Thread: Issue with .so (Shared Object) Files

Hello there!

I'm dealing with a piece of C code today, which is supposed to run in MATLAB. Thus, I intend to make use of the MEX interface.

However, first - the c code must be compiled using

1) make clean all
2) make matlab


My make-File looks the following way:

Code:

#
# Choose your compiler
#

# 
#CC = gcc-4.2
#CPP = g++-4.2
#CFLAGS=-O3 -ffast-math -fomit-frame-pointer -fPIC -mtune=k8 -march=k8 -Werror
CC = gcc
CPP = g++
CFLAGS=-O3 -ffast-math -fomit-frame-pointer -fPIC -Werror 
#CC=/agbs/share/sw/icc/bin/icc
#CFLAGS= -fast -DCOMPILE_WITH_ICC -Werror


#
# MATLAB
#    
MATLABDIR=/usr/pack/matlab-7.10r2010a-sd/
MATLAB_INCLUDE=-I$(MATLABDIR)/extern/include


#
# ARCHITECTURE
# 

# 64 bit
SUFFIX=mexa64
MATLAB_LIB=-L$(MATLABDIR)/bin/glnxa64 -lmex

#LIBS=/usr/lib/gcc/x86_64-linux-gnu/4.3/libstdc++.a /usr/lib/

#
# MPI KMEANS FLAGS
#
#VERBOSEFLAG=-DKMEANS_VERBOSE=0 # 0: silent, 1:iteration counter, 2:everything
#PRECISION=-DINPUT_TYPE=0 # 0: double, 1:float 




matlab: mpi_kmeans_mex.$(SUFFIX) mpi_assign_mex.$(SUFFIX)


libmpikmeans:    mpi_kmeans.o
    ar rc libmpikmeans.a mpi_kmeans.o
    ranlib libmpikmeans.a
    $(CC) -shared -Wl,-soname=libmpikmeans.so -fPIC $(CFLAGS) $(VERBOSEFLAG) -o libmpikmeans.so $(VERBOSEFLAGS) $(PRECISION) mpi_kmeans.cxx


mpi_kmeans_mex.$(SUFFIX):    libmpikmeans mpi_kmeans_mex.o 
    $(CC) mpi_kmeans_mex.o -shared -o mpi_kmeans_mex.$(SUFFIX) libmpikmeans.a $(MATLAB_LIB) 

mpi_assign_mex.$(SUFFIX):    libmpikmeans mpi_assign_mex.o
    $(CC) mpi_assign_mex.o -shared -o mpi_assign_mex.$(SUFFIX) libmpikmeans.a $(MATLAB_LIB)

test:    
    matlab -nojvm -r "test_code;exit"

clean:    
    rm -f *.o
    rm -f *.mexglx
    rm -f *.mexa64
    rm -f libmpikmeans.so
    rm -f libmpikmeans.a
    rm -f mpi_assign mpi_kmeans

After Step 1) I receive the following error message:

ld: unknown option: -soname=libmpikmeans.so
collect2: ld returned 1 exit status
make: *** [libmpikmeans] Error 1

I understand the problem here. the .so file extension is used for Linux only. However, I'm using a Mac.

Is there an equivalent to the command -soname= for Mac?


Looking forward to your replies.

Thanks!

Originally Posted by manual

-soname=name
When creating an ELF shared object, set the internal DT_SONAME field to the specified name. When an executable is linked with a shared object which has a DT_SONAME
field, then when the executable is run the dynamic linker will attempt to load the shared object specified by the DT_SONAME field rather than the using the file
name given to the linker.

Since the names are the same, perhaps you could just delete -Wl,-soname=libmpikmeans.so and see what happens.

It seems a moot point given that the names are the same to begin with.

> Undefined symbols:
> "___gxx_personality_v0", referenced from:
You need to invoke the linker through g++, not gcc.

As in
g++ -shared -fPIC -O3 -ffast-math -fomit-frame-pointer -fPIC -Werror -o libmpikmeans.so mpi_kmeans.cxx

Originally Posted by Salem

>
As in
g++ -shared -fPIC -O3 -ffast-math -fomit-frame-pointer -fPIC -Werror -o libmpikmeans.so mpi_kmeans.cxx

I see. Very interesting. I tried it out - the old error message is gone.

Instead, I have another main error now.

ar rc libmpikmeans.a mpi_kmeans.o
ranlib libmpikmeans.a
g++ -shared -fPIC -O3 -ffast-math -fomit-frame-pointer -fPIC -Werror -o libmpikmeans.so mpi_kmeans.cxx
gcc -O3 -ffast-math -fomit-frame-pointer -fPIC -Werror -I/usr/pack/matlab-7.10r2010a-sd//extern/include -c mpi_kmeans_mex.cxx -o mpi_kmeans_mex.o
mpi_kmeans_mex.cxx:2:17: error: mex.h: No such file or directory
mpi_kmeans_mex.cxx:6: error: ‘mxArray’ has not been declared
mpi_kmeans_mex.cxx:6: error: expected ‘,’ or ‘...’ before ‘*’ token
mpi_kmeans_mex.cxx:6: error: ISO C++ forbids declaration of ‘mxArray’ with no type
mpi_kmeans_mex.cxx: In function ‘void mexFunction(int, int**, int, int)’:
mpi_kmeans_mex.cxx:12: error: ‘mwSize’ was not declared in this scope
mpi_kmeans_mex.cxx:12: error: expected `;' before ‘dims’
mpi_kmeans_mex.cxx:16: error: ‘mexPrintf’ was not declared in this scope
mpi_kmeans_mex.cxx:21: error: ‘prhs’ was not declared in this scope
mpi_kmeans_mex.cxx:21: error: ‘mxGetPr’ was not declared in this scope
mpi_kmeans_mex.cxx:25: error: ‘prhs’ was not declared in this scope
mpi_kmeans_mex.cxx:25: error: ‘mxGetPr’ was not declared in this scope
mpi_kmeans_mex.cxx:30: error: ‘prhs’ was not declared in this scope
mpi_kmeans_mex.cxx:30: error: ‘mxGetPr’ was not declared in this scope
mpi_kmeans_mex.cxx:40: error: ‘mexPrintf’ was not declared in this scope
mpi_kmeans_mex.cxx:46: error: ‘prhs’ was not declared in this scope
mpi_kmeans_mex.cxx:46: error: ‘mxIsDouble’ was not declared in this scope
mpi_kmeans_mex.cxx:46: error: ‘mxIsComplex’ was not declared in this scope
mpi_kmeans_mex.cxx:47: error: ‘mxGetNumberOfDimensions’ was not declared in this scope
mpi_kmeans_mex.cxx:49: error: ‘mexPrintf’ was not declared in this scope
mpi_kmeans_mex.cxx:62: error: ‘prhs’ was not declared in this scope
mpi_kmeans_mex.cxx:62: error: ‘mxGetM’ was not declared in this scope
mpi_kmeans_mex.cxx:63: error: ‘mxGetN’ was not declared in this scope
mpi_kmeans_mex.cxx:67: error: ‘mxGetPr’ was not declared in this scope
mpi_kmeans_mex.cxx:72: error: ‘mexErrMsgTxt’ was not declared in this scope
mpi_kmeans_mex.cxx:75: error: ‘mexErrMsgTxt’ was not declared in this scope
mpi_kmeans_mex.cxx:78: error: ‘mexErrMsgTxt’ was not declared in this scope
mpi_kmeans_mex.cxx:84: error: ‘mxIsComplex’ was not declared in this scope
mpi_kmeans_mex.cxx:85: error: ‘mxGetNumberOfDimensions’ was not declared in this scope
mpi_kmeans_mex.cxx:87: error: ‘mexPrintf’ was not declared in this scope
mpi_kmeans_mex.cxx:94: error: ‘mexErrMsgTxt’ was not declared in this scope
mpi_kmeans_mex.cxx:96: error: ‘mexErrMsgTxt’ was not declared in this scope
mpi_kmeans_mex.cxx:99: error: ‘dims’ was not declared in this scope
mpi_kmeans_mex.cxx:105: error: ‘mxDOUBLE_CLASS’ was not declared in this scope
mpi_kmeans_mex.cxx:105: error: ‘mxREAL’ was not declared in this scope
mpi_kmeans_mex.cxx:105: error: ‘mxCreateNumericArray’ was not declared in this scope
mpi_kmeans_mex.cxx:113: error: ‘mxGetPr’ was not declared in this scope
mpi_kmeans_mex.cxx:121: error: ‘mxIsNaN’ was not declared in this scope
mpi_kmeans_mex.cxx:121: error: ‘mxIsInf’ was not declared in this scope
mpi_kmeans_mex.cxx:122: error: ‘mexErrMsgTxt’ was not declared in this scope
mpi_kmeans_mex.cxx:130: error: ‘mxUINT32_CLASS’ was not declared in this scope
mpi_kmeans_mex.cxx:149: error: ‘mxCreateScalarDouble’ was not declared in this scope
make: *** [mpi_kmeans_mex.o] Error 1

Clearly, the error is coming from the fact, that the c-Files are not being interpreted as mex, since mex.h is not localizable on the system.

The mpi_kmeans_mex.cxx - Filesays: #include "mex.h"
I tried using #include <mex.h>, since there was no mex.h file in the folder.

I still get the same error!
What's going on here?

I have the feeling that the hardcoded MATLAB directory does not exist on my system (I'm using a different version of MATLAB).

Here is the relevant part of makefile again:

#
# Choose your compiler
#

#
#CC = gcc-4.2
#CPP = g++-4.2
#CFLAGS=-O3 -ffast-math -fomit-frame-pointer -fPIC -mtune=k8 -march=k8 -Werror
CC = gcc
CPP = g++
CFLAGS=-O3 -ffast-math -fomit-frame-pointer -fPIC -Werror
#CC=/agbs/share/sw/icc/bin/icc
#CFLAGS= -fast -DCOMPILE_WITH_ICC -Werror


#
# MATLAB
#
MATLABDIR=/usr/pack/matlab-7.10r2010a-sd/
MATLAB_INCLUDE=-I$(MATLABDIR)/extern/include



#
# ARCHITECURE
#

# 32 bit
#SUFFIX=mexglx
#MATLAB_LIB=-L$(MATLABDIR)/bin/glnx86 -lmex

# 64 bit
SUFFIX=mexa64
MATLAB_LIB=-L$(MATLABDIR)/bin/glnxa64 -lmex

#LIBS=/usr/lib/gcc/x86_64-linux-gnu/4.3/libstdc++.a /usr/lib/libm.a




matlab: mpi_kmeans_mex.$(SUFFIX) mpi_assign_mex.$(SUFFIX)

%_mex.o: %_mex.cxx
$(CC) $(CFLAGS) $(VERBOSEFLAG) $(MATLAB_INCLUDE) $(PRECISION) -c $^ -o $@

mpi_kmeans_mex.$(SUFFIX): libmpikmeans mpi_kmeans_mex.o
$(CC) mpi_kmeans_mex.o -shared -o mpi_kmeans_mex.$(SUFFIX) libmpikmeans.a $(MATLAB_LIB)

mpi_assign_mex.$(SUFFIX): libmpikmeans mpi_assign_mex.o
$(CC) mpi_assign_mex.o -shared -o mpi_assign_mex.$(SUFFIX) libmpikmeans.a $(MATLAB_LIB)

The path for MATLAB_LIB seems more appropriate for Linux, rather than Mac. Additionally, MATLABDIR has to be changed - how to find it on my system?

Originally Posted by in_ship

Did now help - I got an the same error again, this time for -install_name.

Same error as what? ld: Unknown option?

Originally Posted by man ld

-install_name name
Sets an internal "install path" (LC_ID_DYLIB) in a dynamic library. Any clients linked against the library will record that path as the way dyld should locate this library. If this option is not
specified, then the -o path will be used. This option is also called -dylib_install_name for compatibility.

You did ask for a -soname equivalent, there is no -soname on OSX so it would make sense that it gives you a "Unknown option" error.