"Communication-free and Parallel Simulation of Neutral Biodiversity Models": Interactive Demonstration¶
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import demo
Cell #1: Independent Reverse-Time Simulation
In [2]:
!rustcoalescence simulate '(
speciation: 0.75,
sample: Sample(percentage: 1.0),
rng: Seed(7206077791098137251),
scenario: SpatiallyExplicitUniformTurnover(
habitat: "maps/demo/habitat.tif",
dispersal: "maps/demo/dispersal.tif",
),
algorithm: Independent(
delta_t: 1.0,
dedup_cache: None,
),
reporters: [ Plugin(
library: "plugins/demo.so",
reporters: [ Demo(
ignore: [
Location(x: 0, y: 0),
Location(x: 1, y: 0),
Location(x: 5, y: 0),
],
) ],
) ],
)'
INFO Starting to load the dispersal map "maps/demo/dispersal.tif" ... WARN No GDAL no data value was found ... INFO Successfully loaded the dispersal map "maps/demo/dispersal.tif" with dimensions 6x6 [cols x rows]. INFO Starting to load the habitat map "maps/demo/habitat.tif" ... WARN No GDAL no data value was found ... INFO Successfully loaded the habitat map "maps/demo/habitat.tif" with dimensions 6x1 [cols x rows]. =========================== Simulation Configuration =========================== ( speciation: 0.75, sample: Sample( percentage: 1.0, origin: Habitat, mode: Genesis, ), pause: None, rng: Seed(7206077791098137251), scenario: SpatiallyExplicitUniformTurnover( habitat: "maps/demo/habitat.tif", dispersal: "maps/demo/dispersal.tif", turnover: 0.5, mode: OffByOne, ), algorithm: Independent( delta_t: 1.0, step_slice: 10, dedup_cache: None, parallelism_mode: Monolithic( event_slice: Relative( factor: 2.0, ), ), ), partitioning: Monolithic(), log: None, reporters: [ Plugin( library: "plugins/demo.so", reporters: [ Demo( ignore: [ Location( x: 5, y: 0, ), Location( x: 1, y: 0, ), Location( x: 0, y: 0, ), ], ), ], ), ], ) =========================== Simulation Configuration =========================== INFO The simulation will start fresh. INFO The scenario will be simulated as one monolithic partition. INFO The simulation will be run on one processing unit. INFO The simulation will report speciation events live. INFO The simulation will report dispersal events live. INFO Events will be reported using the live water-level algorithm ... ================================================================================ = Starting Event Report ... = ================================================================================ 0.35: <3> disperses from (3,0):0 to (2,0):0 ... 0.55: <4> disperses from (4,0):0 to (3,0):0 ... 1.39: <2> disperses from (2,0):0 to (3,0):0 ... 1.39: <3> disperses from (2,0):0 to (3,0):0 ... 2.08: <4> speciates at (3,0):0 ... 2.08: <2> speciates at (3,0):0 ... 2.08: <3> speciates at (3,0):0 ... =============================== Reporter Summary =============================== =============================== Reporter Summary =============================== INFO The simulation finished at time 4.853330974676176 after 12 steps.
Cell #2: Only simulate individual <2>
In [3]:
!rustcoalescence simulate '(
speciation: 0.75,
sample: Sample(percentage: 1.0),
rng: Seed(7206077791098137251),
scenario: SpatiallyExplicitUniformTurnover(
habitat: "maps/demo/habitat.tif",
dispersal: "maps/demo/dispersal.tif",
),
algorithm: Independent(
delta_t: 1.0,
dedup_cache: None,
parallelism_mode: IsolatedLandscape(
partition: Partition(
rank: 2,
size: 6,
),
event_slice: Absolute(capacity: 10),
)
),
reporters: [ Plugin(
library: "plugins/demo.so",
reporters: [ Demo() ],
) ],
)' | grep "<[0-9]*>"
1.39: <2> disperses from (2,0):0 to (3,0):0 ... 2.08: <2> speciates at (3,0):0 ...
Cell #3: Only simulate individual <3>
In [4]:
!rustcoalescence simulate '(
speciation: 0.75,
sample: Sample(percentage: 1.0),
rng: Seed(7206077791098137251),
scenario: SpatiallyExplicitUniformTurnover(
habitat: "maps/demo/habitat.tif",
dispersal: "maps/demo/dispersal.tif",
),
algorithm: Independent(
delta_t: 1.0,
dedup_cache: None,
parallelism_mode: IsolatedLandscape(
partition: Partition(
rank: 3,
size: 6,
),
event_slice: Absolute(capacity: 10),
)
),
reporters: [ Plugin(
library: "plugins/demo.so",
reporters: [ Demo() ],
) ],
)' | grep "<[0-9]*>"
0.35: <3> disperses from (3,0):0 to (2,0):0 ... 1.39: <3> disperses from (2,0):0 to (3,0):0 ... 2.08: <3> speciates at (3,0):0 ...
Cell #4: Only simulate individual <4>
In [5]:
!rustcoalescence simulate '(
speciation: 0.75,
sample: Sample(percentage: 1.0),
rng: Seed(7206077791098137251),
scenario: SpatiallyExplicitUniformTurnover(
habitat: "maps/demo/habitat.tif",
dispersal: "maps/demo/dispersal.tif",
),
algorithm: Independent(
delta_t: 1.0,
dedup_cache: None,
parallelism_mode: IsolatedLandscape(
partition: Partition(
rank: 4,
size: 6,
),
event_slice: Absolute(capacity: 10),
)
),
reporters: [ Plugin(
library: "plugins/demo.so",
reporters: [ Demo() ],
) ],
)' | grep "<[0-9]*>"
0.55: <4> disperses from (4,0):0 to (3,0):0 ... 2.08: <4> speciates at (3,0):0 ...
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