Field Detail

• protected java.util.Map<java.lang.Object, QueueStatus> fQueueStatus

  Store jobs status

• protected nextflow.util.Duration queueInterval

Method Detail

• boolean checkActiveStatus(java.lang.Object jobId, java.lang.Object queue)

  Verify that a job in a 'active' state i.e. RUNNING or HOLD

  Parameters:

  jobId - The job for which verify the status

  Returns:

  true if the job is in RUNNING or HOLD status, or even if it is temporarily unable to retrieve the job status for some

• protected BashWrapperBuilder createBashWrapperBuilder(TaskRun task)

• GridTaskHandler createTaskHandler(TaskRun task)

• TaskMonitor createTaskMonitor()

  Create a a queue holder for this executor

  Returns:

• final java.util.List<java.lang.String> getDirectives(TaskRun task)

  Parameters:

  task - The current task object

  Returns:

  A list of directives for this task used for the job submission

• protected java.util.List<java.lang.String> getDirectives(TaskRun task, java.util.List<java.lang.String> initial)

  Parameters:

  task - The current task object

  initial - An initial list of directives

  Returns:

  A list of directives for this task used for the job submission

• protected java.lang.String getHeaderToken()

  Returns:

  String used to declare job directives in the job script wrapper

• java.lang.String getHeaders(TaskRun task)

  Defines the jobs directive headers

  Parameters:

  task

  Returns:

  A multi-line string containing the job directives

• protected java.lang.String getJobNameFor(TaskRun task)

  Given a task returns a *clean* name used to submit the job to the grid engine. That string must not contain blank or special shell characters e.g. parenthesis, etc

  Parameters:

  task - A TaskRun instance

  Returns:

  A string that represent to submit job name

• protected java.util.List<java.lang.String> getKillCommand()

  The command to be used to kill a grid job

  Returns:

  The command line to be used to kill the specified job

• java.util.Map<?, QueueStatus> getQueueStatus(java.lang.Object queue)

  Returns:

  The status for all the scheduled and running jobs

• java.util.List<java.lang.String> getSubmitCommandLine(TaskRun task, java.nio.file.Path scriptFile)

  Build up the platform native command line used to submit the job wrapper execution request to the underlying grid, e.g. qsub -q something script.job

  Parameters:

  task - The task instance descriptor

  Returns:

  A list holding the command line

• void init()

  Initialize the executor class

• void killTask(java.lang.Object jobId)

  Kill a grid job

  Parameters:

  jobId - The ID of the job to kill

• protected java.util.List<java.lang.String> killTaskCommand(java.lang.Object jobId)

  The command to be used to kill a grid job

  Parameters:

  jobId - The job ID to be kill

  Returns:

  The command line to be used to kill the specified job

• java.lang.Object parseJobId(java.lang.String text)

  Given the string returned the by grid submit command, extract the process handle i.e. the grid jobId

• protected java.util.Map<?, QueueStatus> parseQueueStatus(java.lang.String text)

  Parse the command stdout produced by the command line #queueStatusCommand

  Parameters:

  text

  Returns:

• protected boolean pipeLauncherScript()

  Defines how script is run the by the grid-engine.

  Returns:

  When true the launcher script is piped over the submit tool stdin stream, if false is specified as an argument on the command line

• protected java.util.List<java.lang.String> queueStatusCommand(java.lang.Object queue)

  Parameters:

  queue - The command for which the status of jobs has be to read

  Returns:

  The command line to be used to retried the job statuses

• protected java.lang.String quote(java.nio.file.Path path)

• protected java.lang.String wrapHeader(java.lang.String str)