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 hsw.sl and sub.sh 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

The file hsw.sl 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

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

export vasp_std="srun -n 4 -c 16 --cpu_bind=cores /global/homes/u/usgsw/vasp/20161014/hsw/intel/bin/vasp_std"