/project/projectdirs/training/www/VASPWorkshop2016/exercises
- 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
- 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.
- 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
