Creating sbatch script - Revision history

Sun092: /* partition for resource allocation */

2024-04-24T08:07:39Z

partition for resource allocation

← Older revision		Revision as of 10:07, 24 April 2024
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	===partition for resource allocation===		===partition for resource allocation===
	<pre>		<pre>
	#SBATCH --partition=~~ABGC_Std~~		#SBATCH --partition=gpu
	</pre>		</pre>
	Request a specific partition for the resource allocation~~. It is prefered to use your organizations partition~~.		Request a specific partition for the resource allocation.

	=== Adding accounting information or project number ===		=== Adding accounting information or project number ===

Prins0891: fixed syntax to put code back in code blocks in

2023-06-15T13:32:50Z

fixed syntax to put code back in code blocks in <pre></pre>

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Dawes001 at 15:05, 15 July 2019

2019-07-15T15:05:38Z

← Older revision		Revision as of 17:05, 15 July 2019
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	===constraints: selecting by feature===		===constraints: selecting by feature===
	<source lang='bash'>		<source lang='bash'>
	#SBATCH --constraint=~~normalmem~~		#SBATCH --constraint=4gpercpu
	</source>		</source>
	The HPC nodes have features associated with them, such as Intel CPU's, or the amount of memory per node. If you know that your job requires a specific architecture or memory size, you can elect to constrain your job to only these features.		The HPC nodes have features associated with them, such as Intel CPU's, or the amount of memory per node. If you know that your job requires a specific architecture or memory size, you can elect to constrain your job to only these features.

	The example above will result in jobs being scheduled to the ~~regular~~ compute nodes. By using <code>~~largemem~~</code> as option the job will specifically be scheduled to one of the ~~fat~~ nodes.		The example above will result in jobs being scheduled to the compute nodes with 4GB of memory per CPU. By using <code>12gpercpu</code> as option the job will specifically be scheduled to one of the larger nodes with 12GB per CPU.

	All features can be seen using:		All features can be seen using:

Dawes001 at 14:58, 15 July 2019

2019-07-15T14:58:38Z

← Older revision		Revision as of 16:58, 15 July 2019
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	#-----------------------------Other information------------------------		#-----------------------------Other information------------------------
	#SBATCH --comment=		#SBATCH --comment=
			#SBATCH --qos=
	#-----------------------------Required resources-----------------------		#-----------------------------Required resources-----------------------
	~~#SBATCH --partition=~~
	#SBATCH --time=0-0:0:0		#SBATCH --time=0-0:0:0
	#SBATCH --ntasks=		#SBATCH --ntasks=

Dawes001 at 13:44, 19 March 2019

2019-03-19T13:44:25Z

← Older revision		Revision as of 15:44, 19 March 2019
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	== See also ==		== See also ==
	* [[~~B4F_cluster~~ \| ~~HPC Agrogenomics Cluster~~]]		* [[Anunna \| Anunna]]
	* [[~~SLURM_on_B4F_cluster~~#Batch_script \| ~~Redirect~~ to ~~SLURM on B4F cluster~~]]		* [[Using_Slurm#Batch_script \| Submitting jobs to Slurm]]
	* [[Array_jobs\|Array job hints]]		* [[Array_jobs\|Array job hints]]

Dawes001 at 10:49, 8 May 2018

2018-05-08T10:49:08Z

← Older revision		Revision as of 12:49, 8 May 2018
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	#-----------------------------Other information------------------------		#-----------------------------Other information------------------------
	#SBATCH --comment=		#SBATCH --comment=
	~~##SBATCH --account=~~
	#-----------------------------Required resources-----------------------		#-----------------------------Required resources-----------------------
	#SBATCH --partition=		#SBATCH --partition=
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	=== Adding accounting information or project number ===		=== Adding accounting information or project number ===
	<source lang='bash'>		<source lang='bash'>
	#SBATCH --~~account~~=773320000		#SBATCH --comment=773320000
	</source>		</source>
	Charge resources used by this job to specified account. The ~~account~~ is an arbitrary string. The ~~account name~~ may be changed after job submission using the <tt>scontrol</tt> command. For WUR users a projectnumber or KTP number would be advisable.		Charge resources used by this job to specified account. The comment is an arbitrary string. The comment may be changed after job submission using the <tt>scontrol</tt> command. For WUR users a projectnumber or KTP number would be advisable.

	===time limit===		===time limit===

Dawes001: /* See also */

2017-09-06T10:01:17Z

Dawes001: /* Explanation of used SBATCH parameters */

2017-08-25T08:14:59Z

Explanation of used SBATCH parameters

← Older revision		Revision as of 10:14, 25 August 2017
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	==Explanation of used SBATCH parameters==		==Explanation of used SBATCH parameters==
			===partition for resource allocation===
			<source lang='bash'>
			#SBATCH --partition=ABGC_Std
			</source>
			Request a specific partition for the resource allocation. It is prefered to use your organizations partition.

	=== Adding accounting information or project number ===		=== Adding accounting information or project number ===
	<source lang='bash'>		<source lang='bash'>
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	Because the cluster has a hybrid configuration, i.e. normal and fat nodes, it may be prudent to schedule your job specifically for one or the other node type, depending for instance on memory requirements. This can be done by using the <code>-C</code> or <code>--constraints</code> flag.		Because the cluster has a hybrid configuration, i.e. normal and fat nodes, it may be prudent to schedule your job specifically for one or the other node type, depending for instance on memory requirements. This can be done by using the <code>-C</code> or <code>--constraints</code> flag.

	===constraints: selecting ~~the normal or fat nodes~~===		===constraints: selecting by feature===
	<source lang='bash'>		<source lang='bash'>
	#SBATCH --constraint=normalmem		#SBATCH --constraint=normalmem
	</source>		</source>
			The HPC nodes have features associated with them, such as Intel CPU's, or the amount of memory per node. If you know that your job requires a specific architecture or memory size, you can elect to constrain your job to only these features.

	The example above will result in jobs being scheduled to the regular compute nodes. By using <code>largemem</code> as option the job will specifically be scheduled to one of the fat nodes.		The example above will result in jobs being scheduled to the regular compute nodes. By using <code>largemem</code> as option the job will specifically be scheduled to one of the fat nodes.

			All features can be seen using:
			<source lang='bash'>
			scontrol show nodes \| grep ActiveFeatures \| sort \| uniq
			</source>

			===requesting specific resources===
			<source lang='bash'>
			#SBATCH --gres=gpu:1
			</source>
			In order to be able to use specific hardware resources, you need to request a Generic Resource. Once you do this, one of the resources will be allocated to your job when they are available. In the above example, one GPU is requested for use.

	===output (stderr,stdout) directed to file===		===output (stderr,stdout) directed to file===
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	</source>		</source>
	Specify a name for the job allocation. The specified name will appear along with the job id number when querying running jobs on the system. The default is the name of the batch script, or just "sbatch" if the script is read on sbatch's standard input.		Specify a name for the job allocation. The specified name will appear along with the job id number when querying running jobs on the system. The default is the name of the batch script, or just "sbatch" if the script is read on sbatch's standard input.

	~~===partition for resource allocation===~~
	~~<source lang='bash'>~~
	~~#SBATCH --partition=ABGC_Std~~
	~~</source>~~
	~~Request a specific partition for the resource allocation. It is prefered to use your organizations partition.~~

	===receiving mailed updates===		===receiving mailed updates===

Megen002: /* receiving mailed updates */

2017-06-07T14:26:35Z

receiving mailed updates

← Older revision		Revision as of 16:26, 7 June 2017
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	Notify user by email when certain event types occur. Valid type values are BEGIN, END, FAIL, REQUEUE, and ALL (any state change). The user to be notified is indicated with --mail-user.		Notify user by email when certain event types occur. Valid type values are BEGIN, END, FAIL, REQUEUE, and ALL (any state change). The user to be notified is indicated with --mail-user.
	<source lang='bash'>		<source lang='bash'>
	#SBATCH --mail-user=~~email~~@~~org~~.nl		#SBATCH --mail-user=yourname001@wur.nl
	</source>		</source>
	Email address to use.		Email address to use.

Megen002: /* time limit */

2017-06-07T14:25:52Z

time limit

← Older revision		Revision as of 16:25, 7 June 2017
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	</source>		</source>
	A time limit of zero requests that no time limit be imposed. Acceptable time formats include "minutes", "minutes:seconds", "hours:minutes:seconds", "days-hours", "days-hours:minutes" and "days-hours:minutes:seconds". So in this example the job will run for a maximum of 1200 minutes.		A time limit of zero requests that no time limit be imposed. Acceptable time formats include "minutes", "minutes:seconds", "hours:minutes:seconds", "days-hours", "days-hours:minutes" and "days-hours:minutes:seconds". So in this example the job will run for a maximum of 1200 minutes.


	===memory limit===		===memory limit===

← Older revision		Revision as of 12:01, 6 September 2017
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	* [[B4F_cluster \| HPC Agrogenomics Cluster]]		* [[B4F_cluster \| HPC Agrogenomics Cluster]]
	* [[SLURM_on_B4F_cluster#Batch_script \| Redirect to SLURM on B4F cluster]]		* [[SLURM_on_B4F_cluster#Batch_script \| Redirect to SLURM on B4F cluster]]
			* [[Array_jobs\|Array job hints]]