HPC/Submitting and Managing Jobs/Advanced node selection - Revision history

Stern: /* Memory constraints for partial-node jobs */

2025-08-04T17:40:19Z

Memory constraints for partial-node jobs

← Older revision		Revision as of 17:40, August 4, 2025
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	with the proportion being considered at a granularity of the number of CPU sockets.		with the proportion being considered at a granularity of the number of CPU sockets.
	Since all nodes on Carbon (at time of writing) have 2 CPU sockets,		Since all nodes on Carbon (at time of writing) have 2 CPU sockets,
	this means that if a job claims <code>ppn</code> less than half the number of ~~all~~ cores of a node <code>''n''<sub>core</sub></code>,		this means that if a job claims <code>ppn</code>
	the job gets access to only ''half the node's entire memory''.		''less than half the number of cores'' of a node <code>''n''<sub>core</sub></code>,
			the job gets access to only
			''half the node's entire memory''.

	A job can '''claim all resources on a node''' by claiming all cores, even while not ''using'' all cores for calculation,		A job can '''claim all resources on a node''' by claiming all cores, even while not ''using'' all cores for calculation,

Stern: /* Memory constraints for partial-node jobs */

2025-08-04T17:39:39Z

Memory constraints for partial-node jobs

← Older revision		Revision as of 17:39, August 4, 2025
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	Jobs get granted memory hardware access in rough proportion of the fraction of CPUs cores claimed on each node,		Jobs get granted memory hardware access in rough proportion of the fraction of CPUs cores claimed on each node,
	with the proportion being considered at a granularity of the number of CPU sockets.		with the proportion being considered at a granularity of the number of CPU sockets.

	Since all nodes on Carbon (at time of writing) have 2 CPU sockets,		Since all nodes on Carbon (at time of writing) have 2 CPU sockets,
	this means that if a job claims <code>ppn</code> less than half the number of all cores of a node <code>''n''<sub>core</sub></code>,		this means that if a job claims <code>ppn</code> less than half the number of all cores of a node <code>''n''<sub>core</sub></code>,

Stern: /* Advanced control of processeors-per-node (PPN) */

2025-08-04T17:29:42Z

Advanced control of processeors-per-node (PPN)

@@ Line 37: / Line 37: @@
 == Advanced control of processeors-per-node (PPN) ==
 Each ''Carbon'' node has nodes with different CPU core counts.
-A request of <code>ppn=16</code> in the job submission can get routed onto a node with exactly 16 cores, or the job can get routed to a node with more cores, shareable by other jobs.
+A request of <code>ppn=16</code> in the job submission can get routed onto a node with exactly 16 cores, or the job can get routed to a node with ''more'' cores, the other nodes normally being usable by other jobs.
 You can specify if your application is fine to run on ''shared'' nodes or needs nodes for ''exclusive'' use, such as for the following reasons:
@@ Line 72: / Line 72: @@
 Select an option from the following scenarios.
 === Shared vs. Exclusive Node Access ===
 ; Permit other users and jobs:
@@ Line 90: / Line 116: @@
   #PBS '''-l naccesspolicy=UNIQUEUSER'''
 : The node is shared, but limited to one job for any given user.
 === Different PPN by node ===

Stern: /* Selecting node types for jobs */

2025-04-11T16:35:04Z

Selecting node types for jobs

← Older revision		Revision as of 16:35, April 11, 2025
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	-->		-->

	* [[HPC/~~Software/Catalog~~/vasp \| '''Special note for VASP''']]		* [[HPC/Applications/vasp \| '''Special note for VASP''']]

	=== Recommendations ===		=== Recommendations ===

Stern: /* Unix-like basics */

2024-08-30T17:41:00Z

Unix-like basics

← Older revision		Revision as of 17:41, August 30, 2024
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	PBS_O_HOME=/home/username		PBS_O_HOME=/home/username
	PBS_O_HOST=n123.carboncluster		PBS_O_HOST=n123.carboncluster
	PBS_O_LANG=C # Unix locale(7), used for date formats, sorting, etc.		PBS_O_LANG=C # Unix locale(7), used for date formats, sorting, etc.
	PBS_O_LOGNAME=username		PBS_O_LOGNAME=username
	PBS_O_MAIL=/var/spool/mail/username		PBS_O_MAIL=/var/spool/mail/username

Stern: /* Unix-like basics */

2024-08-30T17:40:48Z

Unix-like basics

← Older revision		Revision as of 17:40, August 30, 2024
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	PBS_O_HOME=/home/username		PBS_O_HOME=/home/username
	PBS_O_HOST=n123.carboncluster		PBS_O_HOST=n123.carboncluster
	PBS_O_LANG=C # Unix locale(7)		PBS_O_LANG=C # Unix locale(7), used for date formats, sorting, etc.
	PBS_O_LOGNAME=username		PBS_O_LOGNAME=username
	PBS_O_MAIL=/var/spool/mail/username		PBS_O_MAIL=/var/spool/mail/username

Stern: /* Advanced: PBS_* Variables */

2024-08-30T17:40:15Z

Advanced: PBS_* Variables

@@ Line 210: / Line 210: @@
      '''PBS_ENVIRONMENT'''				# useful for detection in scripts. Usually "PBS_BATCH", but "PBS_INTERACTIVE" under "qsub -I"
      '''PBS_JOBNAME'''=''jobname''				# from -N option, useful in job script for file names
 === PBS internals ===
@@ Line 224: / Line 233: @@
      PBS_O_SUBMIT_FILTER=/usr/local/sbin/torque_submitfilter
 <!--
 $ strings /usr/sbin/pbs_mom | grep -E "^[A-Z]+_[A-Z_]{5,}$" | grep -Ev '^(A[UVW]|SIG|SUB|GLIB|CXX|MPI|WAIT|RADIX|NOT)' | sort | pr -w100 -Tv3

Stern: /* Particularly useful in job scripts */

2024-08-30T17:39:39Z

Particularly useful in job scripts

← Older revision		Revision as of 17:39, August 30, 2024
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	=== Particularly useful in job scripts ===		=== Particularly useful in job scripts ===
	'''PBS_O_WORKDIR'''=/home/username/foo/bar # directory qsub was running in (or its -w ''dir'' option)		'''PBS_O_WORKDIR'''=/home/username/foo/bar # directory qsub was running in (or its -w ''dir'' option)

	'''PBS_NP'''=1 # number of processors requested, '''automatically used for "mpirun -n …"'''		'''PBS_NP'''=1 # number of processors requested, '''automatically used for "mpirun -n …"'''
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	'''PBS_ENVIRONMENT''' # useful for detection in scripts. Usually "PBS_BATCH", but "PBS_INTERACTIVE" under "qsub -I"		'''PBS_ENVIRONMENT''' # useful for detection in scripts. Usually "PBS_BATCH", but "PBS_INTERACTIVE" under "qsub -I"
	'''PBS_JOBNAME'''=''jobname'' # from -N option, useful in job script for file names		'''PBS_JOBNAME'''=''jobname'' # from -N option, useful in job script for file names

	=== PBS internals ===		=== PBS internals ===
	PBS_JOBCOOKIE=643…31D7		PBS_JOBCOOKIE=643…31D7

Stern: /* Advanced: PBS_* Variables */

2024-08-30T17:39:23Z

Advanced: PBS_* Variables

← Older revision		Revision as of 17:39, August 30, 2024
Line 197:		Line 197:

	=== Particularly useful in job scripts ===		=== Particularly useful in job scripts ===
	'''~~PBS_JOBNAME~~'''=''~~jobname~~'' ~~# from -N~~ option~~, useful in job script for file names~~		'''PBS_O_WORKDIR'''=/home/username/foo/bar # directory qsub was running in (or its -w ''dir'' option)

	'''PBS_NP'''=1 # number of processors requested, '''automatically used for "mpirun -n …"'''		'''PBS_NP'''=1 # number of processors requested, '''automatically used for "mpirun -n …"'''
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	'''PBS_WALLTIME'''=3600 # requested (or default) walltime, in seconds		'''PBS_WALLTIME'''=3600 # requested (or default) walltime, in seconds
	'''PBS_ENVIRONMENT''' # useful for detection in scripts. Usually "PBS_BATCH", but "PBS_INTERACTIVE" under "qsub -I"		'''PBS_ENVIRONMENT''' # useful for detection in scripts. Usually "PBS_BATCH", but "PBS_INTERACTIVE" under "qsub -I"
			'''PBS_JOBNAME'''=''jobname'' # from -N option, useful in job script for file names

	=== PBS internals ===		=== PBS internals ===
	PBS_JOBCOOKIE=643…31D7		PBS_JOBCOOKIE=643…31D7
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	=== Unix-like basics ===		=== Unix-like basics ===
	~~'''PBS_O_WORKDIR'''=/home/username/foo/bar # directory qsub was running in (or its -w ''dir'' option)~~
	PBS_O_HOME=/home/username		PBS_O_HOME=/home/username
	PBS_O_HOST=n123.carboncluster		PBS_O_HOST=n123.carboncluster

Stern: /* Useful in job scripts */

2024-08-30T17:38:33Z

Useful in job scripts

← Older revision		Revision as of 17:38, August 30, 2024
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	</source>		</source>

	=== ~~Useful~~ in job scripts ===		=== Particularly useful in job scripts ===
	'''PBS_JOBNAME'''=''jobname'' # from -N option, useful in job script for file names		'''PBS_JOBNAME'''=''jobname'' # from -N option, useful in job script for file names

Line 209:		Line 209:
	'''PBS_WALLTIME'''=3600 # requested (or default) walltime, in seconds		'''PBS_WALLTIME'''=3600 # requested (or default) walltime, in seconds
	'''PBS_ENVIRONMENT''' # useful for detection in scripts. Usually "PBS_BATCH", but "PBS_INTERACTIVE" under "qsub -I"		'''PBS_ENVIRONMENT''' # useful for detection in scripts. Usually "PBS_BATCH", but "PBS_INTERACTIVE" under "qsub -I"

	=== PBS internals ===		=== PBS internals ===
	PBS_JOBCOOKIE=643…31D7		PBS_JOBCOOKIE=643…31D7