SGE-Slurm - Revision history

Mhanby@uab.edu: /* SGE-Slurm user comamnds */

2016-10-22T13:37:37Z

SGE-Slurm user comamnds

← Older revision		Revision as of 13:37, 22 October 2016
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	<td>qmon</td>		<td>qmon</td>
	<td>sview</td>		<td>sview</td>
	~~</tr><tr><td> </td>~~
	~~<td> </td>~~
	~~<td> </td>~~

	</tr><tr><td><strong>Job ID</strong></td>		</tr><tr><td><strong>Job ID</strong></td>
	<td>$JOB_ID</td>		<td>$JOB_ID</td>

Mhanby@uab.edu at 13:37, 22 October 2016

2016-10-22T13:37:13Z

← Older revision		Revision as of 13:37, 22 October 2016
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	sbatch --mail-user=$USER@uab.edu<br />		sbatch --mail-user=$USER@uab.edu<br />
	sbatch -t 24:00:00<br />		sbatch -t 24:00:00<br />
	sbatch -p ~~node~~ -n 16<br />		sbatch -p ''partition'' -n 16<br />
	sbatch --mem=4096<br />		sbatch --mem-per-cpu=4096<br />
	sbatch -A projectname<br />		sbatch -A projectname<br />
	sbatch -o filename<br />		sbatch -o filename<br />

Mhanby@uab.edu: Added table border for easier readibility

2016-10-21T21:06:41Z

Added table border for easier readibility

← Older revision		Revision as of 21:06, 21 October 2016
Line 2:		Line 2:
	<p>Some common commands and flags in SGE and Slurm with their respective equivalents:</p>		<p>Some common commands and flags in SGE and Slurm with their respective equivalents:</p>
	<p> </p>		<p> </p>
	<table><tr><td><strong>User Commands</strong></td>		<table border="1"><tr><td><strong>User Commands</strong></td>
	<td><strong>SGE</strong></td>		<td><strong>SGE</strong></td>
	<td><strong>Slurm</strong></td>		<td><strong>Slurm</strong></td>
Line 153:		Line 153:

	== SGE - Slurm conversion examples ==		== SGE - Slurm conversion examples ==
	<table><tr><th>'''SGE'''</th>		<table border="1"><tr><th>'''SGE'''</th>
	<th>'''Slurm'''</th>		<th>'''Slurm'''</th>
	</tr><tr>		</tr><tr>

Mhanby@uab.edu: Replaced SLURM with Slurm

2016-10-21T21:03:44Z

Replaced SLURM with Slurm

← Older revision		Revision as of 21:03, 21 October 2016
Line 1:		Line 1:
	== SGE-~~SLURM~~ user comamnds ==		== SGE-Slurm user comamnds ==
	<p>Some common commands and flags in SGE and ~~SLURM~~ with their respective equivalents:</p>		<p>Some common commands and flags in SGE and Slurm with their respective equivalents:</p>
	<p> </p>		<p> </p>
	<table><tr><td><strong>User Commands</strong></td>		<table><tr><td><strong>User Commands</strong></td>
	<td><strong>SGE</strong></td>		<td><strong>SGE</strong></td>
	<td><strong>~~SLURM~~</strong></td>		<td><strong>Slurm</strong></td>

	</tr><tr><td><strong>Interactive login</strong></td>		</tr><tr><td><strong>Interactive login</strong></td>
Line 152:		Line 152:
	</tr></table><p> </p>		</tr></table><p> </p>

	== SGE - ~~SLURM~~ conversion examples ==		== SGE - Slurm conversion examples ==
	<table><tr><th>'''SGE'''</th>		<table><tr><th>'''SGE'''</th>
	<th>'''~~SLURM~~'''</th>		<th>'''Slurm'''</th>
	</tr><tr>		</tr><tr>

Mhanby@uab.edu: Mhanby@uab.edu moved page SGE-SLURM to SGE-Slurm: Renaming to SGE-Slurm to reflect SchedMD syntax

2016-10-21T21:02:22Z

Mhanby@uab.edu moved page SGE-SLURM to SGE-Slurm: Renaming to SGE-Slurm to reflect SchedMD syntax

← Older revision	Revision as of 21:02, 21 October 2016
(No difference)

Tanthony@uab.edu at 12:46, 21 October 2016

2016-10-21T12:46:56Z

← Older revision		Revision as of 12:46, 21 October 2016
Line 5:		Line 5:
	<td><strong>SGE</strong></td>		<td><strong>SGE</strong></td>
	<td><strong>SLURM</strong></td>		<td><strong>SLURM</strong></td>

	</tr><tr><td><strong>Interactive login</strong></td>		</tr><tr><td><strong>Interactive login</strong></td>
	<td>qrsh</td>		<td>qrsh</td>
Line 10:		Line 11:
	srun --pty bash		srun --pty bash
	</td>		</td>

	</tr><tr><td><strong>Job submission</strong></td>		</tr><tr><td><strong>Job submission</strong></td>
	<td>qsub [script_file]</td>		<td>qsub [script_file]</td>
Line 158:		Line 160:
	qstat -f</blockquote>		qstat -f</blockquote>
	</td>		</td>
	<td>squeue<br /><blockquote>squeue -u username<br />		<td>'''squeue'''<br /><blockquote>squeue -u username<br />
	squeue -al</blockquote>		squeue -al</blockquote>
	</td>		</td>
Line 173:		Line 175:
	</blockquote>		</blockquote>
	</td>		</td>
	<td>sbatch<br /><blockquote>sbatch -J jobname<br />		<td>'''sbatch'''<br /><blockquote>sbatch -J jobname<br />
	sbatch --mail-type=ALL<br />		sbatch --mail-type=ALL<br />
	sbatch --mail-user=$USER@uab.edu<br />		sbatch --mail-user=$USER@uab.edu<br />
	sbatch -t 24:00:00<br />		sbatch -t 24:00:00<br />
	sbatch -p node -n 16</~~blockquote~~>		sbatch -p node -n 16<br />
	~~<blockquote>~~sbatch --mem=4096<br />		sbatch --mem=4096<br />
	sbatch -A projectname<br />		sbatch -A projectname<br />
	sbatch -o filename<br />		sbatch -o filename<br />
Line 185:		Line 187:
	</td>		</td>

	</tr><tr><td>'''qlogin for ~~interctive~~ via vnc'''</td>		</tr><tr><td>'''qlogin for interactive via vnc'''</td>
			<td>'''sinteractive for interactive via vnc'''</td>
	</tr><tr><td>~~'''~~qlogin~~'''~~ -l h_rt=8:00:00, vf=1G</td>		</tr><tr><td> <blockquote>qlogin -l h_rt=8:00:00, vf=1G <br /></blockquote></td>
	<td> sinteractive --time=8:00:00 --mem=1024</td>		<td> <blockquote>sinteractive --time=8:00:00 --mem=1024 <br /></blockquote></td>
	</tr></table><p> </p>		</tr></table><p> </p>
	<p> </p>		<p> </p>

Tanthony@uab.edu at 12:35, 21 October 2016

2016-10-21T12:35:09Z

← Older revision		Revision as of 12:35, 21 October 2016
Line 1:		Line 1:
	= SGE-SLURM user comamnds =		== SGE-SLURM user comamnds ==
	<p>Some common commands and flags in SGE and SLURM with their respective equivalents:</p>		<p>Some common commands and flags in SGE and SLURM with their respective equivalents:</p>
	<p> </p>		<p> </p>
Line 150:		Line 150:
	</tr></table><p> </p>		</tr></table><p> </p>

	= SGE - SLURM conversion examples =		== SGE - SLURM conversion examples ==
	<table><tr><th>'''SGE'''</th>		<table><tr><th>'''SGE'''</th>
	<th>'''SLURM'''</th>		<th>'''SLURM'''</th>

Tanthony@uab.edu: First edit of page from - https://srcc.stanford.edu/sge-slurm-conversion

2016-10-21T12:33:41Z

First edit of page from - https://srcc.stanford.edu/sge-slurm-conversion

New page

= SGE-SLURM user comamnds =
Some common commands and flags in SGE and SLURM with their respective equivalents:
 
<table><tr><td>User Commands</td>
<td>SGE</td>
<td>SLURM</td>
</tr><tr><td>Interactive login</td>
<td>qrsh</td>
<td>
srun --pty bash
</td>
</tr><tr><td>Job submission</td>
<td>qsub [script_file]</td>
<td>sbatch [script_file]</td>
</tr><tr><td>Job deletion</td>
<td>qdel [job_id]</td>
<td>scancel [job_id]</td>
</tr><tr><td>Job status by job</td>
<td>qstat -u \* [-j job_id]</td>
<td>squeue [job_id]</td>
</tr><tr><td>Job status by user</td>
<td>qstat [-u user_name]</td>
<td>
squeue -u [user_name]
</td>
</tr><tr><td>Job hold</td>
<td>qhold [job_id]</td>
<td>scontrol hold [job_id]</td>
</tr><tr><td>Job release</td>
<td>qrls [job_id]</td>
<td>scontrol release [job_id]</td>
</tr><tr><td>Queue list</td>
<td>qconf -sql</td>
<td>squeue</td>
</tr><tr><td>List nodes</td>
<td>qhost</td>
<td>sinfo -N OR scontrol show nodes</td>
</tr><tr><td>Cluster status</td>
<td>qhost -q</td>
<td>sinfo</td>
</tr><tr><td> Graphical queue view</td>
<td>qmon</td>
<td>sview</td>
</tr><tr><td> </td>
<td> </td>
<td> </td>

</tr><tr><td>Job ID</td>
<td>$JOB_ID</td>
<td>$SLURM_JOBID</td>
</tr><tr><td>Submit directory</td>
<td>$SGE_O_WORKDIR</td>
<td>$SLURM_SUBMIT_DIR</td>
</tr><tr><td>Submit host</td>
<td>$SGE_O_HOST</td>
<td>$SLURM_SUBMIT_HOST</td>
</tr><tr><td>Node list</td>
<td>$PE_HOSTFILE</td>
<td>$SLURM_JOB_NODELIST</td>
</tr><tr><td>Job Array Index</td>
<td>$SGE_TASK_ID</td>
<td>$SLURM_ARRAY_TASK_ID</td>

</tr><tr><td>Script directive</td>
<td>#$</td>
<td>#SBATCH</td>
</tr><tr><td>queue</td>
<td>-q [queue]</td>
<td>-p [queue]</td>
</tr><tr><td>count of nodes</td>
<td>N/A</td>
<td>-N [min[-max]]</td>
</tr><tr><td>CPU count</td>
<td>-pe [PE] [count]</td>
<td>-n [count]</td>
</tr><tr><td>Wall clock limit</td>
<td>-l h_rt=[seconds]</td>
<td>-t [min] OR -t [days-hh:mm:ss]</td>
</tr><tr><td>Standard out file</td>
<td>-o [file_name]</td>
<td>-o [file_name]</td>
</tr><tr><td>Standard error file</td>
<td>-e [file_name]</td>
<td>e [file_name]</td>
</tr><tr><td>Combine STDOUT & STDERR files </td>
<td>-j yes</td>
<td>(use -o without -e)</td>
</tr><tr><td>Copy environment</td>
<td>-V</td>
<td>--export=[ALL | NONE | variables]</td>
</tr><tr><td>Event notification</td>
<td>-m abe</td>
<td>--mail-type=[events]</td>
</tr><tr><td>send notification email</td>
<td>-M [address]</td>
<td>--mail-user=[address]</td>
</tr><tr><td>Job name</td>
<td>-N [name]</td>
<td>--job-name=[name]</td>
</tr><tr><td>Restart job</td>
<td>-r [yes|no]</td>
<td>--requeue OR --no-requeue (NOTE: 
configurable default)</td>
</tr><tr><td>Set working directory</td>
<td>-wd [directory]</td>
<td>--workdir=[dir_name]</td>
</tr><tr><td>Resource sharing</td>
<td>-l exclusive</td>
<td>--exclusive OR--shared</td>
</tr><tr><td>Memory size</td>
<td>-l mem_free=[memory][K|M|G]</td>
<td>--mem=[mem][M|G|T] OR --mem-per-cpu= 
[mem][M|G|T]</td>
</tr><tr><td>Charge to an account</td>
<td>-A [account]</td>
<td>--account=[account]</td>
</tr><tr><td>Tasks per node</td>
<td>(Fixed allocation_rule in PE)</td>
<td>--tasks-per-node=[count]</td>
</tr><tr><td> </td>
<td> </td>
<td>--cpus-per-task=[count]</td>
</tr><tr><td>Job dependancy</td>
<td>-hold_jid [job_id | job_name]</td>
<td>--depend=[state:job_id]</td>
</tr><tr><td>Job project</td>
<td>-P [name]</td>
<td>--wckey=[name]</td>
</tr><tr><td>Job host preference</td>
<td>-q [queue]@[node] OR -q 
[queue]@@[hostgroup]</td>
<td>--nodelist=[nodes] AND/OR --exclude= 
[nodes]</td>
</tr><tr><td>Quality of service</td>
<td> </td>
<td>--qos=[name]</td>
</tr><tr><td>Job arrays</td>
<td>-t [array_spec]</td>
<td>--array=[array_spec] (Slurm version 2.6+)</td>
</tr><tr><td>Generic Resources</td>
<td>-l [resource]=[value]</td>
<td>--gres=[resource_spec]</td>
</tr><tr><td>Licenses</td>
<td>-l [license]=[count]</td>
<td>--licenses=[license_spec]</td>
</tr><tr><td>Begin Time</td>
<td>-a [YYMMDDhhmm]</td>
<td>--begin=YYYY-MM-DD[THH:MM[:SS]]</td>
</tr></table> 

= SGE - SLURM conversion examples =
<table><tr><th>'''SGE'''</th>
<th>'''SLURM'''</th>
</tr><tr>

<td>'''qstat''' <blockquote>qstat -u username 
qstat -f</blockquote>
</td>
<td>squeue <blockquote>squeue -u username 
squeue -al</blockquote>
</td>

</tr><tr><td>'''qsub''' <blockquote>qsub -N jobname 
qsub -m beas 
qsub -M $USER@uab.edu 
qsub -l h_rt=24:00:00 
qsub -pe smp 16 
qsub -l vf=4G 
qsub -P projectname 
qsub -o filename 
qsub -e filename 
</blockquote>
</td>
<td>sbatch <blockquote>sbatch -J jobname 
sbatch --mail-type=ALL 
sbatch --mail-user=$USER@uab.edu 
sbatch -t 24:00:00 
sbatch -p node -n 16</blockquote>
<blockquote>sbatch --mem=4096 
sbatch -A projectname 
sbatch -o filename 
sbatch -e filename 
</blockquote>
</td>

</tr><tr><td>'''qlogin for interctive via vnc'''</td>

</tr><tr><td>'''qlogin''' -l h_rt=8:00:00, vf=1G</td>
<td> sinteractive --time=8:00:00 --mem=1024</td>
</tr></table>