diff --git a/experiments/batch/julian-animation b/experiments/batch/julian-animation
new file mode 100644
index 0000000..eddb902
--- /dev/null
+++ b/experiments/batch/julian-animation
@@ -0,0 +1,24 @@
+#!/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}"
diff --git a/experiments/batch/measurements/.gitkeep b/experiments/batch/measurements/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/experiments/configs/julian-animation.json b/experiments/configs/julian-animation.json
new file mode 100644
index 0000000..228749a
--- /dev/null
+++ b/experiments/configs/julian-animation.json
@@ -0,0 +1,330 @@
+{
+ "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"
+}
diff --git a/experiments/scripts/gen/weak.py b/experiments/scripts/gen/weak.py
new file mode 100644
index 0000000..cfa7180
--- /dev/null
+++ b/experiments/scripts/gen/weak.py
@@ -0,0 +1,107 @@
+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)
diff --git a/experiments/scripts/timing.py b/experiments/scripts/timing.py
index 2ac7c96..1c5cc5b 100644
--- a/experiments/scripts/timing.py
+++ b/experiments/scripts/timing.py
@@ -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()
diff --git a/experiments/templates/spheroid_weak.json b/experiments/templates/spheroid_weak.json
new file mode 100644
index 0000000..c132bf9
--- /dev/null
+++ b/experiments/templates/spheroid_weak.json
@@ -0,0 +1,100 @@
+{
+ "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
+ }
+}