[gmx-users] cannot compile parallel version

[Andre Farias de Moura]

dear Oliver,

I have tried your scripts with minor changes, as follows:

(1) script to install lam-mpi latest version:

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

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
make
make install


(2) script to install fftw:

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

export  LAM_D=/usr/local/lam/;
export FFTW_D=/usr/local/fftw/;
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
make install


(3) script ot install mdrun parallel version:

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

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

after half an hour running these script I ran mdrun parallel
version as follows:

grompp -f bpcdi -c bpcdi -p bpcdi -po out -o bpcdi -np 2
mpirun -np 2 mdrun_mpi -s bpcdi -o bpcdi -c out -e out -g out -x bpcdi -v
-np 2

then I got these error messages:

mdrun_mpi: relocation error: /usr/local/lib/libsfftw_mpi.so.2: symbol
errno, version GLIBC_2.0 not defined in file libc.so.6 with link time
reference
mdrun_mpi: relocation error: /usr/local/lib/libsfftw_mpi.so.2: symbol
errno, version GLIBC_2.0 not defined in file libc.so.6 with link time
reference
-----------------------------------------------------------------------------
It seems that [at least] one of the processes that was started with
mpirun did not invoke MPI_INIT before quitting (it is possible that
more than one process did not invoke MPI_INIT -- mpirun was only
notified of the first one, which was on node n0).

mpirun can *only* be used with MPI programs (i.e., programs that
invoke MPI_INIT and MPI_FINALIZE).  You can use the "lamexec" program
to run non-MPI programs over the lambooted nodes.
-----------------------------------------------------------------------------

I'm not pretty sure tha there was no error message at all during
the installation procedure described above, due to the huge amount
of output these scripts generated, but certainly the last message
I got from them was something like: installation is ok, go on.

can you figure out any reason why it is not working?

the strangest thing about it is that it worked previously on the
same machine running the same OS and using the default procedure
described in the gromacs homepage.

thank you in advance for any further suggestion.

andre'


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