<br><br><div class="gmail_quote">On Mon, Dec 20, 2010 at 8:20 PM, <span dir="ltr"><<a href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</a>></span> wrote:<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Just for completeness, I could not get fftw to compile with --enable-shared (although I don't need to any more):<br>
<br>
$ ./configure --enable-float --enable-threads --enable-shared --prefix=/project/pomes/cneale/GPC/exe/intel/fftw-3.1.2/exec<br>
$ make<br>
<br>
.. <snip> ...<br>
rm -fr .libs/libfftw3f.a .libs/<a href="http://libfftw3f.la" target="_blank">libfftw3f.la</a> .libs/libfftw3f.lai<br>
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<br>
icc: command line remark #10010: option '-c99' is deprecated and will be removed in a future release. See '-help deprecated'<br>
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<br>
kernel/.libs/libkernel.a(alloc.o): could not read symbols: Bad value<br>
make[2]: *** [<a href="http://libfftw3f.la" target="_blank">libfftw3f.la</a>] Error 1<br>
make[2]: Leaving directory `/project/pomes/cneale/GPC/exe/intel/fftw-3.1.2_again'<br>
make[1]: *** [all-recursive] Error 1<br>
make[1]: Leaving directory `/project/pomes/cneale/GPC/exe/intel/fftw-3.1.2_again'<br>
make: *** [all] Error 2<br></blockquote><div><br></div><div>You need to run "make clean" when you change the configure options.</div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
It will be nice to see some example build instructions on the gromacs site as people have time to add them.<br></blockquote><div>Please contribute you experience to the wiki pages. Good documentation requires many people to help. The (main) developers are often too busy too write detailed documentation. </div>
<div><br></div><div>Roland</div><div><br></div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
From: Roland Schulz <<a href="mailto:roland@utk.edu" target="_blank">roland@utk.edu</a>><br>
Subject: Re: [gmx-users] cmake --> relocation R_X86_64_32S against `a<br>
local symbol' can not be used when making a shared object; recompile<br>
with -fPIC<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
Message-ID:<br>
<<a href="mailto:AANLkTik%2BV%2B7738y6EqGy6fNm4ygCVk-Mzh1Aw1sgJaeF@mail.gmail.com" target="_blank">AANLkTik+V+7738y6EqGy6fNm4ygCVk-Mzh1Aw1sgJaeF@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
You want to compile fftw with either --enable-shared or with --with-pic. Or<br>
you need to compile a static version of Gromacs. As the message says you<br>
can't use fftw without pic with shared libraries in GROMACS.<br>
<br>
Roland<br>
<br>
On Mon, Dec 20, 2010 at 6:31 PM, Chris Neale <<a href="mailto:chris.neale@utoronto.ca" target="_blank">chris.neale@utoronto.ca</a>>wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Gromacs users:<br>
<br>
I pulled the master version of the source code today at 2pm via:<br>
git clone git://<a href="http://git.gromacs.org/gromacs.git" target="_blank">git.gromacs.org/gromacs.git</a><br>
and I tried to compile it following the instructions posted here:<br>
<a href="http://www.gromacs.org/Developer_Zone/Cmake" target="_blank">http://www.gromacs.org/Developer_Zone/Cmake</a> but I was unsuccessful. This<br>
is my first attempt at using cmake, but I have been compiling gromacs<br>
successfully with autoconf since version 3.3.1<br>
<br>
I have a recent enough version of cmake:<br>
$ cmake --version<br>
cmake version 2.8.0<br>
<br>
And I have installed fftw:<br>
$ echo $FFTW_LOCATION<br>
/project/pomes/cneale/GPC/exe/intel/fftw-3.1.2_again/exec<br>
$ ls $FFTW_LOCATION/lib<br>
libfftw3f.a <a href="http://libfftw3f.la" target="_blank">libfftw3f.la</a> libfftw3f_threads.a <a href="http://libfftw3f_threads.la" target="_blank">libfftw3f_threads.la</a> pkgconfig<br>
<br>
But then when I try to compile gromacs:<br>
$ cmake ../ -DFFTW3F_INCLUDE_DIR=$FFTW_LOCATION/include<br>
-DFFTW3F_LIBRARIES=$FFTW_LOCATION/lib/libfftw3f.a<br>
-DCMAKE_INSTALL_PREFIX=$(pwd) -DGMX_X11=OFF<br>
-DCMAKE_CXX_COMPILER=/scinet/gpc/intel/Compiler/11.1/072/bin/intel64/icpc<br>
-DCMAKE_C_COMPILER=/scinet/gpc/intel/Compiler/11.1/072/bin/intel64/icc<br>
$ make -j 4<br>
<br>
I get the error:<br>
... <snip> ...<br>
[ 72%] Building C object src/mdlib/CMakeFiles/md.dir/tables.c.o<br>
Linking C shared library libmd.so<br>
ld:<br>
/project/pomes/cneale/GPC/exe/intel/fftw-3.1.2_again/exec/lib/libfftw3f.a(mapflags.o):<br>
relocation R_X86_64_32S against `a local symbol' can not be used when making<br>
a shared object; recompile with -fPIC<br>
/project/pomes/cneale/GPC/exe/intel/fftw-3.1.2_again/exec/lib/libfftw3f.a:<br>
could not read symbols: Bad value<br>
make[2]: *** [src/mdlib/libmd.so.6] Error 1<br>
make[1]: *** [src/mdlib/CMakeFiles/md.dir/all] Error 2<br>
make: *** [all] Error 2<br>
<br>
Just to be sure, I recompiled my FFTW and also tried a few different<br>
options for FFTW3F_LIBRARIES, all with errors.<br>
This fftw was compiled the same way I did previously, but just in case our<br>
version of icc was updated and this is causing the problem:<br>
export CC=icc<br>
export CXX=icpc<br>
./configure --enable-float --enable-threads --prefix=$(pwd)/exec<br>
make<br>
make install<br>
<br>
############################ USING<br>
-DFFTW3F_LIBRARIES=$FFTW_LOCATION/lib/libfftw3f_threads.a<br>
... <snip> ...<br>
../mdlib/libmd.so.6: undefined reference to `fftwf_plan_dft_c2r_3d'<br>
../mdlib/libmd.so.6: undefined reference to `fftwf_plan_guru_dft_r2c'<br>
../mdlib/libmd.so.6: undefined reference to `fftwf_plan_dft_r2c_2d'<br>
<br>
... <snip> ...<br>
<br>
78%] Building C object src/kernel/CMakeFiles/g_luck.dir/g_luck.c.o<br>
Linking C executable g_luck<br>
Scanning dependencies of target g_protonate<br>
[ 79%] Building C object<br>
src/kernel/CMakeFiles/g_protonate.dir/g_protonate.c.o<br>
[ 79%] /scinet/gpc/intel/Compiler/11.1/072/lib/intel64//libimf.so: warning:<br>
warning: feupdateenv is not implemented and will always fail<br>
Building C object src/tools/CMakeFiles/gmxana.dir/gmx_bundle.c.o<br>
../mdlib/libmd.so.6: undefined reference to `fftwf_plan_dft_3d'<br>
../mdlib/libmd.so.6: undefined reference to `fftwf_execute_dft_r2c'<br>
<br>
... <snip> ...<br>
<br>
Building C object src/tools/CMakeFiles/gmxana.dir/edittop.c.o<br>
[ 88%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_bar.c.o<br>
[ 89%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_pme_error.c.o<br>
Linking C shared library libgmxana.so<br>
[ 89%] Built target gmxana<br>
make: *** [all] Error 2<br>
<br>
############################ USING -DFFTW3F_LIBRARIES=$FFTW_LOCATION/lib/<br>
<a href="http://libfftw3f.la" target="_blank">libfftw3f.la</a><br>
... <snip> ...<br>
[ 72%] Building C object src/mdlib/CMakeFiles/md.dir/tables.c.o<br>
Linking C shared library libmd.so<br>
/project/pomes/cneale/GPC/exe/intel/fftw-3.1.2_again/exec/lib/<a href="http://libfftw3f.la" target="_blank">libfftw3f.la</a>:<br>
file not recognized: File format not recognized<br>
<br>
############################ USING -DFFTW3F_LIBRARIES=$FFTW_LOCATION/lib/<br>
<a href="http://libfftw3f_threads.la" target="_blank">libfftw3f_threads.la</a><br>
... <snip> ...<br>
[ 72%] Building C object src/mdlib/CMakeFiles/md.dir/mvxvf.c.o<br>
[ 72%] Building C object src/mdlib/CMakeFiles/md.dir/tables.c.o<br>
Linking C shared library libmd.so<br>
/project/pomes/cneale/GPC/exe/intel/fftw-3.1.2_again/exec/lib/<br>
<a href="http://libfftw3f_threads.la" target="_blank">libfftw3f_threads.la</a>: file not recognized: File format not recognized<br>
make[2]: *** [src/mdlib/libmd.so.6] Error 1<br>
make[1]: *** [src/mdlib/CMakeFiles/md.dir/all] Error 2<br>
make: *** [all] Error 2<br>
<br>
<br>
Thank you,<br>
Chris.<br>
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