toil.batchSystems.slurm

Module Contents

Classes

SlurmBatchSystem

A partial implementation of BatchSystemSupport for batch systems run on a

Attributes

logger

toil.batchSystems.slurm.logger

class toil.batchSystems.slurm.SlurmBatchSystem(config, maxCores, maxMemory, maxDisk)

Bases: toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem

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

class Worker(newJobsQueue, updatedJobsQueue, killQueue, killedJobsQueue, boss)

Bases: toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem.Worker

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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.

Parameters:

• newJobsQueue (queue.Queue) –

• updatedJobsQueue (queue.Queue) –

• killQueue (queue.Queue) –

• killedJobsQueue (queue.Queue) –

• boss (AbstractGridEngineBatchSystem) –

getRunningJobIDs()

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

Return type:

list

killJob(jobID)

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

Parameters:

jobID (string) – Toil job ID

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

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)

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

coalesce_job_exit_codes(batch_job_id_list)

Collect all job exit codes in a single call. :param batch_job_id_list: list of Job ID strings, where each string has the form “<job>[.<task>]”. :return: list of job exit codes, associated with the list of job IDs.

Parameters:

batch_job_id_list (list) –

Return type:

list

getJobExitCode(batchJobID)

Get job exit code for given batch job ID. :param batchJobID: string of the form “<job>[.<task>]”. :return: integer job exit code.

Parameters:

batchJobID (str) –

Return type:

int

prepareSbatch(cpu, mem, jobID, jobName, job_environment, gpus)

Parameters:

• cpu (int) –

• mem (int) –

• jobID (int) –

• jobName (str) –

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

• gpus (Optional[int]) –

Return type:

List[str]

parse_elapsed(elapsed)

OptionType

classmethod add_options(parser)

If this batch system provides any command line options, add them to the given parser.

Parameters:

parser (Union[argparse.ArgumentParser, argparse._ArgumentGroup]) –

classmethod setOptions(setOption)

Process command line or configuration options relevant to this batch system.

Parameters:

setOption (toil.batchSystems.options.OptionSetter) – A function with signature setOption(option_name, parsing_function=None, check_function=None, default=None, env=None) returning nothing, used to update run configuration as a side effect.

Return type:

None