Andrew Severin

Andrew Severin

Andrew manages the Genome Informatics Facility at Iowa State University. His academic background is in biochemistry with a Ph.D. in Biophysics/NMR spectroscopy. He is an interdisciplinary scientist working at the interface of Genetics and Bioinformatics, translating Big Data into informative data for interesting biological questions. He is passionate about evolution and the science behind the genome.

DataScience Workbook / 06: High-Performance Computing (HPC) / 5. Introduction to job scheduling / 5.1. SLURM: basics of workload manager / 5.1.2. SLURM commands

Introduction

Quick reference sheet for SLURM resource manager

Job scheduling commands

Commands Function Basic Usage Example
sbatch submit a slurm job sbatch [script] $ sbatch job.sub
scancel delete slurm batch job scancel [job_id] $ scancel 123456
scontrol hold hold slurm batch jobs scontrol hold [job_id] $ scontrol hold 123456
scontrol release release hold on slurm batch jobs scontrol release [job_id] $ scontrol release 123456

Job management commands

Job Status Commands
sinfo -a list all queues
squeue list all jobs
squeue -u userid list jobs for userid
squeue -t R list running jobs
smap show jobs, partitions and nodes in a graphical network topology

Job script basics

A typical job script will look like this:

#!/bin/bash
#SBATCH --nodes=1
#SBATCH --cpus-per-task=8
#SBATCH --time=02:00:00
#SBATCH --mem=128G
#SBATCH --mail-user=netid@gmail.com
#SBATCH --mail-type=begin
#SBATCH --mail-type=end
#SBATCH --error=JobName.%J.err
#SBATCH --output=JobName.%J.out

cd $SLURM_SUBMIT_DIR

module load <modulename>

# your commands goes below

Lines starting with #SBATCH are for SLURM resource manager to request resources for HPC. Some important options are as follows:

Option Examples Description
--nodes #SBATCH --nodes=1 Number of nodes
--cpus-per-task #SBATCH --cpus-per-task=16 Number of CPUs per node
--time #SBATCH --time=HH:MM:SS Total time requested for your job
--output #SBATCH -output filename STDOUT to a file
--error #SBATCH --error filename STDERR to a file
--mail-user #SBATCH --mail-user user@domain.edu< Email address to send notifications

Interactive session

To start a interactive session execute the following:

srun -N 1 -t 4:00:00 --pty /bin/bash

This command will give 1 Node for a time of 4 hours.

Getting info on past jobs

You can use slurm database to see how much memory your previous jobs used”

sacct -j <JOBID> --format JobID,Partition,Submit,Start,End,NodeList%40,ReqMem,MaxRSS,MaxRSSNode,MaxRSSTask,MaxVMSize,ExitCode

The following command will report requested memory and used residential and virtual memory for job JOBID.

Useful aliases

Here you have a few aliases that provide useful information parsed from the SLURM commands.

Place these aliases into your .bashrc. Follow the instructions in this practical tutorial.

alias si="sinfo -o \"%20P %5D %14F %8z %10m %10d %11l %16f %N\""
alias sq="squeue -o \"%8i %12j %4t %10u %20q %20a %10g %20P %10Q %5D %11l %11L %R\""

Resources

More information about Slurm can be found in external resources: