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NERSC Berkeley 2016 HOWTO

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  • The examples:
  • can be copied from:
/project/projectdirs/training/www/VASPWorkshop2016/exercises
  • Running the examples:
Almost all examples come with a bash-script that runs them. These scripts are called job.sh, doall.sh, loop.sh, run.sh or something original 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 /project/projectdirs/training/www/VASPWorkshop2016/exercises/hsw.sl .
cp /project/projectdirs/training/www/VASPWorkshop2016/exercises/sub.sh .
  • To submit for instance the jobscripts run.sh, you specify:
./sub.sh run.sh
  • hsw.sl
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/20161102-hsw

export vasp_std="srun -n 4 -c 16 --cpu_bind=cores /global/homes/u/usgsw/vasp/20161102/hsw/intel/bin/vasp_std"
In this case hsw.sl requests 1 Haswell node (32 cores), and the vasp_std command will run VASP using 4 MPI-ranks, that each will be able to start 4 openMP-threads.
  • sub.sh
The bash-script sub.sh does very little but concatenate hsw.sl and a call to the jobscript specified as its argument, and submits the result (sub.sl):
#!/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 sub.sl 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/20161102-hsw

export vasp_std="srun -n 4 -c 16 --cpu_bind=cores /global/homes/u/usgsw/vasp/20161102/hsw/intel/bin/vasp_std"
./run.sh