msub

4.0 Scheduler Commands > Commands > msub

msub

Synopsis

msub [-a datetime][-A account][-c interval][-C directive_prefix][-d path] [-e path][-E][-F][-h][-I][-j join][-k keep][-K][-l resourcelist][-m mailoptions] [-M user_list][-N name][-o path][-p priority][-q destination][-r] [-S pathlist][-t jobarrays][-u userlist][-v variablelist][-V] [-W additionalattributes][-x][-z][script]

Overview

msub allows users to submit jobs directly to Moab. When a job is submitted directly to a resource manager (such as TORQUE), it is constrained to run on only those nodes that the resource manager is directly monitoring. In many instances, a site may be controlling multiple resource managers. When a job is submitted to Moab rather than to a specific resource manager, it is not constrained as to what nodes it is executed on. msub can accept command line arguments (with the same syntax as qsub), job scripts (in either PBS or LoadLeveler syntax), or the SSS Job XML specification.

Moab must run as a root user in order for msub submissions to work. Workload submitted via msub when Moab is running as a non-root user fail immediately.

Submitted jobs can then be viewed and controlled via the mjobctl command.

Flags specified in the following table are not necessarily supported by all resource managers.

Access

When Moab is configured to run as root, any user may submit jobs via msub.

Flags

-a
Name	Eligible Date
Format	[[[[CC]YY]MM]DD]hhmm[.SS]
Description	Declares the time after which the job is eligible for execution.
Example	> msub -a 12041300 cmd.pbs Moab will not schedule the job until 1:00 pm on December 4, of the current year.

-A
Name	Account
Format	<ACCOUNT NAME>
Description	Defines the account associated with the job.
Example	> msub -A research cmd.pbs Moab will associate this job with account research.

-c
Name	Checkpoint Interval
Format	[n\|s\|c\|c=<minutes>]
Description	Checkpoint of the will occur at the specified interval. n — No Checkpoint is to be performed. s — Checkpointing is to be performed only when the server executing the job is shut down. c — Checkpoint is to be performed at the default minimum time for the server executing the job. c=<minutes> — Checkpoint is to be performed at an interval of minutes.
Example	> msub -c c=12 cmd.pbs The job will be checkpointed every 12 minutes.

-C
Name	Directive Prefix
Format	'<PREFIX NAME>'
Default	First known prefix (#PBS, #@, #BSUB, #!, #MOAB, #MSUB)
Description	Specifies which directive prefix should be used from a job script. It is best to submit with single quotes. '#PBS' An empty prefix will cause Moab to not search for any prefix. -C '' Command line arguments have precedence over script arguments. Custom prefixes can be used with the -C flag. -C '#MYPREFIX' Custom directive prefixes must use PBS syntax. If the -C flag is not given, Moab will take the first default prefix found. Once a directive is found, others are ignored.
Example	> msub -C '#MYPREFIX' cmd.pbs #MYPREFIX -l walltime=5:00:00 (in cmd.pbs) Moab will use the #MYPREFIX directive specified in cmd.pbs, setting the wallclock limit to five hours.

-d
Name	Execution Directory
Format	<path>
Default	Depends on the RM being used. If using TORQUE, the default is $HOME. If using SLURM, the default is the submission directory.
Description	Specifies which directory the job should execute in.
Example	> msub -d /home/test/job12 cmd.pbs The job will begin execution in the /home/test/job12 directory.

-e
Name	Error Path
Format	[<hostname>:]<path>
Default	$SUBMISSIONDIR/$JOBNAME.e$JOBID
Description	Defines the path to be used for the standard error stream of the batch job.
Example	> msub -e test12/stderr.txt The STDERR stream of the job will be placed in the relative (to execution) directory specified.

-E
Name	Environment Variables
Description	Moab adds the following variables, if populated, to the job's environment: MOAB_ACCOUNT — Account name. MOAB_BATCH — Set if a batch job (non-interactive). MOAB_CLASS — Class name. MOAB_DEPEND — Job dependency string. MOAB_GROUP — Group name. MOAB_JOBARRAYINDEX —For a job in an array, the index of the job. MOAB_JOBARRAYRANGE — For a system with job arrays, the range of all job arrays. MOAB_JOBID — Job ID. MOAB_JOBNAME — Job name. MOAB_MACHINE — Name of the machine (i.e. Destination RM) that the job is running on. MOAB_NODECOUNT — Number of nodes allocated to job. MOAB_NODELIST — Comma-separated list of nodes (listed singly with no ppn info). MOAB_PARTITION — Partition name the job is running in. MOAB_PROCCOUNT — Number of processors allocated to job. MOAB_QOS — QoS name. MOAB_TASKMAP — Node list with procs per node listed. <nodename>.<procs> MOAB_USER — User name. In SLURM environments, not all variables will be populated since the variables are added at submission (such as NODELIST). With TORQUE/PBS, the variables are added just before the job is started. This feature only works with SLURM and TORQUE/PBS.
Example:	> msub -E mySim.cmd The job mySim will be submitted with extra environment variables.

-E

Name

Environment Variables

Description

Moab adds the following variables, if populated, to the job's environment:

MOAB_ACCOUNT — Account name.
MOAB_BATCH — Set if a batch job (non-interactive).
MOAB_CLASS — Class name.
MOAB_DEPEND — Job dependency string.
MOAB_GROUP — Group name.
MOAB_JOBARRAYINDEX —For a job in an array, the index of the job.
MOAB_JOBARRAYRANGE — For a system with job arrays, the range of all job arrays.
MOAB_JOBID — Job ID.
MOAB_JOBNAME — Job name.
MOAB_MACHINE — Name of the machine (i.e. Destination RM) that the job is running on.
MOAB_NODECOUNT — Number of nodes allocated to job.
MOAB_NODELIST — Comma-separated list of nodes (listed singly with no ppn info).
MOAB_PARTITION — Partition name the job is running in.
MOAB_PROCCOUNT — Number of processors allocated to job.
MOAB_QOS — QoS name.
MOAB_TASKMAP — Node list with procs per node listed. <nodename>.<procs>
MOAB_USER — User name.

In SLURM environments, not all variables will be populated since the variables are added at submission (such as NODELIST). With TORQUE/PBS, the variables are added just before the job is started.

This feature only works with SLURM and TORQUE/PBS.

Example:

> msub -E mySim.cmd

The job mySim will be submitted with extra environment variables.

-F
Name	Script Flags
Format	"\"<STRING>\""
Description	Specifies the flags TORQUE will pass to the job script at execution time. The -F flag is only compatible with TORQUE resource managers.
Example	> msub -F "\"arg1 arg2\"" -1 nodes=1,walltime=60 files/job.sh TORQUE will pass parameters arg1 and arg2 to the job.sh script when the job executes.

-h
Name	Hold
Description	Specifies that a user hold be applied to the job at submission time.
Example	> msub -h cmd.ll The job will be submitted with a user hold on it.

-I
Name	Interactive
Description	Declares the job is to be run interactively. qsub must exist on the same host as msub if the interactive job is destined for a TORQUE cluster, because the interactive msub request will be converted to a qsub -I request.
Example	> msub -I job117.sh The job will be submitted in interactive mode.

-j
Name	Join
Format	[eo\|oe\|n]
Default	n (not merged)
Description	If eo is specified, the error and output streams are merged into the error stream. If oe is specified, the error and output streams will be merged into the output stream. If using either the -e or the -o option and the -j eo\|oe option, the -j option takes precedence and all standard error and output messages go to the chosen output file.
Example	> msub -j oe cmd.sh STDOUT and STDERR will be merged into one file.

-k
Name	Keep
Format	[e\|o\|eo\|oe\|n]
Default	n (not retained)
Description	Defines which (if either) of output and error streams will be retained on the execution host (overrides path for stream).
Example	> msub -k oe myjob.sh STDOUT and STDERR for the job will be retained on the execution host.

-K
Name	Continue Running
Format	N/A
Description	Tells the client to continue running until the submitted job is completed. The client will query the status of the job every 5 seconds. The time interval between queries can be specified or disabled via MSUBQUERYINTERVAL. Use the -K option sparingly (if at all) as it slows down the Moab scheduler with frequent queries. Running ten jobs with the -K option creates an additional fifty queries per minute for the scheduler.
Example	> msub -K newjob.sh 3 Job 3 completed* *Only shows up after job completion.

-l
Name	Resource List
Format	<STRING> -l [BANDWIDTH\|DDISK\|DEADLINE\|DEPEND\|DMEM\|EXCLUDENODES\|FEATURE...\|] Additional options can be referenced on the resource manager extensions page.
Description	Defines the resources that are required by the job and establishes a limit to the amount of resource that can be consumed. Resources native to the resource manager, scheduler resource manager extensions, or job flags may be specified. Note that resource lists are dependent on the resource manager in use. For information on specifying multiple types of resources for allocation, see Multi-Req Support.
Example	> msub -l nodes=32:ppn=2,pmem=1800mb,walltime=3600,VAR=testvar:myvalue cmd.sh The job requires 32 nodes with 2 processors each, 1800 MB per task, a walltime of 3600 seconds, and a variable named testvar with a value of myvalue. If JOBNODEMATCHPOLICY is not set, Moab does not reserve the requested number of processors on the requested number of nodes. It reserves the total number of requested processors (nodes x ppn) on any number of nodes. Rather than setting nodes=<value>:ppn=<value>, set procs=<value>, replacing <value> with the total number of processors the job requires. Note that JOBNODEMATCHPOLICY is not set by default. > msub -l nodes=32:ppn=2 -l advres=!<resvid> This entry would tell Moab to only consider resources outside of the specified <reservation id>.

-m
Name	Mail Options
Format	<STRING> (either n or one or more of the characters a, b, and e)
Description	Defines the set of conditions (abort,begin,end) when the server will send a mail message about the job to the user.
Example	> msub -m be cmd.sh Mail notifications will be sent when the job begins and ends.

-M
Name	Mail List
Format	<user>[@<host>][,<user>[@<host>],...]
Default	$JOBOWNER
Description	Specifies the list of users to whom mail is sent by the execution server. Overrides the EMAILADDRESS specified on the USERCFG credential.
Example	> msub -M jon@node01,bill@node01,jill@node02 cmd.sh Mail will be sent to the specified users if the job is aborted.

-N
Name	Name
Format	<STRING>
Default	STDIN or name of job script
Description	Specifies the user-specified job name attribute.
Example	> msub -N chemjob3 cmd.sh Job will be associated with the name chemjob3.

-o
Name	Output Path
Format	[<hostname>:]<path> - %J and %I are acceptable variables. %J is the master array name and %I is the array member index in the array.
Default	$SUBMISSIONDIR/$JOBNAME.o$JOBID
Description:	Defines the path to be used for the standard output stream of the batch job. More variables are allowed when they are used in the job script instead of msub -o. In the job script, specify a #PBS -o line and input your desired variables. The allowable variables are: OID OTYPE USER OWNER JOBID JOBNAME Submitting a job script that has the line #PBS -o $(USER)_$(JOBID)_$(JOBNAME).txt results in a file called <username>_<jobID>_<jobName>.txt. Do not use msub -o when submitting a job script that has a #PBS -o line defined.
Example	> msub -o test12/stdout.txt The STDOUT stream of the job will be placed in the relative (to execution) directory specified. > msub -t 1-2 -o /home/jsmith/simulations/%J-%I.out ~/sim5.sh A job array is submitted and the name of the output files includes the master array index and the array member index.

-p
Name	Priority
Format	<INTEGER> (between -1024 and 0)
Default	0
Description	Defines the priority of the job. To enable priority range from -1024 to +1023, see ENABLEPOSUSERPRIORITY.
Example	> msub -p 25 cmd.sh The job will have a user priority of 25.

-q
Name	Destination Queue (Class)
Format	[<queue>][@<server>]
Default	[<DEFAULT>]
Description	Defines the destination of the job.
Example	> msub -q priority cmd.sh The job will be submitted to the priority queue.

-r
Name	Rerunable
Format	[y\|n]
Default	n
Description:	Declares whether the job is rerunable.
Example	> msub -r n cmd.sh The job cannot be rerun.

-S
Name	Shell
Format	<path>[@<host>][,<path>[@<host>],...]
Default	$SHELL
Description	Declares the shell that interprets the job script.
Example	> msub -S /bin/bash The job script will be interpreted by the /bin/bash shell.

-t
Name	Job Arrays
Format	<name>.[<indexlist>]%<limit>
Description	Starts a job array with the jobs in the index list. The limit variable specifies how many jobs may run at a time. For more information, see Submitting Job Arrays. Moab enforces an internal limit of 100,000 sub-jobs that a single array job submission can specify.
Example	> msub -t myarray.[1-1000]%4

-u
Name	User List
Format	<user>[@<host>[,<user>[@<host>],...]
Default	UID of msub command
Description	Defines the user name under which the job is to run on the execution system.
Example	> msub -u bill@node01 cmd.sh On node01 the job will run under Bill's UID, if permitted.

-v
Name	Variable List
Format	<string>[,<string>,...] The -v flag is limited to about 500 characters.
Description	Expands the list the environment variables that are exported to the job (taken from the msub command environment).
Example	> msub -v DEBUG cmd.sh The DEBUG environment variable will be defined for the job.

-V
Name	All Variables
Description	Declares that all environment variables in the msub environment are exported to the batch job
Example	> msub -V cmd.sh All environment variables will be exported to the job.

-W
Name	Additional Attributes
Format	<string>
Description	Allows for specification of additional job attributes (See Resource Manager Extension)
Example	> msub -W x=GRES:matlab:1 cmd.sh The job requires one resource of matlab. This flag can be used to set a filter for what name spaces will be passed from a job to a trigger using a comma-delimited list. This limits the trigger's action to objects contained in certain workflows. For more information, see Requesting name space variables. > msub -W x="trigns=vc1,vc2" The job passes name spaces vc1 and vc2 to triggers.

-x
Format	<script> or <command>
Description	When running an interactive job, the -x flag makes it so that the corresponding script won't be parsed for PBS directives, but is instead a command that is launched once the interactive job has started. The job terminates at the completion of this command. This option works only when using TORQUE. The -x option for msub differs from qsub in that qsub does not require the script name to come directly after the flag. The msub command requires a script or command immediately after the -x declaration.
Example	> msub -I -x ./script.pl > msub -I -x /tmp/command

-z
Name	Silent Mode
Description	The job's identifier will not be printed to stdout upon submission.
Example	> msub -z cmd.sh No job identifier will be printout the stdout upon successful submission.

Job Script

The msub command supports job scripts written in any one of the following languages:

Language	Notes
PBS/TORQUE Job Submission Language	---
LoadLeveler Job Submission Language	Use the INSTANTSTAGE parameter as only a subset of the command file keywords are interpreted by Moab.
SSS XML Job Object Specification	---
LSF Job Submission Language	enabled in Moab 4.2.4 and higher

/etc/msubrc

Sites that wish to automatically add parameters to every job submission can populate the file /etc/msubrc with global parameters that every job submission will inherit.

For example, if a site wished every job to request a particular generic resource they could use the following /etc/msubrc:

-W x=GRES:matlab:2

Usage Notes

msub is designed to be as flexible as possible, allowing users accustomed to PBS, LSF, or LoadLeveler syntax, to continue submitting jobs as they normally would. It is not recommended that different styles be mixed together in the same msub command.

When only one resource manager is configured inside of Moab, all jobs are immediately staged to the only resource manager available. However, when multiple resource managers are configured Moab will determine which resource manager can run the job soonest. Once this has been determined, Moab will stage the job to the resource manager.

It is possible to have Moab take a best effort approach at submission time using the forward flag. When this flag is specified, Moab will do a quick check and make an intelligent guess as to which resource manager can run the job soonest and then immediately stage the job.

Moab can be configured to instantly stage a job to the underlying resource manager (like TORQUE/LOADLEVELER) through the parameter INSTANTSTAGE. When set inside moab.cfg, Moab will migrate the job instantly to an appropriate resource manager. Once migrated, Moab will destroy all knowledge of the job and refresh itself based on the information given to it from the underlying resource manager.

In most instances Moab can determine what syntax style the job belongs to (PBS or LoadLeveler); if Moab is unable to make a guess, it will default the style to whatever resource manager was configured at compile time. If LoadLeveler and PBS were both compiled then LoadLeveler takes precedence.

Moab can translate a subset of job attributes from one syntax to another. It is therefore possible to submit a PBS style job to a LoadLeveler resource manager, and vice versa, though not all job attributes will be translated.

Examples

Example 4-39:

> msub -l nodes=3:ppn=2,walltime=1:00:00,pmem=100kb script2.pbs.cmd
4364.orion

Example 4-40:

This example is the XML-formatted version of the above example. See Submitting Jobs via msub in XML for more information.

<job>
  <InitialWorkingDirectory>/home/user/test/perlAPI
  </InitialWorkingDirectory>
  <Executable>/home/user/test/perlAPI/script2.pbs.cmd
  </Executable>
  <SubmitLanguage>PBS</SubmitLanguage>
  <Requested>
    <Feature>ppn2</Feature>
    <Processors>3</Processors>
    <WallclockDuration>3600</WallclockDuration>
  </Requested>
</job>