netpyne.batch.batch module

Module for setting up and running batch simulations

netpyne.batch.batch.tupleToStr(obj)[source]

Function for/to <short description of netpyne.batch.batch.tupleToStr>

Parameters:

obj (<type>) – <Short description of obj> Default: required

class netpyne.batch.batch.Batch(cfgFile='cfg.py', netParamsFile='netParams.py', cfg=None, netParams=None, params=None, groupedParams=None, initCfg=None, seed=None)[source]

Bases: object

Class that handles batch simulations on NetPyNE.

batchLabel

The label of the batch used for directory/file naming of batch generated files.

Type:

str

cfgFile

The path of the file containing the netpyne.simConfig.SimConfig object

Type:

str

cfg

The netpyne.simConfig.SimConfig object

Type:

netpyne.simConfig.SimConfig

N.B. either cfg or cfgFile should be specified #TODO
Type:

replace with typechecked single argument

netParamsFile

The path of the file containing the netpyne.netParams.NetParams object

Type:

str

netParams

The netpyne.netParams.NetParams object

Type:

netpyne.netParams.NetParams

N.B. either netParams or netParamsFile should be specified #TODO
Type:

replace with typechecked single argument

initCfg

params dictionary that is used to modify the batch cfg prior to any algorithm based parameter modifications

Type:

dict

saveFolder

The path of the folder where the batch will be saved (defaults to batchLabel)

Type:

str

method

The algorithm method used for batch

Type:

str

runCfg

Keyword: Arg dictionary used to generate submission templates (see utils.py)

Type:

dict

evolCfg

Keyword: Arg dictionary used to define evolutionary algorithm parameters (see evol.py)

Type:

dict #TODO: replace with algoCfg? to merge with optimCfg

optimCfg

Keyword: Arg dictionary used to define optimization algorithm parameters (see asd_parallel.py, optuna_parallel.py, sbi_parallel.py)

Type:

dict #TODO: replace with algoCfg? to merge with evolCfg

params

Dictionary of parameters to be explored per algorithm (grid, evol, asd, optuna, sbi) (see relevant algorithm script for details)

Type:

list

seed

Seed for random number generator for some algorithms

Type:

int

save(filename)[source]

Function to save batch object to file

Parameters:

filename (str) – The path of the file to save batch object in required

setCfgNestedParam(paramLabel, paramVal)[source]
saveScripts()[source]
openFiles2SaveStats()[source]
getParamCombinations()[source]
run()[source]
property mpiCommandDefault