On Mon, Dec 20, 2010 at 8:20 PM, <chris.ne...@utoronto.ca> wrote: > > 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 >
You need to run "make clean" when you change the configure options. It will be nice to see some example build instructions on the gromacs site > as people have time to add them. > 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. Roland 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<aanlktik%2bv%2b7738y6eqgy6fnm4ygcvk-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.lapkgconfig >>> >>> 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. >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> Please don't post (un)subscribe requests to the list. Use the www >>> interface >>> or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> >>> >>> >> >> -- >> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov >> 865-241-1537, ORNL PO BOX 2008 MS6309 >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://lists.gromacs.org/pipermail/gmx-users/attachments/20101220/a6a71aac/attachment.html >> >> ------------------------------ >> >> -- >> gmx-users mailing list >> gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> >> End of gmx-users Digest, Vol 80, Issue 135 >> ****************************************** >> >> > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use thewww interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309
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