Hoffman2:Batch Mode - Revision history

Hwang: /* Part 3: Call your job script */

2022-09-30T17:29:34Z

Part 3: Call your job script

← Older revision		Revision as of 17:29, 30 September 2022
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	qsub myjob.sh		qsub myjob.sh


			To confirm the status of the submitted job, use command "myjob"

			myjob

			This will show the status of your jobs

	= Other methods =		= Other methods =

Hwang at 17:27, 30 September 2022

2022-09-30T17:27:44Z

← Older revision		Revision as of 17:27, 30 September 2022
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	For example:		For example:
	/bin/bash mycode.sh		/bin/bash mycode.sh

			Once the batch script is ready, you can submit it with qsub

			qsub myjob.sh

	= Other methods =		= Other methods =

Hwang: /* Part 3: Call your job script */

2022-09-30T17:25:57Z

Part 3: Call your job script

← Older revision		Revision as of 17:25, 30 September 2022
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	chmod ug+x mycode.sh		chmod ug+x mycode.sh

			call your script at the last part of your batch script
	~~The rest is to~~ call your script ~~for analysis.~~

	For example:		For example:

Hwang: /* Part 3: Call your job script */

2022-09-30T17:25:14Z

Part 3: Call your job script

← Older revision		Revision as of 17:25, 30 September 2022
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	= Part 3: Call your job script =		= Part 3: Call your job script =

			The third part of the batch script should call commands or other scrip for analysis.

			For example, if you run feat

			feat /my/path/to/design.fsf


			Or if you have a script named as mycode.sh containing all the commands for your analysis,

	Make sure your job script has executive privileges by using chmod command		Make sure your job script has executive privileges by using chmod command

Hwang: /* Part 2: Setup the Environment */

2022-09-30T17:22:55Z

Part 2: Setup the Environment

← Older revision		Revision as of 17:22, 30 September 2022
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	= Part 2: Setup the Environment =		= Part 2: Setup the Environment =
	In the second part, you should setup your Unix environment for your code to run, which includes loading modules and export paths for libraries.		In the second part of the batch script, you should setup your Unix environment for your code to run, which includes loading modules and export paths for libraries.

	To use any module provided by Hoffman and CCN, you'll need the following two lines		To use any module provided by Hoffman and CCN, you'll need the following two lines

Hwang: /* Part 1: Request Computing Resource */

2022-09-30T17:22:41Z

Part 1: Request Computing Resource

← Older revision		Revision as of 17:22, 30 September 2022
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	'''[[Hoffman2:Submit_job\|Submit Job]]''' template.		'''[[Hoffman2:Submit_job\|Submit Job]]''' template.

	The first part of the batch file should let the Hoffman job scheduler know what resources you want to reserve for your job:		The first part of the batch script file should let the Hoffman job scheduler know what resources you want to reserve for your job:
	#!/bin/bash		#!/bin/bash
	#$ -cwd		#$ -cwd

Hwang: /* Part 3: Call your job script */

2022-09-30T17:21:35Z

Part 3: Call your job script

← Older revision		Revision as of 17:21, 30 September 2022
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	The rest is to call your ~~batch job script in the batch~~ script.		The rest is to call your script for analysis.

	For example:		For example:

Hwang: /* Part 3: Submit your job script */

2022-09-30T17:21:06Z

Part 3: Submit your job script

← Older revision		Revision as of 17:21, 30 September 2022
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	export PATH=$HOME/.local/bin:$PATH		export PATH=$HOME/.local/bin:$PATH

	= Part 3: ~~Submit~~ your job script =		= Part 3: Call your job script =


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	The rest is to ~~submit~~ your batch job script ~~with qsub~~.		The rest is to call your batch job script in the batch script.

	For example:		For example:
	~~qsub~~ mycode.sh		/bin/bash mycode.sh

	= Other methods =		= Other methods =

Hwang: /* Part 3: Call your job script */

2022-09-30T17:14:18Z

Part 3: Call your job script

← Older revision		Revision as of 17:14, 30 September 2022
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	export PATH=$HOME/.local/bin:$PATH		export PATH=$HOME/.local/bin:$PATH

	= Part 3: ~~Call~~ your job script =		= Part 3: Submit your job script =

	~~The rest is to call your job script.~~

	~~For example:~~		Make sure your job script has executive privileges by using chmod command
	~~/bin/bash~~ mycode.sh
			chmod ug+x mycode.sh


	~~Make sure~~ your job script ~~has executive privileges by using chmod command~~		The rest is to submit your batch job script with qsub.

	~~chmod ug+x~~ mycode.sh		For example:
			qsub mycode.sh

	= Other methods =		= Other methods =

Jpdiaz: /* Part 1: Request Computing Resource */ remove redundant information

2020-08-05T02:40:53Z

Part 1: Request Computing Resource: remove redundant information

← Older revision		Revision as of 02:40, 5 August 2020
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	:*Part 1: List all the resources you want to reserve for your job		:*Part 1: List all the resources you want to reserve for your job
	:*Part 2: Load your modules, export the Linux environment that needed for your script to run		:*Part 2: Load your modules, export the Linux environment that is needed for your script to run
	:*Part 3: Call your job script		:*Part 3: Call your job script

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	= Job Submission Templates =		= Job Submission Templates =
	Here are some batch file templates you can start with:		Here are some batch file templates you can start with:
	:[[Hoffman2:Job_Submission_Templates\|~~job submission template scripts~~]]		:[[Hoffman2:Job_Submission_Templates\|Job Submission Template Scripts]]

	= Part 1: Request Computing Resource =		= Part 1: Request Computing Resource =

	This example ~~uses the~~ code from the ~~following template~~		This example is based on code from the
	'''[[Hoffman2:Submit_job\|Submit ~~job~~]]'''		'''[[Hoffman2:Submit_job\|Submit Job]]''' template.

	The first part of the batch file should let the Hoffman job scheduler know ~~how much~~ resources you want to reserve for your job		The first part of the batch file should let the Hoffman job scheduler know what resources you want to reserve for your job:
	#!/bin/bash		#!/bin/bash
	#$ -cwd		#$ -cwd
	~~# error = Merged with joblog~~
	#$ -o joblog.$JOB_ID		#$ -o joblog.$JOB_ID
	#$ -j y		#$ -j y
	#$ -pe shared 2		#$ -pe shared 2
	#$ -l h_rt=8:00:00,h_data=4G		#$ -l h_rt=8:00:00,h_data=4G
	~~# Email address to notify~~
	#$ -M $USER@mail		#$ -M $USER@mail
	~~# Notify when~~
	#$ -m bea		#$ -m bea


	Here's the meaning of each line:		Here's the meaning of each line:
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	#$ -cwd		#$ -cwd
	:Use the current directory for the job		:Use the current directory for the job


	#$ -o joblog.$JOB_ID		#$ -o joblog.$JOB_ID
	:Write standard output to file joblog.$JOB_ID. $JOB_ID will be replaced by your job ID which is assigned once you submit your job.		:Write standard output to file joblog.$JOB_ID. $JOB_ID will be replaced by your job ID which is assigned once you submit your job.


	#$ -j y		#$ -j y
	:Merge error log with standard output (in file joblog.$JOB_ID)		:Merge error log with standard output (in file joblog.$JOB_ID)


	#$ -pe shared 2		#$ -pe shared 2
	:Request 2 processor cores		:Request 2 processor cores


	#$ -l h_rt=8:00:00,h_data=4G		#$ -l h_rt=8:00:00,h_data=4G
	:Use -l option to specify job running time length and reserve memory		:Use -l option to specify job running time length and reserve memory

	:<code>h_rt=8:00:00</code> : reserve 8 hours for your job running time		:<code>h_rt=8:00:00</code> : reserve 8 hours for your job running time
	:<code>h_data=4G</code>: reserve 4G per-core (since -pe 2 is used above, it will reserve 2 core x 4G memory = 8G total memory)		:<code>h_data=4G</code>: reserve 4G per-core (since -pe 2 is used above, it will reserve 2 core x 4G memory = 8G total memory)


	#$ -M $USER@mail		#$ -M $USER@mail
	:Send notification ~~email~~ to your user email address		:Send notification to your user email address


	#$ -m bea		#$ -m bea