org.kepler.actor.job

Class GenericJobLauncher

java.lang.Object

ptolemy.kernel.util.NamedObj

ptolemy.kernel.InstantiableNamedObj

ptolemy.kernel.Entity<T>

ptolemy.kernel.ComponentEntity<T>

ptolemy.actor.AtomicActor<TypedIOPort>

ptolemy.actor.TypedAtomicActor

org.kepler.actor.job.GenericJobLauncher

All Implemented Interfaces:

java.lang.Cloneable, Actor, Executable, FiringsRecordable, Initializable, TypedActor, Changeable, Debuggable, DebugListener, Derivable, Instantiable, ModelErrorHandler, MoMLExportable, Moveable, Nameable

public class GenericJobLauncher
extends TypedAtomicActor

A generic job launcher actor that can launch a job using PBS, NCCS, Condor, Loadleveler, SGE, Moab or LSF, and wait till a user specified status.

JobLauncher actor is based on code from Norbert Podhorszki's JobCreator, JobManager, JobStatus, and JobSubmitter actors. It uses JobLauncher.properties to find the list of supported job schedulers and the corresponding support class. Additionally it can support multi task jobs

Author:

Frankie Kwok, Chandrika Sivaramakrishnan, Jared Chase

Nested Class Summary

Nested classes/interfaces inherited from class ptolemy.kernel.Entity

Entity.ContainedObjectsIterator

Field Summary

Fields

Modifier and Type	Field and Description
Parameter	binPath The path to the job manager commands on the target machines.
PortParameter	cmdFile The submit file to be used at job submission.
Parameter	cmdFileLocal Specifying whether the cmdFile is locally stored or on the remote target.
PortParameter	cmdText The text of the job specification.
Parameter	defaultForkScript Boolean flag to indicate if the default fork script should be staged.
TypedIOPort	dependentJob One or more jobs that must successfully complete before this job can run.
Parameter	executable The executable file to be used at job submission.
PortParameter	inputfiles The string array of inputfiles.
TypedIOPort	jobID The real job ID generated from the job scheduler.
TypedIOPort	jobOut The job is passed on in this actor.
Parameter	jobSubmitOptions The Options of the job submission.
TypedIOPort	logPort Logging information of job status query.
Parameter	numTasks The number of tasks for the job - used in a task parallel job
PortParameter	remotefiles The string array of remote input files.
PortParameter	scheduler The name of the jobmanager to be used It should be a name, for which a supporter class exist as org.kepler.job.JobSupport.class This parameter is read each time in fire().
Parameter	sleepWhileWaiting Amount of time (in seconds) to sleep between checking job status.
TypedIOPort	success boolean flag to indicate if job launch was successful
PortParameter	target The machine to be used at job submission.
Parameter	usegivendir By default, Kepler creates a unique sub directory within workdir based on the the job id it creates for the job.
Parameter	waitUntil Wait until the job has a reached specific status.
PortParameter	workdir The working directory in which the actual job submission command will be executed (on the remote machine if the job manager is a remote jobmanager).

Fields inherited from class ptolemy.actor.TypedAtomicActor

_typesValid

Fields inherited from class ptolemy.actor.AtomicActor

_actorFiringListeners, _initializables, _notifyingActorFiring, _stopRequested

Fields inherited from class ptolemy.kernel.util.NamedObj

_changeListeners, _changeLock, _changeRequests, _debugging, _debugListeners, _deferChangeRequests, _elementName, _isPersistent, _verbose, _workspace, ATTRIBUTES, CLASSNAME, COMPLETE, CONTENTS, DEEP, FULLNAME, LINKS

Fields inherited from interface ptolemy.actor.Executable

COMPLETED, NOT_READY, STOP_ITERATING

Constructor Summary

Constructors

Constructor and Description
GenericJobLauncher(CompositeEntity container, java.lang.String name)

Method Summary

Modifier and Type	Method and Description
void	attributeChanged(Attribute attribute) React to a change in an attribute.
void	fire() fire

Methods inherited from class ptolemy.actor.TypedAtomicActor

_containedTypeConstraints, _customTypeConstraints, _defaultTypeConstraints, _fireAt, _fireAt, attributeTypeChanged, clone, clone, isBackwardTypeInferenceEnabled, newPort, typeConstraintList, typeConstraints

Methods inherited from class ptolemy.actor.AtomicActor

_actorFiring, _actorFiring, _declareDelayDependency, addActorFiringListener, addInitializable, connectionsChanged, createReceivers, declareDelayDependency, getCausalityInterface, getDirector, getExecutiveDirector, getManager, initialize, inputPortList, isFireFunctional, isStrict, iterate, newReceiver, outputPortList, postfire, prefire, preinitialize, pruneDependencies, recordFiring, removeActorFiringListener, removeDependency, removeInitializable, setContainer, stop, stopFire, terminate, wrapup

Methods inherited from class ptolemy.kernel.ComponentEntity

_adjustDeferrals, _checkContainer, _getContainedObject, _propagateExistence, getContainer, instantiate, isAtomic, isOpaque, moveDown, moveToFirst, moveToIndex, moveToLast, moveUp, propagateExistence, setName

Methods inherited from class ptolemy.kernel.Entity

_addPort, _description, _exportMoMLContents, _removePort, _validateSettables, connectedPortList, connectedPorts, containedObjectsIterator, getAttribute, getPort, getPorts, linkedRelationList, linkedRelations, portList, removeAllPorts, setClassDefinition, uniqueName

Methods inherited from class ptolemy.kernel.InstantiableNamedObj

_setParent, exportMoML, getChildren, getElementName, getParent, getPrototypeList, isClassDefinition, isWithinClassDefinition

Methods inherited from class ptolemy.kernel.util.NamedObj

_addAttribute, _adjustOverride, _attachText, _cloneFixAttributeFields, _containedDecorators, _copyChangeRequestList, _debug, _debug, _debug, _debug, _debug, _executeChangeRequests, _getIndentPrefix, _isMoMLSuppressed, _markContentsDerived, _notifyHierarchyListenersAfterChange, _notifyHierarchyListenersBeforeChange, _propagateValue, _removeAttribute, _splitName, _stripNumericSuffix, addChangeListener, addDebugListener, addHierarchyListener, attributeDeleted, attributeList, attributeList, decorators, deepContains, depthInHierarchy, description, description, event, executeChangeRequests, exportMoML, exportMoML, exportMoML, exportMoML, exportMoMLPlain, getAttribute, getAttributes, getChangeListeners, getClassName, getDecoratorAttribute, getDecoratorAttributes, getDerivedLevel, getDerivedList, getDisplayName, getFullName, getModelErrorHandler, getName, getName, getSource, handleModelError, isDeferringChangeRequests, isOverridden, isPersistent, lazyContainedObjectsIterator, message, notifyOfNameChange, propagateValue, propagateValues, removeAttribute, removeChangeListener, removeDebugListener, removeHierarchyListener, requestChange, setClassName, setDeferringChangeRequests, setDerivedLevel, setDisplayName, setModelErrorHandler, setPersistent, setSource, sortContainedObjects, toplevel, toString, validateSettables, workspace

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface ptolemy.actor.Actor

createReceivers, getCausalityInterface, getDirector, getExecutiveDirector, getManager, inputPortList, newReceiver, outputPortList

Methods inherited from interface ptolemy.actor.Executable

isFireFunctional, isStrict, iterate, postfire, prefire, stop, stopFire, terminate

Methods inherited from interface ptolemy.actor.Initializable

addInitializable, initialize, preinitialize, removeInitializable, wrapup

Methods inherited from interface ptolemy.kernel.util.Nameable

description, getContainer, getDisplayName, getFullName, getName, getName, setName

Methods inherited from interface ptolemy.kernel.util.Derivable

getDerivedLevel, getDerivedList, propagateValue

Field Detail

cmdFile

public PortParameter cmdFile

The submit file to be used at job submission. Absolute (or relative to current dir of Java) file path should be provided. The job file must be provided here, or the contents can be specified in cmdText.

This parameter is read each time in fire().

cmdFileLocal

public Parameter cmdFileLocal

Specifying whether the cmdFile is locally stored or on the remote target.

This parameter is read each time in fire().

executable

public Parameter executable

The executable file to be used at job submission. Absolute path names, or relative to current dir of the running java virtual machine, should be provided. If it is "" then it is considered to be already at the remote site, otherwise the actor will look for it locally and stage it to the workdir before job submission.

This parameter is read each time in fire().

workdir

public PortParameter workdir

The working directory in which the actual job submission command will be executed (on the remote machine if the job manager is a remote jobmanager).

It should be an absolute path, or a relative one. In the latter case on remote machine, the directory path will be relative to the user's home directory (coming from the use of ssh).

By default, a new unique sub directory is created within this workdir based on the job id created by kepler. Job is run from this sub directory. This can be overwritten by setting the parameter "use given workdir"

This parameter is read each time in fire().

usegivendir

public Parameter usegivendir

By default, Kepler creates a unique sub directory within workdir based on the the job id it creates for the job. Job is run from this sub directory. Set this flag to true if you want job to be run directly from workdir instead of a subdir

This parameter is read each time in fire().

inputfiles

public PortParameter inputfiles

The string array of inputfiles. Absolute path names, or relative to current dir of the running java virtual machine, should be provided.

This parameter is read each time in fire().

remotefiles

public PortParameter remotefiles

The string array of remote input files. Absolute path names, or relative to the user home dir on the remote host should be provided.

This parameter is read each time in fire().

scheduler

public PortParameter scheduler

The name of the jobmanager to be used It should be a name, for which a supporter class exist as org.kepler.job.JobSupport.class This parameter is read each time in fire().

defaultForkScript

public Parameter defaultForkScript

Boolean flag to indicate if the default fork script should be staged. If bin path is provided the default script is uploaded to bin path, else it is uploaded to the working directory

target

public PortParameter target

The machine to be used at job submission. It should be null, "" or "local" for the local machine or [user@]host to denote a remote machine accessible with ssh. This parameter is read each time in fire().

binPath

public Parameter binPath

The path to the job manager commands on the target machines. Commands are constructed as binPath/command and they should be executable this way. This parameter is read each time in fire().

numTasks

public Parameter numTasks

The number of tasks for the job - used in a task parallel job

jobSubmitOptions

public Parameter jobSubmitOptions

The Options of the job submission. Such as "-o /u/joboutput/ -j y -l h_rt=24:00:00" for SGE job scheduler. Its default value is empty.

jobOut

public TypedIOPort jobOut

The job is passed on in this actor. This token can be used (delaying it with a Sleep actor) to ask its Status again and again until the job is finished or aborted. This port is an output port of type Object.

jobID

public TypedIOPort jobID

The real job ID generated from the job scheduler.

logPort

public TypedIOPort logPort

Logging information of job status query. Useful to inform user about problems at unsuccessful status query but it also prints out job status and job id on successful query. This port is an output port of type String. The name of port on canvas is 'log'

waitUntil

public Parameter waitUntil

Wait until the job has a reached specific status. The available status' that can be reached are: any, wait, running, not in queue, and error.

sleepWhileWaiting

public Parameter sleepWhileWaiting

Amount of time (in seconds) to sleep between checking job status.

success

public TypedIOPort success

boolean flag to indicate if job launch was successful

cmdText

public PortParameter cmdText

The text of the job specification. The job specification must either be provided in this parameter or the file name in cmdFile.

dependentJob

public TypedIOPort dependentJob

One or more jobs that must successfully complete before this job can run.

Constructor Detail

GenericJobLauncher

public GenericJobLauncher(CompositeEntity container,
                          java.lang.String name)
                   throws NameDuplicationException,
                          IllegalActionException

Throws:

NameDuplicationException

IllegalActionException

Method Detail

fire

public void fire()
          throws IllegalActionException

fire

Specified by:

fire in interface Executable

Overrides:

fire in class AtomicActor<TypedIOPort>

Throws:

IllegalActionException - Not thrown.

attributeChanged

public void attributeChanged(Attribute attribute)
                      throws IllegalActionException

React to a change in an attribute.

Overrides:

attributeChanged in class NamedObj

Parameters:

attribute - The attribute that changed.

Throws:

IllegalActionException - If the change is not acceptable to this container (not thrown in this base class).