From 47496d125bcba7176032bd34f92216019821d770 Mon Sep 17 00:00:00 2001
From: Daniel Vedder <daniel.vedder@idiv.de>
Date: Tue, 24 Jan 2023 11:35:47 +0100
Subject: [PATCH] Added run parallelisation and cleaned up `simulation.jl`
---
Manifest.toml | 2 +-
Project.toml | 3 +-
src/Persephone.jl | 3 +-
src/core/input.jl | 39 ++++++-----
src/core/landscape.jl | 1 +
src/core/output.jl | 6 +-
src/core/simulation.jl | 154 +++++++++++++++++------------------------
src/nature/nature.jl | 21 ++----
src/parameters.toml | 1 +
9 files changed, 103 insertions(+), 127 deletions(-)
diff --git a/Manifest.toml b/Manifest.toml
index b9a4d2b..1429f06 100644
--- a/Manifest.toml
+++ b/Manifest.toml
@@ -2,7 +2,7 @@
julia_version = "1.9.0-alpha1"
manifest_format = "2.0"
-project_hash = "f0da7d5ff50bf02c651315826a4a291410c6b984"
+project_hash = "6a6afac02132d4ea401777f7459614dc2d5cfa37"
[[deps.AbstractFFTs]]
deps = ["ChainRulesCore", "LinearAlgebra"]
diff --git a/Project.toml b/Project.toml
index 9add9d6..60bac47 100644
--- a/Project.toml
+++ b/Project.toml
@@ -7,6 +7,7 @@ version = "0.0.1"
Agents = "46ada45e-f475-11e8-01d0-f70cc89e6671"
ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"
Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
+Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
GeoArrays = "2fb1d81b-e6a0-5fc5-82e6-8e06903437ab"
Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
LoggingExtras = "e6f89c97-d47a-5376-807f-9c37f3926c36"
@@ -16,5 +17,5 @@ StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
TOML = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
[compat]
+Agents = ">= 5.6"
julia = ">= 1.9"
-Agents = ">= 5.6"
\ No newline at end of file
diff --git a/src/Persephone.jl b/src/Persephone.jl
index 4c1341b..571eb1e 100644
--- a/src/Persephone.jl
+++ b/src/Persephone.jl
@@ -16,10 +16,11 @@ using
Agents,
ArgParse,
Dates,
+ Distributed,
GeoArrays, #XXX this is a big dependency - can we get rid of it?
Logging,
LoggingExtras,
- #MacroTools, #http://fluxml.ai/MacroTools.jl/stable/utilities/
+ #MacroTools, #may be useful: http://fluxml.ai/MacroTools.jl/stable/utilities/
Random,
StableRNGs,
TOML
diff --git a/src/core/input.jl b/src/core/input.jl
index a049e71..d493d21 100644
--- a/src/core/input.jl
+++ b/src/core/input.jl
@@ -31,24 +31,6 @@ macro param(domainparam)
:($(esc(:model)).settings[$(domain*"."*paramname)])
end
-"""
- flattenTOML(dict)
-
-An internal utility function to convert the two-dimensional dict returned
-by `TOML.parsefile()` into a one-dimensional dict, so that instead of
-writing `settings["domain"]["param"]` one can use `settings["domain.param"]`.
-Can be reversed with `expandTOML()`.
-"""
-function flattenTOML(tomldict)
- flatdict = Dict{String, Any}()
- for domain in keys(tomldict)
- for param in keys(tomldict[domain])
- flatdict[domain*"."*param] = tomldict[domain][param]
- end
- end
- flatdict
-end
-
"""
getsettings(configfile, seed=nothing)
@@ -95,12 +77,31 @@ function getsettings(configfile::String, seed::Union{Int64,Nothing}=nothing)
settings["core.outdir"] = outdir
end
if settings["core.startdate"] > settings["core.enddate"]
- Base.error("Enddate is earlier than startdate.")
+ Base.error("Enddate is earlier than startdate.") #TODO replace with exception
end
+ !isempty(scanparams) && addprocs(settings["core.processors"])
settings["internal.scanparams"] = scanparams
settings
end
+"""
+ flattenTOML(dict)
+
+An internal utility function to convert the two-dimensional dict returned
+by `TOML.parsefile()` into a one-dimensional dict, so that instead of
+writing `settings["domain"]["param"]` one can use `settings["domain.param"]`.
+Can be reversed with `expandTOML()`.
+"""
+function flattenTOML(tomldict)
+ flatdict = Dict{String, Any}()
+ for domain in keys(tomldict)
+ for param in keys(tomldict[domain])
+ flatdict[domain*"."*param] = tomldict[domain][param]
+ end
+ end
+ flatdict
+end
+
"""
parsecommandline()
diff --git a/src/core/landscape.jl b/src/core/landscape.jl
index a7f1085..2d2cbaf 100644
--- a/src/core/landscape.jl
+++ b/src/core/landscape.jl
@@ -45,6 +45,7 @@ function initlandscape(landcovermap::String, farmfieldsmap::String)
@debug "Initialising landscape"
landcover = GeoArrays.read(landcovermap)
farmfields = GeoArrays.read(farmfieldsmap)
+ #TODO replace error with exception
(size(landcover) != size(farmfields)) && Base.error("Input map sizes don't match.")
width, height = size(landcover)[1:2]
landscape = Matrix{Pixel}(undef, width, height)
diff --git a/src/core/output.jl b/src/core/output.jl
index 09f621e..6711ff5 100644
--- a/src/core/output.jl
+++ b/src/core/output.jl
@@ -23,7 +23,8 @@ function createdatadir(outdir::String, overwrite::Union{Bool,String})
(answer == "yes") && (overwrite = true)
end
if !overwrite
- Base.error("Output directory exists, will not overwrite. Aborting.")
+ #TODO replace with exception
+ Base.error("Output directory exists, will not overwrite. Aborting.")
else
@warn "Overwriting existing output directory $(outdir)."
end
@@ -76,6 +77,7 @@ function saveinputfiles(model::AgentBasedModel)
# Copy the map files to the output folder
lcmap = @param(core.landcovermap)
ffmap = @param(core.farmfieldsmap)
+ #TODO replace errors with exceptions
!(isfile(lcmap)) && Base.error("The map file $(lcmap) doesn't exist.")
!(isfile(ffmap)) && Base.error("The map file $(ffmap) doesn't exist.")
cp(lcmap, joinpath(@param(core.outdir), basename(lcmap)), force = true)
@@ -127,7 +129,7 @@ that want to have their output functions called regularly.
function newdataoutput!(model::AgentBasedModel, filename::String, header::String,
outputfunction::Function, frequency::String)
if !(frequency in ("daily", "monthly", "yearly", "end", "never"))
- Base.error("Invalid frequency '$frequency' for $filename.")
+ Base.error("Invalid frequency '$frequency' for $filename.") #TODO replace with exception
end
ndo = DataOutput(filename, header, outputfunction, frequency)
append!(model.dataoutputs, [ndo])
diff --git a/src/core/simulation.jl b/src/core/simulation.jl
index 0195a97..492d3e7 100644
--- a/src/core/simulation.jl
+++ b/src/core/simulation.jl
@@ -3,15 +3,59 @@
### This file includes the core functions for initialising and running simulations.
###
-#XXX With the parameter scanning, code execution has become rather difficult to follow.
-# Can I refactor this into two clear, separate paths - one for the normal case (single
-# run) and one for parameter scanning?
+#XXX How can I make the model output during a parallel run clearer?
+
+"""
+ simulate(config=PARAMFILE, seed=nothing)
+
+Initialise one or more model objects and carry out a full simulation experiment,
+optionally specifying a configuration file and a seed for the RNG.
+
+This is the default way to run a Persephone simulation.
+"""
+function simulate(config::String=PARAMFILE, seed::Union{Int64,Nothing}=nothing)
+ models = initialise(config, seed)
+ isa(models, Vector) ?
+ pmap(simulate!, models) :
+ simulate!(models)
+end
+
+"""
+ simulate!(model)
+
+Carry out a complete simulation run using a pre-initialised model object.
+"""
+function simulate!(model::AgentBasedModel)
+ runtime = Dates.value(@param(core.enddate)-@param(core.startdate))+1
+ step!(model, dummystep, stepsimulation!, runtime)
+ finalise!(model)
+end
+
+"""
+ initialise(config=PARAMFILE, seed=nothing)
+
+Initialise the model: read in parameters, create the output data directory,
+and instantiate the AgentBasedModel object(s). Optionally allows specifying the
+configuration file and overriding the `seed` parameter. This returns a single
+model object, unless the config file contains multiple values for one or more
+parameters, in which case it creates a full-factorial simulation experiment
+and returns a vector of model objects.
+"""
+function initialise(config::String=PARAMFILE, seed::Union{Int64,Nothing}=nothing)
+ @info "Simulation run started at $(Dates.now())."
+ settings = getsettings(config, seed)
+ scanparams = settings["internal.scanparams"]
+ delete!(settings, "internal.scanparams")
+ isempty(scanparams) ?
+ initmodel(settings) :
+ pmap(initmodel, paramscan(settings, scanparams))
+end
"""
initmodel(settings)
Initialise a model object using a ready-made settings dict. This is
-a helper function for `initialise()` and `initmodelsparallel()`.
+a helper function for `initialise()`.
"""
function initmodel(settings::Dict{String, Any})
@debug "Initialising model object."
@@ -38,69 +82,32 @@ function initmodel(settings::Dict{String, Any})
end
end
-"""
- initmodelsparallel(settings)
-
-Initialise multiple model objects using ready-made settings dicts. This is
-a helper function for `initialise()`.
-"""
-function initmodelsparallel(settingsdicts::Vector{Dict{String, Any}})
- #TODO parallelise model initialisation
- @debug "Beginning to initialise model objects."
- models = Vector{AgentBasedModel}()
- for settings in settingsdicts
- push!(models, initmodel(settings))
- end
- models
-end
-
"""
paramscan(settings)
-Initialise a list of model objects, covering all possible parameter combinations
-given by the settings (i.e. a full-factorial experiment). This is a helper function
-for `initialise()`.
+Create a list of settings dicts, covering all possible parameter combinations
+given by the input settings (i.e. a full-factorial experiment). This is a helper
+function for `initialise()`.
"""
function paramscan(settings::Dict{String,Any}, scanparams::Vector{String})
+ isempty(scanparams) && return [settings]
+ param = pop!(scanparams)
+ combinations = Vector{Dict{String,Any}}()
# recursively generate a set of settings dicts covering all combinations
- function generatecombinations(params::Vector{String})
- (length(params) == 0) && return [settings]
- param = pop!(params)
- combinations = Vector{Dict{String,Any}}()
- for comb in generatecombinations(params)
- for value in settings[param]
- newcombination = deepcopy(comb)
- newcombination[param] = value
- if comb["core.outdir"] == settings["core.outdir"]
- outdir = joinpath(comb["core.outdir"], "$(split(param, ".")[2])_$(value)")
- else
- outdir = "$(comb["core.outdir"])_$(split(param, ".")[2])_$(value)"
- end
- newcombination["core.outdir"] = outdir
- push!(combinations, newcombination)
+ for comb in paramscan(settings, scanparams)
+ for value in settings[param]
+ newcombination = deepcopy(comb)
+ newcombination[param] = value
+ if comb["core.outdir"] == settings["core.outdir"]
+ outdir = joinpath(comb["core.outdir"], "$(split(param, ".")[2])_$(value)")
+ else
+ outdir = "$(comb["core.outdir"])_$(split(param, ".")[2])_$(value)"
end
+ newcombination["core.outdir"] = outdir
+ push!(combinations, newcombination)
end
- combinations
end
- generatecombinations(scanparams)
-end
-
-"""
- initialise(config=PARAMFILE, seed=nothing)
-
-Initialise the model: read in parameters, create the output data directory,
-and instantiate the AgentBasedModel object(s). Optionally allows specifying the
-configuration file and overriding the `seed` parameter. This returns a single
-model object unless the config file contains multiple values for one or more
-parameters, in which case it creates a full-factorial simulation experiment
-and returns a vector of model objects.
-"""
-function initialise(config::String=PARAMFILE, seed::Union{Int64,Nothing}=nothing)
- @info "Simulation run started at $(Dates.now())."
- settings = getsettings(config, seed)
- scanparams = settings["internal.scanparams"]
- delete!(settings, "internal.scanparams")
- isempty(scanparams) ? initmodel(settings) : initmodelsparallel(settings, scanparameters)
+ combinations
end
"""
@@ -139,34 +146,3 @@ function finalise!(model::AgentBasedModel)
model
end
end
-
-"""
- simulate!(model)
-
-Carry out a complete simulation run using a pre-initialised model object.
-"""
-function simulate!(model::AgentBasedModel)
- runtime = Dates.value(@param(core.enddate)-@param(core.startdate))+1
- step!(model, dummystep, stepsimulation!, runtime)
- finalise!(model)
-end
-
-"""
- simulate(config=PARAMFILE, seed=nothing)
-
-Initialise one or more model objects and carry out a full simulation experiment,
-optionally specifying a configuration file and a seed for the RNG.
-
-This is the default way to run a Persephone simulation.
-"""
-function simulate(config::String=PARAMFILE, seed::Union{Int64,Nothing}=nothing)
- models = initialise(config, seed)
- if isa(models, Vector)
- for m in models
- @info "Executing run $(m.settings["core.outdir"])"
- simulate!(m) #TODO parallelise
- end
- else
- simulate!(models)
- end
-end
diff --git a/src/nature/nature.jl b/src/nature/nature.jl
index ffee8c2..8f4eba6 100644
--- a/src/nature/nature.jl
+++ b/src/nature/nature.jl
@@ -25,6 +25,9 @@ by trait dictionaries passed by them during initialisation.
age::Int32
end
+#TODO If I write a `getproperty` method for `Animal`, I could get around the ugly
+# `animal.traits[property]` syntax (like Agents.jl does in `model.jl`).
+
"""
animalid(animal)
@@ -155,8 +158,8 @@ variables:
information).
Several utility macros can be used within the body of `@phase` as a short-hand for
-common expressions: `@trait`, `@setphase`, `@respond`, `@here`, `@kill`,
-`@reproduce`, `@neighbours`, `@rand`.
+common expressions: `@trait`, `@setphase`, `@respond`, `@kill`, `@reproduce`,
+`@neighbours`, `@rand`.
Note that the first phase that is defined in a species definition block will be
the phase that animals are assigned at birth, unless the variable `phase` is
@@ -215,17 +218,6 @@ macro respond(eventname, body)
end
end
-"""
- @here(property)
-
-A utility macro to quickly access a property of the animal's current position
-(i.e. `landcover`, `fieldid`, or `events` - see the `Pixel` struct).
-This can only be used nested within `@phase`.
-"""
-macro here(property)
- :($(esc(:model)).landscape[$(esc(:animal)).pos...].$(property))
-end
-
"""
@kill
@@ -369,7 +361,8 @@ end
@rand(args...)
Return a random number or element from the sample, using the model RNG.
-This is a utility wrapper that can only be used nested within `@phase` or `@habitat`.
+This is a utility wrapper that can only be used nested within `@phase` or `@habitat`
+(or in other contexts where the `model` object is available).
"""
macro rand(args...)
:($(esc(:rand))($(esc(:model)).rng, $(map(esc, args)...)))
diff --git a/src/parameters.toml b/src/parameters.toml
index e3359e3..ea33de6 100644
--- a/src/parameters.toml
+++ b/src/parameters.toml
@@ -13,6 +13,7 @@ farmfieldsmap = "data/fields_jena.tif" # location of the field geometry map
outdir = "results" # location and name of the output folder
overwrite = "ask" # overwrite the output directory? (true/false/"ask")
loglevel = "debug" # verbosity level: "debug", "info", "warn"
+processors = 2 # number of processors to use on parallel runs
seed = 2 # seed value for the RNG (0 -> random value)
# dates to start and end the simulation
startdate = 2022-01-01
--
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