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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:

pip install ezlaunch

To install the latest version on GitHub, run:

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

Verify installation by running launch -h.

EZ Launch

In contrast to launch, which is relatively low level, ezlaunch manages command, batch script, and output files automatically. To use ezlaunch, set the BATCHDIR environment variable to indicate the directory in which job commands, slurm options, and output should be saved.

For example, you could submit a job to a slurm cluster using something like:

ezlaunch -J myjob 'echo "hello world"' -N 1 -n 1 -r 00:10:00 -p normal

After the job runs, you would have the following files:

$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.

Running a command for multiple subjects

The scripts slaunch and rlaunch run a given command on combinations of subjects and runs. These scripts can optionally use the SUBJIDFORMAT environment variable. This allows automatic conversion between subject numbers (e.g., 5) and subject IDs (e.g., sub-05). For that example, you would set:

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