[gmx-users] compilation of gromacs-4.5.4 with fftw-3.3 for double precision versition
Qinghua Liao
fantasticqhl at gmail.com
Wed Mar 27 15:03:19 CET 2013
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 <ahmedo047 at 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 <fantasticqhl at 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 <jalemkul at 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 at 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-request at 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 at 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-request at gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
>
>
>
> --
> Ahmet Yıldırım
> --
> gmx-users mailing list gmx-users at 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-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
--
Best Regards,
Qinghua
More information about the gromacs.org_gmx-users
mailing list