Serpent

Here are some simple instructions to get your first test case running.

First connect to cluster and create case directory under your home directory and change to that directory:

mkdir BWR
cd BWR

Copy job file template and BWR example to that newly created directory:

cp /shared/tutorials/serpent/template.sh ~/BWR/BWR_2D.sh
cp /shared/tutorials/serpent/BWR_2D.sss ~/BWR

Modify your job file BWR_2D.sh next. Follow instructions inside job script. When ready hit Ctrl+X and choose to save and overwrite.

nano BWR_2D.sh

Then send job to queue. If you get errors just check std.err and std.out files. Correct things which lead to errors and requeue.

sbatch BWR_2D.sh

Example of the runscript needed for Slurm.

#!/bin/bash -l
###
### BWR_2D example case
###
 
## name of your job
#SBATCH -J BWR_2D
 
## system error message output file
#SBATCH -e BWR_2D.std.err%j
 
## system message output file
#SBATCH -o BWR_2D.std.out%j
 
## send mail after job is finished
#SBATCH --mail-type=end
#SBATCH --mail-user=<username>@lut.fi
 
## a per-process (soft) memory limit
## limit is specified in MB
## example: 1 GB is 1000
#SBATCH --mem-per-cpu=900
 
## how long a job takes, wallclock time d-hh:mm:ss
#SBATCH -t 01:00:00
 
## the number of processes (number of cores)
## number of nodes
#SBATCH -N 1
 
## number of cores (amount of MPI processes)
#SBATCH -n 2
## threads per process (amount of OpenMP threads per MPI process)
#SBATCH --cpus-per-task=8
 
## name of queue
#SBATCH -p phase2
 
## load modules
module load serpent/openmpi-2.1.1-gcc-local/gcc-4.8.5/2.1.29
 
## change directory
cd /home/<username>/BWR
 
## run my MPI executable
srun sss2 BWR_2D.sss