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

[Chris Neale]

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.