> Date: Wed, 27 Mar 2013 15:14:19 +0100 > From: Mark Abraham <mark.j.abra...@gmail.com> > Subject: Re: [gmx-users] compilation of gromacs-4.5.4 with fftw-3.3 > for double precision versition > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <camnumatt-1hbt1jr8bwpfnxhxmcdtegszlvp4wk-18cqgfs...@mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Yes, --enable-long-double is useless for FFTW+GROMACS. Actually long-double is, like single precision, a different library - libffwl. Same is true for fftw's quad precision
> > Mark > > On Wed, Mar 27, 2013 at 3:03 PM, Qinghua Liao <fantastic...@gmail.com>wrote: > >> Hi all, >> >> Finally I compiled it successfully when I used the following commands: >> >> 1077 ./configure --prefix=/usr/users/iff_th2/liao/fftw-3.3 >> --enable-threads --enable-shared --enable-mpi CC=gcc >> 1078 make >> 1079 make install >> 1080 history | grep export >> 1081 export CPPFLAGS=-I/usr/users/iff_th2/liao/fftw-3.3/include >> 1082 export LDFLAGS=-L/usr/users/iff_th2/liao/fftw-3.3/lib >> 1083 cd ../gromacs454/ >> 1084 history | grep configure >> 1085 ./configure --prefix=/usr/users/iff_th2/liao/gromacs454/ >> --enable-double --enable-threads CC=gcc --disable-gcc41-check --enable-mpi >> --program-suffix=_d --enable-shared >> 1086 make >> 1087 make install >> >> The only difference is that I delete the option of --enable-long-double for >> compiling fftw and add the option of --enable-shared for compiling gromacs. >> >> Thanks all for the suggestions. >> >> All the best. >> Qinghua Liao >> >> >> On Wed, Mar 27, 2013 at 2:04 PM, Ahmet yıldırım <ahmedo...@gmail.com> >> wrote: >> >> > 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 >> > >> >> >> >> -- >> 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 >> > > > ------------------------------ > > -- > 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 107, Issue 116 > ******************************************* -- Christoph Junghans Web: http://www.compphys.de -- 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