Command-Line Arguments
Note
In cases where a behavior can be controlled by both a command line argument, and a configuration file (.json file), the command line argument will ALWAYS take precedence.
run
ASCENT: Automated Simulations to Characterize Electrical Nerve Thresholds
usage: run [-h] [-v] [--version] [-l {runs,samples,sims}]
{pipeline,tidy_samples,import_n_sims,clean_samples,mock_morphology_generator,install,env_setup,build_dataset}
...
Positional Arguments
- script
Possible choices: pipeline, tidy_samples, import_n_sims, clean_samples, mock_morphology_generator, install, env_setup, build_dataset
which script to run
Named Arguments
- -v, --verbose
verbose printing
Default: False
- --version
show program’s version number and exit
- -l, --list
Possible choices: runs, samples, sims
List all available indices for the specified option
Sub-commands
pipeline
main ASCENT pipeline
run pipeline [-h]
[-b {pre_geom_run,post_geom_run,pre_java,post_mesh_distal,pre_mesh_distal,post_material_assign,pre_loop_currents,pre_mesh_proximal,post_mesh_proximal,pre_solve}]
[-w WAIT_FOR_LICENSE] [-P {cuff_only,nerve_only}]
[-E {overwrite,error,selective}] [-e] [-r] [-S] [-c | -C]
run_indices [run_indices ...]
Positional Arguments
- run_indices
Space separated indices to run the pipeline over
Named Arguments
- -b, --break-point
Possible choices: pre_geom_run, post_geom_run, pre_java, post_mesh_distal, pre_mesh_distal, post_material_assign, pre_loop_currents, pre_mesh_proximal, post_mesh_proximal, pre_solve
Point in pipeline to exit and continue to next run
- -w, --wait-for-license
Wait the specified number of hours for a comsol license to become available.
- -P, --partial-fem
Possible choices: cuff_only, nerve_only
Only generate the specified geometry.
- -E, --export-behavior
Possible choices: overwrite, error, selective
Behavior if n_sim export encounters extant data. Default is selective.
- -e, --endo-only-solution
Store basis solutions for endoneurial geometry ONLY
Default: False
- -r, --render-deform
Pop-up window will render deformation operations
Default: False
- -S, --auto-submit
Automatically submit fibers after each run
Default: False
- -c, --comsol-progress
Print COMSOL progress to stdout
Default: False
- -C, --comsol-progress-popup
Show COMSOL progress in a pop-up window
Default: False
tidy_samples
Remove specified files from Sample directories
run tidy_samples [-h] [-f FILENAME] sample_indices [sample_indices ...]
Positional Arguments
- sample_indices
Space separated sample indices to tidy
Named Arguments
- -f, --filename
Filename to clear
import_n_sims
Move NEURON outputs into ASCENT directories for analysis
run import_n_sims [-h] [-f | -D] run_indices [run_indices ...]
Positional Arguments
- run_indices
Space separated run indices to import
Named Arguments
- -f, --force
Import n_sims even if all thresholds are not found
Default: False
- -D, --delete-nsims
After importing delete n_sim folder from NSIM_EXPORT_PATH
Default: False
clean_samples
Remove all files except those specified from Sample directories
run clean_samples [-h] [-R] sample_indices [sample_indices ...]
Positional Arguments
- sample_indices
Space separated sample indices to clean
Named Arguments
- -R, --full-reset
Clear all files except sample.json and model.json
Default: False
mock_morphology_generator
Generate mock morpology for an ASCENT run
run mock_morphology_generator [-h] mock_sample_index
Positional Arguments
- mock_sample_index
Mock Sample Index to generate
install
install ASCENT
run install [-h] [--no-conda]
Named Arguments
- --no-conda
Skip conda portion of installation
Default: False
env_setup
Set ASCENT environment variables
run env_setup [-h]
build_dataset
Export dataset from ASCENT runs in SPARC format
run build_dataset [-h]
dataset_indices [dataset_indices ...] {query,generate} ...
Positional Arguments
- dataset_indices
Space separated dataset indices to export
- stage
Possible choices: query, generate
build_dataset stage
Sub-commands
query
Use query criteria to build excel output
run build_dataset query [-h]
generate
Generate dataset (keeps files) from excel output
run build_dataset generate [-h] [-f]
Named Arguments
- -f, --force
Overwrite existing dataset
Default: False
submit.py
ASCENT: Automated Simulations to Characterize Electrical Nerve Thresholds
usage: submit.py [-h] [-p PARTITION] [-n NUM_CPU] [-m JOB_MEM] [-j NUM_JOBS]
[-l] [-A] [-s] [-S SLURM_PARAMS] [-c] [-L | -C] [-v]
[run_indices ...]
Positional Arguments
- run_indices
Space separated indices to submit NEURON sims for
Named Arguments
- -p, --partition
If submitting on a cluster, overrides slurm_params.json
- -n, --num-cpu
For local submission: set number of CPUs to use, overrides run.json
- -m, --job-mem
For cluster submission: set amount of RAM per job (in MB), overrides slurm_params.json
- -j, --num-jobs
For cluster submission: set number of jobs per array, overrides slurm_params.json
- -l, --list-runs
List info for available runs.z If supplying this argument, do not pass any run indices
- -A, --all-runs
Submit all runs in the present export folder. If supplying this argument, do not pass any run indices
Default: False
- -s, --skip-summary
Begin submitting fibers without asking for confirmation
Default: False
- -S, --slurm-params
For cluster submission: string for additional slurm parameters (enclose in quotes)
- -c, --force-recompile
Force submit.py to recompile NEURON files
Default: False
- -L, --local-submit
Set submission context to local, overrides run.json
Default: False
- -C, --cluster-submit
Set submission context to cluster, overrides run.json
Default: False
- -v, --verbose
Print detailed submission info
Default: False