EZLaunch: Tools to run slurm jobs with launcher
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
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
The launch programs can use information about cluster configuration to fill in blanks (e.g., the number of cores available on each node) and to make sure you're not going over limits of the queue you're submitting to (e.g., a maximum number of nodes).
The configuration is specified using TOML files, which have a simple format.
Global settings should go under a
[global] heading, while partition-specific
settings should go under a heading with the name of that partition.
For example (here, "normal" and "development" are two partitions):
[global] account = "myAccountName" [normal] cores = 56 max-nodes = 1280 [development] cores = 56 max-nodes = 40
This sets the default account to use when submitting jobs. It also sets the number of
cores and the maximum number of nodes per job for the
normal and development partitions. You may also set a
max-cores option to
restrict the number of total cores used by a job.
The launch programs will look for a configuration file at
If you set the
LAUNCH_CONFIG environment variable, launch will look there
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:
Then subject number lists can be converted, for example
- Neal Morton
- Russ Poldrack - wrote original launch script
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