Dear Justin, Thanks very much for your reply! Yeah, I did not add the option of --enable-shared for compilation of gromacs 4.5.4, but it still failed after I added this option for the compilation. For the compilations I posted in the last e-mail, I do add the option of --enable-shared in compilation of fftw 3.3, but not for compilation of gromacs 4.5.4. Problem remains unsolved.
I choose this old version is to keep the simulations consistent with previous simulations. Thanks for the suggestion! All the best, Qinghua Liao On Wed, Mar 27, 2013 at 12:59 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 3/27/13 6:57 AM, Qinghua Liao wrote: > >> Dear gmx users, >> >> I tried to compile gromacs 4.5.4 with double precision, but it failed. The >> reason was a little wired. >> >> Firstly, I used the following commands to compile gromacs 4.5.4 together >> with fftw 3.3 for serial and parallel version with single precision, and I >> made it successfully. >> >> >> 1014 ./configure --prefix=/usr/users/iff_th2/**liao/fftw-3.3 >> --enable-sse >> --enable-threads --enable-float --enable-shared CC=gcc >> 1015 make >> 1016 make install >> 1017 make distclean >> 1018 export CPPFLAGS=-I/usr/users/iff_th2/**liao/fftw-3.3/include >> 1019 export LDFLAGS=-L/usr/users/iff_th2/**liao/fftw-3.3/lib >> >> 1022 mv gromacs-4.5.4 gromacs454 >> 1023 cd gromacs454/ >> >> 1026 ./configure --prefix=/usr/users/iff_th2/**liao/gromacs454/ >> --enable-float --enable-threads CC=gcc --disable-gcc41-check >> 1027 make >> 1028 make install >> >> 1031 make distclean >> 1032 cd ../fftw-3.3 >> 1034 ./configure --prefix=/usr/users/iff_th2/**liao/fftw-3.3 >> --enable-sse >> --enable-threads --enable-float --enable-shared --enable-mpi CC=gcc >> 1035 make >> 1036 make install >> 1037 make distclean >> 1038 cd ../gromacs454/ >> 1039 ls >> 1040 make distclean >> 1041 ./configure --prefix=/usr/users/iff_th2/**liao/gromacs454/ >> --enable-float --enable-threads CC=gcc --disable-gcc41-check --enable-mpi >> --program-suffix=_mpi >> 1042 make >> 1043 make install >> 1044 make distclean >> >> But when I used these similar commands to compile for the double >> precision, >> it failed. >> >> >> 1049 ./configure --prefix=/usr/users/iff_th2/**liao/fftw-3.3 >> --enable-long-double --enable-threads --enable-shared --enable-mpi CC=gcc >> 1050 make >> 1051 make install >> 1052 make distclean >> 1053 cd ../gromacs454/ >> 1054 make distclean >> 1055 ./configure --prefix=/usr/users/iff_th2/**liao/gromacs454/ >> --enable-double --enable-threads CC=gcc --disable-gcc41-check --enable-mpi >> --program-suffix=_d >> 1056 make >> >> The error showed to me was: >> >> /usr/bin/ld: /usr/local/lib/libfftw3.a(**plan-dft-c2r-2d.o): relocation >> R_X86_64_32 against `a local symbol' can not be used when making a shared >> object; recompile with -fPIC /usr/local/lib/libfftw3.a: could not read >> symbols: Bad value >> >> I added the option of --with-fPIC, but it was not recognized, and then I >> changed it to --with-pic, but the error was still the same. >> >> I don't know why gromacs can recognize the fftw library when doing the >> single float compilation, but not for the double float compilation, I >> already used the shared option. Could someone give me some suggestions to >> help me this out? Any reply will be appreciated. >> >> > In your last step, you're not using --enable-shared like you did in every > preceding step. Adding that flag should fix it. > > http://www.gromacs.org/**Documentation/Installation_** > Instructions_4.5#Details_for_**building_the_FFTW_prerequisite<http://www.gromacs.org/Documentation/Installation_Instructions_4.5#Details_for_building_the_FFTW_prerequisite> > > Gromacs 4.5.4 is pretty old; is there any reason you're not using a new > version? You'll get much better performance from 4.6.1. > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- Best Regards, Qinghua -- 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
