View source for NERSC Berkeley 2016 HOWTO

* '''Running the examples''':
:Almost all examples come with a bash-script that runs them. In most cases these scripts are called ''job.sh'', ''doall.sh'', ''loop.sh'', ''run.sh'' or something like that.
:To submit these jobscripts to the Haswell nodes on Cori you may do the following:
:* copy the files <tt>hsw.sl</tt> and <tt>sub.sh</tt> to the directory where you want to run the example:

 cd path-to-your-directory
 cp /.../hsw.sl .
 cp /.../sub.sh .

:* then to submit for instance the jobscripts ''run.sh'', you specify:

 ./sub.sh run.sh

* '''<tt>hsw.sl</tt>
:The file <tt>hsw.sl</tt> contains the slurm-preamble, loads the relevant environment modules, and sets the command with which VASP will be called by the jobscript:

 #!/bin/bash -l
 #SBATCH -N 1
 #SBATCH -p regular
 #SBATCH -t 30:00
 #SBATCH -C haswell
 
 export OMP_NUM_THREADS=4
 export OMP_PROC_BIND=spread
 export OMP_PLACES=threads
 
 module use ~usgsw/modulefiles
 module load vasp/hsw
 
 export vasp_std="srun -n 4 -c 16 --cpu_bind=cores /global/homes/u/usgsw/vasp/20161014/hsw/intel/bin/vasp_std"

:In this case <tt>hsw.sl</tt> requests 1 Haswell node (32 cores).
:The <tt>vasp_std</tt> command will run VASP using 4 MPI-ranks, that each will be able to start 4 openMP-threads.

* '''<tt>sub.sh</tt>'''
:The bash-script <tt>sub.sh</tt> does very little but concatenate <tt>hsw.sl</tt> and a call to the jobscript specified as its argument, and submits the result (<tt>sub.sl</tt>):

 #!/bin/bash -l
 
 cat ./hsw.sl > sub.sl
 echo ./$1   >> sub.sl
 
 sbatch sub.sl

:To be specific, the command
 ./sub.sh run.sh
:will submit the following <tt>sub.sl</tt> file:
 #!/bin/bash -l
 #SBATCH -N 1
 #SBATCH -p regular
 #SBATCH -t 30:00
 #SBATCH -C haswell
 
 export OMP_NUM_THREADS=4
 export OMP_PROC_BIND=spread
 export OMP_PLACES=threads
 
 module use ~usgsw/modulefiles
 module load vasp/hsw
 
 export vasp_std="srun -n 4 -c 16 --cpu_bind=cores /global/homes/u/usgsw/vasp/20161014/hsw/intel/bin/vasp_std"
 ./run.sh