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

[Justin Lemkul]

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

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

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