Getting Started

This guide assumes you have already installed slim and its dependencies. If you haven’t please check the README.

Run the simulator

The easiest way to run this project is from the command line.

The main script you’ll need to run is SeaLiceMgmt. The general way to launch it is the following:

python -m slim.SeaLiceMgmt output_folder/simulation_name simulation_params_directory

For example:

python -m slim.SeaLiceMgmt output/Loch_Fyne config_data/Fyne

The entry point of this program is the slim.Simulator.Simulator class.

All you have to do is to instantiate an object of that class and provide a slim.Config.Config instance. For example:

from slim.simulation.config import Config
from slim.simulation.Simulator import Simulator

cfg = Config("config_data/config.json", "config_data/Fyne")
sim = Simulator("output", "Fyne_foobar", cfg)
sim.run_model()

Runtime Environment

An environmental setup consists of a subfolder containing three files:

params.json with simulation parameters specific to the organisation;
interfarm_time.csv with travel time of sea lice between any two given farms (as a dense CSV matrix);
interfarm_prob.csv with probability of sea lice travel between any two given farms (as a dense CSV matrix);

See config_data/Fyne for examples.

Additionally, global simulation constants are provided inside config_data/config.json.

Warning

Do not change the values inside config.json! Here are two reasons:

changing those values will impact any simulation;
those values are determined via experimentation and fitting on real world data.

Currently, the only way to overwrite these parameters is via manual overriding, for example as described in Parameter Override.

Advanced features

Parameter Override

If one wishes to modify a runtime option without modifying those files an extra CLI parameter can be passed to the command. In general, for each key in the format a_b_c an automatic parameter in the format --a-b-c will be generated. For example:

python -m slim.SeaLiceMgmt out/0 config_data/Fyne --seed=0 --genetic-mechanism=discrete

For now, nested and list properties are not yet supported.

slim.Config.Config allows you to override the default parameter configuration of either global or environment-specific variables, assuming there is no name clash.

For example:

override = {
    "seed": 42,
    "gain_per_kg": 5.0,
    "dam_unavailability": 3,
    "start_date": "2017-10-01 00:00:00",
    "end_date": "2019-10-01 00:00:00",
}
cfg = Config("config_data/config.json", "config_data/Fyne")
sim = Simulator("output", "Fyne_foobar", cfg)
sim.run_model()

Note

The format of the override options must be consistent with the schema. This also means that overriding with the schema. See config_data/config.schema.json and config_data/params.schema.json.

Artifact Saving

The artifacts are saved inside the output folder under the name simulation_data_${NAME}.pickle.

For efficiency reasons, slim only saves a checkpoint of the simulation state at the end of the simulation.

This has two uses:

introspecting the simulation output with the GUI;
resuming an interrupted simulation.

To generate a dump every n days add the --save-rate=n option. For example:

python -m slim.SeaLiceMgmt outputs/sim_1 config_data/Fyne --save-rate=1"

This will save the output every day.

To resume a session one can instead pass the –resume parameter. Via CLI:

python -m slim.SeaLiceMgmt outputs/sim_1 config_data/Fyne --resume="2017-12-05 00:00:00"

If you only know n days have elapsed since the start use the –resume-after=n option. For example:

python -m slim.SeaLiceMgmt outputs/sim_1 config_data/Fyne --resume-after=365

To generate a dump every n days set up an instance of slim.Config.Config and pass the extra parameter save_rate. The rest follows as usual.

from slim.simulation.Config import Config
from slim.simulation.Simulator import Simulator

n = 10 # every 10 days

cfg = Config("config_data/config.json", "config_data/Fyne", save_rate=n)
sim = Simulator("output", "Fyne_foobar", cfg)
sim.run_model()

# Press Ctrl+C before the end to stop it prematurely

To resume the session you need to know either a timestamp or the number of elapsed days.

from slim.simulation.config import Config, to_dt
from slim.simulation.simulator import Simulator

timestamp = to_dt("2018-12-05 00:00:00")
sim = Simulator.reload("output", "Fyne_foobar", timestamp=timestamp)
# or alternatively
sim = Simulator.reload("output", "Fyne_foobar", resume_after=365)
sim.run_model()

Additionally, one can override the config parameters.

Note

Artifacts are opened in read-only mode when resuming. It is not allowed to combine resuming and dumping.

Run the GUI

We also provide a GUI for debugging and visualisation. Its support is still heavily experimental so please use with caution.

To run the GUI you need to launch slim.SeaLiceMgmtGUI, for example via: `python -m slim.SeaLiceMgmtGUI` and provide your run data (generated via the –save-rate option mentioned above) from the given menu.

TODO: expand on this?