cd mkdir fftw3.3 cd Desktop wget http://www.fftw.org/fftw-3.3.tar.gz tar xzvf fftw-3.3.tar.gz cd fftw-3.3 ./configure --prefix=/home/manchu/fftw3.3 --enable-threads --enable-sse2 --enable-shared make make install
cd mkdir gromacs_install cd Desktop wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.5.tar.gz tar xzvf gromacs-4.5.5.tar.gz cd gromacs-4.5.5 ./configure --prefix=/home/manchu/gromacs_install LDFLAGS=-L/home/manchu/fftw3.3/lib CPPFLAGS=-I/home/manchu/fftw3.3/include --disable-float make make install Executables are in /home/manchu/gromacs/bin Reference:http://www.youtube.com/watch?v=bxWjWmdf6xw 2013/3/27 Qinghua Liao <fantastic...@gmail.com> > 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 > -- Ahmet Yıldırım -- 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
