I'm using LAMMPS software to simulate the movement of moleculars. After screating script for LAMMPS, I type:
If run it parallel, I use MPICH2:
mpiexec -np 4 lmp_linux<in.test
Then I have to use job scheduler, I create script: lmp.sh (using cat ?)
#$ -j y
#$ -S /bin/bash
/share/apps/bin/mpiexec -n $num_np /share/apps/bin/lmp_linux<in.test
After that I use qsub:
qsub lmp.sh (cça SGE)
I use qstat to check, it still work, but I only have an error file: lmp.sh.o83
mpiexec_dudu5.local: cannot connect to local mpd (/tmp/mpd2.console_coffee); possible causes:
1. no mpd is running on this host
2. an mpd is running but was started without a ''console'' (-n option)
In case 1, you can start an mpd on this host with:
and you will be able to run jobs just on this host.
For more details on starting mpds on a set of host, see the MPICH2 installation Guide.
What I have to do now? Please suggest me!
Also please explain for me the structure of the script lmp.sh.