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

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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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