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2
experiments/.gitignore vendored
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@ -3,5 +3,3 @@ venv
logs
__pycache__
generated/*
batch/measurements/strong/*
configs/measurements/strong/*

11
experiments/Makefile
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@ -1,17 +1,8 @@
VARIED_FILLINGS_IS := $(shell seq -w 0 10 100)
VARIED_FILLINGS_JOBS := $(addprefix generated/varied-fillings-, $(addsuffix .json, ${VARIED_FILLINGS_IS}))
all: varied-fillings strong
varied-fillings: ${VARIED_FILLINGS_JOBS}
strong:
python scripts/gen/strong.py
clean-strong:
rm -f batch/measurements/strong/*
rm -f configs/measurements/strong/spheroid*.json
clean:
rm -f generated/*
@ -24,4 +15,4 @@ clean-outs:
generated/varied-fillings-%.json: scripts/gen/varied_fillings.py templates/varied-fillings.json
python scripts/gen/varied_fillings.py $* > $@
.PHONY: varied-fillings strong clean clean-logs clean-outs
.PHONY: varied-fillings clean clean-logs clean-outs

1
experiments/batch/measurements/strong/.gitkeep
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@ -1 +0,0 @@
Generated by scripts/gen/strong.py

102
experiments/configs/comp.json
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@ -1,102 +0,0 @@
{
"#Testing": {
"description": "Small experiment for comparing CPU and GPU implementations"
},
"Application": "Cells",
"Geometry": {
"blocksize": [10, 10, 10],
"blockcount": [1, 1, 1]
},
"Settings": {
"timesteps": 4,
"randomseed": 42
},
"Filling": {
"cells": [
{
"_comment": "This is for the dynamic ECM",
"shape": "cube",
"box": [
[0, 0, 0],
[9, 9, 9]
],
"value": 0,
"celltype": 0
},
{
"shape": "cube",
"box": [
[4, 4, 4],
[7, 7, 7]
],
"celltype": 2
}
]
},
"CellsInSilico": {
"liquid": 1,
"adhesion": {
"matrix": [
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 10, 5],
[0, 0, 5, 5]
]
},
"temperature": 15,
"volume": {
"default": [0, 0, 64, 64],
"lambda": {
"storage": "const",
"value": 10
}
},
"surface": {
"default": [0, 0, 80, 80],
"lambda": {
"storage": "const",
"value": 10
}
},
"cleaner": {
"killdistance": 100
},
"checkerboard": "00",
"energyfunctions": ["Volume00", "Surface00", "Adhesion00", "DynamicECM00"],
"centerofmass": {
"steps": 10
},
"dynamicecm": {
"enabled": true,
"stepsPerMcs": 10,
"pushSteps": 10,
"pushWeight": 2,
"ecmCellID": 0,
"deltat": 0.1,
"eta": 0.25,
"k0": 0.1,
"k1": 0.1,
"c": 4,
"alpha": 2,
"d": 0.3,
"phi": 1,
"lambda": 50
}
},
"Writers": {
"ParallelVTK_Cells": {
"writer": "ParallelVtkImage",
"outputtype": "UInt32",
"field": "cells",
"steps": 1
},
"ParallelVTK_Displacement": {
"writer": "ParallelVtkImage",
"outputtype": "Float32",
"field": "dynamicecm",
"components": [0, 1, 2],
"steps": 1
}
},
"WriteActions": ["ParallelVTK_Cells", "ParallelVTK_Displacement"]
}

1
experiments/configs/measurements/.gitkeep
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@ -1 +0,0 @@
Autogenerated by scripts/gen/strong.py

44
experiments/configs/measurements/strong/config_filling_1.json
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@ -1,44 +0,0 @@
{
"DefineFunctions": [
"r_angle()=360*rnd()",
"r_size()=400*rnd()"
],
"Filling": {
"cells": [
{
"_comment": "This is for the dynamic ECM",
"shape": "cube",
"box": [
[0, 0, 0],
[399, 399, 401]
],
"value": 0,
"celltype": 0
},
{
"shape": "sphere",
"pattern": "voronoi",
"count": 5500,
"radius": 75,
"center": [
200,
200,
200
],
"box": [
[
110,
110,
110
],
[
290,
290,
290
]
],
"celltype": 9
}
]
}
}

109
experiments/configs/medium.json
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@ -1,109 +0,0 @@
{
"#Testing": {
"description": "Cellular Potts Model with dynamic ECM"
},
"Application": "Cells",
"Geometry": {
"blocksize": [90, 90, 60],
"blockcount": [2, 2, 3]
},
"Settings": {
"timesteps": 100,
"randomseed": 42
},
"Filling": {
"cells": [
{
"_comment": "This is for the dynamic ECM",
"shape": "cube",
"box": [
[0, 0, 0],
[179, 179, 179]
],
"value": 0,
"celltype": 0
},
{
"shape": "cube",
"pattern": "voronoi",
"box": [
[20, 20, 20],
[159, 159, 159]
],
"count": 1500,
"celltype": [0, 0, 750, 750]
}
]
},
"CellsInSilico": {
"liquid": 1,
"adhesion": {
"matrix": [
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 10, 5],
[0, 0, 5, 5]
]
},
"temperature": 15,
"volume": {
"default": {
"storage": "const",
"value": 2000
},
"lambda": {
"storage": "const",
"value": 10
}
},
"surface": {
"default": {
"storage": "const",
"value": 800
},
"lambda": {
"storage": "const",
"value": 10
}
},
"cleaner": {
"killdistance": 100
},
"checkerboard": "00",
"energyfunctions": ["Volume00", "Surface00", "Adhesion00", "DynamicECM00"],
"centerofmass": {
"steps": 10
},
"dynamicecm": {
"enabled": true,
"stepsPerMcs": 100,
"pushSteps": 10,
"pushWeight": 2,
"ecmCellID": 0,
"deltat": 0.1,
"eta": 0.25,
"k0": 0.1,
"k1": 0.1,
"c": 4,
"alpha": 2,
"d": 0.3,
"phi": 1
}
},
"Writers": {
"ParallelVTK_Cells": {
"writer": "ParallelVtkImage",
"outputtype": "UInt32",
"field": "cells",
"steps": 1
},
"ParallelVTK_Displacement": {
"writer": "ParallelVtkImage",
"outputtype": "Float32",
"field": "dynamicecm",
"components": [0, 1, 2],
"steps": 1
}
},
"WriteActions": ["ParallelVTK_Cells", "ParallelVTK_Displacement"]
}

8
experiments/configs/mini.json
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@ -4,11 +4,11 @@
},
"Application": "Cells",
"Geometry": {
"blocksize": [40, 20, 20],
"blockcount": [1, 1, 1]
"blocksize": [20, 20, 20],
"blockcount": [2, 1, 1]
},
"Settings": {
"timesteps": 200,
"timesteps": 500,
"randomseed": 42
},
"Filling": {
@ -76,7 +76,7 @@
},
"dynamicecm": {
"enabled": true,
"stepsPerMcs": 10,
"stepsPerMcs": 100,
"pushSteps": 10,
"pushWeight": 2,
"ecmCellID": 0,

2
experiments/configs/small.json
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@ -8,7 +8,7 @@
"blockcount": [1, 1, 1]
},
"Settings": {
"timesteps": 3,
"timesteps": 1,
"randomseed": 42
},
"Filling": {

116
experiments/configs/spheroid/config.json
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@ -1,116 +0,0 @@
{
"Comments": ["Celltype Usage", "0 Not Used", "1-5 Solids for blood vessels / ECM", "6 Liquid ", "7 Apoptotic cell Type ", "8 Basic Non Dividing Cell type (surrounding)", "9 Cancer"],
"Application": "Cells",
"CellsInSilico": {
"ecmdegradation": {
"enabled": "false",
"steps": 99999,
"stochastic": "true",
"probability": 0.5
},
"energyfunctions": ["Volume00", "Surface01", "Motility00", "Adhesion01", "DynamicECM00"],
"liquid": 6,
"volume": {
"default": {
"storage": "const",
"value": 500
},
"lambda": [0, 0, 0, 0, 0, 0, 0, 7.5, 7.5, 7.5],
"sizechange": [0, 0, 0, 0, 0, 0, 0, -0.05, 0, 0, 0, 0, 0, 0, 0]
},
"surface": {
"default": {
"storage": "const",
"value": 400
},
"lambda": [0, 0, 0, 0, 0, 0, 0, 5.625, 5.625, 1],
"sizechange": [0, 0, 0, 0, 0, 0, 0, -0.05, 0, 0, 0, 0, 0, 0, 0, 0]
},
"adhesion": {
"matrix": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 450],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 450, 0, 0, 0, 0, 0, 0, 0, 50]
]
},
"temperature": 50,
"division": {
"enabled": "true",
"condition": ["", "", "", "", "", "", "", "", "", "( volume >= 0.9 * volume0 ) & ( rnd() <= 0.00001 ) & generation < 1"]
},
"centerofmass": {
"steps": 1
},
"signaling": {
"enabled": false
},
"orientation": {
"enabled": true,
"motility": "persistentRandomWalk",
"persistenceMagnitude": 0.0,
"recalculationtime": 200,
"motilityamount": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
},
"visitor": {
"stepwidth": 10,
"checkerboard": "01"
},
"cleaner": {
"killDistance": 20
},
"dynamicecm": {
"enabled": true,
"stepsPerMcs": 100,
"pushSteps": 10,
"pushWeight": 2,
"ecmCellID": 0,
"deltat": 0.1,
"eta": 0.25,
"k0": 0.1,
"k1": 0.1,
"c": 4,
"alpha": 2,
"d": 0.3,
"phi": 1
}
},
"Geometry": {
"blockcount": [8, 8, 6],
"blocksize": [50, 50, 67]
},
"Settings": {
"randomseed": 0,
"timesteps": 100
},
"WriteActions": ["CellInfo"],
"Writers": {
"CellInfo": {
"field": "",
"groupsize": 0,
"steps": 1,
"writer": "CellInfo"
},
"ParallelVTK_Cells": {
"field": "cells",
"outputtype": "UInt32",
"printhints": false,
"steps": 1,
"writer": "ParallelVtkImage"
},
"ParallelVTK_Displacement": {
"writer": "ParallelVtkImage",
"outputtype": "Float32",
"field": "dynamicecm",
"components": [0, 1, 2],
"steps": 1
}
},
"Include": "config_filling_1.json"
}

44
experiments/configs/spheroid/config_filling_1.json
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@ -1,44 +0,0 @@
{
"DefineFunctions": [
"r_angle()=360*rnd()",
"r_size()=400*rnd()"
],
"Filling": {
"cells": [
{
"_comment": "This is for the dynamic ECM",
"shape": "cube",
"box": [
[0, 0, 0],
[399, 399, 401]
],
"value": 0,
"celltype": 0
},
{
"shape": "sphere",
"pattern": "voronoi",
"count": 5500,
"radius": 75,
"center": [
200,
200,
200
],
"box": [
[
110,
110,
110
],
[
290,
290,
290
]
],
"celltype": 9
}
]
}
}

77
experiments/scripts/gen/strong.py
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@ -1,77 +0,0 @@
import copy
import json
from dataclasses import dataclass
from typing import Tuple
@dataclass
class Configuration:
nodes: int
tasks: int
gpus_per_node: int
blockcount: Tuple[int, int, int]
blocksize: Tuple[int, int, int]
def get_domain_size(self) -> int:
return self.blockcount[0] * self.blocksize[0] * self.blockcount[1] * self.blocksize[1] * self.blockcount[2] * self.blocksize[2]
configurations = [
Configuration( 1, 12, 1, ( 1, 4, 3), (400, 100, 134)),
Configuration( 1, 24, 2, ( 2, 4, 3), (200, 100, 134)),
Configuration( 1, 48, 4, ( 4, 4, 3), (100, 100, 134)),
Configuration( 2, 96, 4, ( 4, 4, 6), (100, 100, 67)),
Configuration( 4, 192, 4, ( 4, 8, 6), (100, 50, 67)),
Configuration( 8, 384, 4, ( 8, 8, 6), ( 50, 50, 67)),
Configuration(16, 768, 4, ( 8, 16, 6), ( 50, 25, 67)),
Configuration(32, 1536, 4, (16, 16, 6), ( 25, 25, 67))
]
with open("templates/spheroid.json") as template_file:
template = json.load(template_file)
for c in configurations:
print(c)
assert(c.get_domain_size() == configurations[0].get_domain_size())
nastja_config = copy.deepcopy(template)
nastja_config["Geometry"]["blockcount"] = c.blockcount
nastja_config["Geometry"]["blocksize"] = c.blocksize
label = f"{c.nodes:02}"
if c.gpus_per_node < 4:
label += f"g{c.gpus_per_node}"
with open(f"configs/measurements/strong/spheroid_{label}.json", "w") as config_file:
json.dump(nastja_config, config_file, indent=2)
batch_config = f"""#!/usr/bin/env bash
#SBATCH --job-name=strong-{label}
#SBATCH --account=hkf6
#SBATCH --partition=booster
#SBATCH --nodes={c.nodes}
#SBATCH --ntasks={c.tasks}
# Counted per node
#SBATCH --gres=gpu:{c.gpus_per_node}
#SBATCH --time=06:00:00
#SBATCH --output=logs/strong-{label}-%A_%a.log
#SBATCH --error=logs/strong-{label}-%A_%a.log
#SBATCH --array=1-5
SOURCE_DIR=/p/project/cellsinsilico/paulslustigebude
OUTPUT_DIR="/p/scratch/cellsinsilico/paul/nastja-out/strong-{label}-${{SLURM_ARRAY_TASK_ID}}"
echo "${{OUTPUT_DIR}}"
mkdir -p "${{OUTPUT_DIR}}"
source "${{SOURCE_DIR}}/activate-nastja-modules"
srun --unbuffered "${{SOURCE_DIR}}/nastja/build-cuda/nastja" \\
-c "${{SOURCE_DIR}}/ma/experiments/configs/measurements/strong/spheroid_{c.nodes:02}.json" \\
-o "${{OUTPUT_DIR}}"
"""
with open(f"batch/measurements/strong/strong-{label}", "w", encoding="utf8") as batch_config_file:
batch_config_file.write(batch_config)

116
experiments/templates/spheroid.json
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@ -1,116 +0,0 @@
{
"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"],
"Application": "Cells",
"CellsInSilico": {
"ecmdegradation": {
"enabled": "false",
"steps": 99999,
"stochastic": "true",
"probability": 0.5
},
"energyfunctions": ["Volume00", "Surface01", "Motility00", "Adhesion01", "DynamicECM00"],
"liquid": 6,
"volume": {
"default": {
"storage": "const",
"value": 500
},
"lambda": [0, 0, 0, 0, 0, 0, 0, 7.5, 7.5, 7.5],
"sizechange": [0, 0, 0, 0, 0, 0, 0, -0.05, 0, 0, 0, 0, 0, 0, 0]
},
"surface": {
"default": {
"storage": "const",
"value": 400
},
"lambda": [0, 0, 0, 0, 0, 0, 0, 5.625, 5.625, 1],
"sizechange": [0, 0, 0, 0, 0, 0, 0, -0.05, 0, 0, 0, 0, 0, 0, 0, 0]
},
"adhesion": {
"matrix": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 450],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 450, 0, 0, 0, 0, 0, 0, 0, 50]
]
},
"temperature": 50,
"division": {
"enabled": "true",
"condition": ["", "", "", "", "", "", "", "", "", "( volume >= 0.9 * volume0 ) & ( rnd() <= 0.00001 ) & generation < 1"]
},
"centerofmass": {
"steps": 1
},
"signaling": {
"enabled": false
},
"orientation": {
"enabled": true,
"motility": "persistentRandomWalk",
"persistenceMagnitude": 0.0,
"recalculationtime": 200,
"motilityamount": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
},
"visitor": {
"stepwidth": 10,
"checkerboard": "01"
},
"cleaner": {
"killDistance": 20
},
"dynamicecm": {
"enabled": true,
"stepsPerMcs": 100,
"pushSteps": 10,
"pushWeight": 2,
"ecmCellID": 0,
"deltat": 0.1,
"eta": 0.25,
"k0": 0.1,
"k1": 0.1,
"c": 4,
"alpha": 2,
"d": 0.3,
"phi": 1
}
},
"Geometry": {
"blockcount": [4, 4, 3],
"blocksize": [100, 100, 134]
},
"Settings": {
"randomseed": 0,
"timesteps": 100
},
"WriteActions": ["CellInfo"],
"Writers": {
"CellInfo": {
"field": "",
"groupsize": 0,
"steps": 1,
"writer": "CellInfo"
},
"ParallelVTK_Cells": {
"field": "cells",
"outputtype": "UInt32",
"printhints": false,
"steps": 100,
"writer": "ParallelVtkImage"
},
"ParallelVTK_Displacement": {
"writer": "ParallelVtkImage",
"outputtype": "Float32",
"field": "dynamicecm",
"components": [0, 1, 2],
"steps": 100
}
},
"Include": "config_filling_1.json"
}