This version (2019/04/02 11:24) is a draft.
Approvals: 0/1

Batch Pipeline Execution: Run jobs that wait with the execution on each other.

Usage in command line

sp_batch.py  submission_command  input_run_dir --hold_flag=HOLD_FLAG --first_hold_number=FIRST_HOLD_NUMBER

sp_batch exists only in non-MPI version.

The pipeline directory can be easily added within the GUI.

Run sp_batch locally with bash:

sp_batch.py bash input_run_dir

Run sp_batch within a SGE/PBS/Torque queuing environment:

sp_batch.py 'qsub' input_run_dir --hold_flag='-hold_jid'

Run sp_batch within a SGE/PBS/Torque queuing environment waiting for another job with the id 3456:

sp_batch.py 'qsub' input_run_dir --hold_flag='-hold_jid' --first_hold_number=3456

Main Parameters

Submission command
Submission command, e.g., qsub, qsub -V, sbatch, bash (default required string)
input_run_dir: Pipeline directory
Directory containin the pipeline submission files (default required string)
--hold_flag: Hold flag: Hold flag for the submission command, e.g. -hold_jid=, –wait=, –dependency=afterany:; Default is None and should be used in combination with a local execution with bash (default none)
--first_hold_number: First hold number
Wait number for the first job that is submitted. By default, the first job will not wait for others (default none)

Content of the commands in the PIPELINE folder.

Markus Stabrin



Beta:: Under evaluation and testing. Please let us know if there are any bugs.

There are no known bugs so far.

  • pipeline/utilities/sp_batch.txt
  • Last modified: 2019/04/02 11:24
  • by lusnig