[gmx-users] cannot compile parallel version

Oliver Beckstein oliver at biop.ox.ac.uk
Thu Jul 8 00:14:08 CEST 2004

Hi Andre',

did you install LAM/MPI, too? And if yes, is mpicc found in your shell's 
PATH, ie does 'which mpicc' give something like '/usr/local/bin/mpicc' (or 
wherever it is installed)? 

Also, you will need to tell configure explicitly if your libraries are 
not in standard places. For example, assuming that your lam installation 
resided in /nfs/lam-mpi/7.0.4 (and fftw in /nfs/fftw/2.1.5) then you could 
run configure  like this (in bash):

export  LAM_D=/nfs/lam-mpi/7.0.4; 
export FFTW_D=/nfs/fftw/2.1.5; 

CPPFLAGS="-I${LAM_D}/include -I${FFTW_D}/include" \ 
  LDFLAGS="-L${LAM_D}/lib -L${FFTW_D}/lib" \
  ./configure --prefix=/opt/gromacs/3.2.1 --without-x \
      --enable-mpi --program-suffix=_mpi
make mdrun
make install-mdrun

(at least that's more or less what I use).

In case you need to install LAM then you can download it and compile it 
like this:

wget http://www.lam-mpi.org/download/files/lam-7.0.4.tar.bz2
tar -jxvf lam-7.0.4.tar.bz2
cd lam-7.0.4
./configure --prefix=${LAM_D} --with-tcp-short=524288 \
  --with-rpi=usysv --with-rsh=ssh
make install

Note that in this case you will have to compile fftw against the same 
version of lam/mpi, hence:

wget --passive ftp://ftp.fftw.org/pub/fftw/fftw-2.1.5.tar.gz
tar -xvf 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

Hope this helps,

> dear all,
> I'm trying to compile the gromacs parallel version
> on a dual athlon mp 2000 running linux redhat 9.0
> but I allways get the error message at the configure
> step:
> checking whether the MPI cc command works... configure: error: Cannot
> compile and link MPI code with mpicc
> any clue to what is going on?
> thanks in advance,
> andre'
> /-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
>     Dr. Andre' Farias de Moura
>   Laboratorio de Quimica Teorica
> Universidade Federal de Sao Carlos
>      Sao Carlos - SP - Brasil
> /-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/

Oliver Beckstein * oliver at biop.ox.ac.uk

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