I am just getting started with Cython and am trying to compile a "Hello World" script. I am trying to use gcc -Os /User/Documents/Python/Test\ Python/helloCopy.c -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -l, but I don't know what to add after the -l. Other forum pages say to "include -lpython2.7 (or whatever version of Python you're using) on the linker command-line" but that produces ld: library not found for -lpython3.5
clang: error: linker command failed with exit code 1 (use -v to see invocation)
Should I be directing the -l to a particular folder?
I do not know what resource you're using, but this does not say anything about a -l flag. It suggests
cython -a helloCopy.pyx
This creates a yourmod.c file, and the -a switch produces an annotated html file of the source code. Pass the -h flag for a complete list of supported flags.
gcc -shared -pthread -fPIC -fwrapv -O2 -Wall -fno-strict-aliasing -I/usr/include/python2.7 -o helloCopy.so helloCopy.c
(Linux)
On macOS I would try to compile with
gcc -I/usr/bin/python -o helloCopy.so helloCopy.c
to use the standard version of Python.
Related
I have troubles using a Python interface generated with SWIG (I have OSX 10.11.12). After compiling and linking everything together as such:
swig -python erk_integrator.i
gcc -c -fPIC -O3 model.c auxiliary_functions.c timing_functions.c
gcc -c -fPIC -O3 erk_integrator.c erk_integrator_wrap.c -I. -I/usr/local/include/python2.7
gcc -lpython -dynamiclib model.o erk_integrator.o erk_integrator_wrap.o auxiliary_functions.o timing_functions.o -o _erk_integrator.so
I try a test script, but Python throws a fatal error:
/usr/local/bin/python test_erk.py
Fatal Python error: PyThreadState_Get: no current thread
Abort trap: 6
But when I run
/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7 test_erk.py
everything works as it should. However, I need to use /usr/local/bin/python (from Homebrew) instead of the system Python.
I think something goes wrong in the linking step. Many thanks for helping!
This blog post helped me solve it: blog.tim-smith.us/2015/09/python-extension-modules-os-x
It turns out on OSX you need
-undefined dynamic_lookup
instead of
-lpython
I'm trying to install Distance for python on my mac (OS X Yosemite).
After downloading the package and unpacking it, I run (as described on their page):
python setup.py install --with-c
From this I get the following error message:
running build_ext
building 'distance.cdistance' extension
gcc -fno-strict-aliasing -I/Users/me/anaconda/envs/name/include - arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/me/anaconda/envs/name/include/python2.7 -c cdistance/distance.c -o build/temp.macosx-10.5-x86_64-2.7/cdistance/distance.o
gcc -bundle -undefined dynamic_lookup -L/Users/me/anaconda/envs/name/lib -arch x86_64 -arch x86_64 build/temp.macosx-10.5-x86_64-2.7/cdistance/distance.o -L/Users/me/anaconda/envs/name/lib -o build/lib.macosx-10.5-x86_64-2.7/distance/cdistance.so
ld: library not found for -lgcc_s.10.5
clang: error: linker command failed with exit code 1 (use -v to see invocation)
error: command 'gcc' failed with exit status 1
From what I understood from several posts like this one or this previously asked question, it looks like clang, which is called through the command gcc, can't find the libgcc library.
I ran find /usr/ -name libgcc*and this if what I get:
/usr//lib/libgcc_s.1.dylib
/usr//lib/libgcc_s.10.4.tbd
/usr//lib/libgcc_s.10.5.tbd
/usr//local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.4.0/5.2.0/i386/libgcc.a
/usr//local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.4.0/5.2.0/i386/libgcc_eh.a
/usr//local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.4.0/5.2.0/libgcc.a
/usr//local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.4.0/5.2.0/libgcc_eh.a
/usr//local/Cellar/gcc/5.2.0/lib/gcc/5/libgcc_ext.10.4.dylib
/usr//local/Cellar/gcc/5.2.0/lib/gcc/5/libgcc_ext.10.5.dylib
/usr//local/Cellar/gcc/5.2.0/lib/gcc/5/libgcc_s.1.dylib
/usr//local/Cellar/gcc/5.2.0/lib/gcc/5/libgcc_s_ppc64.1.dylib
/usr//local/Cellar/gcc/5.2.0/lib/gcc/5/libgcc_s_x86_64.1.dylib
/usr//local/gfortran/lib/gcc/x86_64-apple-darwin14/5.1.0/i386/libgcc.a
/usr//local/gfortran/lib/gcc/x86_64-apple-darwin14/5.1.0/i386/libgcc_eh.a
/usr//local/gfortran/lib/gcc/x86_64-apple-darwin14/5.1.0/libgcc.a
/usr//local/gfortran/lib/gcc/x86_64-apple-darwin14/5.1.0/libgcc_eh.a
/usr//local/gfortran/lib/libgcc_ext.10.4.dylib
/usr//local/gfortran/lib/libgcc_ext.10.5.dylib
/usr//local/gfortran/lib/libgcc_s.1.dylib
/usr//local/gfortran/lib/libgcc_s_ppc64.1.dylib
/usr//local/gfortran/lib/libgcc_s_x86_64.1.dylib
And now I'm stuck because I don't know what to do next. Basically the question is: how do I make clang to know where the library is ?
I solved the issue thanks to this link which showed that this is a very recent issue with Xcode6.
You just need to upgrade Xcode to Xcode7 and set it up as your default toolkit chain. Easy.
I've been provisioned a very bare-bones RHEL 4.4 at work; e.g., it didn't have java or gcc installed.
I have followed this guide to install python 2.7.6 on another VM (RHEM 4.6) successfully. However on this new vm, I cannot make without getting this error:
gcc -pthread -c -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE \
-DSVNVERSION="\"`LC_ALL=C echo Unversioned directory`\"" \
-DHGVERSION="\"`LC_ALL=C `\"" \
-DHGTAG="\"`LC_ALL=C `\"" \
-DHGBRANCH="\"`LC_ALL=C `\"" \
-o Modules/getbuildinfo.o ./Modules/getbuildinfo.c
gcc.orig: directory": No such file or directory
<command-line>: warning: missing terminating " character
./Modules/getbuildinfo.c: In function â_Py_svnversionâ:
./Modules/getbuildinfo.c:63: error: missing terminating " character
./Modules/getbuildinfo.c:63: error: expected expression before â;â token
make: *** [Modules/getbuildinfo.o] Error 1
I tried what was suggested in this unrelated bug report:
SVNVERSION="Unversioned directory"
./configure
make
but received the same error.
I saw this question on super user, which suggests to check the output of the svnversion command in the Modules directory, but I don't have svn or svnversion on this machine. It also suggests to edit the function _PY_svnversion in Modules/getbuildinfo.c, which I did but received the same error.
Any ideas?
Ok I found the answer in my case:
issue configure which will create a new Makefile
edit the Makefile with vi.
search for SVNVERSION and set it to
SVNVERSION= ""
make will then work.
I want to embed python in C. But I find that the version of python interpreter which is embedded in my program is 2.7 (The default version on mac).
How could I specify particular version of python interpreter when I compile the c codes in mac os x. The gcc in os x is definitely different from in linux.
I have already installed python3 through HomeBrew.
Thanks a lot.
UPDATE:
I try to use python3.4-config --cflags and python3.4-config --ldflags to find out the required compiler and linker flags. Then I get these recommended flags when compiling & linking:
-I/usr/local/Cellar/python3/3.4.1/Frameworks/Python.framework/Versions/3.4/include/python3.4m -I/usr/local/Cellar/python3/3.4.1/Frameworks/Python.framework/Versions/3.4/include/python3.4m -Wno-unused-result -Werror=declaration-after-statement -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/include -I/usr/local/opt/sqlite/include
and
-L/usr/local/Cellar/python3/3.4.1/Frameworks/Python.framework/Versions/3.4/lib/python3.4/config-3.4m -ldl -framework CoreFoundation -lpython3.4m
After this, I assemble these flags along with source file into gcc, and obtain an error:
Undefined symbols for architecture x86_64:
"_PyUnicodeUCS2_FromString", referenced from:
_main in py2-5d8da5.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
The C code which I test here comes from Python Documentation
I got the same errors when trying to do this tutorial on OSX. You don't need all of the flags that the config utility spits out. You definitely don't need the corefoundation framework if you're just doing the embedding tutorial. Just use the include directory for headers:
-I/usr/local/Cellar/python3/3.4.1/Frameworks/Python.framework/Versions/3.4/include/python3.4m -I/usr/local/Cellar/python3/3.4.1/Frameworks/Python.framework/Versions/3.4/include/python3.4m
, and the library to link to:
-L/usr/local/Cellar/python3/3.4.1/Frameworks/Python.framework/Versions/3.4/lib/python3.4/config-3.4m -lpython3.4m
so here's a one-liner to compile and link:
gcc -I/usr/local/Cellar/python3/3.4.1/Frameworks/Python.framework/Versions/3.4/include/python3.4m -I/usr/local/Cellar/python3/3.4.1/Frameworks/Python.framework/Versions/3.4/include/python3.4m -L/usr/local/Cellar/python3/3.4.1/Frameworks/Python.framework/Versions/3.4/lib/python3.4/config-3.4m -lpython3.4m /path/to/main.c -o /path/to/output/executable
I am implementing a C++ program that uses python/C++ Extensions. As of now I am explicitly linking my program to python static library I compiled. I am wondering is there any way to link my program with system installed python(i mean the default python installation that comes with linux)
Yes. There is a command line utility called python-config:
Usage: /usr/bin/python-config [--prefix|--exec-prefix|--includes|--libs|--cflags|--ldflags|--help]
For linkage purposes, you have to invoke it with --ldflags parameter. It will print a list of flags you have to pass to the linker (or g++) in order to link with system installed python libraries:
$ python-config --ldflags
-L/usr/lib/python2.6/config -lpthread -ldl -lutil -lm -lpython2.6
It also can give you flags to compilation with --cflags parameter:
$ python-config --cflags
-I/usr/include/python2.6 -I/usr/include/python2.6 -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes
Say you have a test program in test.cpp file, then you can do something like this in order to compile and link:
g++ $(python-config --cflags) -o test $(python-config --ldflags) ./test.cpp
That will link your program with shared libraries. If you want to go static, you can pass -static option to the linker. But that will link with all static stuff, including a runtime. If you want to go just with static python, you have to find those libraries yourself. One of the option is to parse python-config --ldflags output and look for libraries with .a extensions. But I'd rather stick to all dynamic or all static.
Hope it helps. Good luck!