[gmx-users] parallel run error

[Lianqing Zheng]

Thanks, David! Do I need to recompile lam, fftw, and gromacs or just
gromacs? I did it for gromacs but still got the same error.

We actually have libxml2 at /usr/lib/libxml2.so.2. It's only on
the master node. Do I need to install it on all nodes?

Thanks,
Lianqing


On Tue, 23 Nov 2004, David wrote:

>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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