[gmx-users] parallel run error

[David]

On Tue, 2004-11-23 at 11:46 -0500, Lianqing Zheng wrote:
> 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
Your cluster does not have libxml2 installed. Either ask your sysadm to
install libxml2 or configure --without-libxml2

Note that xml may become obligatory in the next (4.0) release.

> /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
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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