Rocky Job Anatomy - Revision history

Jondale at 15:04, 12 September 2023

2023-09-12T15:04:59Z

← Older revision		Revision as of 15:04, 12 September 2023
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	<pre>		<pre>
	#!/bin/bash		#!/bin/bash
	#SBATCH --job-name=MY_JOB ### ~~Job Name~~		#SBATCH --job-name=MY_JOB ### job name
	#SBATCH --output=my_job_%j.out ### ~~File in which~~ to store job output		#SBATCH --output=my_job_%j.out ### file to store job output
	#SBATCH --time=00:10:00 ### ~~Wall clock~~ time limit in Days-HH:MM:SS		#SBATCH --time=1-00:00:00 ### maximum time limit for job (Days-HH:MM:SS)
	#SBATCH --mem-per-cpu=2G ### ~~How much RAM~~ per cpu		#SBATCH --mem-per-cpu=2G ### amount of memory per cpu to allocate
	#SBATCH --cpus-per-task=1 ### ~~How many~~ cpu to ~~use per task~~		#SBATCH --cpus-per-task=1 ### number of cpu to allocate
	#SBATCH --mail-user=me@test.com ### My email address		#SBATCH --mail-user=me@test.com ### email address to notify
	#SBATCH --mail-type=END ### ~~Which events to~~ send email		#SBATCH --mail-type=END ### send an email when the job ends

	module load R/4.2.1-foss-2022a		module load R/4.2.1-foss-2022a

Jondale at 14:47, 12 September 2023

2023-09-12T14:47:10Z

← Older revision		Revision as of 14:47, 12 September 2023
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	Job parameters are defined one per line and start with <code>#SBATCH</code>.<br/>		Job parameters are defined one per line and start with <code>#SBATCH</code>.<br/>
	All parameters have default values and are optional but most batch scripts will use ~~them~~.		All parameters have default values and are optional but most batch scripts will use some.<br/>

			You can view all of the sbatch options at:<br/>
			https://slurm.schedmd.com/sbatch.html

			Below is an example batch file using some of the most common options:

	'''my_job.run'''		'''my_job.run'''
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	#SBATCH --output=my_job_%j.out ### File in which to store job output		#SBATCH --output=my_job_%j.out ### File in which to store job output
	#SBATCH --time=00:10:00 ### Wall clock time limit in Days-HH:MM:SS		#SBATCH --time=00:10:00 ### Wall clock time limit in Days-HH:MM:SS
	#SBATCH --~~nodes~~=1 ### ~~Node count required for the job~~		#SBATCH --mem-per-cpu=2G ### How much RAM per cpu
	#SBATCH --~~ntasks~~-per-~~node~~=1 ### ~~Number of tasks~~ to ~~be launched~~ per ~~Node~~		#SBATCH --cpus-per-task=1 ### How many cpu to use per task
	#SBATCH --~~mem~~-~~per-cpu~~=2G		#SBATCH --mail-user=me@test.com ### My email address
	#SBATCH --~~cpus-per~~-~~task~~=40		#SBATCH --mail-type=END ### Which events to send email

	module load R/4.2.1-foss-2022a		module load R/4.2.1-foss-2022a

Jstratt7 at 20:41, 17 April 2023

2023-04-17T20:41:49Z

← Older revision		Revision as of 20:41, 17 April 2023
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	Job parameters are defined one per line and start with <code>#SBATCH</code>.<br/>		Job parameters are defined one per line and start with <code>#SBATCH</code>.<br/>
	All parameters have default values ~~are~~ are optional but most batch scripts will use them.		All parameters have default values and are optional but most batch scripts will use them.

Jstratt7 at 17:21, 10 April 2023

2023-04-10T17:21:09Z

← Older revision		Revision as of 17:21, 10 April 2023
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	scancel 2947		scancel 2947
	</pre>		</pre>


	~~= Example Jobs =~~


	~~==== Python ====~~
	* [[ Rocky_Python_HelloWorld \| Hello World ]]

	~~==== R ====~~
	* [[ Rocky_R_HelloWorld \| Hello World ]]
	* [[ Rocky_R_Prime \| Calculate Prime Numbers ]]

Jstratt7: /* Example Jobs */

2023-04-10T17:17:48Z

Example Jobs

← Older revision		Revision as of 17:17, 10 April 2023
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	==== Python ====		==== Python ====
	* [[Rocky_Python_HelloWorld \| Hello World]]		* [[ Rocky_Python_HelloWorld \| Hello World ]]

	==== R ====		==== R ====
	* [[Rocky_R_Prime \| Calculate Prime Numbers ]]		* [[ Rocky_R_HelloWorld \| Hello World ]]
			* [[ Rocky_R_Prime \| Calculate Prime Numbers ]]

Jstratt7: /* Example Jobs */

2023-04-10T17:00:01Z

Example Jobs

← Older revision		Revision as of 17:00, 10 April 2023
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	= Example Jobs =		= Example Jobs =


	==== Python ====		==== Python ====
			* [[Rocky_Python_HelloWorld \| Hello World]]

	==== R ====		==== R ====
	* [[Rocky_R_Prime \| Calculate Prime Numbers ~~in R~~ ]]		* [[Rocky_R_Prime \| Calculate Prime Numbers ]]

Jstratt7: /* R */

2023-04-10T16:47:04Z

← Older revision		Revision as of 16:47, 10 April 2023
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	==== R ====		==== R ====
	[[Rocky_R_Prime \| Calculate Prime Numbers in R ]]		* [[Rocky_R_Prime \| Calculate Prime Numbers in R ]]

Jstratt7: Created page with "= Anatomy of a Rocky Job = Setting up a job to run on Rocky starts by creating or uploading your project's files to the project directory within your home directory on Rocky. These files will include the code you've written, any data files needed, and a batch file. ==== Your Code ==== Your code is what is submitted and executed on Rocky's compute nodes.
It can be written in any of the languages supported by Rocky environment modules (Lmod). ==== Your Data ===..."

2023-04-10T16:45:42Z

Created page with "= Anatomy of a Rocky Job = Setting up a job to run on Rocky starts by creating or uploading your project's files to the project directory within your home directory on Rocky. These files will include the code you've written, any data files needed, and a batch file. ==== Your Code ==== Your code is what is submitted and executed on Rocky's compute nodes.<br/> It can be written in any of the languages supported by Rocky environment modules (Lmod). ==== Your Data ===..."

New page

= Anatomy of a Rocky Job =

Setting up a job to run on Rocky starts by creating or uploading your project's files to the project directory within your home directory on Rocky. These files will include the code you've written, any data files needed, and a batch file.

==== Your Code ====

Your code is what is submitted and executed on Rocky's compute nodes.<br/>
It can be written in any of the languages supported by Rocky environment modules (Lmod).

==== Your Data ====

If your job will be processing data, you'll need to upload that data to your project's directory.

Your home directory is shared amongst all compute nodes. No matter which node your job is assigned, it will have access to your data.

==== Batch Script ====

The batch script is a shell script that brings everything together by defining job parameters, loading any environment modules needed, and finally executing your code.

Job parameters are defined one per line and start with <code>#SBATCH</code>.<br/>
All parameters have default values are are optional but most batch scripts will use them.

'''my_job.run'''
<pre>
#!/bin/bash
#SBATCH --job-name=MY_JOB ### Job Name
#SBATCH --output=my_job_%j.out ### File in which to store job output
#SBATCH --time=00:10:00 ### Wall clock time limit in Days-HH:MM:SS
#SBATCH --nodes=1 ### Node count required for the job
#SBATCH --ntasks-per-node=1 ### Number of tasks to be launched per Node
#SBATCH --mem-per-cpu=2G
#SBATCH --cpus-per-task=40

module load R/4.2.1-foss-2022a

Rscript my_code.R
</pre>

= Running Job =

==== Submitting Job ====

Jobs are submitted using the <code>sbatch</code> command and passed your batch script as a parameter. This will add your job to the queue.

<pre>
sbatch my_job.run
</pre>

==== Watching Job ====

While your job is in the queue or being executed you may see it's status using the <code>squeue</code> command. If the job is currently running it will show which node(s) it is assigned.

<pre>
[test_user@rocky7 ~]$ squeue
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
2947 compute_all my_job test_use R 0:05 1 moose1
</pre>

==== Cancelling Job ====

To cancel a job, use the <code>scancel</code> command and pass the JOBID (as returned by <code>squeue</code>).

<pre>
scancel 2947
</pre>

= Example Jobs =

==== Python ====

==== R ====
[[Rocky_R_Prime | Calculate Prime Numbers in R ]]