CP/MM Tutorial

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Some batch script templates called launch_XXX.job can be found in:
/home/ei250498/TUTORIALS/ACETONE
If you open them you will found some initial lines starting with #BSUB word that
represents commands for the batch system:
#BSUB -J Template
#BSUB -o output
#BSUB -e error
#BSUB -n 2
#BSUB -W 00:15
#BSUB -M 700
#BSUB -a intelmpi
ß Batch system’s job name
ß Filename of the batch system’s output messages (and error if no option -e used)
ß Filename of the batch system’s error messages
ß Number of cores to be reserve for the job
ß Hard runtime limit: after the expiration of this time (here 15’) the job will be killed
ß Set the per-process memory limit in MB
ß Specify which MPI version you want to use in the parallel run
followed by some lines which are the commands that the batch system has to run on
the computational nodes and that are similar to the ones you use in the interactive
way.
Refer to the HPC user guide for a more detailed description of all the useful
commands available for the batch script.
To check the status of your batched jobs you can use the command:
bjobs –w
and to remove a job from the batch list you can use the command:
bkill
where the job_id can be read from the list got with the bjobs command.
A batch script template called launch.job can be found in:
/home/ei250498/TUTORIALS/ACETONE
Refer to the HPC user guide to learn how to create a batch script for your jobs.
To run CPMD with for example 2 cores (everything on the same line):
mpirun –np 2 cpmd.x /home/ei250498/PROGRAMS/SRC/cpmd/PP
> &
/home/ei250498/PROGRAMS/SRC/cpmd/PP is the location where CPMD will look for
the pseudopotentials files which will be specified in the input file. All the
pseudopotentials we will use are already present there.
In order to calculate the dipole moment of the acetone in vacuum we first have to
optimize the geometry of the molecule we have constructed in the previous step. So,