PyJobRunner 2023.6

Job runner for scientific computing workloads

Jobrunner is a command line tool to manage and deploy computing jobs, organize complex workloads, and enforce a directory based hierarchy to enable reuse of files and bash scripts within a project. Organization details of a directory tree are encoded in Jobfiles which serve as an index of files/scripts, and indicate their purpose when deploying or setting up a job. It is a flexible tool that allows users to design their own directory structure, perserve their design, and maintain consistency with increase in complexity of the project.

Installation

Stable releases of Jobrunner are hosted on Python Package Index website (https://pypi.org/project/PyJobRunner/) and can be installed by executing,

pip install PyJobrunner

Note that pip should point to python3+ installation package pip3.

Upgrading and uninstallation is easily managed through this interface using,

pip install --upgrade PyJobrunner
pip uninstall PyJobRunner

There maybe situations where users may want to install Jobrunner in development mode $\textemdash$ to design new features, debug, or customize options/commands to their needs. This can be easily accomplished using the setup script located in the project root directory and executing,

./setup develop

Development mode enables testing of features/updates directly from the source code and is an effective method for debugging. Note that the setup script relies on click, which can be installed using,

pip install click

The jobrunner script is installed in $HOME/.local/bin directory and therfore the environment variable, PATH, should be updated to include this location for command line use.

Dependencies

python3.8+ click toml pyyaml

Writing a Jobfile

A Jobfile provides details on functionality of each file in a directory tree along with schedular configuration. Consider the following directory tree for a project,

$ tree Project

├── Jobfile
├── environment.sh
├── JobObject1
├── JobObject2
    ├── Jobfile
    ├── application.input
    ├── application.exe
    ├── setupScript.sh
    ├── submitScript.sh
    ├── preProcess.sh
    ├── Config1
    ├── Config2
        ├── Jobfile
        ├── application.input

The base directory Project contains two different job object subdirectories /Project/JobObject1 and /Project/JobObject2 which share a common environment defined in environment.sh,

# module for OpenMPI
module load openmpi

# environment variables common to different job objects
export COMMON_ENV_VARIABLE_1=/path/to/a/library
export COMMON_ENV_VARIABLE_2="value"

It makes sense to places this file at the level of project home directory and define it in Jobfile as given below, indicating that environment.sh should be included when executing both jobrunner setup and jobrunner submit commands. Details regarding the job schedular are also defined at this level. The schedular command $\textemdash$ slurm in this case $\textemdash$ is used to dispatch the jobs with desired options.

# scripts to include during jobrunner setup and submit commands
job:
  setup:
    - environment.sh
  submit:
    - environment.sh

# schedular command and options to dispatch jobs
schedular:
  command: slurm
  options:
    - "#SBATCH -t 0-30:00"
    - "#SBATCH --job-name=myjob"
    - "#SBATCH --ntasks=5"

At the level of subdirectory /Project/JobObject2 more files are added and lead to a Jobfile that looks like,

job:

  # list of scripts and input files that need to execute during setup command
  setup:
    - setupScript.sh

  # input for the job
  input:
    - application.input

  # target file/executable for the job
  target: application.exe

  # list of scripts that need to execute when running submit command
  submit:
    - preProcess.sh
    - submitScript.sh

The field, job:input, refers to the inputs required to run job:target executable common for configurations /Project/JobObject2/Config1 and /Project/JobObject2/Config2. Each configuration contains additional input files with values that are appended to the ones provided at the current level. The Jobfile at /Project/JobObject2/Config2 becomes,

job:

  # append to input file
  input:
    - application.input

  # list of file/patterns to archive
  archive:
    - "*_hdf5_*"
    - "*.log"

The field, job.archive, provides a list of file/patterns that are moved over to the /Project/JobObject2/Config2/jobnode.archive/<tagID> directory when running jobrunner archive --tag=<tagID>. This feature is provided to store results before cleaning up working directory for fresh runs

Jobrunner commands

Setup

jobrunner setup <JobWorkDir> creates a job.setup file in <workdir> using job.setup scripts defined in Jobfiles along the directory tree. Jobrunner executes each script serially by changing the working directory to the location of the script. A special environment variable JobWorkDir provides the value of <JobWorkDir> supplied during invocation of the command.

The --show option can be used to check which bash scripts will be included during invocation. Following is the result of jobrunner setup --show JobObject2 for the example above,

Working directory: /Project/JobObject2
Parsing Jobfiles in directory tree

job.setup: [
        /Project/environment.sh
        /Project/JobObject2/setupScript.sh
        ]

Submit

jobrunner submit <JobWorkDir> creates a job.submit file in <JobWorkDir> using job.submit scripts and schedular.options values defined in Jobfiles along the directory tree. schedular.command is used to dispatch the result script.

The --show option can be used to check schedular configuration and list of bash scripts that will be included during invocation. Following is the result of jobrunner submit --show JobObject2/Config2 for the example above,

Working directory: /Project/JobObject2/Config2
Parsing Jobfiles in directory tree

schedular.command:
        slurm
schedular.options: [
        #SBATCH -t 0-30:00
        #SBATCH --job-name=myjob
        #SBATCH --ntasks=5
        ]
job.input: [
        /Project/JobObject2/flash.par
        /Project/JobObject2/Config2/flash.par
        ]
job.target:
        /Project/JobObject2/flashx
job.submit: [
        /Project/environment.sh
        /Project/JobObject2/preProcess.sh
        /Project/JobObject2/submitScript.sh
        ]

Along with the job.submit script, job.input and job.target files are also created in <JobWorkDir> and created using values defined in Jobfiles.

Archive

jobrunner archive --tag=<tagID> <JobWorkDir> creates archives along the directory tree using the list of values defined job.archive. The archives are created under the sub-directory jobnode.archive/<tagID> and represent the state of the directory tree during the invocation.

Export

jobrunner export --tag=<pathToArchive> <JobWorkDir> exports directory tree and archives objects to an external directory <pathToArchive> to preserve state and curate execution environment.

Clean

jobrunner clean <JobWorkDir> removes Jobrunner artifacts from the working directory

Examples

Functionality of Jobrunner is best understood through example projects which can be found in following repositories:

• akashdhruv/Multiphase-Simulations: A collection of high-fidelity flow/pool boiling simulations

Citation

@software{akash_dhruv_2022_7255620,
   author       = {Akash Dhruv},
   title        = {akashdhruv/Jobrunner: October 2022},
   month        = oct,
   year         = 2022,
   publisher    = {Zenodo},
   version      = {22.10},
   doi          = {10.5281/zenodo.7255620},
   url          = {https://doi.org/10.5281/zenodo.7255620}
}