[gmx-users] compiling paralel version

Andre Farias de Moura andre at qt.dq.ufscar.br
Wed Jul 14 15:04:23 CEST 2004

Hi Andrei,

I just asked the same question and managed to compile mdrun
parallel version with the help from Oliver and David. The
script I used was as follows:

export  LAM_D=/usr/local/;
export FFTW_D=/usr/local/;

tar -jxvf lam-7.0.6.tar.bz2
cd lam-7.0.6
./configure --prefix=${LAM_D} --with-tcp-short=524288 --with-rpi=usysv
--with-rsh=ssh --with-shm-short=524288
make install

cd ..
tar -zxvf fftw-2.1.5.tar.gz
cd fftw-2.1.5

export PATH=${LAM_D}/bin:${PATH}   # so mpicc gets found

CPPFLAGS="-I${LAM_D}/include" \
LDFLAGS="-L${LAM_D}/lib" \
./configure --prefix=${FFTW_D} --enable-type-prefix --enable-mpi
make install

make distclean

./configure --prefix=${FFTW_D} --enable-type-prefix --enable-mpi
make install

cd ..
tar -zxvf gromacs-3.2.1.tar.gz
cd gromacs-3.2.1

CPPFLAGS="-I${LAM_D}/include -I${FFTW_D}/include" \
LDFLAGS="-L${LAM_D}/lib -L${FFTW_D}/lib" \

make install
make links

make distclean

./configure --without-x --enable-mpi --program-suffix=_mpi
make mdrun
make install-mdrun
make links

(end of script)

you just have to download lam-mpi and fftw from their
homepages and run a script like this (edit it to your

I hope it helps,

best regards,


    Dr. Andre' Farias de Moura
  Laboratorio de Quimica Teorica
Universidade Federal de Sao Carlos
     Sao Carlos - SP - Brasil

On 14 Jul 2004, Andrei Neamtu wrote:

> Hello,
> I try to compile the MPI version of mdrun but I receive the following
> message:
> 'checking wether the MPI cc command works... configure: error: Cannot
> compile and link MPI code with mpicc'
> I use SuSE 9.1
> The non-MPI version is compilling fine.
> Can anyone tell what this message means and how can I resolve this
> problem?
> Thank you very much,
> Andrei
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