toil.batchSystems.htcondor

Module Contents

Classes

HTCondorBatchSystem

A partial implementation of BatchSystemSupport for batch systems run on a

Attributes

logger

JobTuple

schedd_lock

toil.batchSystems.htcondor.logger
toil.batchSystems.htcondor.JobTuple
toil.batchSystems.htcondor.schedd_lock
class toil.batchSystems.htcondor.HTCondorBatchSystem(config, maxCores, maxMemory, maxDisk)

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.

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

Bases: toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem.Worker

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:
createJobs(newJob)

Create a new job with the given attributes.

Implementation-specific; called by AbstractGridEngineWorker.run()

Parameters:

newJob (JobTuple) –

Return type:

bool

prepareSubmission(cpu, memory, disk, jobID, jobName, command, environment)

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) –

  • disk (int) –

  • jobID (int) –

  • jobName (str) –

  • command (str) –

  • environment (Dict[str, str]) –

submitJob(submitObj)

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

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

getJobExitCode(batchJobID)

Returns job exit code or an instance of abstractBatchSystem.BatchJobExitReason. if something else happened other than the job exiting. Implementation-specific; called by AbstractGridEngineWorker.checkOnJobs()

Parameters:

batchjobID (string) – batch system job ID

Return type:

int|toil.batchSystems.abstractBatchSystem.BatchJobExitReason: exit code int or BatchJobExitReason if something else happened other than job exiting.

connectSchedd()

Connect to HTCondor Schedd and yield a Schedd object.

You can only use it inside the context. Handles locking to make sure that only one thread is trying to do this at a time.

duplicate_quotes(value)

Escape a string by doubling up all single and double quotes.

This is used for arguments we pass to htcondor that need to be inside both double and single quote enclosures.

Parameters:

value (str) –

Return type:

str

getEnvString(overrides)

Build an environment string that a HTCondor Submit object can use.

For examples of valid strings, see: http://research.cs.wisc.edu/htcondor/manual/current/condor_submit.html#man-condor-submit-environment

Parameters:

overrides (Dict[str, str]) –

Return type:

str

issueBatchJob(jobNode, job_environment=None)

Issues a job with the specified command to the batch system and returns a unique jobID.

Parameters:

  • jobDesc – a toil.job.JobDescription

  • job_environment (Optional[Dict[str, str]]) – a collection of job-specific environment variables to be set on the worker.

Returns:

a unique jobID that can be used to reference the newly issued job