Add stuff for strong scaling measurements
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7e3778757c
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2
experiments/.gitignore
vendored
2
experiments/.gitignore
vendored
@ -3,3 +3,5 @@ venv
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logs
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__pycache__
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generated/*
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batch/measurements/strong/*
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configs/measurements/strong/*
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1
experiments/batch/measurements/strong/.gitkeep
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1
experiments/batch/measurements/strong/.gitkeep
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Generated by scripts/gen/strong.py
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1
experiments/configs/measurements/.gitkeep
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1
experiments/configs/measurements/.gitkeep
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Autogenerated by scripts/gen/strong.py
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{
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"DefineFunctions": [
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"r_angle()=360*rnd()",
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"r_size()=400*rnd()"
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],
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"Filling": {
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"cells": [
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{
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"_comment": "This is for the dynamic ECM",
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"shape": "cube",
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"box": [
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[0, 0, 0],
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[399, 399, 401]
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],
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"value": 0,
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"celltype": 0
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},
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{
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"shape": "sphere",
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"pattern": "voronoi",
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"count": 5500,
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"radius": 75,
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"center": [
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200,
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200,
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200
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],
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"box": [
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[
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110,
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110,
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110
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],
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[
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290,
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290,
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290
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]
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],
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"celltype": 9
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}
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]
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}
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}
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77
experiments/scripts/gen/strong.py
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77
experiments/scripts/gen/strong.py
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import copy
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import json
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from dataclasses import dataclass
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from typing import Tuple
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@dataclass
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class Configuration:
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nodes: int
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tasks: int
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gpus_per_node: int
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blockcount: Tuple[int, int, int]
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blocksize: Tuple[int, int, int]
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def get_domain_size(self) -> int:
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return self.blockcount[0] * self.blocksize[0] * self.blockcount[1] * self.blocksize[1] * self.blockcount[2] * self.blocksize[2]
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configurations = [
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Configuration( 1, 12, 1, ( 1, 4, 3), (400, 100, 134)),
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Configuration( 1, 24, 2, ( 2, 4, 3), (200, 100, 134)),
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Configuration( 1, 48, 4, ( 4, 4, 3), (100, 100, 134)),
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Configuration( 2, 96, 4, ( 4, 4, 6), (100, 100, 67)),
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Configuration( 4, 192, 4, ( 4, 8, 6), (100, 50, 67)),
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Configuration( 8, 384, 4, ( 8, 8, 6), ( 50, 50, 67)),
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Configuration(16, 768, 4, ( 8, 16, 6), ( 50, 25, 67)),
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Configuration(32, 1536, 4, (16, 16, 6), ( 25, 25, 67))
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]
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with open("templates/spheroid.json") as template_file:
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template = json.load(template_file)
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for c in configurations:
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print(c)
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assert(c.get_domain_size() == configurations[0].get_domain_size())
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nastja_config = copy.deepcopy(template)
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nastja_config["Geometry"]["blockcount"] = c.blockcount
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nastja_config["Geometry"]["blocksize"] = c.blocksize
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label = f"{c.nodes:02}"
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if c.gpus_per_node < 4:
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label += f"g{c.gpus_per_node}"
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with open(f"configs/measurements/strong/spheroid_{label}.json", "w") as config_file:
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json.dump(nastja_config, config_file, indent=2)
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batch_config = f"""#!/usr/bin/env bash
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#SBATCH --job-name=strong-{label}
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#SBATCH --account=hkf6
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#SBATCH --partition=booster
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#SBATCH --nodes={c.nodes}
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#SBATCH --ntasks={c.tasks}
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# Counted per node
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#SBATCH --gres=gpu:{c.gpus_per_node}
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#SBATCH --time=06:00:00
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#SBATCH --output=logs/strong-{label}-%A_%a.log
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#SBATCH --error=logs/strong-{label}-%A_%a.log
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#SBATCH --array=1-5
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SOURCE_DIR=/p/project/cellsinsilico/paulslustigebude
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OUTPUT_DIR="/p/scratch/cellsinsilico/paul/nastja-out/strong-{label}-${{SLURM_ARRAY_TASK_ID}}"
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echo "${{OUTPUT_DIR}}"
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mkdir -p "${{OUTPUT_DIR}}"
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source "${{SOURCE_DIR}}/activate-nastja-modules"
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srun --unbuffered "${{SOURCE_DIR}}/nastja/build-cuda/nastja" \\
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-c "${{SOURCE_DIR}}/ma/experiments/configs/measurements/strong/spheroid_{c.nodes:02}.json" \\
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-o "${{OUTPUT_DIR}}"
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"""
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with open(f"batch/measurements/strong/strong-{label}", "w", encoding="utf8") as batch_config_file:
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batch_config_file.write(batch_config)
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116
experiments/templates/spheroid.json
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experiments/templates/spheroid.json
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{
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"Comments": ["Celltype Usage", "0 Dynamic ECM", "1-5 Not Used", "6 Liquid ", "7 Apoptotic cell Type ", "8 Basic Non Dividing Cell type (surrounding)", "9 Cancer"],
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"Application": "Cells",
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"CellsInSilico": {
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"ecmdegradation": {
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"enabled": "false",
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"steps": 99999,
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"stochastic": "true",
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"probability": 0.5
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},
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"energyfunctions": ["Volume00", "Surface01", "Motility00", "Adhesion01", "DynamicECM00"],
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"liquid": 6,
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"volume": {
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"default": {
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"storage": "const",
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"value": 500
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},
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"lambda": [0, 0, 0, 0, 0, 0, 0, 7.5, 7.5, 7.5],
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"sizechange": [0, 0, 0, 0, 0, 0, 0, -0.05, 0, 0, 0, 0, 0, 0, 0]
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},
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"surface": {
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"default": {
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"storage": "const",
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"value": 400
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},
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"lambda": [0, 0, 0, 0, 0, 0, 0, 5.625, 5.625, 1],
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"sizechange": [0, 0, 0, 0, 0, 0, 0, -0.05, 0, 0, 0, 0, 0, 0, 0, 0]
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},
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"adhesion": {
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"matrix": [
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[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
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[0, 0, 0, 0, 0, 0, 0, 0, 0, 450],
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[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
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[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
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[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
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[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
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[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
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[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
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[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
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[0, 450, 0, 0, 0, 0, 0, 0, 0, 50]
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]
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},
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"temperature": 50,
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"division": {
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"enabled": "true",
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"condition": ["", "", "", "", "", "", "", "", "", "( volume >= 0.9 * volume0 ) & ( rnd() <= 0.00001 ) & generation < 1"]
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},
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"centerofmass": {
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"steps": 1
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},
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"signaling": {
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"enabled": false
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},
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"orientation": {
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"enabled": true,
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"motility": "persistentRandomWalk",
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"persistenceMagnitude": 0.0,
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"recalculationtime": 200,
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"motilityamount": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
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},
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"visitor": {
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"stepwidth": 10,
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"checkerboard": "01"
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},
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"cleaner": {
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"killDistance": 20
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},
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"dynamicecm": {
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"enabled": true,
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"stepsPerMcs": 100,
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"pushSteps": 10,
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"pushWeight": 2,
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"ecmCellID": 0,
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"deltat": 0.1,
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"eta": 0.25,
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"k0": 0.1,
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"k1": 0.1,
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"c": 4,
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"alpha": 2,
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"d": 0.3,
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"phi": 1
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}
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},
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"Geometry": {
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"blockcount": [4, 4, 3],
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"blocksize": [100, 100, 134]
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},
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"Settings": {
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"randomseed": 0,
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"timesteps": 100
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},
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"WriteActions": ["CellInfo"],
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"Writers": {
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"CellInfo": {
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"field": "",
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"groupsize": 0,
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"steps": 1,
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"writer": "CellInfo"
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},
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"ParallelVTK_Cells": {
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"field": "cells",
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"outputtype": "UInt32",
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"printhints": false,
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"steps": 100,
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"writer": "ParallelVtkImage"
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},
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"ParallelVTK_Displacement": {
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"writer": "ParallelVtkImage",
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"outputtype": "Float32",
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"field": "dynamicecm",
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"components": [0, 1, 2],
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"steps": 100
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}
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},
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"Include": "config_filling_1.json"
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}
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