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Paul Brinkmeier 2024-03-08 17:04:58 +01:00
parent 4661646b4f
commit b36d8a748d
6 changed files with 575 additions and 0 deletions
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24
experiments/batch/julian-animation Normal file
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#!/usr/bin/env bash
#SBATCH --job-name=julian-animation
#SBATCH --account=hkf6
#SBATCH --partition=booster
#SBATCH --nodes=8
#SBATCH --ntasks=32
# Counted per node
#SBATCH --gres=gpu:4
#SBATCH --time=03:30:00
#SBATCH --output=logs/%x-%A_%a.log
#SBATCH --error=logs/%x-%A_%a.log
SOURCE_DIR=/p/project/cellsinsilico/paulslustigebude
OUTPUT_DIR="/p/scratch/cellsinsilico/paul/nastja-out/${SLURM_JOB_NAME}"
echo "outdir is ${OUTPUT_DIR}"
mkdir -p "${OUTPUT_DIR}"
source "${SOURCE_DIR}/activate-nastja-modules"
srun --unbuffered "${SOURCE_DIR}/nastja/build-cuda/nastja" \
-c "${SOURCE_DIR}/ma/experiments/configs/${SLURM_JOB_NAME}.json" \
-o "${OUTPUT_DIR}"

0
experiments/batch/measurements/.gitkeep Normal file
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330
experiments/configs/julian-animation.json Normal file
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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"
],
"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": [
2,
4,
4
],
"blocksize": [
200,
100,
100
]
},
"Settings": {
"randomseed": 0,
"timesteps": 5000,
"statusoutput": 1
},
"WriteActions": ["ParallelVTK_Cells", "ParallelVTK_Displacement"],
"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": "measurements/strong/config_filling_1.json"
}

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experiments/scripts/gen/weak.py Normal file
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import copy
import json
from dataclasses import dataclass
configurations = [
(1, 1, 1),
(1, 1, 2),
(1, 2, 2),
(2, 2, 2),
(2, 2, 4),
(2, 4, 4),
(4, 4, 4),
(4, 4, 8),
(4, 8, 8),
(8, 8, 8)
]
with open("templates/spheroid_weak.json") as template_file:
template = json.load(template_file)
SIZE_X = 400
SIZE_Y = 400
SIZE_Z = 400
for bx, by, bz in configurations:
nastja_config = copy.deepcopy(template)
nastja_config["Geometry"]["blockcount"] = [bx, by, bz]
nastja_config["Geometry"]["blocksize"] = [SIZE_X, SIZE_Y, SIZE_Z]
# Fill the whole domain with ECM
cells_filling = [
{
"shape": "cube",
"box": [
[0, 0, 0],
[bx * SIZE_X, by * SIZE_Y, bz * SIZE_Z]
],
"value": 0,
"celltype": 0
}
]
# Place a bunch of cells in each block to keep each rank busy
for z in range(bz):
for y in range(by):
for x in range(bx):
sx = x * SIZE_X
sy = y * SIZE_Y
sz = z * SIZE_Z
cells_filling.append({
"shape": "sphere",
"pattern": "voronoi",
"count": 5500,
"radius": 75,
"center": [sx + 200, sy + 200, sz + 200],
"box": [
[sx + 110, sy + 110, sz + 110],
[sx + 290, sy + 290, sz + 290]
],
"celltype": 9
})
nastja_config["Filling"]["cells"] = cells_filling
ntasks = bx * by * bz
if ntasks < 4:
nodes = 1
gpus_per_node = ntasks
else:
assert ntasks % 4 == 0
nodes = ntasks // 4
gpus_per_node = 4
label = f"weak400-t{ntasks:04}n{nodes:03}g{gpus_per_node}x{bx}y{by}z{bz}"
with open(f"configs/measurements/weak/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={label}
#SBATCH --account=hkf6
#SBATCH --partition=booster
#SBATCH --nodes={nodes}
#SBATCH --ntasks={ntasks}
# Counted per node
#SBATCH --gres=gpu:{gpus_per_node}
#SBATCH --time=00:15:00
#SBATCH --output=logs/{label}-%A_%a.log
#SBATCH --error=logs/{label}-%A_%a.log
#SBATCH --array=1-5
SOURCE_DIR=/p/project/cellsinsilico/paulslustigebude
OUTPUT_DIR="/p/scratch/cellsinsilico/paul/nastja-out/{label}-${{SLURM_ARRAY_TASK_ID}}"
echo "outdir is ${{OUTPUT_DIR}}"
mkdir -p "${{OUTPUT_DIR}}"
source "${{SOURCE_DIR}}/activate-nastja-modules"
srun --unbuffered "${{SOURCE_DIR}}/nastja/build-cuda/nastja" \\
-c "${{SOURCE_DIR}}/ma/experiments/configs/measurements/weak/spheroid_{label}.json" \\
-o "${{OUTPUT_DIR}}"
"""
with open(f"batch/measurements/weak/{label}", "w", encoding="utf8") as batch_config_file:
batch_config_file.write(batch_config)

14
experiments/scripts/timing.py
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@ -128,5 +128,19 @@ def strong_dat(db, time):
for tasks, time in values:
print(f"{tasks}\t{time}")
@timing.command()
@click.option("--db", default="timings.db", help="Path of sqlite database file")
def weak_dat(db):
db = sqlite3.connect(db)
c = db.cursor()
res = c.execute("""
select tasks, avg(averagetime) as mean from timings group by tasks order by tasks asc
""")
values = res.fetchall()
print("gpus\tefficiency")
for tasks, mean in values:
print(f"{tasks}\t{values[0][1] / mean}")
if __name__ == "__main__":
timing()

100
experiments/templates/spheroid_weak.json Normal file
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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"],
"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": null,
"blocksize": null
},
"Settings": {
"randomseed": 0,
"timesteps": 20,
"statusoutput": 1
},
"DefineFunctions": [
"r_angle()=360*rnd()",
"r_size()=400*rnd()"
],
"Filling": {
"cells": null
}
}