Quick Reference Guide - Revision history

Anovak: /* General Commands */

2023-05-15T19:59:29Z

General Commands

← Older revision		Revision as of 12:59, 15 May 2023
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	man squeue		man squeue
	man scancel		man scancel
			man srun

	== Submitting jobs ==		== Submitting jobs ==
	The following example script specifies a partition, time limit, memory allocation and number of cores. All your scripts should specify values for these four parameters. You can also set additional parameters as shown, such as jobname and output file. For This script performs a simple task — it generates of file of random numbers and then sorts it. A detailed explanation the script is available here.		The following example script specifies a partition, time limit, memory allocation and number of cores. All your scripts should specify values for these four parameters. You can also set additional parameters as shown, such as jobname and output file. For This script performs a simple task — it generates of file of random numbers and then sorts it. A detailed explanation the script is available here.

Weiler: /* Advanced (but useful!) Commands */

2023-03-09T03:52:20Z

Advanced (but useful!) Commands

← Older revision		Revision as of 20:52, 8 March 2023
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	After resuming, check if any are still suspended:		After resuming, check if any are still suspended:
	squeue -ho %A -u $USER -t S \| wc -l		squeue -ho %A -u $USER -t S \| wc -l
	View Cluster State		View Cluster State:
	shost		shost

Weiler at 03:51, 9 March 2023

2023-03-09T03:51:22Z

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Weiler: Created page with "== Job scheduling commands == {| class="wikitable" |- ! Commands ! Function ! Basic Usage ! Example |- ! sbatch ! submit a slurm job ! sbatch [script] ! $ sbatch job.sub |- !..."

2023-03-09T03:39:31Z

Created page with "== Job scheduling commands == {| class="wikitable" |- ! Commands ! Function ! Basic Usage ! Example |- ! sbatch ! submit a slurm job ! sbatch [script] ! $ sbatch job.sub |- !..."

New page

== Job scheduling commands ==
{| class="wikitable"
|-
! 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_here

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

{| class="wikitable"
|+ Caption: Batch File
|-
! 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:

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#this command will give 1 Node for a time of 4 hours

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

Getting information on past jobs

You can use slurm database to see how much memory your previous jobs used, e.g. the following command will report requested memory and used residential and virtual memory for job

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

Aliases that provide useful information parsed from the SLURM commands

Place these alias’ into your .bashrc

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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\""