netpyne.batch.batch

Module for setting up and running batch simulations

Functions:

tupleToStr(obj)

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

Classes:

Batch([cfgFile, netParamsFile, cfg, ...])

Class that handles batch simulations on NetPyNE. Relevant Attributes: batchLabel : str The label of the batch used for directory/file naming of batch generated files. cfgFile : str The path of the file containing the netpyne.simConfig.SimConfig object cfg : netpyne.simConfig.SimConfig The netpyne.simConfig.SimConfig object N.B. either cfg or cfgFile should be specified #TODO: replace with typechecked single argument netParamsFile : str The path of the file containing the netpyne.netParams.NetParams object netParams : netpyne.netParams.NetParams The netpyne.netParams.NetParams object N.B. either netParams or netParamsFile should be specified #TODO: replace with typechecked single argument initCfg : dict params dictionary that is used to modify the batch cfg prior to any algorithm based parameter modifications saveFolder : str The path of the folder where the batch will be saved (defaults to batchLabel) method : str The algorithm method used for batch runCfg : dict Keyword: Arg dictionary used to generate submission templates (see utils.py) evolCfg : dict #TODO: replace with algoCfg? to merge with optimCfg Keyword: Arg dictionary used to define evolutionary algorithm parameters (see evol.py) optimCfg : dict #TODO: replace with algoCfg? to merge with evolCfg Keyword: Arg dictionary used to define optimization algorithm parameters (see asd_parallel.py, optuna_parallel.py, sbi_parallel.py) params : list Dictionary of parameters to be explored per algorithm (grid, evol, asd, optuna, sbi) (see relevant algorithm script for details) seed : int Seed for random number generator for some algorithms.

netpyne.batch.batch.tupleToStr(obj)

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)

Bases: object

Class that handles batch simulations on NetPyNE. Relevant Attributes:

batchLabelstr

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

cfgFilestr

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

cfgnetpyne.simConfig.SimConfig

The netpyne.simConfig.SimConfig object

N.B. either cfg or cfgFile should be specified #TODO: replace with typechecked single argument netParamsFile : str

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

netParamsnetpyne.netParams.NetParams

The netpyne.netParams.NetParams object

N.B. either netParams or netParamsFile should be specified #TODO: replace with typechecked single argument initCfg : dict

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

saveFolderstr

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

methodstr

The algorithm method used for batch

runCfgdict

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

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

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

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

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

paramslist

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

seedint

Seed for random number generator for some algorithms

Methods:

save(filename)	Function to save batch object to file
setCfgNestedParam(paramLabel, paramVal)
saveScripts()
openFiles2SaveStats()
getParamCombinations()
run()

Attributes:

mpiCommandDefault

save(filename)

Function to save batch object to file

Parameters:

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

setCfgNestedParam(paramLabel, paramVal)

saveScripts()

openFiles2SaveStats()

getParamCombinations()

run()

property mpiCommandDefault