toil.batchSystems.gridengine
¶
Module Contents¶
Classes¶
A partial implementation of BatchSystemSupport for batch systems run on a |
Attributes¶
- toil.batchSystems.gridengine.logger¶
- class toil.batchSystems.gridengine.GridEngineBatchSystem(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.
- class Worker(newJobsQueue, updatedJobsQueue, killQueue, killedJobsQueue, boss)[source]¶
Bases:
toil.batchSystems.abstractGridEngineBatchSystem.AbstractGridEngineBatchSystem.Worker
Grid Engine-specific AbstractGridEngineWorker methods
- Parameters
newJobsQueue (queue.Queue) –
updatedJobsQueue (queue.Queue) –
killQueue (queue.Queue) –
killedJobsQueue (queue.Queue) –
boss (AbstractGridEngineBatchSystem) –
- getRunningJobIDs()[source]¶
Get a list of running job IDs. Implementation-specific; called by boss AbstractGridEngineBatchSystem implementation via AbstractGridEngineBatchSystem.getRunningBatchJobIDs()
- Return type
- killJob(jobID)[source]¶
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)[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
- 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