Cannot build because of lstdc++ (no PETSc)

[Timothée Lecomte]

Hi,

Following previous reports, I am now trying to build libadjoint without its PETSc-related features, to workaround the fact that my PETSc built does not have C support. I realize that the cleaner way would be to build PETSc with C support, but I have already had so much of a hard time building it that I am afraid to start again, even changing the smallest option.

So now I am trying to build libadjoint (r418) with:

PETSC_ARCH="" PETSC_DIR="" SLEPC_ARCH="" SLEPC_DIR="" make install

(Note that PETSC_ARCH="" PETSC_DIR="" is not enough since SLEPC headers include PETSc ones)

Unfortunately, I am still getting an error (and a bunch of warnings), all related to the use of -lstdc++. Below is the full output. Thank you in advance for your help to fix my issues !

  CC src/adj_adjointer_routines.c
mpicc -g -O0 -fPIC -Iinclude/ -Wall -Wextra -Wunused-parameter -Wunsafe-loop-optimizations -Wpointer-arith -Wstrict-prototypes -ggdb3 -fstack-protector-all -lstdc++ -c -o obj/adj_adjointer_routines.o src/adj_adjointer_routines.c
i686-apple-darwin10-gcc-4.2.1: -lstdc++: linker input file unused because linking not done
  CC src/adj_adjointer_visualisation.c
mpicc -g -O0 -fPIC -Iinclude/ -Wall -Wextra -Wunused-parameter -Wunsafe-loop-optimizations -Wpointer-arith -Wstrict-prototypes -ggdb3 -fstack-protector-all -lstdc++ -c -o obj/adj_adjointer_visualisation.o src/adj_adjointer_visualisation.c
i686-apple-darwin10-gcc-4.2.1: -lstdc++: linker input file unused because linking not done
  CC src/adj_core.c
mpicc -g -O0 -fPIC -Iinclude/ -Wall -Wextra -Wunused-parameter -Wunsafe-loop-optimizations -Wpointer-arith -Wstrict-prototypes -ggdb3 -fstack-protector-all -lstdc++ -c -o obj/adj_core.o src/adj_core.c
i686-apple-darwin10-gcc-4.2.1: -lstdc++: linker input file unused because linking not done
  CC src/adj_data_structures.c
mpicc -g -O0 -fPIC -Iinclude/ -Wall -Wextra -Wunused-parameter -Wunsafe-loop-optimizations -Wpointer-arith -Wstrict-prototypes -ggdb3 -fstack-protector-all -lstdc++ -c -o obj/adj_data_structures.o src/adj_data_structures.c
i686-apple-darwin10-gcc-4.2.1: -lstdc++: linker input file unused because linking not done
  CC src/adj_debug.c
mpicc -g -O0 -fPIC -Iinclude/ -Wall -Wextra -Wunused-parameter -Wunsafe-loop-optimizations -Wpointer-arith -Wstrict-prototypes -ggdb3 -fstack-protector-all -lstdc++ -c -o obj/adj_debug.o src/adj_debug.c
i686-apple-darwin10-gcc-4.2.1: -lstdc++: linker input file unused because linking not done
  CC src/adj_dictionary.c
mpicc -g -O0 -fPIC -Iinclude/ -Wall -Wextra -Wunused-parameter -Wunsafe-loop-optimizations -Wpointer-arith -Wstrict-prototypes -ggdb3 -fstack-protector-all -lstdc++ -c -o obj/adj_dictionary.o src/adj_dictionary.c
i686-apple-darwin10-gcc-4.2.1: -lstdc++: linker input file unused because linking not done
  CC src/adj_error_handling.c
mpicc -g -O0 -fPIC -Iinclude/ -Wall -Wextra -Wunused-parameter -Wunsafe-loop-optimizations -Wpointer-arith -Wstrict-prototypes -ggdb3 -fstack-protector-all -lstdc++ -c -o obj/adj_error_handling.o src/adj_error_handling.c
i686-apple-darwin10-gcc-4.2.1: -lstdc++: linker input file unused because linking not done
  CC src/adj_evaluation.c
mpicc -g -O0 -fPIC -Iinclude/ -Wall -Wextra -Wunused-parameter -Wunsafe-loop-optimizations -Wpointer-arith -Wstrict-prototypes -ggdb3 -fstack-protector-all -lstdc++ -c -o obj/adj_evaluation.o src/adj_evaluation.c
i686-apple-darwin10-gcc-4.2.1: -lstdc++: linker input file unused because linking not done
  CC src/adj_petsc_data_structures.c
mpicc -g -O0 -fPIC -Iinclude/ -Wall -Wextra -Wunused-parameter -Wunsafe-loop-optimizations -Wpointer-arith -Wstrict-prototypes -ggdb3 -fstack-protector-all -lstdc++ -c -o obj/adj_petsc_data_structures.o src/adj_petsc_data_structures.c
i686-apple-darwin10-gcc-4.2.1: -lstdc++: linker input file unused because linking not done
  CC src/adj_predictability.c
mpicc -g -O0 -fPIC -Iinclude/ -Wall -Wextra -Wunused-parameter -Wunsafe-loop-optimizations -Wpointer-arith -Wstrict-prototypes -ggdb3 -fstack-protector-all -lstdc++ -c -o obj/adj_predictability.o src/adj_predictability.c
i686-apple-darwin10-gcc-4.2.1: -lstdc++: linker input file unused because linking not done
  CC src/adj_simplification.c
mpicc -g -O0 -fPIC -Iinclude/ -Wall -Wextra -Wunused-parameter -Wunsafe-loop-optimizations -Wpointer-arith -Wstrict-prototypes -ggdb3 -fstack-protector-all -lstdc++ -c -o obj/adj_simplification.o src/adj_simplification.c
i686-apple-darwin10-gcc-4.2.1: -lstdc++: linker input file unused because linking not done
  CC src/adj_test_tools.c
mpicc -g -O0 -fPIC -Iinclude/ -Wall -Wextra -Wunused-parameter -Wunsafe-loop-optimizations -Wpointer-arith -Wstrict-prototypes -ggdb3 -fstack-protector-all -lstdc++ -c -o obj/adj_test_tools.o src/adj_test_tools.c
i686-apple-darwin10-gcc-4.2.1: -lstdc++: linker input file unused because linking not done
  CC src/adj_variable_lookup.c
mpicc -g -O0 -fPIC -Iinclude/ -Wall -Wextra -Wunused-parameter -Wunsafe-loop-optimizations -Wpointer-arith -Wstrict-prototypes -ggdb3 -fstack-protector-all -lstdc++ -c -o obj/adj_variable_lookup.o src/adj_variable_lookup.c
i686-apple-darwin10-gcc-4.2.1: -lstdc++: linker input file unused because linking not done
  CC src/html_encode.c
mpicc -g -O0 -fPIC -Iinclude/ -Wall -Wextra -Wunused-parameter -Wunsafe-loop-optimizations -Wpointer-arith -Wstrict-prototypes -ggdb3 -fstack-protector-all -lstdc++ -c -o obj/html_encode.o src/html_encode.c
i686-apple-darwin10-gcc-4.2.1: -lstdc++: linker input file unused because linking not done
  SED include/libadjoint/adj_constants_f.h
  SED include/libadjoint/adj_error_handling_f.h
  FC src/adj_fortran.F90
  C++ src/revolve.cpp
  C++ src/revolve_c.cpp
  AR lib/libadjoint.a
  LD lib/libadjoint.dylib
ld: library not found for -lstdc++
collect2: error: ld returned 1 exit status
make: *** [lib/libadjoint.dylib] Error 1

[Timothée Lecomte (timothee-lecomte-5)]

And for reference:

minerve:dorsal tlecomte$ mpicc --version
i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5666) (dot 3)
minerve:dorsal tlecomte$ uname -a
Darwin #### 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64

[Patrick Farrell (pefarrell)]

I don't blame you for not wanting to recompile PETSc! However, I *think* the only thing you have to do is to add

--with-c-support

to your configure line.

Anyway, on to your bug. Could you please paste the output of:

find /usr -name 'libstdc++*'

?

On my machine it gives:
/usr/lib/libstdc++.6.0.9.dylib
/usr/lib/libstdc++.6.dylib
/usr/lib/libstdc++.dylib

which is why -lstdc++ works for me (it automatically looks in /usr/lib).

Thanks!

Patrick

[Timothée Lecomte (timothee-lecomte-5)]

Thanks for looking into it ! Here is what I have on mine:

minerve:dorsal tlecomte$ find /usr -name 'libstdc++*'
/usr/lib/gcc/i686-apple-darwin10/4.0.1/libstdc++.dylib
/usr/lib/gcc/i686-apple-darwin10/4.2.1/libstdc++.dylib
/usr/lib/gcc/powerpc-apple-darwin10/4.0.1/libstdc++.dylib
/usr/lib/gcc/powerpc-apple-darwin10/4.2.1/libstdc++.dylib
/usr/lib/libstdc++-static.a
/usr/lib/libstdc++.6.0.9.dylib
/usr/lib/libstdc++.6.dylib
/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin10/4.2.1/libstdc++.dylib
/usr/llvm-gcc-4.2/lib/gcc/powerpc-apple-darwin10/4.2.1/libstdc++.dylib

So I have no /usr/lib/libstdc++.dylib

May I ask why you need the C++ standard library to build a C project ?

[Timothée Lecomte (timothee-lecomte-5)]

Hi Patrick,

For reference for future readers of this page, here is the solution that appeared on bug #1135519:

Thanks again for your help and your explanation. I am sorry that the compiler situation is so messy on OS X...

It looks like my stdc++ problem comes from the fact that I have gfortran is used for the linking, and I have gfortran 4.7.2 installed (from Homebrew):
minerve:dorsal tlecomte$ gfortran --version
GNU Fortran (GCC) 4.7.2

'gfortran -lstdc++' complains while 'gcc -lstdc++' and 'g++ -lstdc++' do not,

Well, as you suggested, I changed '-lstdc++' to '-lstdc++.6' in line 176 of the Makefile, and got rid of that error. Finally, I had to install greadlink (through Homebrew coreutils) to get the python bindings properly built, and now I have a fully working libadjoint where all tests pass ! Thanks !!