Submitting NEURON jobs

We provide scripts for the user to submit NEURON jobs in src/neuron/. It is suggested that the script ending in “.sh” is used for Linux-based cluster contexts; on the other hand, if running locally, the environment setup will likely be more specific to the machine, and the script ending in “.py” is the better choice. The submit.sh acts as a buffer for submit.py to set up the environment and load appropriate modules for job submission. The submit.py script takes the input of the Run configuration and submits a NEURON call for each independent fiber within an n_sim/. These scripts are called using similar syntax as pipeline.py: “./submit.<ext> <run indices>,” where <run indices> is a space-separated list of integers. Note that these submission scripts expect to be called from a directory with the structure generated by Simulation.export_nsims() at the location defined by “ASCENT_NSIM_EXPORT_PATH” in env.json.

Cluster submissions

When using a high-performance computing cluster running SLURM:

Set your default parameters, particularly your partition (can be found in "config/system/slurm_params.json"). The partition you set here (default is “common” ) will apply to all submit.py runs.
Optionally, set your "submission_context" to "auto", and configure your run.json with the appropriate hostname prefix. (Only necessary if you plan to submit runs both locally and on a cluster, see S8 Text.)
Many parameters which submit.py sources from JSON configuration files can be overridden with command line arguments. For more information, see Command-Line Arguments.