compbio.engine.cluster.drmaa

Class ClusterRunner

java.lang.Object

compbio.engine.cluster.drmaa.ClusterRunner

All Implemented Interfaces:

SyncExecutor

public class ClusterRunner
extends java.lang.Object
implements SyncExecutor

Single cluster job runner class

Author:

pvtroshin

Field Summary

Fields

Modifier and Type	Field and Description
(package private) static ClusterSession	clustSession
(package private) ConfiguredExecutable<?>	confExecutable
(package private) java.lang.String	jobId
(package private) org.ggf.drmaa.JobTemplate	jobtempl
(package private) static org.apache.log4j.Logger	log
(package private) static org.ggf.drmaa.Session	session
private java.lang.String	workDirectory

Constructor Summary

Constructors

Constructor and Description
ClusterRunner(ConfiguredExecutable<?> confExec)

Method Summary

Modifier and Type	Method and Description
boolean	cancelJob() Stops running job.
(package private) boolean	cancelJob(java.lang.String jobId)
boolean	cleanup() Clean up after the job
boolean	deepClean()
void	executeJob() Execute the job
static ClusterRunner	getInstance(ConfiguredExecutable<?> executable)
org.ggf.drmaa.JobInfo	getJobInfo() This method will block before the calculation has completed and then return the object containing a job execution statistics
JobStatus	getJobStatus() Query the status of the job by its id.
(package private) static JobStatus	getJobStatus(java.lang.String jobId) This will never return clust.engine.JobStatus.CANCELLED as for sun grid engine cancelled job is the same as failed.
(package private) static JobStatus	getRecordedJobStatus(java.lang.String jobId)
java.lang.String	getWorkDirectory()
private static java.lang.String	makeLocalPath(java.lang.String path)
(package private) void	setEmail(java.lang.String email)
(package private) void	setJobEnvironmentVariables(java.util.Map<java.lang.String,java.lang.String> env_variables)
(package private) void	setJobName(java.lang.String name)
(package private) void	setNativeSpecs(Executable<?> executable)
(package private) void	setPipes(ConfiguredExecutable<?> executable)
(package private) java.lang.String	submitJob()
(package private) org.ggf.drmaa.JobInfo	waitForJob(java.lang.String jobId)
ConfiguredExecutable<?>	waitForResult() Call to this method block for as long as it is required for an executable to finish its job.

Methods inherited from class java.lang.Object

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

Field Detail

jobtempl

final org.ggf.drmaa.JobTemplate jobtempl

clustSession

static ClusterSession clustSession

session

static org.ggf.drmaa.Session session

log

static final org.apache.log4j.Logger log

confExecutable

final ConfiguredExecutable<?> confExecutable

workDirectory

private final java.lang.String workDirectory

jobId

java.lang.String jobId

Constructor Detail

ClusterRunner

public ClusterRunner(ConfiguredExecutable<?> confExec)
              throws JobSubmissionException

Throws:

JobSubmissionException

Method Detail

setPipes

void setPipes(ConfiguredExecutable<?> executable)
       throws org.ggf.drmaa.DrmaaException

Throws:

org.ggf.drmaa.DrmaaException

setNativeSpecs

void setNativeSpecs(Executable<?> executable)
             throws org.ggf.drmaa.DrmaaException

Throws:

org.ggf.drmaa.DrmaaException

setEmail

void setEmail(java.lang.String email)

setJobName

void setJobName(java.lang.String name)

setJobEnvironmentVariables

void setJobEnvironmentVariables(java.util.Map<java.lang.String,java.lang.String> env_variables)

makeLocalPath

private static java.lang.String makeLocalPath(java.lang.String path)

deepClean

public boolean deepClean()

getJobStatus

static JobStatus getJobStatus(java.lang.String jobId)

This will never return clust.engine.JobStatus.CANCELLED as for sun grid engine cancelled job is the same as failed. Cancelled jobs needs to be tracked manually!

getRecordedJobStatus

static JobStatus getRecordedJobStatus(java.lang.String jobId)

cleanup

public boolean cleanup()

Description copied from interface: SyncExecutor

Clean up after the job

Specified by:

cleanup in interface SyncExecutor

Returns:

true if all the files created by this job have been removed successfully, false otherwise

waitForJob

org.ggf.drmaa.JobInfo waitForJob(java.lang.String jobId)
                          throws JobExecutionException

Throws:

JobExecutionException

cancelJob

boolean cancelJob(java.lang.String jobId)

cancelJob

public boolean cancelJob()

Description copied from interface: SyncExecutor

Stops running job. Clean up is not performed.

Specified by:

cancelJob in interface SyncExecutor

Returns:

true if job was cancelled successfully, false otherwise

submitJob

java.lang.String submitJob()
                    throws JobSubmissionException

Throws:

JobSubmissionException

getWorkDirectory

public java.lang.String getWorkDirectory()

Specified by:

getWorkDirectory in interface SyncExecutor

Returns:

working directory if the task

executeJob

public void executeJob()
                throws JobSubmissionException

Description copied from interface: SyncExecutor

Execute the job

Specified by:

executeJob in interface SyncExecutor

Throws:

JobSubmissionException - if submission fails

getJobInfo

public org.ggf.drmaa.JobInfo getJobInfo()
                                 throws JobExecutionException

This method will block before the calculation has completed and then return the object containing a job execution statistics

Returns:

Throws:

JobExecutionException

waitForResult

public ConfiguredExecutable<?> waitForResult()
                                      throws JobExecutionException

Description copied from interface: SyncExecutor

Call to this method block for as long as it is required for an executable to finish its job. If the calculation has been completed already, the this method returns results immediately. This could return the result directly, but that would be type unsafe

Specified by:

waitForResult in interface SyncExecutor

Returns:

object from wich the result can be obtained

Throws:

JobExecutionException

getJobStatus

public JobStatus getJobStatus()

Description copied from interface: SyncExecutor

Query the status of the job by its id.

Specified by:

getJobStatus in interface SyncExecutor

Returns:

- JobStatus

getInstance

public static ClusterRunner getInstance(ConfiguredExecutable<?> executable)
                                 throws JobSubmissionException

Throws:

JobSubmissionException