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Add stuff for eval

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Paul Brinkmeier 2024-03-08 21:42:24 +01:00
parent b36d8a748d
commit 6de64dd5d0
11 changed files with 414 additions and 0 deletions
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1
experiments/.gitignore vendored
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@ -7,3 +7,4 @@ batch/measurements/strong/*
configs/measurements/strong/* configs/measurements/strong/*
*.dat *.dat
*.db *.db
eval/generated/*

7
experiments/eval/Makefile Normal file
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@ -0,0 +1,7 @@
generate-batch-strong-cpu:
python scripts/substitute.py strong-batch.j2 < strong-cpu.json
clean-logs:
rm logs/*
.PHONY: generate-batch-strong-cpu clean-logs

0
experiments/eval/generated/batch/.gitkeep Normal file
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0
experiments/eval/generated/config/.gitkeep Normal file
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1
experiments/eval/load-modules Normal file
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@ -0,0 +1 @@
module load SciPy-Stack

0
experiments/eval/logs/.gitkeep Normal file
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34
experiments/eval/scripts/generate-strong-cpu-configs.py Normal file
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#!/usr/bin/env python
import copy
import json
from pathlib import Path
SIZE = [384, 384, 384]
with (Path(__file__).parent.parent / "templates" / "strong-cpu.json").open(encoding="utf8") as f:
template = json.load(f)
configs = [
[ 4, 4, 3],
[ 4, 4, 6],
[ 4, 4, 12],
[ 4, 8, 12],
[ 8, 8, 12],
[ 8, 8, 24],
[ 8, 16, 24],
[ 16, 16, 24]
]
out_path = Path(__file__).parent.parent / "generated" / "config"
for c in configs:
nc = copy.deepcopy(template)
nc["Geometry"]["blockcount"] = c
nc["Geometry"]["blocksize"] = [bs // bc for bc, bs in zip(c, SIZE)]
nc_out_path = out_path / f"strong-cpu-{c[0]:02}-{c[1]:02}-{c[2]:02}.json"
print(f"Dumping {(c[0] * c[1] * c[2]) // 48} to {nc_out_path}")
with nc_out_path.open("w", encoding="utf8") as f:
json.dump(nc, f)

21
experiments/eval/scripts/substitute.py Normal file
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@ -0,0 +1,21 @@
#!/usr/bin/env python
import jinja2
import json
import sys
from pathlib import Path
data = json.load(sys.stdin)
templates_env = jinja2.Environment(
loader=jinja2.FileSystemLoader(Path(__file__).parent.parent / "templates"),
autoescape=jinja2.select_autoescape()
)
for possibly_incomplete_batch in data["batches"]:
batch = dict(list(data["common"].items()) + list(possibly_incomplete_batch.items()))
out_path = Path(__file__).parent.parent / "generated" / "batch" / batch["name"]
t = templates_env.get_template(sys.argv[1])
print(f"Dumping to {out_path}")
t.stream(**batch).dump(str(out_path))

61
experiments/eval/strong-cpu.json Normal file
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@ -0,0 +1,61 @@
{
"common": {
"account": "cellsinsilico",
"partition": "batch",
"extra_sbatch_line": "",
"logfile_path": "/p/project/cellsinsilico/paulslustigebude/ma/experiments/eval/logs/%x-%A.%a",
"nastja_binary_path": "/p/project/cellsinsilico/paulslustigebude/nastja/build-nocuda/nastja",
"config_path": "/p/project/cellsinsilico/paulslustigebude/ma/experiments/eval/generated/config/${SLURM_JOB_NAME}.json",
"output_dir_path": "/p/scratch/cellsinsilico/paul/nastja-out/${SLURM_JOB_NAME}-${SLURM_JOB_ID}.${SLURM_ARRAY_TASK_ID}"
},
"batches": [
{
"name": "strong-cpu-04-04-03",
"nodes": 1,
"tasks": 48,
"time": "00:30:00"
},
{
"name": "strong-cpu-04-04-06",
"nodes": 2,
"tasks": 96,
"time": "00:30:00"
},
{
"name": "strong-cpu-04-04-12",
"nodes": 4,
"tasks": 192,
"time": "00:10:00"
},
{
"name": "strong-cpu-04-08-12",
"nodes": 8,
"tasks": 384,
"time": "00:10:00"
},
{
"name": "strong-cpu-08-08-12",
"nodes": 16,
"tasks": 768,
"time": "00:10:00"
},
{
"name": "strong-cpu-08-08-24",
"nodes": 32,
"tasks": 1536,
"time": "00:10:00"
},
{
"name": "strong-cpu-08-16-24",
"nodes": 64,
"tasks": 3072,
"time": "00:10:00"
},
{
"name": "strong-cpu-16-16-24",
"nodes": 128,
"tasks": 6144,
"time": "00:10:00"
}
]
}

31
experiments/eval/templates/strong-batch.j2 Normal file
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#!/usr/bin/env bash
#SBATCH --job-name={{ name }}
#SBATCH --account={{ account }}
#SBATCH --partition={{ partition }}
#SBATCH --nodes={{ nodes }}
#SBATCH --ntasks={{ tasks }}
# Counted per node
{{ extra_sbatch_line }}
#SBATCH --time={{ time }}
#SBATCH --output={{ logfile_path }}
#SBATCH --error={{ logfile_path }}
#SBATCH --array=1-5
NASTJA_BINARY="{{ nastja_binary_path }}"
CONFIG_FILE="{{ config_path }}"
OUTPUT_DIR="{{ output_dir_path }}"
module load Stages/2024 GCC/12.3.0 ParaStationMPI/5.9.2-1 CMake/3.26.3 mold/1.11.0 jq/1.6 git Python
echo "${NASTJA_BINARY_PATH}"
echo "${CONFIG_FILE}"
echo "${OUTPUT_DIR}"
cat "${CONFIG_FILE}"
mkdir -p "${OUTPUT_DIR}"
srun "${NASTJA_BINARY}" \
-c "${CONFIG_FILE}" \
-o "${OUTPUT_DIR}"

258
experiments/eval/templates/strong-cpu.json Normal file
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@ -0,0 +1,258 @@
{
"Application": "Cells",
"CellsInSilico": {
"2D": false,
"adhesion": {
"matrix": [
[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, 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, 0.0, 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, 0.0, 0.0, 0.0, 0.0, 50.0]
],
"polarityenabled": false
},
"centerofmass": {
"steps": 1
},
"cleaner": {
"killdistance": 0,
"steps": 100
},
"contactinhibition": {
"enabled": false
},
"division": {
"condition": [
"",
"",
"",
"",
"",
"",
"",
"",
"",
"( volume >= 0.9 * volume0 ) & ( rnd() <= 0.00001 ) & generation < 1"
],
"enabled": true,
"halveSignals": false
},
"dynamicecm": {
"alpha": 2.0,
"beta": 0.5,
"c": 4.0,
"deltat": 0.10000000149011612,
"ecmCellID": 0,
"enabled": true,
"eta": 0.25,
"k0": 0.10000000149011612,
"k1": 0.10000000149011612,
"lambda": 10.0,
"phi": 1.0,
"pushSteps": 10,
"pushWeight": 0.5,
"stepsPerMcs": 100
},
"ecmdegradation": {
"enabled": false
},
"energyfunctions": [
"Volume00",
"Surface01",
"Motility00",
"Adhesion01",
"DynamicECM00"
],
"liquid": 6,
"logcellproperties": {
"enabled": false
},
"orientation": {
"enabled": true,
"motility": "persistentRandomWalk",
"motilityamount": [
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0
],
"numRandomNumbers": 5,
"persistenceMagnitude": 0.0,
"persistentDecay": 0.8,
"recalculationtime": 200
},
"polarity": {
"enabled": false
},
"signaling": {
"constant": false,
"enabled": false
},
"surface": {
"default": {
"storage": "const",
"value": 400.0
},
"lambda": [
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
5.625,
5.625,
1.0
],
"sizechange": [
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
-0.05,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0
]
},
"temperature": 50.0,
"visitor": {
"checkerboard": "01",
"stepwidth": 10
},
"volume": {
"default": {
"storage": "const",
"value": 500.0
},
"lambda": [
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
7.5,
7.5,
7.5
],
"sizechange": [
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
-0.05,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0
]
}
},
"DefineFunctions": [
"r_angle()=360*rnd()",
"r_size()=400*rnd()"
],
"Filling": {
"cells": [
{
"box": [
[
0,
0,
0
],
[
384,
384,
384
]
],
"celltype": 0,
"component": 0,
"pattern": "const",
"seed": 0,
"shape": "cube",
"value": 0
},
{
"box": [
[117, 117, 177],
[267, 267, 267]
],
"celltype": 9,
"center": [192, 192, 192],
"component": 0,
"count": 5500,
"pattern": "voronoi",
"radius": 75,
"seed": 758960,
"shape": "sphere",
"value": 8
}
],
"initialoutput": false,
"randomseed": 758959
},
"Geometry": {
"blockcount": [
4,
4,
3
],
"blockdefault": "fill",
"blocksize": [
96,
96,
128
],
"blocktype": [
[
[
1
]
]
]
},
"Settings": {
"deltat": 1.0,
"deltax": 1.0,
"handleFPE": "signal",
"logger": {
"group": 0,
"steps": 100
},
"randomseed": 42,
"statusoutput": 1,
"timestepguard": 1,
"timesteps": 5
}
}