Thank you Roland.
The static build of gromacs worked:
$ 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
-DGMX_PREFER_STATIC_LIBS=ON
$ make
$ make install
Just for completeness, I could not get fftw to compile with
--enable-shared (although I don't need to any more):
$ ./configure --enable-float --enable-threads --enable-shared
--prefix=/project/pomes/cneale/GPC/exe/intel/fftw-3.1.2/exec
$ make
.. <snip> ...
rm -fr .libs/libfftw3f.a .libs/libfftw3f.la .libs/libfftw3f.lai
icc -c99 -shared -Wl,--whole-archive kernel/.libs/libkernel.a
dft/.libs/libdft.a dft/codelets/.libs/libdft_codelets.a
dft/codelets/standard/.libs/libdft_standard.a rdft/.libs/librdft.a
rdft/codelets/.libs/librdft_codelets.a
rdft/codelets/r2hc/.libs/librdft_codelets_r2hc.a
rdft/codelets/hc2r/.libs/librdft_codelets_hc2r.a
rdft/codelets/r2r/.libs/librdft_codelets_r2r.a
reodft/.libs/libreodft.a api/.libs/libapi.a -Wl,--no-whole-archive
-L/scratch/cneale/GPC/exe/intel/fftw-3.1.2/exec/lib -lm -pthread
-Wl,-soname -Wl,libfftw3f.so.3 -o .libs/libfftw3f.so.3.1.2
icc: command line remark #10010: option '-c99' is deprecated and will
be removed in a future release. See '-help deprecated'
ld: kernel/.libs/libkernel.a(alloc.o): relocation R_X86_64_32 against
`a local symbol' can not be used when making a shared object;
recompile with -fPIC
kernel/.libs/libkernel.a(alloc.o): could not read symbols: Bad value
make[2]: *** [libfftw3f.la] Error 1
make[2]: Leaving directory
`/project/pomes/cneale/GPC/exe/intel/fftw-3.1.2_again'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory
`/project/pomes/cneale/GPC/exe/intel/fftw-3.1.2_again'
make: *** [all] Error 2
It will be nice to see some example build instructions on the gromacs
site as people have time to add them.
Chris.
From: Roland Schulz <rol...@utk.edu>
Subject: Re: [gmx-users] cmake --> relocation R_X86_64_32S against `a
local symbol' can not be used when making a shared object;
recompile
with -fPIC
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID:
<aanlktik+v+7738y6eqgy6fnm4ygcvk-mzh1aw1sgj...@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
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.ne...@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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