Getting started on clusters - Revision history

Pelibby16 at 20:12, 2 April 2026

2026-04-02T20:12:36Z

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	This document gives you all the information you need to choose a system, log in to a cluster/phat node, write a script, submit it via sbatch to the scheduler, and find the output. As such, these notes cover hardware and software. (If you're a sysadmin, you may be interested in [[Sysadmin:Services:ClusterOverview \|this page]] instead.)		This document gives you all the information you need to choose a system, log in to a cluster/phat node, write a script, submit it via sbatch to the scheduler, and find the output. As such, these notes cover hardware and software. (If you're a sysadmin, you may be interested in [[Sysadmin:Services:ClusterOverview \|this page]] instead.)

	~~Please review~~ the ~~information here~~ and ~~consider which machine fits your purpose best~~.		Before you get started, make sure you have a CS account. You can email <code>admin@cs.earlham.edu</code> or a current CS faculty member to get started. Your user account will grant access to all the servers below, and you will have a home directory at <code>~username</code> that you can access when you connect to any of them.

	~~__TOC__~~		# First, read about what machines you can pick from. Take a look at [[#Cluster systems to choose from]], and see which machines fit your needs the best.
			# Open and terminal and connect to Hopper: <code>ssh username@hopper.cluster.earlham.edu</code>
			# Once you are connected to Hopper, you can SSH to the machine you need: <code>ssh username@hamilton.cluster.earlham.edu</code> (In this example, we connect to the Hamilton cluster).
			# Now you are ready to start using Slurm on that cluster. Check out [[#Using Slurm]] for more examples and information on how to use the scheduler on that machine.

	~~= Prerequisites =~~

	* Get a cluster account. You can email <code>admin@cs.earlham.edu</code> or a current CS faculty member to get started. Your user account will grant access to all the servers below, and you will have a home directory at <code>~username</code> that you can access when you connect to any of them.		__TOC__
	** Note: if you have a CS account, you will use the same username and password for your cluster account.
	* Connect through a terminal via ssh to <code>username@hopper.cluster.earlham.edu</code>. If you intend to work with these machines a lot, you should also configure your [[How To Set Up SSH Keys \| ssh keys]].
	* Once you are connected to Hopper, you can connect to any of the machines below.

	~~For example, if I want to connect to Hamilton:~~
	~~# <code>ssh username@hopper.cluster.earlham.edu</code>~~
	~~# <code>ssh username@hamilton.cluster.earlham.edu</code>~~
	~~# Now you are ready to start using Slurm on that cluster. Keep reading for more information on how to get started with Slurm.~~

	= Using Slurm =		= Using Slurm =

Pelibby16 at 20:08, 2 April 2026

2026-04-02T20:08:34Z

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Pelibby16: /* Prerequisites */

2026-04-02T20:07:51Z

Prerequisites

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	# <code>ssh username@hopper.cluster.earlham.edu</code>		# <code>ssh username@hopper.cluster.earlham.edu</code>
	# <code>ssh username@hamilton.cluster.earlham.edu</code>		# <code>ssh username@hamilton.cluster.earlham.edu</code>
			# Now you are ready to start using Slurm on that cluster. Keep reading for more information on how to get started with Slurm.

	= Cluster systems to choose from =		= Cluster systems to choose from =

Pelibby16: /* Useful Slurm Commands */

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Useful Slurm Commands

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	== Useful Slurm Commands ==		== Useful Slurm Commands ==
			Slurm has some other useful commands that you can use to interact with or view jobs that are running.
	~~To submit a job to~~ Slurm, you~~'ll need~~ to ~~write a shell script wrapper and submit it through sbatch on your system of choice. For people familiar~~ with ~~pbs the pattern is very similar~~. ~~For example (change the specific options):~~


	{\| class="wikitable"		{\| class="wikitable"

Pelibby16: /* Using Slurm */

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Using Slurm

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Pelibby16: /* Using Slurm */

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Using Slurm

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	Slurm is our batch scheduler.		Slurm is our batch scheduler.

	~~You can check that it's working by running: <code>$ srun -l hostname</code>~~

	You can submit a job in a script with the following: <code>$ sbatch my_good_script.sbatch</code>		You can submit a job in a script with the following: <code>$ sbatch my_good_script.sbatch</code>

Pelibby16: /* Conversion from Torque to Slurm */

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Conversion from Torque to Slurm

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	There's some more CPU management information [https://slurm.schedmd.com/cpu_management.html here].		There's some more CPU management information [https://slurm.schedmd.com/cpu_management.html here].

	== ~~Conversion from Torque to~~ Slurm ==		== Useful Slurm Commands ==

	To submit a job to Slurm, you'll need to write a shell script wrapper and submit it through sbatch on your system of choice. For people familiar with pbs the pattern is very similar. For example (change the specific options):		To submit a job to Slurm, you'll need to write a shell script wrapper and submit it through sbatch on your system of choice. For people familiar with pbs the pattern is very similar. For example (change the specific options):
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	\|-		\|-
	\| <code>sbatch</code>		\| <code>sbatch</code>
	\| run/submit a batch job		\| run/submit a batch job (.sbatch file, see above)
	\|-		\|-
	\| <code>squeue</code>		\| <code>squeue</code>
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	\|-		\|-
	\| <code>scancel</code>		\| <code>scancel</code>
	\| cancel a job		\| cancel a job by its ID
	\|-		\|-
	\| <code>scontrol show nodes</code>		\| <code>scontrol show nodes</code>

Pelibby16: /* Conversion from Torque to Slurm */

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Conversion from Torque to Slurm

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	\|+ Commands		\|+ Commands
	\|-		\|-
	~~! Torque~~
	! Slurm		! Slurm
	! Description		! Description
	\|-		\|-
	~~\| <code>qsub</code>~~
	\| <code>sbatch</code>		\| <code>sbatch</code>
	\| run/submit a batch job		\| run/submit a batch job
	\|-		\|-
	~~\| <code>qstat</code>~~
	\| <code>squeue</code>		\| <code>squeue</code>
	\| show jobs currently in the queue		\| show jobs currently in the queue
	\|-		\|-
	~~\| <code>qdel</code>~~
	\| <code>scancel</code>		\| <code>scancel</code>
	\| cancel a job		\| cancel a job
	\|-		\|-
	~~\| <code>pbsnodes -a</code>~~
	\| <code>scontrol show nodes</code>		\| <code>scontrol show nodes</code>
	\| show nodes in the cluster		\| show nodes in the cluster
	\|-
	~~\| <code>qstat ...</code>~~
	~~\| <code>scontrol update NodeName=w[0-6] State=RESUME</code>~~
	~~\| resurrect nodes that are offline~~
	\|}		\|}

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	\|+ Environment Variables		\|+ Environment Variables
	\|-		\|-
	~~! Torque~~
	! Slurm		! Slurm
	! Description		! Description
	\|-		\|-
	~~\| <code>$PBS_QUEUE</code>~~
	\| <code>$SLURM_JOB_PARTITION</code>		\| <code>$SLURM_JOB_PARTITION</code>
	\| the queue/partition you are in		\| the queue/partition you are in
	\|-		\|-
	~~\| <code>cat $PBS_NODEFILE</code>~~
	\| <code>$SLURM_JOB_NODELIST</code>		\| <code>$SLURM_JOB_NODELIST</code>
	\| there's no equivalent of the nodes file but there is an environment variable that stores that information		\| there's no equivalent of the nodes file but there is an environment variable that stores that information
	\|-		\|-
	~~\| <code>$PBS_O_WORKDIR</code>~~
	\| <code>$SLURM_SUBMIT_DIR</code>		\| <code>$SLURM_SUBMIT_DIR</code>
	\| working directory from which the command was run		\| working directory from which the command was run

Pelibby16: /* Prerequisites */

2026-04-02T18:56:48Z

Prerequisites

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	= Prerequisites =		= Prerequisites =

	# Get a cluster account. You can email <code>admin@cs.earlham.edu</code> or a current CS faculty member to get started. Your user account will grant access to all the servers below, and you will have a home directory at <code>~username</code> that you can access when you connect to any of them.		* Get a cluster account. You can email <code>admin@cs.earlham.edu</code> or a current CS faculty member to get started. Your user account will grant access to all the servers below, and you will have a home directory at <code>~username</code> that you can access when you connect to any of them.
	## Note: if you have a CS account, you will use the same username and password for your cluster account.		** Note: if you have a CS account, you will use the same username and password for your cluster account.
	# Connect through a terminal via ssh to <code>username@hopper.cluster.earlham.edu</code>. If you intend to work with these machines a lot, you should also configure your [[How To Set Up SSH Keys \| ssh keys]].		* Connect through a terminal via ssh to <code>username@hopper.cluster.earlham.edu</code>. If you intend to work with these machines a lot, you should also configure your [[How To Set Up SSH Keys \| ssh keys]].
	# Once you are connected to Hopper, you can connect to any of the machines below.		* Once you are connected to Hopper, you can connect to any of the machines below.

	For example, if I want to connect to Hamilton:		For example, if I want to connect to Hamilton:
	# 1. <code>ssh username@hopper.cluster.earlham.edu</code>		# <code>ssh username@hopper.cluster.earlham.edu</code>
	# 2. <code>ssh username@hamilton.cluster.earlham.edu</code>		# <code>ssh username@hamilton.cluster.earlham.edu</code>

	= Cluster systems to choose from =		= Cluster systems to choose from =

Pelibby16: /* Prerequisites */

2026-04-02T18:56:31Z

Prerequisites

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	For example, if I want to connect to Hamilton:		For example, if I want to connect to Hamilton:
	1. <code>ssh username@hopper.cluster.earlham.edu</code>		# 1. <code>ssh username@hopper.cluster.earlham.edu</code>
	2. <code>ssh username@hamilton.cluster.earlham.edu</code>		# 2. <code>ssh username@hamilton.cluster.earlham.edu</code>

	= Cluster systems to choose from =		= Cluster systems to choose from =