAGS : -O2 -DNDEBUG
CXXDEBUGFLAGS : -g
LDXX : /usr/bin/xcrun -sdk macosx10.11 clang++
LDFLAGS : -Wl,-twolevel_namespace -undefined error -arch x86_64 -mmacosx-version-min=10.11 -Wl,-syslibroot,/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk -framework Cocoa -bundle -Wl,-exported_symbols_list,"/Applications/MATLAB_R2014b.app/extern/lib/maci64/mexFunction.map"
LDBUNDLE : -bundle
LINKEXPORT : -Wl,-exported_symbols_list,"/Applications/MATLAB_R2014b.app/extern/lib/maci64/mexFunction.map"
LINKLIBS : -lfftw3 -L/usr/local/lib -L"/Applications/MATLAB_R2014b.app/bin/maci64" -lmx -lmex -lmat
LDOPTIMFLAGS : -O
LDDEBUGFLAGS : -g
OBJEXT : .o
LDEXT : .mexmaci64
DEVELOPER_DIR_CHECK :
XCODE_DIR : /Applications/Xcode.app/Contents/Developer
XCRUN_DIR : /usr/bin
XCODE_AGREED_VERSION : 7.1.1
ISYSROOT : /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk
SDKVER : 10.11
MATLABROOT : /Applications/MATLAB_R2014b.app
ARCH : maci64
SRC : /path/to/file/mex.cpp
OBJ : /var/folders/09/dysbhb1d5zn98sq8lzkwpn5r0000gn/T//mex_291104578803706_45753/mex.o
OBJS : /var/folders/09/dysbhb1d5zn98sq8lzkwpn5r0000gn/T//mex_291104578803706_45753/mex.o
SRCROOT : /path/to/file/mex
DEF : /var/folders/09/dysbhb1d5zn98sq8lzkwpn5r0000gn/T//mex_291104578803706_45753/mex.def
EXP : mex.exp
LIB : mex.lib
EXE : mex.mexmaci64
ILK : mex.ilk
MANIFEST : mex.mexmaci64.manifest
TEMPNAME : mex
EXEDIR :
EXENAME : mex
OPTIM : -O2 -DNDEBUG
LINKOPTIM : -O
-------------------------------------------------------------------
Building with 'Xcode Clang++'.
/usr/bin/xcrun -sdk macosx10.11 clang++ -c -DMX_COMPAT_32 -DMATLAB_MEX_FILE -I"/Applications/MATLAB_R2014b.app/extern/include" -I"/Applications/MATLAB_R2014b.app/simulink/include" -L/usr/local/lib -lfftw3 -O2 -DNDEBUG /path/to/file/mex.cpp -o /var/folders/09/dysbhb1d5zn98sq8lzkwpn5r0000gn/T//mex_291104578803706_45753/mex.o
Error using mex
clang: warning: -lfftw3: 'linker' input unused
clang: warning: argument unused during compilation: '-L/usr/local/lib'
/path/to/file/mex.cpp:4:10:
fatal error: 'fftw3.h' file not found
#include "fftw3.h"
^
1 error generated.
The warnings
clang: warning: -lfftw3: 'linker' input unused
clang: warning: argument unused during compilation: '-L/usr/local/lib'
are there because you are setting CXXFLAGS to contain these flags. This variable is for compiler flags, but -L and -l are linker flags. Simply remove the CXXFLAGS definition from your mex command.
The error
/path/to/file/mex.cpp:4:10:
fatal error: 'fftw3.h' file not found
#include "fftw3.h"
^
1 error generated.
is because the compiler cannot find the fftw4.h header file. You need to tell the compiler where to find it:
mex -I/usr/local/include -L/usr/local/lib -lfftw3 mex.cpp
Note that in your first case, where you call clang++ directly, it is likely that CLang is configured to look for header files in /usr/local/include, it's a standard place. But when mex invokes your compiler (I don't even know if it's the same one?) apparently this location is not added to the search path.
I have cross compiled tool chain for armv7eb. Now I have copied the tools to my target machine and tried to build perl on target. In this process of building perl, there is a binary called 'miniperl' which crashes, outputting "ILLEGAL INSTRUCTION".
Can someone help me point out what I should be doing?
PERL VERSION: 5.8.8
GCC: 4.1.3
Please find the crash log below. Does anybody have any suggestions?
sh cflags "optimize='-O'" opmini.o` -DPIC -fPIC -DPERL_EXTERNAL_GLOB opmini.c
CCCMD = cc -DPERL_CORE -c -msoft-float -dynamic -fno-strict-aliasing -pipe -Wdeclaration-after-statement -O -Wall
LD_LIBRARY_PATH=/usr/pkg/src/perl-5.8.8:/lib:/usr/lib:/usr/pkg/lib:/usr/pkg/src/PTHREAD/lib cc -Wl,-rpath,/usr/pkg/lib -Wl,-rpath,/usr/local/lib -L/usr/pkg/lib -L/lib -L/usr/lib -o miniperl miniperlmain.o opmini.o -L. -lperl -lm -lcrypt -lutil -lc -lposix
LD_LIBRARY_PATH=/usr/pkg/src/perl-5.8.8:/lib:/usr/lib:/usr/pkg/lpid 25563 (miniperl), uid 0: exited on signal 4 (core not dumped, err = 2)
ib:/usr/pkg/src/PTHREAD/lib ./miniperl -w -Ilib -MExporter -e '<?>' || make minitest
[1] Illegal instruction LD_LIBRARY_PATH=...
cp ext/re/re.pm lib/re.pm
LD_LIBRARY_PATH=/usr/pkg/src/perpid 8052 (miniperl), uid 0: exited on signal 4 (core not dumped, err = 2)
l-5.8.8:/lib:/usr/lib:/usr/pkg/lib:/usr/pkg/src/PTHREAD/lib ./miniperl -Ilib configpm --heavy=lib/Config_heavy.pl lib/Config.pm
[1] Illegal instruction LD_LIBRARY_PATH=...
*** Error code 132
Stop.
make: stopped in /upid 25595 (miniperl), uid 0: exited on signal 4 (core not dumped, err = 2)
sr/pkg/src/perl-5.8.8
*** Error code 1 (ignored)
You may see some irrelevant test failures if you have been unable
to build lib/Config.pm, lib/lib.pm or the Unicode data files.
cd t && (rm -f perl; /bin/ln -s ../miniperl perl) && LD_LIBRARY_PATH=/usr/pkg/src/perl-5.8.8:/lib:/usr/lib:/usr/pkg/lib:/usr/pkg/src/PTHREAD/lib ./perl TEST -minitest base/*.t comp/*.t cmd/*.t run/*.t io/*.t op/*.t uni/*.t </dev/tty
[1] Illegal instruction LD_LIBRARY_PATH=...
*** Error code 132 (ignored)
*** Error code 1 (ignored)
LD_LIBRARY_PATH=/usr/pkg/src/perpid 703 (miniperl), uid 0: exited on signal 4 (core not dumped, err = 2)
l-5.8.8:/lib:/usr/lib:/usr/pkg/lib:/usr/pkg/src/PTHREAD/lib ./miniperl -Ilib configpm --heavy=lib/Config_heavy.pl lib/Config.pm
So I have been trying to compile this code using mex to on avail. The issue is it can not seem to find lstdc++ and lpthread and libm are for whatever reason incompatible. My /usr/lib32 folder looks like the following:
iggy#ThinkpadX1:~/Applications/Matlab_2012a/bin$ ls /usr/lib32/
crt1.o libanl.so libc_nonshared.a libg.a libmcheck.a libnss_files.so libpthread.so librt.so libz.so.1
crti.o libBrokenLocale.a libcrypt.a libgcc_s.so.1 libm.so libnss_hesiod.so libquadmath.so.0 libstdc++.so.6 libz.so.1.2.3.4
crtn.o libBrokenLocale.so libcrypt.so libgomp.so.1 libnsl.a libnss_nisplus.so libquadmath.so.0.0.0 libstdc++.so.6.0.16 Mcrt1.o
gconv libbsd-compat.a libc.so libgomp.so.1.0.0 libnsl.so libnss_nis.so libresolv.a libthread_db.so Scrt1.o
gcrt1.o libc.a libdl.a libieee.a libnss_compat.so libpthread.a libresolv.so libutil.a
libanl.a libcidn.so libdl.so libm.a libnss_dns.so libpthread_nonshared.a librt.a libutil.so
And the errors I am recieving are the following:
K>> make_csolve
**************************************************************************
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/techdoc/matlab_external/bsflnue-1.html
**************************************************************************
/home/iggy/Applications/Matlab_2012a/bin/mex: 1: /home/iggy/Applications/Matlab_2012a/bin/util/oscheck.sh: /lib64/libc.so.6: not found
/home/iggy/Applications/Matlab_2012a/bin/mex: 1: /home/iggy/Applications/Matlab_2012a/bin/util/oscheck.sh: /lib64/libc.so.6: not found
-> mexopts.sh sourced from directory (DIR = $MATLAB/bin)
FILE = /home/iggy/Applications/Matlab_2012a/bin/mexopts.sh
----------------------------------------------------------------
-> MATLAB = /home/iggy/Applications/Matlab_2012a
-> CC = gcc-4.4
-> CC flags:
CFLAGS = -ansi -D_GNU_SOURCE -fexceptions -fPIC -fno-omit-frame-pointer -pthread
CDEBUGFLAGS = -g
COPTIMFLAGS = -O -DNDEBUG
CLIBS = -Wl,-rpath-link,/home/iggy/Applications/Matlab_2012a/bin/glnxa64 -L/usr/lib32 -L/home/iggy/Applications/Matlab_2012a/bin/glnxa64 -lmx -lmex -lmat -lm -lstdc++
arguments = -DMX_COMPAT_32
-> CXX = g++-4.4
-> CXX flags:
CXXFLAGS = -ansi -D_GNU_SOURCE -fPIC -fno-omit-frame-pointer -pthread
CXXDEBUGFLAGS = -g
CXXOPTIMFLAGS = -O -DNDEBUG
CXXLIBS = -Wl,-rpath-link,/home/iggy/Applications/Matlab_2012a/bin/glnxa64 -L/home/iggy/Applications/Matlab_2012a/bin/glnxa64 -lmx -lmex -lmat -lm
arguments = -DMX_COMPAT_32
-> FC = gfortran
-> FC flags:
FFLAGS = -fexceptions -fbackslash -fPIC -fno-omit-frame-pointer
FDEBUGFLAGS = -g
FOPTIMFLAGS = -O
FLIBS = -Wl,-rpath-link,/home/iggy/Applications/Matlab_2012a/bin/glnxa64 -L/home/iggy/Applications/Matlab_2012a/bin/glnxa64 -lmx -lmex -lmat -lm
arguments = -DMX_COMPAT_32
-> LD = gcc-4.4
-> Link flags:
LDFLAGS = -pthread -shared -Wl,--version-script,/home/iggy/Applications/Matlab_2012a/extern/lib/glnxa64/mexFunction.map -Wl,--no-undefined
LDDEBUGFLAGS = -g
LDOPTIMFLAGS = -O
LDEXTENSION = .mexa64
arguments =
-> LDCXX =
-> Link flags:
LDCXXFLAGS =
LDCXXDEBUGFLAGS =
LDCXXOPTIMFLAGS =
LDCXXEXTENSION =
arguments =
----------------------------------------------------------------
-> gcc-4.4 -c -I/home/iggy/Applications/Matlab_2012a/extern/include -I/home/iggy/Applications/Matlab_2012a/simulink/include -DMATLAB_MEX_FILE -ansi -D_GNU_SOURCE -fexceptions -fPIC -fno-omit-frame-pointer -pthread -DMX_COMPAT_32 -O -DNDEBUG "csolve.c"
-> gcc-4.4 -c -I/home/iggy/Applications/Matlab_2012a/extern/include -I/home/iggy/Applications/Matlab_2012a/simulink/include -DMATLAB_MEX_FILE -ansi -D_GNU_SOURCE -fexceptions -fPIC -fno-omit-frame-pointer -pthread -DMX_COMPAT_32 -O -DNDEBUG "ldl.c"
-> gcc-4.4 -c -I/home/iggy/Applications/Matlab_2012a/extern/include -I/home/iggy/Applications/Matlab_2012a/simulink/include -DMATLAB_MEX_FILE -ansi -D_GNU_SOURCE -fexceptions -fPIC -fno-omit-frame-pointer -pthread -DMX_COMPAT_32 -O -DNDEBUG "matrix_support.c"
-> gcc-4.4 -c -I/home/iggy/Applications/Matlab_2012a/extern/include -I/home/iggy/Applications/Matlab_2012a/simulink/include -DMATLAB_MEX_FILE -ansi -D_GNU_SOURCE -fexceptions -fPIC -fno-omit-frame-pointer -pthread -DMX_COMPAT_32 -O -DNDEBUG "solver.c"
-> gcc-4.4 -c -I/home/iggy/Applications/Matlab_2012a/extern/include -I/home/iggy/Applications/Matlab_2012a/simulink/include -DMATLAB_MEX_FILE -ansi -D_GNU_SOURCE -fexceptions -fPIC -fno-omit-frame-pointer -pthread -DMX_COMPAT_32 -O -DNDEBUG "util.c"
-> gcc-4.4 -O -pthread -shared -Wl,--version-script,/home/iggy/Applications/Matlab_2012a/extern/lib/glnxa64/mexFunction.map -Wl,--no-undefined -o "csolve.mexa64" csolve.o ldl.o matrix_support.o solver.o util.o -Wl,-rpath-link,/home/iggy/Applications/Matlab_2012a/bin/glnxa64 -L/usr/lib32 -L/home/iggy/Applications/Matlab_2012a/bin/glnxa64 -lmx -lmex -lmat -lm -lstdc++
/usr/bin/ld: skipping incompatible /usr/lib32/libm.so when searching for -lm
/usr/bin/ld: skipping incompatible /usr/lib32/libm.a when searching for -lm
/usr/bin/ld: cannot find -lstdc++
/usr/bin/ld: skipping incompatible /usr/lib32/libpthread.so when searching for -lpthread
/usr/bin/ld: skipping incompatible /usr/lib32/libpthread.a when searching for -lpthread
collect2: ld returned 1 exit status
mex: link of ' "csolve.mexa64"' failed.
Error using mex (line 206)
Unable to complete successfully.
Error in make_csolve (line 10)
mex -v csolve.c ldl.c matrix_support.c solver.c util.c
Any advice would be greatly appreciated (I am on Ubuntu 12.04 64-bit running MATLAB R2012a).
The libraries in /use/lib32 are incompatible because they are the wrong architecture (32-bit instead of 64-bit). Try running mex -setup again first. I'm assuming you're using 64-bit MATLAB (check with ver) since there are glnxa64 folders in the current setup.
However, the real error seems to be the following:
/home/iggy/Applications/Matlab_2012a/bin/mex: 1: /home/iggy/Applications/Matlab_2012a/bin/util/oscheck.sh: /lib64/libc.so.6: not found
Since oscheck.sh fails to find /lib64/libc.so.6, you might need to go into the package manage and look for libc and libstdc++, install them and try again. But first try to make a link to any existing libc.so.6 in another folder. Typical locations for Ubuntu are below.
64-bit Ubuntu:
sudo ln -s /lib/x86_64-linux-gnu/libc.so.6 /lib64/libc.so.6
32-bit Ubuntu:
sudo ln -s /lib/i386-linux-gnu/libc.so.6 /lib/libc.so.6
I'm unable to build Doxygen on x86_64-linux.
I have Doxygen-1.8.6 unpacked.
I have libiconv-1.14 unpacked, built, installed.
I keep getting:
g++ -c -pipe -fsigned-char -D_LARGEFILE_SOURCE -Wall -W -O2 -I../qtools -I../libmd5 -I. -o ../objects/main.o main.cpp
g++ -o ../bin/doxygen ../objects/main.o -L../lib -ldoxygen -ldoxycfg -lqtools -lmd5 -lpthread
../lib/libdoxycfg.a(portable_c.o): In function `portable_iconv_close':
portable_c.c:(.text+0x1): undefined reference to `libiconv_close'
../lib/libdoxycfg.a(portable_c.o): In function `portable_iconv':
portable_c.c:(.text+0x11): undefined reference to `libiconv'
../lib/libdoxycfg.a(portable_c.o): In function `portable_iconv_open':
portable_c.c:(.text+0x21): undefined reference to `libiconv_open'
collect2: ld returned 1 exit status
Which iconv gives:
/usr/local/bin/iconv
as expected.
Any ideas?
add -liconv to the end of the line in src/doxygen.pro.in:
unix:LIBS += -L../lib -ldoxygen -lvhdlparser -ldoxycfg -lqtools -lmd5 -lpthread %%SQLITE3_LIBS%% %%LIBCLANG_LIBS%% -liconv
Up until recently I've been able to compile mex functions fine on my mac osx 10.8.4
but now it gives me the error as follows (for convenience I have included the entire -v invocation):
**************************************************************************
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/munanxu/Dropbox/Code/CUDA/mexThomasTDM/mexopts.sh
----------------------------------------------------------------
-> MATLAB = /Applications/MATLAB_R2013a.app
-> CC = xcrun -sdk macosx10.7 clang
-> CC flags:
CFLAGS = -fno-common -arch x86_64 -isysroot
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOS
X10.7.sdk -mmacosx-version-min=10.7 -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 macosx10.7 clang++
-> CXX flags:
CXXFLAGS = -fno-common -fexceptions -arch x86_64 -isysroot
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX
10.7.sdk -mmacosx-version-min=10.7
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 macosx10.7 clang
-> Link flags:
LDFLAGS = -arch x86_64 -Wl,-
syslibroot,/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/
SDKs/MacOSX10.7.sdk -mmacosx-version-min=10.7 -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 macosx10.7 clang -g -arch x86_64 -Wl,-
syslibroot,/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/
SDKs/MacOSX10.7.sdk -mmacosx-version-min=10.7 -bundle -Wl,-
exported_symbols_list,/Applications/MATLAB_R2013a.app/extern/lib/maci64/mexFunction.map -o
"inputsTest.mexmaci64" "inputsTest.o" -L/Applications/MATLAB_R2013a.app/bin/maci64 -lmx
-lmex -lmat -lstdc++
Undefined symbols for architecture x86_64:
"_mexFunction", referenced from:
-exported_symbol[s_list] command line option
ld: symbol(s) not found for architecture x86_64
I had copied the original mexopts.sh file to the local directory to ensure that the mex compiler was using the correct version. I had also previously compiled my cpp file using g++ just to make sure the code was compiled natively for the x86_64 architecture. However, the same result occurs when I attempt to use the mex compiler to do compilation and linking.
Any ideas on what might be going on here? It seems that people have had this issue before, but mostly with missing libraries or definitions. I have definitely defined a mexFunction in my source file.
I think Amro is correct, I would put this as a comment, but it's a bit large, I find this for clang command line options to select target CPU
Registered Targets:
alpha - Alpha [experimental]
arm - ARM
bfin - Analog Devices Blackfin [experimental]
c - C backend ... ...
mblaze - MBlaze
mips - Mips ...
msp430 - MSP430 [experimental] ...
thumb - Thumb
x86 - 32-bit X86: Pentium-Pro and above
x86-64 - 64-bit X86: EM64T and AMD64
xcore - XCoreI'm thinking Amro is correct:
So is -arch x86-64 the right command line switch, rather than x86_64