{ "cells": [ { "cell_type": "markdown", "id": "8ba03726-6b87-48e7-9d5d-d0c6ca77a896", "metadata": {}, "source": [ "# \"Communication-free and Parallel Simulation of Neutral Biodiversity Models\": Interactive Demonstration" ] }, { "cell_type": "code", "execution_count": 1, "id": "8c3f401d-7d54-46dc-906a-e712a4c9ddb0", "metadata": {}, "outputs": [], "source": [ "import demo" ] }, { "cell_type": "markdown", "id": "e25347fe-a014-4dc5-93fa-a706ada101e7", "metadata": {}, "source": [ "

Cell #1: Independent Reverse-Time Simulation

" ] }, { "cell_type": "code", "execution_count": 2, "id": "367bd13d-40c7-4c1e-8b72-24512400ac71", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\u001b[36mINFO \u001b[0m Starting to load the dispersal map \"maps/demo/dispersal.tif\" ...\n", "\u001b[33mWARN \u001b[0m No GDAL no data value was found ...\n", "\u001b[36mINFO \u001b[0m Successfully loaded the dispersal map \"maps/demo/dispersal.tif\" with dimensions 6x6 [cols x rows].\n", "\u001b[36mINFO \u001b[0m Starting to load the habitat map \"maps/demo/habitat.tif\" ...\n", "\u001b[33mWARN \u001b[0m No GDAL no data value was found ...\n", "\u001b[36mINFO \u001b[0m Successfully loaded the habitat map \"maps/demo/habitat.tif\" with dimensions 6x1 [cols x rows].\n", "\n", "=========================== Simulation Configuration ===========================\n", "\n", "(\n", " speciation: 0.75,\n", " sample: Sample(\n", " percentage: 1.0,\n", " origin: Habitat,\n", " mode: Genesis,\n", " ),\n", " pause: None,\n", " rng: Seed(7206077791098137251),\n", " scenario: SpatiallyExplicitUniformTurnover(\n", " habitat: \"maps/demo/habitat.tif\",\n", " dispersal: \"maps/demo/dispersal.tif\",\n", " turnover: 0.5,\n", " mode: OffByOne,\n", " ),\n", " algorithm: Independent(\n", " delta_t: 1.0,\n", " step_slice: 10,\n", " dedup_cache: None,\n", " parallelism_mode: Monolithic(\n", " event_slice: Relative(\n", " factor: 2.0,\n", " ),\n", " ),\n", " ),\n", " partitioning: Monolithic(),\n", " log: None,\n", " reporters: [\n", " Plugin(\n", " library: \"plugins/demo.so\",\n", " reporters: [\n", " Demo(\n", " ignore: [\n", " Location(\n", " x: 5,\n", " y: 0,\n", " ),\n", " Location(\n", " x: 1,\n", " y: 0,\n", " ),\n", " Location(\n", " x: 0,\n", " y: 0,\n", " ),\n", " ],\n", " ),\n", " ],\n", " ),\n", " ],\n", ")\n", "\n", "=========================== Simulation Configuration ===========================\n", "\n", "\u001b[36mINFO \u001b[0m The simulation will start fresh.\n", "\u001b[36mINFO \u001b[0m The scenario will be simulated as one monolithic partition.\n", "\u001b[36mINFO \u001b[0m The simulation will be run on one processing unit.\n", "\u001b[36mINFO \u001b[0m The simulation will report speciation events live.\n", "\u001b[36mINFO \u001b[0m The simulation will report dispersal events live.\n", "\u001b[36mINFO \u001b[0m Events will be reported using the live water-level algorithm ...\n", "================================================================================\n", "= Starting Event Report ... =\n", "================================================================================\n", " 0.35: <3> disperses from (3,0):0 to (2,0):0 ...\n", " 0.55: <4> disperses from (4,0):0 to (3,0):0 ...\n", " 1.39: <2> disperses from (2,0):0 to (3,0):0 ...\n", " 1.39: <3> disperses from (2,0):0 to (3,0):0 ...\n", " 2.08: <4> speciates at (3,0):0 ...\n", " 2.08: <2> speciates at (3,0):0 ...\n", " 2.08: <3> speciates at (3,0):0 ...\n", "\n", "\n", "=============================== Reporter Summary ===============================\n", "\n", "\n", "=============================== Reporter Summary ===============================\n", "\n", "\u001b[36mINFO \u001b[0m The simulation finished at time 4.853330974676176 after 12 steps.\n", "\n" ] } ], "source": [ "!rustcoalescence simulate '(\n", " speciation: 0.75,\n", " sample: Sample(percentage: 1.0),\n", " rng: Seed(7206077791098137251),\n", "\n", " scenario: SpatiallyExplicitUniformTurnover(\n", " habitat: \"maps/demo/habitat.tif\",\n", " dispersal: \"maps/demo/dispersal.tif\",\n", " ),\n", " \n", " algorithm: Independent(\n", " delta_t: 1.0,\n", " dedup_cache: None,\n", " ),\n", " \n", " reporters: [ Plugin(\n", " library: \"plugins/demo.so\",\n", " reporters: [ Demo(\n", " ignore: [\n", " Location(x: 0, y: 0),\n", " Location(x: 1, y: 0),\n", " Location(x: 5, y: 0),\n", " ],\n", " ) ],\n", " ) ],\n", ")'" ] }, { "cell_type": "markdown", "id": "23d44b21-c652-4099-bd87-b9dcc31cd335", "metadata": {}, "source": [ "

Cell #2: Only simulate individual <2>

" ] }, { "cell_type": "code", "execution_count": 3, "id": "5989a9e8-9a6d-48bc-8920-0c5044b9a5dd", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 1.39: <2> disperses from (2,0):0 to (3,0):0 ...\n", " 2.08: <2> speciates at (3,0):0 ...\n" ] } ], "source": [ "!rustcoalescence simulate '(\n", " speciation: 0.75,\n", " sample: Sample(percentage: 1.0),\n", " rng: Seed(7206077791098137251),\n", "\n", " scenario: SpatiallyExplicitUniformTurnover(\n", " habitat: \"maps/demo/habitat.tif\",\n", " dispersal: \"maps/demo/dispersal.tif\",\n", " ),\n", " \n", " algorithm: Independent(\n", " delta_t: 1.0,\n", " dedup_cache: None,\n", " \n", " parallelism_mode: IsolatedLandscape(\n", " partition: Partition(\n", " rank: 2,\n", " size: 6,\n", " ),\n", " event_slice: Absolute(capacity: 10),\n", " )\n", " ),\n", " \n", " reporters: [ Plugin(\n", " library: \"plugins/demo.so\",\n", " reporters: [ Demo() ],\n", " ) ],\n", ")' | grep \"<[0-9]*>\"" ] }, { "cell_type": "markdown", "id": "378f80e2-791f-48a4-abb0-017136ad6f36", "metadata": {}, "source": [ "

Cell #3: Only simulate individual <3>

" ] }, { "cell_type": "code", "execution_count": 4, "id": "358e8b31-3f43-4244-a44a-abe3b7c806ca", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 0.35: <3> disperses from (3,0):0 to (2,0):0 ...\n", " 1.39: <3> disperses from (2,0):0 to (3,0):0 ...\n", " 2.08: <3> speciates at (3,0):0 ...\n" ] } ], "source": [ "!rustcoalescence simulate '(\n", " speciation: 0.75,\n", " sample: Sample(percentage: 1.0),\n", " rng: Seed(7206077791098137251),\n", "\n", " scenario: SpatiallyExplicitUniformTurnover(\n", " habitat: \"maps/demo/habitat.tif\",\n", " dispersal: \"maps/demo/dispersal.tif\",\n", " ),\n", " \n", " algorithm: Independent(\n", " delta_t: 1.0,\n", " dedup_cache: None,\n", " \n", " parallelism_mode: IsolatedLandscape(\n", " partition: Partition(\n", " rank: 3,\n", " size: 6,\n", " ),\n", " event_slice: Absolute(capacity: 10),\n", " )\n", " ),\n", " \n", " reporters: [ Plugin(\n", " library: \"plugins/demo.so\",\n", " reporters: [ Demo() ],\n", " ) ],\n", ")' | grep \"<[0-9]*>\"" ] }, { "cell_type": "markdown", "id": "d38d6ce8-65c1-4328-9810-a85416101e77", "metadata": {}, "source": [ "

Cell #4: Only simulate individual <4>

" ] }, { "cell_type": "code", "execution_count": 5, "id": "7d81f402-be33-48d6-8be4-bec13bff7574", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 0.55: <4> disperses from (4,0):0 to (3,0):0 ...\n", " 2.08: <4> speciates at (3,0):0 ...\n" ] } ], "source": [ "!rustcoalescence simulate '(\n", " speciation: 0.75,\n", " sample: Sample(percentage: 1.0),\n", " rng: Seed(7206077791098137251),\n", "\n", " scenario: SpatiallyExplicitUniformTurnover(\n", " habitat: \"maps/demo/habitat.tif\",\n", " dispersal: \"maps/demo/dispersal.tif\",\n", " ),\n", " \n", " algorithm: Independent(\n", " delta_t: 1.0,\n", " dedup_cache: None,\n", " \n", " parallelism_mode: IsolatedLandscape(\n", " partition: Partition(\n", " rank: 4,\n", " size: 6,\n", " ),\n", " event_slice: Absolute(capacity: 10),\n", " )\n", " ),\n", " \n", " reporters: [ Plugin(\n", " library: \"plugins/demo.so\",\n", " reporters: [ Demo() ],\n", " ) ],\n", ")' | grep \"<[0-9]*>\"" ] }, { "cell_type": "code", "execution_count": null, "id": "finished-shark", "metadata": {}, "outputs": [], "source": [] } ], "metadata": { "kernelspec": { "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.7.12" } }, "nbformat": 4, "nbformat_minor": 5 }