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.
Related
I have installed gcc-plugin in my Ubuntu 16.10-32 bit and the installation have been done correctly:
>$ gcc -print-file-name=plugin
/usr/lib/gcc/i686-linux-gnu/6/plugin
However, when I try to compile the plugin, I get a huge amount of errors, warning, and exceptions ...
I can not understand what is the reason behind this.
Is it a mistake in the compiling command line? or the installation of the gcc-plugin was not the right way?
I have compiled the gcc-plugin file as follow:
gcc -g -I`gcc -print-file-name=plugin`/include -fpic -shared -o my_plugin.so my_plugin.c
any help?
You have to use the C++ compiler g++. The command line looks otherwise ok, but I don't know your source code, of course.
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.
I am compiling a third-part software, with mpif90, that in my case is the mpi version of gcc. The package comes with a makefile. After compiling the object files, the makefile creates the archive with ar, but this fails because there are not input object files. In effect I tried to compile by hand the object files (.o) with
mpif90 -lmkl_gf -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm -openmp -O3 -DMPI -c a.f90
and the a.o is not created, a .mod file is created instead. I don't have much experience with fortran, and I am a bit puzzled, because the -c flag should create an object, shouldn' it?
I have verified that gfortran does create the object file if I remove the flag openmp
Notes:
mpif90 -v
gcc version 4.4.3
OS : Ubuntu 10.04.4 LTS
I changed the flag openmp to fopenmp
http://gcc.gnu.org/onlinedocs/gfortran/OpenMP.html
In case anyone comes across this question in the future ... the flags used by the OP are specific to the intel fortran compiler while it seems the mpif90 wrapper is using the gfortran compiler. The proper flag to use OpenMP with gfortran is -fopenmp and the library is -lgomp. It is possible to use the intel library with a different vendors compiler, but its easiest to stick with one vendor.
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.
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...