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Tools to launch slurm jobs

Project description

# launch Programs for managing job submission through slurm.

These scripts can be used to submit jobs for a cluster running the slurm scheduler. Some scripts are designed with neuroimaging data in mind, for example running a single command to process data from multiple participants in an experiment can be done using slaunch.

## Installation

To install the most recent release from PyPI, run:

`bash pip install ezlaunch `

To install the latest version on GitHub, run:

`bash pip install git+https://github.com/prestonlab/launch `

Verify installation by running launch -h.

Set the BATCHDIR environment variable to indicate the directory in which job commands, slurm options, and job output should be saved. If a job is called “myjob”, then running a job will produce:

`bash $BATCHDIR/myjob1.sh     # job commands $BATCHDIR/myjob1.slurm  # slurm options (run time, number of nodes, etc.) $BATCHDIR/myjob1.out    # output from all commands `

If you run another job named “myjob”, that will be saved under “myjob2.sh”, etc.

You may also define SUBJIDFORMAT. This allows automatic conversion between subject numbers (e.g., 5) and subject IDs (e.g., sub-05). For that example, you would set:

`bash export SUBJIDFORMAT='sub-%02d' `

Then subject number lists can be converted, for example subjids 1:2:3 will produce sub-01:sub-02:sub-03.

## Authors

  • Neal Morton
  • Russ Poldrack - wrote original launch script

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