toil.batchSystems.singleMachine

Module Contents

Classes

SingleMachineBatchSystem	The interface for running jobs on a single machine, runs all the jobs you
Info	Record for a running job.

Attributes

logger

toil.batchSystems.singleMachine.logger

class toil.batchSystems.singleMachine.SingleMachineBatchSystem(config, maxCores, maxMemory, maxDisk, max_jobs=None)

Bases: toil.batchSystems.abstractBatchSystem.BatchSystemSupport

The interface for running jobs on a single machine, runs all the jobs you give it as they come in, but in parallel.

Uses a single “daddy” thread to manage a fleet of child processes.

Communication with the daddy thread happens via two queues: one queue of jobs waiting to be run (the input queue), and one queue of jobs that are finished/stopped and need to be returned by getUpdatedBatchJob (the output queue).

When the batch system is shut down, the daddy thread is stopped.

If running in debug-worker mode, jobs are run immediately as they are sent to the batch system, in the sending thread, and the daddy thread is not run. But the queues are still used.

Parameters

• config (toil.common.Config) –

• maxCores (float) –

• maxMemory (int) –

• maxDisk (int) –

• max_jobs (Optional[int]) –

numCores

minCores = 0.1

The minimal fractional CPU. Tasks with a smaller core requirement will be rounded up to this value.

physicalMemory

classmethod supportsAutoDeployment()

Whether this batch system supports auto-deployment of the user script itself.

If it does, the setUserScript() can be invoked to set the resource object representing the user script.

Note to implementors: If your implementation returns True here, it should also override

classmethod supportsWorkerCleanup()

Indicates whether this batch system invokes BatchSystemSupport.workerCleanup() after the last job for a particular workflow invocation finishes. Note that the term worker refers to an entire node, not just a worker process. A worker process may run more than one job sequentially, and more than one concurrent worker process may exist on a worker node, for the same workflow. The batch system is said to shut down after the last worker process terminates.

daddy()

Be the “daddy” thread.

Our job is to look at jobs from the input queue.

If a job fits in the available resources, we allocate resources for it and kick off a child process.

We also check on our children.

When a child finishes, we reap it, release its resources, and put its information in the output queue.

getSchedulingStatusMessage()

Get a log message fragment for the user about anything that might be going wrong in the batch system, if available.

If no useful message is available, return None.

This can be used to report what resource is the limiting factor when scheduling jobs, for example. If the leader thinks the workflow is stuck, the message can be displayed to the user to help them diagnose why it might be stuck.

Returns

User-directed message about scheduling state.

check_resource_request(requirer)

Check resource request is not greater than that available or allowed.

Parameters

• requirer (toil.job.Requirer) – Object whose requirements are being checked

• job_name (str) – Name of the job being checked, for generating a useful error report.

• detail (str) – Batch-system-specific message to include in the error.

Raises

InsufficientSystemResources – raised when a resource is requested in an amount greater than allowed

Return type

None

issueBatchJob(jobDesc, job_environment=None)

Adds the command and resources to a queue to be run.

Parameters

• jobDesc (toil.job.JobDescription) –

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

Return type

int

killBatchJobs(jobIDs)

Kills jobs by ID.

Parameters

jobIDs (List[int]) –

Return type

None

getIssuedBatchJobIDs()

Just returns all the jobs that have been run, but not yet returned as updated.

Return type

List[int]

getRunningBatchJobIDs()

Gets a map of jobs as jobIDs that are currently running (not just waiting) and how long they have been running, in seconds.

Returns

dictionary with currently running jobID keys and how many seconds they have been running as the value

Return type

Dict[int, float]

shutdown()

Terminate cleanly and join daddy thread.

Return type

None

getUpdatedBatchJob(maxWait)

Returns a tuple of a no-longer-running job, the return value of its process, and its runtime, or None.

Parameters

maxWait (int) –

Return type

Optional[toil.batchSystems.abstractBatchSystem.UpdatedBatchJobInfo]

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]) –

Return type

None

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.

class toil.batchSystems.singleMachine.Info(startTime, popen, resources, killIntended)

Record for a running job.

Stores the start time of the job, the Popen object representing its child (or None), the tuple of (coreFractions, memory, disk) it is using (or None), and whether the job is supposed to be being killed.