[gmx-users] cmake --> relocation R_X86_64_32S against `a local symbol' can not be used when making a shared object; recompile with -fPIC

[Roland Schulz]

You want to compile fftw with either --enable-shared or with --with-pic. Or
you need to compile a static version of Gromacs. As the message says you
can't use fftw without pic with shared libraries in GROMACS.

Roland

On Mon, Dec 20, 2010 at 6:31 PM, Chris Neale <chris.neale at utoronto.ca>wrote:

> Dear Gromacs users:
>
> I pulled the master version of the source code today at 2pm via:
> git clone git://git.gromacs.org/gromacs.git
> and I tried to compile it following the instructions posted here:
> http://www.gromacs.org/Developer_Zone/Cmake but I was unsuccessful.  This
> is my first attempt at using cmake, but I have been compiling gromacs
> successfully with autoconf since version 3.3.1
>
> I have a recent enough version of cmake:
> $ cmake --version
> cmake version 2.8.0
>
> And I have installed fftw:
> $ echo $FFTW_LOCATION
> /project/pomes/cneale/GPC/exe/intel/fftw-3.1.2_again/exec
> $ ls $FFTW_LOCATION/lib
> libfftw3f.a  libfftw3f.la  libfftw3f_threads.a  libfftw3f_threads.la pkgconfig
>
> But then when I try to compile gromacs:
> $ cmake ../ -DFFTW3F_INCLUDE_DIR=$FFTW_LOCATION/include
> -DFFTW3F_LIBRARIES=$FFTW_LOCATION/lib/libfftw3f.a
> -DCMAKE_INSTALL_PREFIX=$(pwd) -DGMX_X11=OFF
> -DCMAKE_CXX_COMPILER=/scinet/gpc/intel/Compiler/11.1/072/bin/intel64/icpc
> -DCMAKE_C_COMPILER=/scinet/gpc/intel/Compiler/11.1/072/bin/intel64/icc
> $ make -j 4
>
> I get the error:
> ... <snip> ...
> [ 72%] Building C object src/mdlib/CMakeFiles/md.dir/tables.c.o
> Linking C shared library libmd.so
> ld:
> /project/pomes/cneale/GPC/exe/intel/fftw-3.1.2_again/exec/lib/libfftw3f.a(mapflags.o):
> relocation R_X86_64_32S against `a local symbol' can not be used when making
> a shared object; recompile with -fPIC
> /project/pomes/cneale/GPC/exe/intel/fftw-3.1.2_again/exec/lib/libfftw3f.a:
> could not read symbols: Bad value
> make[2]: *** [src/mdlib/libmd.so.6] Error 1
> make[1]: *** [src/mdlib/CMakeFiles/md.dir/all] Error 2
> make: *** [all] Error 2
>
> Just to be sure, I recompiled my FFTW and also tried a few different
> options for FFTW3F_LIBRARIES, all with errors.
> This fftw was compiled the same way I did previously, but just in case our
> version of icc was updated and this is causing the problem:
> export CC=icc
> export CXX=icpc
> ./configure --enable-float --enable-threads --prefix=$(pwd)/exec
> make
> make install
>
> ############################ USING
> -DFFTW3F_LIBRARIES=$FFTW_LOCATION/lib/libfftw3f_threads.a
> ... <snip> ...
> ../mdlib/libmd.so.6: undefined reference to `fftwf_plan_dft_c2r_3d'
> ../mdlib/libmd.so.6: undefined reference to `fftwf_plan_guru_dft_r2c'
> ../mdlib/libmd.so.6: undefined reference to `fftwf_plan_dft_r2c_2d'
>
> ... <snip> ...
>
>  78%] Building C object src/kernel/CMakeFiles/g_luck.dir/g_luck.c.o
> Linking C executable g_luck
> Scanning dependencies of target g_protonate
> [ 79%] Building C object
> src/kernel/CMakeFiles/g_protonate.dir/g_protonate.c.o
> [ 79%] /scinet/gpc/intel/Compiler/11.1/072/lib/intel64//libimf.so: warning:
> warning: feupdateenv is not implemented and will always fail
> Building C object src/tools/CMakeFiles/gmxana.dir/gmx_bundle.c.o
> ../mdlib/libmd.so.6: undefined reference to `fftwf_plan_dft_3d'
> ../mdlib/libmd.so.6: undefined reference to `fftwf_execute_dft_r2c'
>
> ... <snip> ...
>
> Building C object src/tools/CMakeFiles/gmxana.dir/edittop.c.o
> [ 88%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_bar.c.o
> [ 89%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_pme_error.c.o
> Linking C shared library libgmxana.so
> [ 89%] Built target gmxana
> make: *** [all] Error 2
>
> ############################ USING -DFFTW3F_LIBRARIES=$FFTW_LOCATION/lib/
> libfftw3f.la
> ... <snip> ...
> [ 72%] Building C object src/mdlib/CMakeFiles/md.dir/tables.c.o
> Linking C shared library libmd.so
> /project/pomes/cneale/GPC/exe/intel/fftw-3.1.2_again/exec/lib/libfftw3f.la:
> file not recognized: File format not recognized
>
> ############################ USING -DFFTW3F_LIBRARIES=$FFTW_LOCATION/lib/
> libfftw3f_threads.la
> ... <snip> ...
> [ 72%] Building C object src/mdlib/CMakeFiles/md.dir/mvxvf.c.o
> [ 72%] Building C object src/mdlib/CMakeFiles/md.dir/tables.c.o
> Linking C shared library libmd.so
> /project/pomes/cneale/GPC/exe/intel/fftw-3.1.2_again/exec/lib/
> libfftw3f_threads.la: file not recognized: File format not recognized
> make[2]: *** [src/mdlib/libmd.so.6] Error 1
> make[1]: *** [src/mdlib/CMakeFiles/md.dir/all] Error 2
> make: *** [all] Error 2
>
>
> Thank you,
> Chris.
> --
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>


-- 
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