Add stuff for eval
This commit is contained in:
parent
b36d8a748d
commit
6de64dd5d0
1
experiments/.gitignore
vendored
1
experiments/.gitignore
vendored
@ -7,3 +7,4 @@ batch/measurements/strong/*
|
||||
configs/measurements/strong/*
|
||||
*.dat
|
||||
*.db
|
||||
eval/generated/*
|
||||
|
||||
7
experiments/eval/Makefile
Normal file
7
experiments/eval/Makefile
Normal file
@ -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
0
experiments/eval/generated/batch/.gitkeep
Normal file
0
experiments/eval/generated/config/.gitkeep
Normal file
0
experiments/eval/generated/config/.gitkeep
Normal file
1
experiments/eval/load-modules
Normal file
1
experiments/eval/load-modules
Normal file
@ -0,0 +1 @@
|
||||
module load SciPy-Stack
|
||||
0
experiments/eval/logs/.gitkeep
Normal file
0
experiments/eval/logs/.gitkeep
Normal file
34
experiments/eval/scripts/generate-strong-cpu-configs.py
Normal file
34
experiments/eval/scripts/generate-strong-cpu-configs.py
Normal file
@ -0,0 +1,34 @@
|
||||
#!/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
21
experiments/eval/scripts/substitute.py
Normal file
@ -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
61
experiments/eval/strong-cpu.json
Normal file
@ -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
31
experiments/eval/templates/strong-batch.j2
Normal file
@ -0,0 +1,31 @@
|
||||
#!/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
258
experiments/eval/templates/strong-cpu.json
Normal file
@ -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
|
||||
}
|
||||
}
|
||||
Loading…
x
Reference in New Issue
Block a user