Check in stuff

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)

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()