• ●  srun can use a subset or all of the job's resources.

An interactive session on one of the compute nodes can most conveniently be initiated by invoking the following:

srun  --pty -p interactive /bin/bash

and where additional resources (e.g. memory, cpus etc) can be specified using the settings indicated in the table above. Alternatively, 

an interactive session can be initiated by using salloc.

EXAMPLE 2: SINGLE CPU JOB 

 In the example below, a simple Python program is submitted as a SLURM job to the ‘short’ partition using ‘sbatch <file_name>’ where 1 CPU and 1GB of memory are requested.  

#!/bin/bash 

#SBATCH --job-name=single_cpu_example 

#SBATCH --partition=short 

#SBATCH –ntasks=1 

#SBATCH --cpus-per-task=1 

#SBATCH –mem-per-cpu=1G 

#SBATCH --output=log%J.out 

#SBATCH --error=log%J.err 

# Load conda with the module of miniforge3 distribution 

module load miniforge3 

# Run a demo python program on a single CPU 

python hello.py 

EXAMPLE 3: MULTIPLE CPU JOB 

In the example below, a Python program is submitted as a SLURM job to the ‘normal’ partition using ‘sbatch <file_name>' where 4 CPUs and 1GB of memory per CPU are requested.  

#!/bin/bash 

#SBATCH --job-name=multi_cpu_example 

#SBATCH --partition=normal 

#SBATCH --ntasks=4 

#SBATCH --cpus-per-task=1 

#SBATCH --mem-per-cpu=1 

#SBATCH --output=log%J.out 

#SBATCH --error=log%J.err 
 

# Run a python program on 4 CPUs that splits the iterations of the loop among each CPU 

python square.py 

EXAMPLE 4: SINGULARITY JOB 

 In the example below, a Python program is run upon the startup of a singularity container and is submitted as a SLURM job to the ‘short’ partition using ‘sbatch <file_name>’.  

#!/bin/bash 

#SBATCH --job-name=singularity_example 

#SBATCH --partition=short 

#SBATCH –ntasks=1 

#SBATCH --mem-per-cpu=2 

#SBATCH --output=singularity-log%J.out 

#SBATCH --error=singularity-log%J.err 

# Check available versions of singularity with ‘module avail singularity’ 

module load singularity 

# Run application using singularity 

singularity exec conda-miniforge3.sif python3 pyTest.py 

More details about Singularity on the ERIS cluster can be found here.

EXAMPLE 5: ARRAY JOB USING R 

 In the example below, an R script is submitted as a SLURM job to the ‘filemove’ partition using ‘sbatch <file_name>'.  

#!/bin/bash 

#SBATCH --job-name=hello-parallel-test 

#SBATCH --partition=filemove 

#SBATCH --array=1-5 

#SBATCH –ntasks=2 

#SBATCH --mem-per-cpu=1 

#SBATCH --output=hello-%j-%a.out 

#SBATCH --error=hello-%j-%a.err 
 

# Check available versions of R using ‘module avail R’ 

module load R/3.5.1-foss-2018b 

# Run application using R passing in the array ID, corresponding to $SLURM_ARRAY_TASK_ID, as a command line argument 

Rscript hello-parallel.R $SLURM_ARRAY_TASK_ID 

The example below is the simple R script used in example 4.

hello-parallel.R 

#!/usr/bin/env Rscript 

args = commandArgs(trailingOnly=TRUE) 

print(paste0('Hello! I am task number: ', args[1])) 

vector = c(1, 10, 100, 1000, 10000) 

multiply = function(x, y) { 

return(x*y) 

} 

num = as.integer(args[1]) 

res = multiply(vector[num],num) 

print(paste0('Result: ', res))