ClusterRun[source]¶cleanUpArrayJob(scriptFile=None, logDir=None)[source]¶Rename all the log files Args: logDir: directory that the logfiles should end up in
getRunningJobList(user='')[source]¶Check a job status int the cluster queue
For LSF output is of form:
JOBID USER STAT QUEUE FROM_HOST EXEC_HOST JOB_NAME SUBMIT_TIME 35340 jxt15-d RUN q1h32 ida7c42 ida2a40 *ep 5;done Mar 25 13:23
ida2a40 ida2a40
monitorQueue(user='', monitor=None)[source]¶Monitor the Cluster queue to see when all jobs are completed
queueDirectives(nproc=None, log_file=None, job_name=None, job_time=None, submit_max_array=None, submit_num_array_jobs=None, submit_pe_sge='mpi', submit_pe_lsf='#BSUB -R "span[ptile={0}]"', submit_qtype=None, submit_queue=None)[source]¶Create a string suitable for writing out as the header of the submission script for submitting to a particular queueing system.
Args: job_scripts – the list of scripts to run as the array job_name – the name of the job in the queue (required for LSF array jobs) job_dir – the directory the job will run in job_time – maximum job runtime in minutes (CHECK) submit_max_array – maximum number of array jobs to run concurrently submit_queue – the name of the queue to submit the job to submit_qtype – the type of the queueing system (e.g. SGE)
Returns: queue directives as a list of EOL-terminated strings
submitArrayJob(job_scripts, job_name=None, job_time=None, submit_max_array=None, submit_queue=None, submit_qtype=None)[source]¶Submit a list of jobs as an array job
Args: job_scripts – the list of scripts to run as the array job_name – the name of the job in the queue (required for LSF array jobs) job_dir – the directory the job will run in job_time – maximum job runtime in minutes (CHECK) submit_max_array – maximum number of array jobs to run concurrently submit_queue – the name of the queue to submit the job to submit_qtype – the type of the queueing system (e.g. SGE)