[gmx-users] compilation of gromacs-4.5.4 with fftw-3.3 for double precision versition

Mark Abraham mark.j.abraham at gmail.com
Wed Mar 27 15:14:19 CET 2013 

Yes, --enable-long-double is useless for FFTW+GROMACS.

Mark

On Wed, Mar 27, 2013 at 3:03 PM, Qinghua Liao <fantasticqhl at 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 <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>
> > > >
> > > > ==============================**==========
> > > > --
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> > >
> > > --
> > > Best Regards,
> > >
> > > Qinghua
> > > --
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> >
> >
> > --
> > Ahmet Yıldırım
> > --
> > gmx-users mailing list    gmx-users at gromacs.org
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>
>
> --
> Best Regards,
>
> Qinghua
> --
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