jobrunner 1.4.0

An abstraction layer to run jobs on HPC clusters using Grid Engine, Torque, or locally.

An abstraction layer to run jobs on HPC clusters using Grid Engine, SLURM, Torque, or locally.

The jobrunner package was developed by the United States Food and Drug Administration, Center for Food Safety and Applied Nutrition.

• Free software

• Documentation: https://jobrunner.readthedocs.io

• Source Code: https://github.com/CFSAN-Biostatistics/jobrunner

• PyPI Distribution: https://pypi.python.org/pypi/jobrunner

Features

• Python API for job submission

• Consistent interface to run jobs on Grid Engine, SLURM, Torque, or locally

• Dependencies between jobs

• Array jobs and normal non-array jobs

• Array job parameter substitution

• Array job slot-dependency

• Limit the CPU resources consumed by array jobs

• Separate log files for each array job task

Citing jobrunner

To cite jobrunner, please reference the jobrunner GitHub repository:

https://github.com/CFSAN-Biostatistics/jobrunner

License

See the LICENSE file included in the jobrunner distribution.

History

1.4.0 (2020-08-21)

• Add support for wall clock time limits.

1.3.1 (2020-08-12)

• Allow array tasks in local mode to process only a portion of the lines in the array file by setting num_tasks to a value less than the number of lines in the array file.

1.3.0 (2020-04-12)

• Add support for the SLURM job scheduler.

• Add capability to request exclusive access to compute nodes when running on SLURM.

1.2.0 (2019-10-11)

• Add the capability to run in quiet mode when running locally on a workstation so the job stdout and stderr are written to log files only.

1.1.0 (2019-06-07)

• HPC array job command lines are quoted and executed in a subshell by default with better support for complex command lines.

1.0.0 (2018-12-03)

• First public release.