|(Moab Job Submit)|
msub [-a datetime][-A account][-c interval][-C directive_prefix][-d path] [-e path][-E][-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][-u userlist][-v variablelist][-V][-W additionalattributes] [-z][script]
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.
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.|
AccessWhen Moab is configured to run as root, any user may submit jobs via msub.
|Description:||Declares the time after which the job is eligible for execution.|
> msub -a 12041300 cmd.pbs
|Description:||Defines the account associated with the job.|
> msub -A research cmd.pbs
|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.
> msub -c c=12 cmd.pbs
|Default:||First known prefix (#PBS, #@, #BSUB, #!, #MOAB, #MSUB)|
|Description:||Specifies which directive prefix should be used from a job script.
> msub -C '#MYPREFIX' cmd.pbs #MYPREFIX -l walltime=5:00:00 (in cmd.pbs)
|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.|
> msub -d /home/test/job12 cmd.pbs
|Description:||Defines the path to be used for the standard error stream of the batch job.|
> msub -e test12/stderr.txt
|Description:||Moab adds the following variables, if populated, to the job's environment:
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.
> msub -E mySim.cmd
|Description:||Specifies that a user hold be applied to the job at submission time.|
> msub -h cmd.ll
|Description:||Declares the the job is to be run interactively.|
> msub -I job117.sh
|Default:||n (not merged)|
|Description:||Declares if the standard error stream of the job will be merged with the standard output stream of the job. If "oe" is specified, the error and output streams will be merged into the output stream.|
> msub -j oe cmd.sh
|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).|
> msub -k oe myjob.sh
|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.
> msub -K newjob.sh 3 Job 3 completed*
<STRING>(either standard PBS/TORQUE options or resource manager extensions)
Defines the resources that are required by the job and establishes a limit to the amount of resource that can be consumed. Either resources native to the resource manager (see PBS/TORQUE resources) or scheduler resource manager extensions may be specified. Note that resource lists are dependent on the resource manager in use.
> 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.
|Description:||Defines the set of conditions (abort,begin,end) when the server will send a mail message about the job to the user.|
> msub -m be cmd.sh
|Description:||Specifies the list of users to whom mail is sent by the execution server.|
> msub -M jon@node01,bill@node01,jill@node02 cmd.sh
|Default:||STDIN or name of job script|
|Description:||Specifies the user-specified job name attribute.|
> msub -N chemjob3 cmd.sh
|Description:||Defines the path to be used for the standard output stream of the batch job.|
> msub -o test12/stdout.txt
|Format:||<INTEGER> (between -1024 and 0)|
|Description:||Defines the priority of the job.
To enable priority range from -1024 to +1023, see ENABLEPOSUSERPRIORITY.
> msub -p 25 cmd.sh
|Name:||Destination Queue (Class)|
|Description:||Defines the destination of the job.|
> msub -q priority cmd.sh
|Description:||Declares whether the job is rerunable.|
> msub -r n cmd.sh
|Description:||Declares the shell that interprets the job script.|
> msub -S /bin/bash
|Default:||UID of msub command|
|Description:||Defines the user name under which the job is to run on the execution system.|
> msub -u bill@node01 cmd.sh
|Description:||Expands the list the environment variables that are exported to the job (taken from the msub command environment).|
> msub -v DEBUG cmd.sh
|Description:||Declares that all environment variables in the msub environment are exported to the batch job|
> msub -V cmd.sh
|Description:||Allows the for the specification of additional job attributes (See Resource Manager Extension)|
> msub -W x=GRES:matlab:1 cmd.sh
|Description:||The job's identifier will not be printed to stdout upon submission.|
> msub -z cmd.sh
The msub command supports job scripts written in any one of the following languages:
|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|
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:
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.
> msub -l nodes=3:ppn=2,walltime=1:00:00,pmem=100kb script2.pbs.cmd 4364.orion
Example 2Example 2 is the XML-formatted version of Example 1. 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>