Importing a simulation

Some developmental models may simulate consecutive stages in development and each stage may be optimized separately during model creation. If the simulations take a lot of time to run it may then be advantageous to use a previous simulation of early stages of development to start simulating a later stage.

This is possible with the Admin_agent.import_simulation method:

fname_old = "output/prev_simulation.db"
fname = "output/new_simulation.db"
sim_volume = [[0., 0., 0.], [100., 100., 100.]]
neuron_types = [MyFront1,MyFront2]
num_procs = 4
admin = Admin_agent(num_procs,fname,sim_volume,neuron_types,seed=1)
admin.import_simulation(fname_old)

There are strict limitations to the use of import_simulation:

1. The database should be importable: this should be set in the previous simulation as admin.importable_db = True, best immediately after Admin_agent class initalization.

2. The importing simulation shoul call import_simulation as the first method after initalization of Admin_agent class.

3. Admin_agent class initalization should be almost identical to that used for the previous simulation: num_procs, sim_volume and neuron_types should be identical (num_procs can be 0 for Interactive mode). The code defining each neuron type should be compatible with the previous simulation. Optional changes to Admin_agent array size attributes should also be identical.

4. The database name for the new simulation should be different from that of the previous one. By default the database contents are copied to the new simulation database, but this can be turned off with the optional copy_db parameter.

5. Admin_agent seed and verbose can be different.

The new simulation will start at the next cycle after the last one stored in the previous simulation database. Because it uses an importable database it has all the information needed to continue the simulation as if it was never interrupted. If any Additional attributes were declared their values should be stored during the previous simulation, this can be done with Storing additional attributes and setting the optional parameter last_only=True.

Several use cases of import_simulation are shown in the Import notebook.