Undefined symbol errors in MEX compilation

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12-05-2012
in_ship

Undefined symbol errors in MEX compilation

Hi there! ;)

I am currently trying to run someone else's code on my machine (Link).
The precompiled MEX files are available for a Linux 64-bit machine. However, I am trying to run it on a Mac using MATLAB 2012b.

I adapted the makefile by adjusting the MATLAB directory. However, I still get some compilation errors.
It seems that certain libraries cannot be located. :(

Quote:

mycomputer:mpi_kmeans-1.5 username$ make matlab
ar rc libmpikmeans.a mpi_kmeans.o
ranlib libmpikmeans.a
g++ -shared -fPIC -O3 -ffast-math -fomit-frame-pointer -fPIC -m64 -o libmpikmeans.so mpi_kmeans.cxx
gcc mpi_kmeans_mex.o -shared -o mpi_kmeans_mex.mexmaci64 libmpikmeans.a -L/Applications/MATLAB_R2012b.app/bin/maci64 -lmex
Undefined symbols:
"_mxGetM", referenced from:
_mexFunction in mpi_kmeans_mex.o
_mexFunction in mpi_kmeans_mex.o
_mexFunction in mpi_kmeans_mex.o
_mexFunction in mpi_kmeans_mex.o
"_mxGetN", referenced from:
_mexFunction in mpi_kmeans_mex.o
_mexFunction in mpi_kmeans_mex.o
_mexFunction in mpi_kmeans_mex.o
_mexFunction in mpi_kmeans_mex.o
"_mxIsDouble", referenced from:
_mexFunction in mpi_kmeans_mex.o
"___gxx_personality_v0", referenced from:
_mexFunction in mpi_kmeans_mex.o
CIE in mpi_kmeans_mex.o
comp_randperm(void const*, void const*)in libmpikmeans.a(mpi_kmeans.o)
remove_point_from_cluster(unsigned int, double*, double const*, unsigned int*, unsigned int)in libmpikmeans.a(mpi_kmeans.o)
add_point_to_cluster(unsigned int, double*, double const*, unsigned int*, unsigned int)in libmpikmeans.a(mpi_kmeans.o)
compute_distance(double const*, double const*, unsigned int)in libmpikmeans.a(mpi_kmeans.o)
randperm(unsigned int*, unsigned int)in libmpikmeans.a(mpi_kmeans.o)
kmeans_error(char*) in libmpikmeans.a(mpi_kmeans.o)
remove_identical_clusters(double*, float*, double const*, unsigned int*, unsigned int*, unsigned int, unsigned int, unsigned int)in libmpikmeans.a(mpi_kmeans.o)
compute_cluster_distances(float*, float*, double const*, unsigned int, unsigned int, bool const*)in libmpikmeans.a(mpi_kmeans.o)
compute_sserror(double const*, double const*, unsigned int const*, unsigned int, unsigned int)in libmpikmeans.a(mpi_kmeans.o)
assign_point_to_cluster(unsigned int, double const*, double const*, unsigned int, unsigned int, unsigned int, double*, float*, float*, float*)in libmpikmeans.a(mpi_kmeans.o)
assign_point_to_cluster_ordinary(double const*, double const*, unsigned int, unsigned int)in libmpikmeans.a(mpi_kmeans.o)
init_point_to_cluster(unsigned int, double const*, double const*, unsigned int, unsigned int, double*, float*, float const*)in libmpikmeans.a(mpi_kmeans.o)
kmeans_run(double*, double const*, unsigned int*, unsigned int, unsigned int, unsigned int, unsigned int)in libmpikmeans.a(mpi_kmeans.o)
_kmeans in libmpikmeans.a(mpi_kmeans.o)
CIE in libmpikmeans.a(mpi_kmeans.o)
"_mxCreateNumericArray_730", referenced from:
_mexFunction in mpi_kmeans_mex.o
_mexFunction in mpi_kmeans_mex.o
"_mxIsComplex", referenced from:
_mexFunction in mpi_kmeans_mex.o
_mexFunction in mpi_kmeans_mex.o
"_mxGetNumberOfDimensions_730", referenced from:
_mexFunction in mpi_kmeans_mex.o
_mexFunction in mpi_kmeans_mex.o
"_mxIsInf", referenced from:
_mexFunction in mpi_kmeans_mex.o
"_mxIsSingle", referenced from:
_mexFunction in mpi_kmeans_mex.o
"_mxIsNaN", referenced from:
_mexFunction in mpi_kmeans_mex.o
"_mxGetPr", referenced from:
_mexFunction in mpi_kmeans_mex.o
_mexFunction in mpi_kmeans_mex.o
_mexFunction in mpi_kmeans_mex.o
_mexFunction in mpi_kmeans_mex.o
_mexFunction in mpi_kmeans_mex.o
_mexFunction in mpi_kmeans_mex.o
_mexFunction in mpi_kmeans_mex.o
_mexFunction in mpi_kmeans_mex.o
"_mxCreateDoubleScalar", referenced from:
_mexFunction in mpi_kmeans_mex.o
ld: symbol(s) not found
collect2: ld returned 1 exit status
make: *** [mpi_kmeans_mex.mexmaci64] Error 1

Any ideas where the problem could be?
12-05-2012
Salem

> g++ -shared -fPIC -O3 -ffast-math -fomit-frame-pointer -fPIC -m64 -o libmpikmeans.so mpi_kmeans.cxx
So why are you overwriting your library with the result of a module compilation?

In fact, the whole sequence seems wrong - you create the library, then build the source.

Try
g++ -shared -fPIC -O3 -ffast-math -fomit-frame-pointer -fPIC -m64 -o mpi_kmeans.o mpi_kmeans.cxx
ar rc libmpikmeans.a mpi_kmeans.o
ranlib libmpikmeans.a

> gcc mpi_kmeans_mex.o -shared -o mpi_kmeans_mex.mexmaci64 libmpikmeans.a -L/Applications/MATLAB_R2012b.app/bin/maci64 -lmex
If you're compiling separate files using g++, then the final executable needs to be linked by invoking g++ as well.
Seeing ___gxx_personality_v0 is a sign you've mixed up the C and C++.
12-05-2012
in_ship

Hey Salem!

Thanks for your willingness to help! :)

I've removed the .so file command and changed g++ to gcc. Unfortunately though, I still seem to be getting an error on the g++ reference:

Quote:

ar rc libmpikmeans.a mpi_kmeans.o
/usr/bin/ranlib: file: libmpikmeans.a(mpi_kmeans.o) is a dynamic library, not added to the static library
ranlib libmpikmeans.a
ranlib: file: libmpikmeans.a(mpi_kmeans.o) is a dynamic library, not added to the static library
ranlib: empty library: libmpikmeans.a (no table of contents added)
gcc -shared -fPIC -O3 -ffast-math -fomit-frame-pointer -fPIC -m64 -DKMEANS_VERBOSE=0 -o mpi_kmeans.o mpi_kmeans.cxx
Undefined symbols:
"___gxx_personality_v0", referenced from:
comp_randperm(void const*, void const*)in ccWhobPa.o
remove_point_from_cluster(unsigned int, double*, double const*, unsigned int*, unsigned int)in ccWhobPa.o
add_point_to_cluster(unsigned int, double*, double const*, unsigned int*, unsigned int)in ccWhobPa.o
compute_distance(double const*, double const*, unsigned int)in ccWhobPa.o
randperm(unsigned int*, unsigned int)in ccWhobPa.o
kmeans_error(char*) in ccWhobPa.o
remove_identical_clusters(double*, float*, double const*, unsigned int*, unsigned int*, unsigned int, unsigned int, unsigned int)in ccWhobPa.o
compute_cluster_distances(float*, float*, double const*, unsigned int, unsigned int, bool const*)in ccWhobPa.o
compute_sserror(double const*, double const*, unsigned int const*, unsigned int, unsigned int)in ccWhobPa.o
assign_point_to_cluster(unsigned int, double const*, double const*, unsigned int, unsigned int, unsigned int, double*, float*, float*, float*)in ccWhobPa.o
assign_point_to_cluster_ordinary(double const*, double const*, unsigned int, unsigned int)in ccWhobPa.o
init_point_to_cluster(unsigned int, double const*, double const*, unsigned int, unsigned int, double*, float*, float const*)in ccWhobPa.o
kmeans_run(double*, double const*, unsigned int*, unsigned int, unsigned int, unsigned int, unsigned int)in ccWhobPa.o
_kmeans in ccWhobPa.o
CIE in ccWhobPa.o
ld: symbol(s) not found
collect2: ld returned 1 exit status
make: *** [libmpikmeans] Error 1
12-05-2012
in_ship

Here's an edit from my side:

I tried what you recommended, i.e. I used a different order for the 3 compile commands and replaced g++ with gcc

Code:

gcc -shared -fPIC -O3 -ffast-math -fomit-frame-pointer -fPIC -m64 -DKMEANS_VERBOSE=0 -o mpi_kmeans.o mpi_kmeans.cxx ar rc libmpikmeans.a mpi_kmeans.o ranlib libmpikmeans.a

Unfortuntely though, I still get some error!

Quote:

Undefined symbols:
"___gxx_personality_v0", referenced from:
comp_randperm(void const*, void const*)in ccs3czSH.o
remove_point_from_cluster(unsigned int, double*, double const*, unsigned int*, unsigned int)in ccs3czSH.o
add_point_to_cluster(unsigned int, double*, double const*, unsigned int*, unsigned int)in ccs3czSH.o
compute_distance(double const*, double const*, unsigned int)in ccs3czSH.o
randperm(unsigned int*, unsigned int)in ccs3czSH.o
kmeans_error(char*) in ccs3czSH.o
remove_identical_clusters(double*, float*, double const*, unsigned int*, unsigned int*, unsigned int, unsigned int, unsigned int)in ccs3czSH.o
compute_cluster_distances(float*, float*, double const*, unsigned int, unsigned int, bool const*)in ccs3czSH.o
compute_sserror(double const*, double const*, unsigned int const*, unsigned int, unsigned int)in ccs3czSH.o
assign_point_to_cluster(unsigned int, double const*, double const*, unsigned int, unsigned int, unsigned int, double*, float*, float*, float*)in ccs3czSH.o
assign_point_to_cluster_ordinary(double const*, double const*, unsigned int, unsigned int)in ccs3czSH.o
init_point_to_cluster(unsigned int, double const*, double const*, unsigned int, unsigned int, double*, float*, float const*)in ccs3czSH.o
kmeans_run(double*, double const*, unsigned int*, unsigned int, unsigned int, unsigned int, unsigned int)in ccs3czSH.o
_kmeans in ccs3czSH.o
CIE in ccs3czSH.o
ld: symbol(s) not found
collect2: ld returned 1 exit status
make: *** [libmpikmeans] Error 1

I have not seen the ccs3czSH.o file ever before?
12-06-2012
in_ship

I change the gcc command in the first line to g++. The references error vanished, but now I seem to have library connection problem! :-(
The code in the Makefile is bold and the errors are highlighted in red.

Code:

gcc -O3 -ffast-math -fomit-frame-pointer -fPIC -m64 -DKMEANS_VERBOSE=0 -c -o mpi_kmeans.o mpi_kmeans.cxx g++ -shared -fPIC -O3 -ffast-math -fomit-frame-pointer -fPIC -m64 -DKMEANS_VERBOSE=0 -o mpi_kmeans.o mpi_kmeans.cxx ar rc libmpikmeans.a mpi_kmeans.o /usr/bin/ranlib: file: libmpikmeans.a(mpi_kmeans.o) is a dynamic library, not added to the static library ranlib libmpikmeans.a ranlib: file: libmpikmeans.a(mpi_kmeans.o) is a dynamic library, not added to the static library ranlib: empty library: libmpikmeans.a (no table of contents added) gcc -O3 -ffast-math -fomit-frame-pointer -fPIC -m64 -I/Applications/MATLAB_R2012b.app/extern/include -DKMEANS_VERBOSE=0 -c mpi_kmeans_mex.cxx -o mpi_kmeans_mex.o g++ mpi_kmeans_mex.o -shared -m64 -o mpi_kmeans_mex.mexmaci64 libmpikmeans.a -L/Applications/MATLAB_R2012b.app/bin/maci64 -lmex ld: warning: in libmpikmeans.a, file was built for unsupported file format which is not the architecture being linked (x86_64) Undefined symbols: "_mxGetM", referenced from: _mexFunction in mpi_kmeans_mex.o ........
12-06-2012
stahta01

IIRC, The "-shared" means make a dynamic library/object file.

I have no idea if you want a dynamic or static library.

The "-static" should make a static library/object file.

http://gcc.gnu.org/onlinedocs/gcc/Link-Options.html

Tim S.
12-06-2012
in_ship

Hey stahta01!

Thanks for the heads-up!

I did try that too. Unfortunately though, I still get errors:

Quote:

gcc -O3 -ffast-math -fomit-frame-pointer -fPIC -m64 -DKMEANS_VERBOSE=0 -c -o mpi_kmeans.o mpi_kmeans.cxx
g++ -static -shared -fPIC -O3 -ffast-math -fomit-frame-pointer -fPIC -m64 -DKMEANS_VERBOSE=0 -o mpi_kmeans.o mpi_kmeans.cxx
ld: warning: in /usr/lib/gcc/i686-apple-darwin10/4.2.1/libgcc_static.a, file was built for unsupported file format which is not the architecture being linked (x86_64)
Undefined symbols:
"___assert_rtn", referenced from:
-----

I understand that there is an incompatibility problem, but which library must be rebuilt and how?
12-06-2012
stahta01

Doing both makes no sense to me "-static -shared". I could be wrong on this.

The "-m64" means 64 bit; "x86_64" means 64 bit.
The i686-apple-darwin10 implies 32 bit.

You might try adding "-shared-libgcc" in case your compiler only has 64 bit Dynamic of libgcc.

Tim S.
12-07-2012
in_ship

Hey Tim!

There is still some issue here.

Quote:

gcc -O3 -ffast-math -fomit-frame-pointer -fPIC -m64 -DKMEANS_VERBOSE=0 -c -o mpi_kmeans.o mpi_kmeans.cxx
g++ -shared-libgcc -fPIC -O3 -ffast-math -fomit-frame-pointer -fPIC -m64 -DKMEANS_VERBOSE=0 -o mpi_kmeans.o mpi_kmeans.cxx
Undefined symbols:
"_main", referenced from:
start in crt1.10.6.o
ld: symbol(s) not found
collect2: ld returned 1 exit status
make: *** [libmpikmeans] Error 1

I used the library path on my system to be '/usr/lib/gcc/i686-apple-darwin10/4.2.1/'
Could this be an issue?
12-07-2012
stahta01

Quote:

Originally Posted by in_ship

Hey Tim!

There is still some issue here.

Code:

Undefined symbols: "_main", referenced from: start in crt1.10.6.o

I used the library path on my system to be '/usr/lib/gcc/i686-apple-darwin10/4.2.1/'
Could this be an issue?

I am guessing your code is missing the main function.

If your code is not supposed to have a main you might need to add another option.
I can not remember the right option; not even sure I ever know about the right option.

Tim S.
12-07-2012
in_ship

mpi_kmeans does not really have a main-file.
However, mpi_kmeans_main.cxx does!
Can I somehow link them together?

Here's the Makefile (compile with make matlab)

Code:

# # Choose your compiler # # CC = gcc CPP = g++ CFLAGS=-O3 -ffast-math -fomit-frame-pointer -fPIC -m64 #-Werror # # MPI KMEANS FLAGS # VERBOSEFLAG=-DKMEANS_VERBOSE=0 # 0: silent, 1:iteration counter, 2:everything #PRECISION=-DINPUT_TYPE=0 # 0: double, 1:float # # MATLAB # MATLABDIR=/Applications/MATLAB_R2012b.app MATLAB_INCLUDE=-I$(MATLABDIR)/extern/include # # ARCHITECURE # # 64 bit SUFFIX=mexmaci64 MATLAB_LIB=-L$(MATLABDIR)/bin/maci64 -lmex LIBS=/usr/lib/gcc/i686-apple-darwin10/4.2.1/ /usr/lib/ matlab: mpi_kmeans_mex.$(SUFFIX) mpi_assign_mex.$(SUFFIX) mpi_kmeans.o: mpi_kmeans.cxx mpi_kmeans.h $(CC) $(CFLAGS) $(VERBOSEFLAG) $(PRECISION) -c -o $@ mpi_kmeans.cxx mpi_kmeans_main.o: mpi_kmeans_main.cxx $(CC) $(CFLAGS) $(BOOST_INCLUDE) -c -o mpi_kmeans_main.o mpi_kmeans_main.cxx libmpikmeans: mpi_kmeans.o ar rc libmpikmeans.a mpi_kmeans.o ranlib libmpikmeans.a $(CPP) -shared-libgcc -fPIC $(CFLAGS) $(VERBOSEFLAG) -o libmpikmeans.so $(VERBOSEFLAGS) $(PRECISION) mpi_kmeans.cxx mpi_assign_main.o: mpi_assign_main.cxx $(CC) $(CFLAGS) $(BOOST_INCLUDE) -c -o mpi_assign_main.o mpi_assign_main.cxx mpi_kmeans_main: libmpikmeans mpi_kmeans_main.o $(CC) mpi_kmeans_main.o $(CFLAGS) -L/usr/lib/ -static -o mpi_kmeans -lm libmpikmeans.a \ $(BOOST_LIB) $(LIBS) mpi_assign_main: libmpikmeans mpi_assign_main.o $(CC) mpi_assign_main.o $(CFLAGS) -L/usr/lib/ -static -o mpi_assign -lm libmpikmeans.a \ $(BOOST_LIB) $(LIBS) mpi_kmeans_mex.$(SUFFIX): libmpikmeans mpi_kmeans_mex.o $(CPP) mpi_kmeans_mex.o -shared -m64 -o mpi_kmeans_mex.$(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)