I'm trying to generate a python wrapper for a C++ library that I am putting together. I have just come across SWIG and am trying to use this in conjunction with distutils. I'm modifying someone elses code, so odd errors were to be expected but this one is just confusing.
I've managed to generate a c++ wrapper file with SWIG and am now attempting to run a modified version of setup.py in order to install the wrapper (which itself may or may not work, but I'll cross that bridge when it comes to it.) When doing this compiler errors pop up about inability to include header files. Specifically - string, ostream, sstream, map and vector. All of which are standard libraries, included as "include ".
The code itself compiles, but in trying to create a wrapper this way it does not.
I'm not entirely sure what information is relevant to this but this is how the extension is made:
## Extension definition
import os
wrapsrc = './project_rewrite_wrap.c'
incdir_src = os.path.abspath('../include/project')
incdir_build = os.path.abspath('../include/project')
libdir = os.path.abspath('../lib')
ext = Extension('_project_rewrite',
[wrapsrc],
include_dirs=[incdir_src, incdir_build],
library_dirs=[libdir, os.path.join(libdir,'.libs')],
libraries=['ProjectMain'])
The gcc command that is run is:
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/home/ben/Project/rewrite/include/Project -I/home/ben/Project/rewrite/include/Project -I/usr/include/python2.6 -c ./project_rewrite_wrap.c -o build/temp.linux-i686-2.6/./project_rewrite_wrap.o
Which results in errors such as:
./project_rewrite_wrap.c:2696:18: error: string: No such file or directory
Any thoughts would be greatly appreciated, thanks.
You are compiling C code - the headers you mention are part of C++, not C. To compile as C++ code, use the g++ driver instead of gcc, and give the source files a .cpp extension instead of .c.
Related
I'm been attempting to compile an open-source C++ library (QuantLib-1.7) on my mac for several days but I seem to be encountering some kind of C++11 compatibility issue.
When I run make && sudo make install from the terminal the compilation seems to work except for a bunch of errors of the form
Making all in BermudanSwaption
g++ -DHAVE_CONFIG_H -I. -I../../ql -I../.. -I../.. -I/opt/local/include -g -O2 -MT BermudanSwaption.o -MD -MP -MF .deps/BermudanSwaption.Tpo -c -o BermudanSwaption.o BermudanSwaption.cpp
In file included from BermudanSwaption.cpp:22:
In file included from ../../ql/quantlib.hpp:43:
In file included from ../../ql/experimental/all.hpp:25:
In file included from ../../ql/experimental/volatility/all.hpp:21:
In file included from ../../ql/experimental/volatility/zabr.hpp:31:
In file included from ../../ql/math/statistics/incrementalstatistics.hpp:35:
In file included from /opt/local/include/boost/accumulators/statistics/stats.hpp:14:
In file included from /opt/local/include/boost/accumulators/statistics_fwd.hpp:12:
/opt/local/include/boost/mpl/print.hpp:50:19: warning: in-class initialization
of non-static data member is a C++11 extension [-Wc++11-extensions]
const int m_x = 1 / (sizeof(T) - sizeof(T));
^
1 warning generated.
I'm guessing this has something to do with g++ not being correctly configured for C++11. I'm familiar with the fact that C++11 can be invoked by compiling with g++ -std=c++11. However, despite a lot of googling I can't find a way to modify the makefile such that -std=c++11 is called when I run make && sudo make install.
Any help would be greatly appreciated.
Here is the section of the makefile which I believe is relevant:
BOOST_INCLUDE = -I/opt/local/include
BOOST_LIB = -L/opt/local/lib
BOOST_THREAD_LIB =
BOOST_UNIT_TEST_DEFINE = -DQL_WORKING_BOOST_STREAMS
BOOST_UNIT_TEST_LIB = boost_unit_test_framework-mt
BOOST_UNIT_TEST_MAIN_CXXFLAGS = -DBOOST_TEST_DYN_LINK
CC = gcc
CCDEPMODE = depmode=gcc3
CFLAGS = -g -O2
CPP = gcc -E
CPPFLAGS = -I/opt/local/include
CXX = g++
CXXCPP = g++ -E
CXXDEPMODE = depmode=gcc3
CXXFLAGS = -g -O2
Here is the output from running "g++ -v":
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 7.0.0 (clang-700.1.76)
Target: x86_64-apple-darwin14.5.0
Thread model: posix
Makefile.am: https://www.dropbox.com/s/v5j7qohwfup81od/Makefile.am?dl=0
Makefile.in: https://www.dropbox.com/s/t92hft9ea2ar1zw/Makefile.in?dl=0
QuantLib-1.7 directory: https://www.dropbox.com/sh/ulj0y68m8x35zg8/AAA-w7L2_YWIP8_KnwURErzYa?dl=0
Full error log: https://www.dropbox.com/s/g09lcnma8skipv7/errors.txt?dl=0
Add something like
CXXFLAGS += -std=c++11
to your Makefile. This will work regardless of the Darwin-specific munging of the g++ executable---it's really clang++.
References:
https://gcc.gnu.org/onlinedocs/gcc-5.2.0/gcc/C_002b_002b-Dialect-Options.html#C_002b_002b-Dialect-Options
https://gcc.gnu.org/projects/cxx0x.html
http://clang.llvm.org/cxx_status.html
https://www.gnu.org/software/make/manual/html_node/Implicit-Variables.html
As you already have, and are familiar with homebrew, my suggestion would be to use that to install and manage quantlib like this:
brew install quantlib
That will then build and put all the files in /usr/local/Cellar/quantlib under some version number that is not of importance. The important thing is the the tools are then linked into /usr/local/bin so all you need to do is make sure that /usr/local/bin is in your PATH.
That gives you access to the tool quantlib-config which is always linked to the latest version and it knows which version that is. So, if you run:
quantlib-config --cflags
it will tell you what the correct path is for your includes like this:
-I/usr/local/Cellar/quantlib/1.6.1/include
Likewise, if you run:
quantlib-config --libs
it will tell you the correct linking directories and libraries for your latest version.
In short, all you need to do to compile is:
g++ $(quantlib-config --cflags --libs)
and it will always pull in the version you are using.
Note that if you use a Makefile, you will need to double the dollar signs.
This is how I eventually managed to compile the Quantlib library for future reference. It is probably not the most efficient/elegant method but it appears to work.
I followed the steps given in http://quantlib.org/install/macosx.shtml and found that running make && sudo make install led to the error reported in the OP.
Create a new static library C++ project in Eclipse called 'Quantlib'
Copy the ql directory located in the .tar file to the Quantlib Eclipse workspace
Right-click Quantlib > Properties > C/C++ Build > Settings > Cross G++ Compiler: Change the Language standard to ISO C++ 11 (-std=c++0x)
Right-click Quantlib > C/C++ General > Paths and Symbols: Add the following include directories for GNU C++
opt/local/include
/Quantlib (check "Is a workspace directory")
/opt/local/include/boost.
Build the Quantlib project (around 34 min on MacBook Air 1.8 GHz Intel Core i7)
Create a new C++ executable project (e.g. BermudanSwaption) and copy the BermudanSwaption.cpp into the BermudanSwaption Eclipse workspace
Repeat steps 4. and 5. for the BermudanSwaption Eclipse project
Right-click BermudanSwaption > Properties > C/C++ General > Paths and Symbols > References: check Quantlib (the Library Paths tab should now contain the entry '/Quantlib/Debug')
Build and run the BermudanSwaption executable project
QuantLib-1.7
OSX Yosemite 10.10.5
Eclipse C/C++ Development Tools Version: 8.8.0.201509131935
Xcode Version 7.1 (7B91b)
xcode-select version 2339.
I'm having some trouble building shared libraries from Ada packages without using GPR's.
I have a package, Numerics, in files "numerics.ads" and "numerics.adb". They have no dependencies. There is a small build script which does:
gnatmake -Os numerics.ad[bs] -cargs -fPIC
gcc -shared numerics.o -o libnumerics.so -Wl,-soname,libnumerics.so
The .so and .ali files are installed at /usr/lib, and the .ads file is installed at /usr/include.
gnatls -v outputs the following relevant parts:
Source Search Path:
<Current_Directory>
/usr/include
/usr/lib/gcc/x86_64-unknown-linux-gnu/5.1.0/adainclude
Object Search Path:
<Current_Directory>
/usr/lib
/usr/lib/gcc/x86_64-unknown-linux-gnu/5.1.0/adalib
So GNAT should have no problem finding the files.
Then, trying to compile a package that depends on Numerics:
gnatmake -O2 mathematics.ad[bs] -cargs -fPIC
outputs:
gcc -c -fPIC mathematics.adb
gcc -c -I./ -fPIC -I- /usr/include/numerics.ads
cannot generate code for file numerics.ads (package spec)
gnatmake: "/usr/include/numerics.ads" compilation error
This error has me thinking GNAT doesn't recognize the shared library, and is trying to rebuild Numerics.
I'd like to be building shared libraries, and only supply the spec for reference/documentation purposes.
edit:
So, it looks like gprbuild does two things I'm not doing. The first, is also passing -lnumerics to the compiler. The second, which shouldn't matter since libnumerics.so is in a standard directory anyways, is -L«ProjectDirectory». GPRbuild is obviously not doing desired behavior either, even though it's building the dependent project. It should be using the installed library /usr/lib/libnumerics.so, but instead is using «path»/Numerics/build/libnumerics.so. Furthermore, after building Numerics with GPRbuild, and then renaming the body to make it as if the body didn't exist (like with the installed files), when building Mathematics with GPRbuild, it complains about the exact same problem. It's as if the libraries aren't even shared, and GPRBuild is just making them look that way (except readelf reports the correct dependencies inside the libraries).
Adding -lnumerics to the build script accomplishes nothing; the build error is exactly the same. I'm completely lost at this point.
edit:
Following the link from Simon, the buildscript has changed to:
gnatmake -O2 mathematics.ad[bs] \
-aI/usr/include \
-aO/usr/lib \
-cargs -fPIC \
-largs -lnumerics
The error is essentially the same:
gcc -c -O2 -I/usr/include/ -fPIC mathematics.adb
gcc -c -I./ -O2 -I/usr/include/ -fPIC -I- /usr/include/numerics.ads
cannot generate code for file numerics.ads (package spec)
gnatmake: "/usr/include/numerics.ads" compilation error
I thought to check libnumerics.so is actually a correct shared library. ldd reports:
linux-vdso.so.1 (0x00007ffd944c1000)
libc.so.6 => /usr/lib/libc.so.6 (0x00007f50d3927000)
/usr/lib64/ld-linux-x86-64.so.2 (0x00007f50d3ed4000)
So I'm thinking yes, the library is fine, and gnatmake still isn't recognizing it.
In general, you need to install the body of the packages as well (numerics.adb in your case). Also, I suspect you want to set the ALI files
(numerics.ali) as read-only, so that gnatmake does not try to recompile them.
One of my users is getting an error message when trying to compile a C part of our mixed C/C++ codebase on ubuntu 12.04 with gcc 4.8.1
We have a library in C++ with some C-linkage functions in, and want to compile a C program linking to it. The library is compiled with g++ and builds fine. The c program fails like this:
> gcc -O3 -g -fPIC -I/media/Repo/lcdm/code/cosmosis/ -Wall -Wextra -pedantic -Werror -std=c99 -o c_datablock_t c_datablock_test.c -L . -lcosmosis
cc1plus: error: command line option ‘-std=c99’ is valid for C/ObjC but not for C++ [-Werror]
The program has a lower case .c file suffix, so why does gcc try to compile it as c++ ? We have not seen this on other OSes.
(I know we could kick the problem down the road by removing -Werror or handle this particular file with -x c but I'd like to solve the real problem.)
why does gcc try to compile it as c++
I can think of only two plausible explanations, and they both are end-user's fault.
It could be that the user transferred sources via Windows, and the file is really called C_DATABLOCK_TEST.C, and the user is misleading you.
It could also be that the user overwrote his gcc with g++ (surprisingly many people believe that gcc and g++ are the same thing, but they are not).
To disprove the first possibility, ask the user to execute his build commands under script, and send you resulting typescript.
To disprove the second, ask the user to add -v to the compile command.
This look like GCC Bug 54641, which has been fixed in a later release of GCC. It is only a warning, but your compile flags are causing GCC to treat all warnings as errors.
For a test I have written a code of matrix multiplication in C(cuda) and compiled it using nvcc to create shared library using following command.
nvcc -c MatMul.cu -o libmatmul.so
Then i wrote a OpenCV code in C and tried to compile with following command.
gcc ImgMul.c `pkg-config --cflags --libs opencv` -L. -L/usr/local/cuda/lib64 -I/usr/local/cuda/include -I. -lmatmul -lcudart -o ImgMul
and I am getting following error.
gputest.c:(.text+0x3f): undefined reference to `matmul'
Could anyone tell me how to include cuda libraries while compiling a code in gcc.
OS: Ubuntu
gcc : 4.4.0
The first point to make is that
nvcc -c MatMul.cu -o libmatmul.so
does not make a shared library, it just compiles to an object file. Shared libraries and object files are not at all the same thing.
That aside, the reason for the symbol not found error is C++ name mangling. Host code in CUDA source files is compiled using the host C++ compiler, not C. So symbol names in the host code emitted by the compiler are subject to name mangling. To get around this, the easiest way is to declare functions which you wish to call from plain C code using the extern "C" declarator (see here for a reasonable overview of the perils of C/C++ interoperability).
I am trying to write a matlab mex function which uses libhdf5; My Linux install provides libhdf5-1.8 shared libraries and headers. However, my version of Matlab, r2007b, provides a libhdf5.so from the 1.6 release. (Matlab .mat files bootstrap hdf5, evidently). When I compile the mex, it segfaults in Matlab. If I downgrade my version of libhdf5 to 1.6 (not a long-term option), the code compiles and runs fine.
question: how do I solve this problem? how do I tell the mex compilation process to link against /usr/lib64/libhdf5.so.6 instead of /opt/matlab/bin/glnxa64/libhdf5.so.0 ? When I try to do this using -Wl,-rpath-link,/usr/lib64 in my compilation, I get errors like:
/usr/lib/gcc/x86_64-pc-linux-gnu/4.3.4/../../../../x86_64-pc-linux-gnu/bin/ld: warning: libhdf5.so.0, needed by /opt/matlab/matlab75/bin/glnxa64/libmat.so, may conflict with libhdf5.so.6
/usr/lib/gcc/x86_64-pc-linux-gnu/4.3.4/../../../../lib64/crt1.o: In function `_start':
(.text+0x20): undefined reference to `main'
collect2: ld returned 1 exit status
mex: link of 'hdf5_read_strings.mexa64' failed.
make: *** [hdf5_read_strings.mexa64] Error 1
ack. the last resort would be to download a local copy of the hdf5-1.6.5 headers and be done with it, but this is not future proof (a Matlab version upgrade is in my future.). any ideas?
EDIT: per Ramashalanka's excellent suggestions, I
A) called mex -v to get the 3 gcc commands; the last is the linker command;
B) called that linker command with a -v to get the collect command;
C) called that collect2 -v -t and the rest of the flags.
The relevant parts of my output:
/usr/bin/ld: mode elf_x86_64
/usr/lib/gcc/x86_64-pc-linux-gnu/4.3.4/../../../../lib64/crti.o
/usr/lib/gcc/x86_64-pc-linux-gnu/4.3.4/crtbeginS.o
hdf5_read_strings.o
mexversion.o
-lmx (/opt/matlab/matlab75/bin/glnxa64/libmx.so)
-lmex (/opt/matlab/matlab75/bin/glnxa64/libmex.so)
-lhdf5 (/usr/lib/gcc/x86_64-pc-linux-gnu/4.3.4/../../../../lib64/libhdf5.so)
/lib64/libz.so
-lm (/usr/lib/gcc/x86_64-pc-linux-gnu/4.3.4/../../../../lib64/libm.so)
-lstdc++ (/usr/lib/gcc/x86_64-pc-linux-gnu/4.3.4/libstdc++.so)
-lgcc_s (/usr/lib/gcc/x86_64-pc-linux-gnu/4.3.4/libgcc_s.so)
/lib64/libpthread.so.0
/lib64/libc.so.6
/lib64/ld-linux-x86-64.so.2
-lgcc_s (/usr/lib/gcc/x86_64-pc-linux-gnu/4.3.4/libgcc_s.so)
/usr/lib/gcc/x86_64-pc-linux-gnu/4.3.4/crtendS.o
/usr/lib/gcc/x86_64-pc-linux-gnu/4.3.4/../../../../lib64/crtn.o
So, in fact the libhdf5.so from /usr/lib64 is being referenced. However, this is being overriden, I believe, by the environment variable LD_LIBRARY_PATH, which my version of Matlab automagically sets at run-time so it can locate its own versions of e.g. libmex.so, etc.
I am thinking that the crt_file.c example works either b/c it does not use the functions I am using (H5DOpen, which had a signature change in the move from 1.6 to 1.8 (yes, I am using -DH5_USE_16_API)), or, less likely, b/c it does not hit the parts of Matlab internals that need hdf5. ack.
The following worked on my system:
Install hdf5 version 1.8.4 (you've already done this: I installed the source and compiled to ensure it is compatible with my system, that I get gcc versions and that I get the static libraries - e.g. the binaries offered for my system are icc specific).
Make a target file. You already have your own file. I used the simple h5_crtfile.c from here (a good idea to start with this simple file first a look for warnings). I changed main to mexFunction with the usual args and included mex.h.
Specify the static 1.8.4 library you want to load explicitly (the full path with no -L for it necessary) and don't include -lhdf5 in the LDFLAGS. Include a -t option so you can ensure that there is no dynamic hdf5 library being loaded. You also need -lz, with zlib installed. For darwin we also need a -bundle in LDFLAGS:
mex CFLAGS='-I/usr/local/hdf5/include' LDFLAGS='-t /usr/local/hdf5/lib/libhdf5.a -lz -bundle' h5_crtfile.c -v
For linux, you need an equivalent position-independent call, e.g. fPIC and maybe -shared, but I don't have a linux system with a matlab license, so I can't check:
mex CFLAGS='-fPIC -I/usr/local/hdf5/include' LDFLAGS='-t /usr/local/hdf5/lib/libhdf5.a -lz -shared' h5_crtfile.c -v
Run the h5_crtfile mex file. This runs without problems on my machine. It just does a H5Fcreate and H5Fclose to create "file.h5" in the current directory, and when I call file file.h5 I get file.h5: Hierarchical Data Format (version 5) data.
Note that if I include a -lhdf5 above in step 3, then matlab aborts when I try to run the executable (because it then uses matlab's dynamic libraries which for me are version 1.6.5), so this is definitely solving the problem on my system.
Thanks for the question. My solution above is definitely much easier for me than what I was doing before. Hopefully the above works for you.
I am accepting Ramashalanka's answer because it led me to the exact solution which I will post here for completeness only:
download the hdf5-1.6.5 library from the hdf5 website, and install the header files in a local directory;
tell mex to look for "hdf5.h" in this local directory, rather than in the standard location (e.g. /usr/include.)
tell mex to compile my code and the shared object library provided by matlab, and do not use the -ldfh5 flag in LDFLAGS.
the command I used is, essentially:
/opt/matlab/matlab_default/bin/mex -v CC#gcc CXX#g++ CFLAGS#"-Wall -O3 -fPIC -I./hdf5_1.6.5/src -I/usr/include -I/opt/matlab/matlab_default/extern/include" CXXFLAGS#"-Wall -O3 -fPIC -I./hdf5_1.6.5/src -I/usr/include -I/opt/matlab/matlab_default/extern/include " -O -lmwblas -largeArrayDims -L/usr/lib64 hdf5_read_strings.c /opt/matlab/matlab_default/bin/glnxa64/libhdf5.so.0
this gets translated by mex into the commands:
gcc -c -I/opt/matlab/matlab75/extern/include -DMATLAB_MEX_FILE -Wall -O3 -fPIC -I./hdf5_1.6.5/src -I/usr/include -I/opt/matlab/matlab_default/extern/include -O -DNDEBUG hdf5_read_strings.c
gcc -c -I/opt/matlab/matlab75/extern/include -DMATLAB_MEX_FILE -Wall -O3 -fPIC -I./hdf5_1.6.5/src -I/usr/include -I/opt/matlab/matlab_default/extern/include -O -DNDEBUG /opt/matlab/matlab75/extern/src/mexversion.c
gcc -O -pthread -shared -Wl,--version-script,/opt/matlab/matlab75/extern/lib/glnxa64/mexFunction.map -Wl,--no-undefined -o hdf5_read_strings.mexa64 hdf5_read_strings.o mexversion.o -lmwblas -L/usr/lib64 /opt/matlab/matlab_default/bin/glnxa64/libhdf5.so.0 -Wl,-rpath-link,/opt/matlab/matlab_default/bin/glnxa64 -L/opt/matlab/matlab_default/bin/glnxa64 -lmx -lmex -lmat -lm -lstdc++
this solution should work on all my various target machines and at least until I upgrade to matlab r2009a, which I believe uses hdf5-1.8. thanks for all the help, sorry for being so dense with this--I think I was overly-committed to using the packaged version of hdf5, rather than a local set of header files.
Note this would all have been trivial if Mathworks had provided a set of the header files with the Matlab distribution...