[gmx-users] parallel run error

[Lianqing Zheng]

Dear GMX-pals,

Here is what I did:

1. Compile and install fftw
a) MPICC=/opt/lam-7.0/bin/mpicc
b) ./configure --prefix=/home/lzheng/fftw-2.1.3 --enable-float
--enable-type-prefix --enable-mpi 
c) make
d) make install

2. Compile and install gromacs 3.2.1
a) export CPPFLAGS=-I/home/lzheng/fftw-2.1.3/include
b) export LDFLAGS=-L/home/lzheng/fftw-2.1.3/lib
c) ./configure --prefix=/home/lzheng/gromacs-3.2.1 --enable-mpi
--without-motif-libraries --without-motif-includes --without-x 
d) make
e) make install

3. Run water simulation in tutorial
a) lamboot -v bhost.def
b) grompp -f grompp.mdp -p water.top -c spc216.gro -o water.tpr -np 4
c) /opt/lam-7.0/bin/mpirun n21-24
/home/lzheng/gromacs-3.2.1/i686-pc-linux-gnu/bin/mdrun  -s water.tpr -o
water.trr -c water_out.gro -v -g water.log -np 4

OK, then I got the following error message:

****begin****
/home/lzheng/gromacs-3.2.1/i686-pc-linux-gnu/bin/mdrun: error while
loading shared libraries: libxml2.so.2: cannot open shared object file: No
such file or directory
/home/lzheng/gromacs-3.2.1/i686-pc-linux-gnu/bin/mdrun: error while
loading shared libraries: libxml2.so.2: cannot open shared object file: No
such file or directory
/home/lzheng/gromacs-3.2.1/i686-pc-linux-gnu/bin/mdrun: error while
loading shared libraries: libxml2.so.2: cannot open shared object file: No
such file or directory
/home/lzheng/gromacs-3.2.1/i686-pc-linux-gnu/bin/mdrun: error while
loading shared libraries: libxml2.so.2: cannot open shared object file: No
such file or directory
-----------------------------------------------------------------------------
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.
-----------------------------------------------------------------------------
****end****

I also tried mpirun -np 4 and got the same error.

Thanks for your kind help!

Lianqing