Add new batch files

experiments/batch/build-cuda

@@ -8,8 +8,8 @@
 #SBATCH --ntasks-per-node=1
 #SBATCH --cpus-per-task=48
 #SBATCH --time=01:00:00
-#SBATCH --output=build-cuda-%j.out
-#SBATCH --error=build-cuda-%j.err
+#SBATCH --output=logs/build-cuda-%j.log
+#SBATCH --error=logs/build-cuda-%j.log
 
 SOURCE_DIR=/p/project/cellsinsilico/paulslustigebude
 

experiments/batch/build-nocuda

@@ -8,8 +8,8 @@
 #SBATCH --ntasks-per-node=1
 #SBATCH --cpus-per-task=48
 #SBATCH --time=01:00:00
-#SBATCH --output=build-nocuda-%j.out
-#SBATCH --error=build-nocuda-%j.err
+#SBATCH --output=logs/build-nocuda-%j.log
+#SBATCH --error=logs/build-nocuda-%j.log
 
 SOURCE_DIR=/p/project/cellsinsilico/paulslustigebude
 

experiments/batch/cuda

@@ -0,0 +1,32 @@
+#!/usr/bin/env bash
+
+#SBATCH --job-name=cuda
+# Forschergruppe Schug
+#SBATCH --account=hkf6
+# 48 Cores, 512GiB RAM, 4x NVIDIA A100 GPUs
+#SBATCH --partition=booster
+# Right now we're using a single node
+#SBATCH --nodes=1
+# Number of MPI processes
+# TODO: Change the config and set to this the maximum of 48
+#SBATCH --ntasks-per-node=16
+#SBATCH --cpus-per-task=1
+# For now, we are using a single GPU only
+#SBATCH --gres=gpu:1
+#SBATCH --time=01:00:00
+#SBATCH --output=logs/cuda-%j.log
+#SBATCH --error=logs/cuda-%j.log
+
+SOURCE_DIR=/p/project/cellsinsilico/paulslustigebude
+OUTPUT_DIR=/p/scratch/cellsinsilico/paul/nastja-out/cuda
+
+mkdir -p "${OUTPUT_DIR}"
+source "${SOURCE_DIR}/activate-nastja-modules"
+
+# This is actually the default behavior for a single task anyways
+# However I'm leaving this here for documentation reasons
+export CUDA_VISIBLE_DEVICES=0
+
+srun "${SOURCE_DIR}/nastja/build-cuda/nastja" \
+  -c "${SOURCE_DIR}/ma/experiments/configs/genesis.json" \
+  -o "${OUTPUT_DIR}"

experiments/batch/nocuda

@@ -12,8 +12,8 @@
 #SBATCH --ntasks-per-node=16
 #SBATCH --cpus-per-task=1
 #SBATCH --time=01:00:00
-#SBATCH --output=nocuda-%j.out
-#SBATCH --error=nocuda-%j.err
+#SBATCH --output=logs/nocuda-%j.log
+#SBATCH --error=logs/nocuda-%j.log
 
 SOURCE_DIR=/p/project/cellsinsilico/paulslustigebude
 OUTPUT_DIR=/p/scratch/cellsinsilico/paul/nastja-out/nocuda

experiments/batch/nocuda-noecm

@@ -0,0 +1,26 @@
+#!/usr/bin/env bash
+
+#SBATCH --job-name=nocuda-noecm
+# Forschergruppe Schug
+#SBATCH --account=hkf6
+# 48 Cores, 512GiB RAM, 4x NVIDIA A100 GPUs
+#SBATCH --partition=booster
+# Right now we're using a single node
+#SBATCH --nodes=1
+# Number of MPI processes
+# TODO: Change the config and set to this the maximum of 48
+#SBATCH --ntasks-per-node=16
+#SBATCH --cpus-per-task=1
+#SBATCH --time=01:00:00
+#SBATCH --output=logs/nocuda-noecm-%j.log
+#SBATCH --error=logs/nocuda-noecm-%j.log
+
+SOURCE_DIR=/p/project/cellsinsilico/paulslustigebude
+OUTPUT_DIR=/p/scratch/cellsinsilico/paul/nastja-out/nocuda-noecm
+
+mkdir -p "${OUTPUT_DIR}"
+source "${SOURCE_DIR}/activate-nastja-modules"
+
+srun "${SOURCE_DIR}/nastja/build-nocuda/nastja" \
+  -c "${SOURCE_DIR}/ma/experiments/configs/genesis-noecm.json" \
+  -o "${OUTPUT_DIR}"

experiments/configs/genesis-noecm.json

@@ -0,0 +1,109 @@
+{
+  "#Testing": {
+    "description": "Cellular Potts Model with dynamic ECM"
+  },
+  "Application": "Cells",
+  "Geometry": {
+    "blocksize": [20, 40, 40],
+    "blockcount": [4, 2, 2]
+  },
+  "Settings": {
+    "timesteps": 250,
+    "randomseed": 42
+  },
+  "Filling": {
+    "cells": [
+      {
+        "_comment": "This is for the dynamic ECM",
+        "shape": "cube",
+        "box": [
+          [0, 0, 0],
+          [79, 79, 79]
+        ],
+        "value": 0,
+        "celltype": 0
+      },
+      {
+        "shape": "cube",
+        "box": [
+          [41, 35, 10],
+          [45, 39, 15]
+        ],
+        "celltype": 2
+      },
+      {
+        "shape": "cube",
+        "box": [
+          [40, 15, 14],
+          [47, 22, 20]
+        ],
+        "celltype": 2
+      },
+      {
+        "shape": "cube",
+        "box": [
+          [40, 20, 20],
+          [47, 27, 26]
+        ],
+        "celltype": 3
+      },
+      {
+        "shape": "cube",
+        "box": [
+          [38, 20, 60],
+          [45, 27, 66]
+        ],
+        "celltype": 3
+      }
+    ]
+  },
+  "CellsInSilico": {
+    "liquid": 1,
+    "adhesion": {
+      "matrix": [
+        [0, 0,  0, 0],
+        [0, 0,  0, 0],
+        [0, 0, 10, 5],
+        [0, 0,  5, 5]
+      ]
+    },
+    "temperature": 15,
+    "volume": {
+      "default": {
+        "storage": "const",
+        "value": 2000
+      },
+      "lambda": {
+        "storage": "const",
+        "value": 10
+      }
+    },
+    "surface": {
+      "default": {
+        "storage": "const",
+        "value": 800
+      },
+      "lambda": {
+        "storage": "const",
+        "value": 10
+      }
+    },
+    "cleaner": {
+      "killdistance": 100
+    },
+    "checkerboard": "00",
+    "energyfunctions": ["Volume00", "Surface00", "Adhesion00"],
+    "centerofmass": {
+      "steps": 10
+    }
+  },
+  "Writers": {
+    "ParallelVTK_Cells": {
+      "writer": "ParallelVtkImage",
+      "outputtype": "UInt32",
+      "field": "cells",
+      "steps": 1
+    }
+  },
+  "WriteActions": ["ParallelVTK_Cells"]
+}