org.kepler.job

Class JobSupportSGE

java.lang.Object

org.kepler.job.JobSupportSGE

public class JobSupportSGE
extends java.lang.Object

Support class for Sun Grid Engine job manager support Class Job uses the methods of a supporter class to submit jobs and check status

Constructor Summary

Constructors

Constructor and Description
JobSupportSGE()

Method Summary

Modifier and Type	Method and Description
boolean	createSubmitFile(java.lang.String filename, Job job) Create a submission file for the specific job manager, based on the information available in Job: - executable name - input files - output files - arguments for the job
java.lang.String	getDeleteCmd(java.lang.String jobID) Get the command to remove a job from queue (either running or waiting jobs). return: the String of command
java.lang.String	getStatusCmd(java.lang.String jobID) Get the command to ask the status of the job return: the String of command
java.lang.String	getSubmitCmd(java.lang.String submitFile, java.lang.String options, Job job) Submit command for SGE return: the command for submission
java.lang.String	getTaskStatusCmd(java.lang.String jobID) Get the command to ask the status of both job and tasks Eg.
void	init(java.lang.String nccsBinPath) Store the binary path given by the user and use that in the methods below
boolean	parseDeleteOutput(java.lang.String jobID, int exitCode, java.lang.String output, java.lang.String error) Parse output of delete command. return: true if stdout is empty and exitCode is 0, otherwise return false
JobStatusInfo	parseStatusOutput(java.lang.String jobID, int exitCode, java.lang.String output, java.lang.String error) Parse output of status check command and get status info return: a JobStatusInfo object, or throws an JobException with the error output
java.lang.String	parseSubmitOutput(java.lang.String output, java.lang.String error) Parse output of submission and get information: jobID return String jobID on success throws JobException at failure (will contain the error stream or output stream)
TaskParallelJobStatusInfo	parseTaskStatusOutput(java.lang.String jobID, int numTasks, int exitCode, java.lang.String output, java.lang.String error) Parse output of task status check command and get status info

Methods inherited from class java.lang.Object

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

Constructor Detail

JobSupportSGE

public JobSupportSGE()

Method Detail

init

public void init(java.lang.String nccsBinPath)

Store the binary path given by the user and use that in the methods below

createSubmitFile

public boolean createSubmitFile(java.lang.String filename,
                                Job job)

Create a submission file for the specific job manager, based on the information available in Job: - executable name - input files - output files - arguments for the job

getSubmitCmd

public java.lang.String getSubmitCmd(java.lang.String submitFile,
                                     java.lang.String options,
                                     Job job)
                              throws JobException

Submit command for SGE return: the command for submission

Throws:

JobException

parseSubmitOutput

public java.lang.String parseSubmitOutput(java.lang.String output,
                                          java.lang.String error)
                                   throws JobException

Parse output of submission and get information: jobID return String jobID on success throws JobException at failure (will contain the error stream or output stream)

Throws:

JobException

getStatusCmd

public java.lang.String getStatusCmd(java.lang.String jobID)

Get the command to ask the status of the job return: the String of command

parseStatusOutput

public JobStatusInfo parseStatusOutput(java.lang.String jobID,
                                       int exitCode,
                                       java.lang.String output,
                                       java.lang.String error)
                                throws JobException

Parse output of status check command and get status info return: a JobStatusInfo object, or throws an JobException with the error output

Throws:

JobException

getDeleteCmd

public java.lang.String getDeleteCmd(java.lang.String jobID)

Get the command to remove a job from queue (either running or waiting jobs). return: the String of command

parseDeleteOutput

public boolean parseDeleteOutput(java.lang.String jobID,
                                 int exitCode,
                                 java.lang.String output,
                                 java.lang.String error)
                          throws JobException

Parse output of delete command. return: true if stdout is empty and exitCode is 0, otherwise return false

Throws:

JobException

getTaskStatusCmd

public java.lang.String getTaskStatusCmd(java.lang.String jobID)
                                  throws NotSupportedException

Get the command to ask the status of both job and tasks Eg. ; return: the String of command or throws a NotSupportedException if the scheduler doesn't support task status

Throws:

NotSupportedException

parseTaskStatusOutput

public TaskParallelJobStatusInfo parseTaskStatusOutput(java.lang.String jobID,
                                                       int numTasks,
                                                       int exitCode,
                                                       java.lang.String output,
                                                       java.lang.String error)
                                                throws JobException,
                                                       NotSupportedException

Parse output of task status check command and get status info

Throws:

JobException

NotSupportedException