Package fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters

Class BpipeTaskScheduler

java.lang.Object

fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler

fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.AbstractClusterTaskScheduler

fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.BpipeTaskScheduler

All Implemented Interfaces:

ClusterTaskScheduler, TaskScheduler

Direct Known Subclasses:

BundledScriptBpipeTaskScheduler, DummyTaskScheduler, TGCCTaskScheduler

public abstract class BpipeTaskScheduler
extends AbstractClusterTaskScheduler

This class allow to submit, stop and get the status of jobs using Bpipe scheduler wrappers.

Since:

2.0

Author:

Laurent Jourdren

Nested Class Summary

Nested classes/interfaces inherited from class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.AbstractClusterTaskScheduler

AbstractClusterTaskScheduler.ProcessThreadOutput

Nested classes/interfaces inherited from interface fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskScheduler

ClusterTaskScheduler.StatusResult, ClusterTaskScheduler.StatusValue

Constructor Summary

Constructors

Constructor	Description
BpipeTaskScheduler()

Method Summary

Modifier and Type	Method	Description
void	cleanupJob(String jobId)	Cleanup after a job.
void	configure(Settings settings)	Configure the scheduler.
ClusterTaskScheduler.StatusResult	statusJob(String jobId)	Get the status of a job.
void	stopJob(String jobId)	Stop a job.
String	submitJob(String jobName, List<String> jobCommand, File jobDirectory, int taskId, int requiredMemory, int requiredProcessors)	Submit a job.

Methods inherited from class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.AbstractClusterTaskScheduler

stop, submit

Methods inherited from class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler

getResult, getStatus, getTaskDoneCount, getTaskRunningCount, getTaskSubmittedCount, getTotalTaskDoneCount, getTotalTaskRunningCount, getTotalTaskSubmittedCount, start, submit, waitEndOfTasks

Methods inherited from class java.lang.Object

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

Methods inherited from interface fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskScheduler

getSchedulerName

Methods inherited from interface fr.ens.biologie.genomique.eoulsan.core.schedulers.TaskScheduler

getResult, getStatus, getTaskDoneCount, getTaskRunningCount, getTaskSubmittedCount, getTotalTaskDoneCount, getTotalTaskRunningCount, getTotalTaskSubmittedCount, start, submit, waitEndOfTasks

Constructor Details

BpipeTaskScheduler

public BpipeTaskScheduler()

Method Details

configure

public void configure(Settings settings)
               throws EoulsanException

Description copied from interface: ClusterTaskScheduler

Configure the scheduler.

Parameters:

settings - Eoulsan settings

Throws:

EoulsanException - if an error occurs while configuring the scheduler

submitJob

public String submitJob(String jobName,
 List<String> jobCommand,
 File jobDirectory,
 int taskId,
 int requiredMemory,
 int requiredProcessors)
                 throws IOException

Description copied from interface: ClusterTaskScheduler

Submit a job.

Parameters:

jobName - job name

jobCommand - job command

jobDirectory - job directory

taskId - task id

requiredMemory - required memory

requiredProcessors - required processors

Returns:

a String with the id of the submitted job

Throws:

IOException - if an error occurs while submitting job

stopJob

public void stopJob(String jobId)
             throws IOException

Description copied from interface: ClusterTaskScheduler

Stop a job.

Parameters:

jobId - job id

Throws:

IOException - if an error occurs while stopping the job

statusJob

public ClusterTaskScheduler.StatusResult statusJob(String jobId)
                                            throws IOException

Description copied from interface: ClusterTaskScheduler

Get the status of a job.

Parameters:

jobId - job id

Returns:

a StatusResult object

Throws:

IOException - if an error occurs while getting the status of the job

cleanupJob

public void cleanupJob(String jobId)
                throws IOException

Description copied from interface: ClusterTaskScheduler

Cleanup after a job.

Parameters:

jobId - job id

Throws:

IOException - if an error occurs while cleanup