I have a linking problem which I cannot explain. The program contains references to FFTW functions in a file called fft.cpp. The linking command is as follows (I skipped the rest of object files):
/usr/bin/g++ common/CleanerND.cpp.2.o ... common/fft.cpp.2.o
-o cleaner3d -Wl,-Bstatic -Wl,-Bdynamic -lmkl_intel_lp64 -lmkl_sequential -lmkl_core
-lfftw3f -lgsl -lgslcblas -lm -lglib-2.0 -lz -lm -lpthread -fopenmp
The superfluous -Wl,-Bstatic -Wl,-Bdynamic options are generated by Waf, which I use as the build system. I use the default toolchain that comes with Ubuntu 12.04: GCC 4.6.3, binutils 2.22.
The problem is that the linker does not detect and resolve the references to the FFTW functions. When run, the program aborts with this message:
cleaner3d: symbol lookup error: cleaner3d: undefined symbol: fftwf_malloc
The output ofldd shows that FFTW is not being linked at all:
$ ldd cleaner3d
linux-vdso.so.1 => (0x00007fffa3193000)
libmkl_intel_lp64.so => /opt/intel/mkl/10.0.1.014/lib/em64t/libmkl_intel_lp64.so (0x00007f6f16683000)
libmkl_sequential.so => /opt/intel/mkl/10.0.1.014/lib/em64t/libmkl_sequential.so (0x00007f6f164d3000)
libmkl_core.so => /opt/intel/mkl/10.0.1.014/lib/em64t/libmkl_core.so (0x00007f6f16300000)
libgsl.so.0 => /usr/lib/libgsl.so.0 (0x00007f6f15ec4000)
libglib-2.0.so.0 => /lib/x86_64-linux-gnu/libglib-2.0.so.0 (0x00007f6f15bcf000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f6f158d4000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f6f156b7000)
libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f6f153b7000)
libgomp.so.1 => /usr/lib/x86_64-linux-gnu/libgomp.so.1 (0x00007f6f151a8000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f6f14f92000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f6f14bd5000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f6f149d0000)
libpcre.so.3 => /lib/x86_64-linux-gnu/libpcre.so.3 (0x00007f6f14793000)
librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f6f1458b000)
/lib64/ld-linux-x86-64.so.2 (0x00007f6f169b2000)
This is clearly the linker's fault, since the output of nm shows that it contains references to FFTW:
$ nm build/common/fft.cpp.2.o | grep fftw
U fftwf_destroy_plan
U fftwf_execute_dft
U fftwf_free
U fftwf_malloc
U fftwf_plan_dft_1d
U fftwf_plan_many_dft
I found out that this might be somehow related to the linker option --as-needed, which is passed by default since Ubuntu 12.04 - and indeed, when I add -Wl,--no-as-needed to the command line, the problem disappears. However, this workaround should not be necessary. I don't understand why the linker won't properly link FFTW with --as-needed enabled. Can anyone shine some light on this? Is this a linker bug? Why only the FFTW library is affected?
