Skip to main content

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+ `

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:

`bash 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:

`bash $BATCHDIR/     # 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 “”, 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:

`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

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for ezlaunch, version 1.0.3
Filename, size File type Python version Upload date Hashes
Filename, size ezlaunch-1.0.3-py3-none-any.whl (25.4 kB) File type Wheel Python version py3 Upload date Hashes View
Filename, size ezlaunch-1.0.3.tar.gz (10.8 kB) File type Source Python version None Upload date Hashes View

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring DigiCert DigiCert EV certificate Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page