I need compile a piece of C code to be called from matlab (mex compiling).
I am doing that on an intel mac and, since I am using Matlab's R2010a (7.10.0.499), I'd like to compile the C code into a version for 64-bits.
For whatever reason, just doing mex with the -arch=maci64 option did not seem to work...
As a way around, I am compiling the C code to a mexmaci64 file directly on the command line.
I used the gcc calls made by mex (with the -v option on) as a starting point.
I managed to compile the C code to an object file, but it looks like I am not compiling the C code to the correct architecture.
Does anyone know how to correct the gcc calls below so the C code gets compiled to 64-bits intel macs?
Details are listed below.
As always, any help greatly appreciated...
Keep thirsty, my friends. :p
G
DETAILS:
Here is how I did the compilation and linking:
gcc -c -I/Applications/MATLAB_R2010a.app/extern/include -DMATLAB_MEX_FILE -fno-common -no-cpp-precomp -fexceptions -D MACVERSION -DMX_COMPAT_32 -O3 -DNDEBUG "BoxQP.c"
gcc -O -bundle -Wl,-flat_namespace -undefined suppress -Wl,-exported_symbols_list,/Applications/MATLAB_R2010a.app/extern/lib/maci64/mexFunction.map -o "BoxQP.mexmaci64" BoxQP.o -L/Applications/MATLAB_R2010a.app/bin/maci64 -lmx -lmex -lmat -lstdc++
Here are the warnings I get:
ld warning: in /Applications/MATLAB_R2010a.app/bin/maci64/libmx.dylib, file is not of required architecture
ld warning: in /Applications/MATLAB_R2010a.app/bin/maci64/libmex.dylib, file is not of required architecture
ld warning: in /Applications/MATLAB_R2010a.app/bin/maci64/libmat.dylib, file is not of required architecture
Ignoring the warnings and calling the BoxQP function from matlab results in the following error message:
??? Invalid MEX-file '/Users/gvrocha/Documents/academic/projects/splice/code/matlab/covsel/BoxQP.mexmaci64':
dlopen(/Users/gvrocha/Documents/academic/projects/splice/code/matlab/covsel/BoxQP.mexmaci64, 1): no suitable image found.
Did find: /Users/gvrocha/Documents/academic/projects/splice/code/matlab/covsel/BoxQP.mexmaci64: mach-o, but wrong architecture.
PS: I tried changing the -DMX_COMPAT_32 flag to -DMX_COMPAT_64 but I do get the same warnings and same error...
PPS: I guess it may be relevant to mention that I am using Mac OS X 10.5.8 (the "tropical"/plain-vanilla Leopard, i.e., not the snow Leopard).
PPPS: The same happens with the yprime.c example provided by MATLAB
Related
I am trying to compile a multi threaded application to WebAssembly. The application uses OpenMP for multithreading.
To compile I am using the Emscripten framework.
I have already downloaded the source files for OpenMP and compiled it for my host machine using make. With the following command I can get it to link with a simple demo application on my machine:
g++ -Wall -Werror -pedantic main.o -o main.x /$PATH_TO_OPENMP/build/runtime/src/libgomp.a -pthread -lstdc++ -Wl,--no-as-needed -ldl
I then tried to compile OpenMP to the llvm bytecode format used by Emscripten. To do so I tried to run 'emmake make', so that the emscripten framework executes the OpenMP makefiles with a suitable compiler. As emscripten does not like shared object files I compiled it to static library .a files.
This works and actually gives me object files to which I can link.
I then wanted to link my demo application with the following command
em++ -Wall -Werror -pedantic main.o -o main.html /home/main/data/Programming/openMP/openmp_web/build/runtime/src/libgomp.a -pthread -lstdc++ -Wl,--no-as-needed -ldl
But I get these warnings, that it couldn't link to OpenMP files:
shared:WARNING: object /tmp/emscripten_temp_ONa0eU_archive_contents/kmp_atomic.cpp.o is not a valid object file for emscripten, cannot link
.
.
shared:WARNING: object /tmp/emscripten_temp_ONa0eU_archive_contents/kmp_str.cpp.o is not a valid object file for emscripten, cannot link
shared:WARNING: object /tmp/emscripten_temp_ONa0eU_archive_contents
So I figured I must have compiled OpenMP with the wrong compiler. I then tried to change the compiler when building the library by using the following commands:
cmake -DCMAKE_C_COMPILER=emcc -DCMAKE_CXX_COMPILER=em++ -DLIBOMP_LIB_TYPE=normal -DLIBOMP_ENABLE_SHARED=OFF -DCMAKE_BUILD_TYPE=Release -DLIBOMP_ARCH=x86_64 OPENMP_STANDALONE_BUILD=1 ..
emmake make
But this just gives strange errors on some missing system variables
/home/main/data/Programming/openMP/openmp_web/runtime/src/kmp_platform.h:82:2: error: Unknown OS
/home/main/data/Programming/openMP/openmp_web/runtime/src/kmp_platform.h:203:2: error: Unknown or unsupported architecture
In file included from /home/main/data/Programming/openMP/openmp_web/runtime/src/kmp_alloc.cpp:13:
In file included from /home/main/data/Programming/openMP/openmp_web/runtime/src/kmp.h:77:
/home/main/data/Programming/openMP/openmp_web/runtime/src/kmp_os.h:171:2: error: "Can't determine size_t printf format specifier."
Does anyone have an idea on what I could do differently?
When I try to compile a trivial example test.c
int main () {
return 0;
}
for a cortex m7 target with hard float ABI by using the following invocation
arm-none-eabi-gcc -mcpu=cortex-m7 -mfpu=fpv5-d16 -mfloat-abi=hard --specs=nosys.specs test.c
I get this error:
/usr/lib/gcc/arm-none-eabi/6.3.1/../../../arm-none-eabi/bin/ld: error: /usr/lib/gcc/arm-none-eabi/6.3.1/../../../arm-none-eabi/lib/crt0.o: Conflicting CPU architectures 13/1
/usr/lib/gcc/arm-none-eabi/6.3.1/../../../arm-none-eabi/bin/ld: failed to merge target specific data of file /usr/lib/gcc/arm-none-eabi/6.3.1/../../../arm-none-eabi/lib/crt0.o
/usr/lib/gcc/arm-none-eabi/6.3.1/../../../arm-none-eabi/bin/ld: error: a.out uses VFP register arguments, /usr/lib/gcc/arm-none-eabi/6.3.1/../../../arm-none-eabi/lib/libc.a(lib_a-atexit.o) does not
[snip]
/usr/lib/gcc/arm-none-eabi/6.3.1/../../../arm-none-eabi/bin/ld: failed to merge target specific data of file /usr/lib/gcc/arm-none-eabi/6.3.1/../../../arm-none-eabi/lib/libnosys.a(_exit.o)
collect2: error: ld returned 1 exit status
So the issue is that gcc is linking to the wrong libc.a. If I use the argument print-multi-directory, it would appear that my version of arm-none-eabi-gcc should support this architecture:
$ arm-none-eabi-gcc -mcpu=cortex-m7 -mfpu=fpv5-d16 -mfloat-abi=hard --specs=nosys.specs --print-multi-directory
thumb/v7e-m/fpv5/hard
And I can list the different versions of libc.a that are provided by arm-none-eabi-gcc:
$ find /usr/lib/arm-none-eabi/ -name libc.a
/usr/lib/arm-none-eabi/newlib/armv7e-m/libc.a
/usr/lib/arm-none-eabi/newlib/armv7e-m/fpu/fpv5-sp-d16/libc.a
/usr/lib/arm-none-eabi/newlib/armv7e-m/fpu/libc.a
/usr/lib/arm-none-eabi/newlib/armv7e-m/fpu/fpv5-d16/libc.a
/usr/lib/arm-none-eabi/newlib/armv7e-m/softfp/fpv5-sp-d16/libc.a
/usr/lib/arm-none-eabi/newlib/armv7e-m/softfp/libc.a
/usr/lib/arm-none-eabi/newlib/armv7e-m/softfp/fpv5-d16/libc.a
/usr/lib/arm-none-eabi/newlib/libc.a
/usr/lib/arm-none-eabi/newlib/armv6-m/libc.a
/usr/lib/arm-none-eabi/newlib/fpu/libc.a
/usr/lib/arm-none-eabi/newlib/thumb/libc.a
/usr/lib/arm-none-eabi/newlib/armv7-m/libc.a
So it looks like there is a version of libc.a compiled for my desired architecture, but gcc isn't linking against it. How can I get gcc to link against the correct version of libc.a?
I'm using arm-none-eabi-gcc version 6.3.1 provided by the gcc-arm-none-eabi package for Ubuntu 18.04.
This is a follow-up to the question at Element-Wise Matrix Multiplication in Rcpp
I have been getting a number of different kinds of errors with RcppArmadillo since upgrading to Mavericks. I have Xcode 5.0.2 and Command Line Tools installed. Also, gfortran from Homebrew. But I keep encountering the error below --
> cppFunction("arma::mat schur(arma::mat& a, arma::mat& b)
{ return(a % b); }", depends="RcppArmadillo")
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [sourceCpp_18474.so] Error 1
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include - I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include" -fPIC "-mtune=native -g -O2 -Wall -pedantic -Wconversion" -c fileaf992bfb8f84.cpp -o fileaf992bfb8f84.o clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o sourceCpp_18474.so fileaf992bfb8f84.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -lgfortran /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
Error in sourceCpp(code = code, env = env, rebuild = rebuild, showOutput = showOutput, :
Error 1 occurred building shared library.
WARNING: The tools required to build C++ code for R were not found.
Please install Command Line Tools for XCode (or equivalent).
# Contents of Makevars
$ cat ~/.R/Makevars
CC=clang
CXX=clang++
CXXFLAGS="-mtune=native -g -O2 -Wall -pedantic -Wconversion"
FLIBS=-lgfortran
Commenting FLIBS=-lgfortran does not help and results in even more error messages --
> cppFunction("arma::mat schur(arma::mat& a, arma::mat& b) { return(a % b); }", depends="RcppArmadillo")
ld: warning: directory not found for option '-L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64'
ld: warning: directory not found for option '-L/usr/local/lib/x86_64'
ld: warning: directory not found for option '-L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [sourceCpp_50381.so] Error 1
Thanks in advance.
Update
Following suggestions from response from Kevin and Dirk below, I re-installed Rcpp, RcppArmadillo and inline from source and updated FLIBS to point to the actual directory. This solved the issue.
# Update FLIBS in ~/.R/Makevars
FLIBS=-L/usr/local/Cellar/gfortran/4.8.2/gfortran
#Re-Install from source
install.packages(c("Rcpp","RcppArmadillo","inline"),type="source")
#Restart R
EDIT: If you're a Homebrew user, you now instead need to use brew install gcc (gfortran is no longer provided separate of gcc), and you can then follow the instructions here to get set up.
You have to symlink the libraries to /usr/local/lib manually:
ln -s /usr/local/Cellar/gfortran/4.8.2/gfortran/lib/libgfortran.* /usr/local/lib/
I thought brew link gfortran would handle this, but apparently it only symlinks the gfortran program and not the actual libraries. So, unfortunately, you have to do it yourself.
(Replace 4.8.2 with whichever version of gfortran you're using from homebrew.)
Alternatively, if you want to keep from modifying /usr/local/lib, you can use
FLIBS=-L/usr/local/Cellar/gfortran/4.8.2/gfortran
in your ~/.R/Makevars file instead, so R knows where to find the gfortran libraries.
I can only suggest you study the numerous threads on the r-sig-mac list, the different answers here on SO as well as the posts on the rcpp-devel list.
As your error comes from the failed Fortran linking, maybe also review the standard page by Simon U. as well as the tools page it points too. AFAIK you should use the (older) gfortran 4.2.* from that page with R -- but then I am not an OS X user.
Edit in late 2016: We now have more detailed instructions in section 2.16 of the Rcpp FAQ.
I wrote like this :
gcc -m elf_i386
it says:
gcc: error: elf_i386: No such file or directory
basically I am trying to compile a 32bit program on 64bit system,but error :
/usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../x86_64-suse-linux/bin/ld:
skipping incompatible /usr/lib/libSDL.so when searching for -lSDL
which I've checked the project built with -m32 and I can see all the *.o file are ELF 32-bit LSB,and the /usr/lib/libSDL.so are ELF 32-bit LSB too...so I might need pass -m elf_i386 to ld right? but I don't use ld directly I just use gcc to compile it.
gcc -m32
is what you want probably. The elf_i386 is passed by gcc to ld (if needed) just as Alan Curry mentioned in the comments.
The "skipping incompatible library" warning is just a warning and if it doesn't come up with "can't find the library", then you can assume it linked to the correct binary (because of the -m32 option).
I need to suppress "-arch x86_64 -arch i386" flags Waf is passing to GCC.
I am building an SDL/Opengl application. If I link against 32 bit SDL runtime I get error
Undefined symbols for architecture i386:
"_SDL_Quit", referenced from:
__del_video in SDL_functions.c.2.o
__init_video in SDL_functions.c.2.o
If I link against 64 bit SDL runtime, I get error "Undefined symbols for architecture x86_64"
The compiler is apparently using flags
-arch x86_64 -arch i386
I understand that this causes GCC on OSX to try to compile for both architectures. I want to either compile for 64 bit, or compile for 32 bit. How do I suppress the flags for one architecture?
I found out in my case that the double arch flags were originating here, specifically from distutils.sysconfig.get_config_var('LDFLAGS'). This returns the LDFLAGS that Python thinks you should link Python modules with. In my case, file $(which python) is a "Mach-O universal binary with 2 architectures", so Python thinks you should link with -arch x86_64 -arch i386 -Wl,F.
My problem was that I was building a Python native module that needed to link against Python and another library which was not built with both arches. When building my module with both arches, linking failed with "symbols not found", because both arches were not available in the third-party library.
Since waf unfortunately doesn't allow you to override its computed flags with your own flags, as Automake does, I could only fix this by messing directly with my ctx() object in my wscript:
for var in ['CFLAGS_PYEMBED', 'CFLAGS_PYEXT', 'CXXFLAGS_PYEMBED',
'CXXFLAGS_PYEXT', 'LINKFLAGS_PYEMBED', 'LINKFLAGS_PYEXT']:
newvar = []
for ix, arg in enumerate(ctx.env[var]):
if '-arch' not in (arg, ctx.env[var][ix - 1]):
newvar.append(arg)
ctx.env[var] = newvar
(This removes all -arch flags and their arguments from the relevant variables. Since I was also passing my own -arch flag in my CFLAGS, it now does not get overridden.)
I don't know of a way to issue a command/flag to suppress other flags. However, to compile for only 64 or 32 bits, you can use -m64 or -m32, respectively. Since you're compiling for both architectures, -m32 might be your only option because -m64 won't work for i386.