toil.batchSystems.torque

Attributes

logger

Classes

TorqueBatchSystem

A partial implementation of BatchSystemSupport for batch systems run on a

Module Contents

toil.batchSystems.torque.logger
class toil.batchSystems.torque.TorqueBatchSystem(config, maxCores, maxMemory, maxDisk)[source]

Bases: toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem

A partial implementation of BatchSystemSupport for batch systems run on a standard HPC cluster. By default auto-deployment is not implemented.

Parameters:
class GridEngineThread(newJobsQueue, updatedJobsQueue, killQueue, killedJobsQueue, boss)[source]

Bases: toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem.GridEngineThread

A class that represents a thread of control.

This class can be safely subclassed in a limited fashion. There are two ways to specify the activity: by passing a callable object to the constructor, or by overriding the run() method in a subclass.

getRunningJobIDs()[source]

Get a list of running job IDs. Implementation-specific; called by boss AbstractGridEngineBatchSystem implementation via AbstractGridEngineBatchSystem.getRunningBatchJobIDs()

Return type:

list

getUpdatedBatchJob(maxWait)[source]
killJob(jobID)[source]

Kill specific job with the Toil job ID. Implementation-specific; called by GridEngineThread.killJobs()

Parameters:

jobID (string) – Toil job ID

prepareSubmission(cpu, memory, jobID, command, jobName, job_environment=None, gpus=None)[source]

Preparation in putting together a command-line string for submitting to batch system (via submitJob().)

Param:

int cpu

Param:

int memory

Param:

int jobID: Toil job ID

Param:

string subLine: the command line string to be called

Param:

string jobName: the name of the Toil job, to provide metadata to batch systems if desired

Param:

dict job_environment: the environment variables to be set on the worker

Return type:

List[str]

Parameters:
  • cpu (int)

  • memory (int)

  • jobID (int)

  • command (str)

  • jobName (str)

  • job_environment (Optional[Dict[str, str]])

  • gpus (Optional[int])

submitJob(subLine)[source]

Wrapper routine for submitting the actual command-line call, then processing the output to get the batch system job ID

Param:

string subLine: the literal command line string to be called

Return type:

string: batch system job ID, which will be stored internally

getJobExitCode(torqueJobID)[source]

Returns job exit code and possibly an instance of abstractBatchSystem.BatchJobExitReason.

Returns None if the job is still running.

If the job is not running but the exit code is not available, it will be EXIT_STATUS_UNAVAILABLE_VALUE. Implementation-specific; called by GridEngineThread.checkOnJobs().

The exit code will only be 0 if the job affirmatively succeeded.

Parameters:

batchjobID (string) – batch system job ID

prepareQsub(cpu, mem, jobID, job_environment)[source]
Parameters:
  • cpu (int)

  • mem (int)

  • jobID (int)

  • job_environment (Optional[Dict[str, str]])

Return type:

List[str]

generateTorqueWrapper(command, jobID)[source]

A very simple script generator that just wraps the command given; for now this goes to default tempdir