Add Erics spheroid config for reference

experiments/.gitignore

@@ -3,3 +3,5 @@ venv
 logs
 __pycache__
 generated/*
+batch/measurements/strong/*
+configs/measurements/strong/*

experiments/Makefile

@@ -1,8 +1,17 @@
 VARIED_FILLINGS_IS := $(shell seq -w 0 10 100)
 VARIED_FILLINGS_JOBS := $(addprefix generated/varied-fillings-, $(addsuffix .json, ${VARIED_FILLINGS_IS}))
 
+all: varied-fillings strong
+
 varied-fillings: ${VARIED_FILLINGS_JOBS}
 
+strong:
+	python scripts/gen/strong.py
+
+clean-strong:
+	rm -f batch/measurements/strong/*
+	rm -f configs/measurements/strong/spheroid*.json
+
 clean:
 	rm -f generated/*
 
@@ -15,4 +24,4 @@ clean-outs:
 generated/varied-fillings-%.json: scripts/gen/varied_fillings.py templates/varied-fillings.json
 	python scripts/gen/varied_fillings.py $* > $@
 
-.PHONY: varied-fillings clean clean-logs clean-outs
+.PHONY: varied-fillings strong clean clean-logs clean-outs

experiments/batch/measurements/strong/.gitkeep

@@ -0,0 +1 @@
+Generated by scripts/gen/strong.py

experiments/configs/comp.json

@@ -0,0 +1,102 @@
+{
+  "#Testing": {
+    "description": "Small experiment for comparing CPU and GPU implementations"
+  },
+  "Application": "Cells",
+  "Geometry": {
+    "blocksize": [10, 10, 10],
+    "blockcount": [1, 1, 1]
+  },
+  "Settings": {
+    "timesteps": 4,
+    "randomseed": 42
+  },
+  "Filling": {
+    "cells": [
+      {
+        "_comment": "This is for the dynamic ECM",
+        "shape": "cube",
+        "box": [
+          [0, 0, 0],
+          [9, 9, 9]
+        ],
+        "value": 0,
+        "celltype": 0
+      },
+      {
+        "shape": "cube",
+        "box": [
+          [4, 4, 4],
+          [7, 7, 7]
+        ],
+        "celltype": 2
+      }
+    ]
+  },
+  "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": [0, 0, 64, 64],
+      "lambda": {
+        "storage": "const",
+        "value": 10
+      }
+    },
+    "surface": {
+      "default": [0, 0, 80, 80],
+      "lambda": {
+        "storage": "const",
+        "value": 10
+      }
+    },
+    "cleaner": {
+      "killdistance": 100
+    },
+    "checkerboard": "00",
+    "energyfunctions": ["Volume00", "Surface00", "Adhesion00", "DynamicECM00"],
+    "centerofmass": {
+      "steps": 10
+    },
+    "dynamicecm": {
+      "enabled": true,
+      "stepsPerMcs": 10,
+      "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,
+      "lambda": 50
+    }
+  },
+  "Writers": {
+    "ParallelVTK_Cells": {
+      "writer": "ParallelVtkImage",
+      "outputtype": "UInt32",
+      "field": "cells",
+      "steps": 1
+    },
+    "ParallelVTK_Displacement": {
+      "writer": "ParallelVtkImage",
+      "outputtype": "Float32",
+      "field": "dynamicecm",
+      "components": [0, 1, 2],
+      "steps": 1
+    }
+  },
+  "WriteActions": ["ParallelVTK_Cells", "ParallelVTK_Displacement"]
+}

experiments/configs/measurements/.gitkeep

@@ -0,0 +1 @@
+Autogenerated by scripts/gen/strong.py

experiments/configs/measurements/strong/config_filling_1.json

@@ -0,0 +1,44 @@
+{
+    "DefineFunctions": [
+        "r_angle()=360*rnd()",
+        "r_size()=400*rnd()"
+    ],
+    "Filling": {
+        "cells": [
+            {
+                "_comment": "This is for the dynamic ECM",
+                "shape": "cube",
+                "box": [
+                  [0, 0, 0],
+                  [399, 399, 401]
+                ],
+                "value": 0,
+                "celltype": 0
+            },
+            {
+                "shape": "sphere",
+                "pattern": "voronoi",
+                "count": 5500,
+                "radius": 75,
+                "center": [
+                    200,
+                    200,
+                    200
+                ],
+                "box": [
+                    [
+                        110,
+                        110,
+                        110
+                    ],
+                    [
+                        290,
+                        290,
+                        290
+                    ]
+                ],
+                "celltype": 9
+            }
+        ]
+    }
+}

experiments/configs/medium.json

@@ -0,0 +1,109 @@
+{
+  "#Testing": {
+    "description": "Cellular Potts Model with dynamic ECM"
+  },
+  "Application": "Cells",
+  "Geometry": {
+    "blocksize": [90, 90, 60],
+    "blockcount": [2, 2, 3]
+  },
+  "Settings": {
+    "timesteps": 100,
+    "randomseed": 42
+  },
+  "Filling": {
+    "cells": [
+      {
+        "_comment": "This is for the dynamic ECM",
+        "shape": "cube",
+        "box": [
+          [0, 0, 0],
+          [179, 179, 179]
+        ],
+        "value": 0,
+        "celltype": 0
+      },
+      {
+        "shape": "cube",
+        "pattern": "voronoi",
+        "box": [
+            [20, 20, 20],
+            [159, 159, 159]
+        ],
+        "count": 1500,
+        "celltype": [0, 0, 750, 750]
+      }
+    ]
+  },
+  "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", "DynamicECM00"],
+    "centerofmass": {
+      "steps": 10
+    },
+    "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
+    }
+  },
+  "Writers": {
+    "ParallelVTK_Cells": {
+      "writer": "ParallelVtkImage",
+      "outputtype": "UInt32",
+      "field": "cells",
+      "steps": 1
+    },
+    "ParallelVTK_Displacement": {
+      "writer": "ParallelVtkImage",
+      "outputtype": "Float32",
+      "field": "dynamicecm",
+      "components": [0, 1, 2],
+      "steps": 1
+    }
+  },
+  "WriteActions": ["ParallelVTK_Cells", "ParallelVTK_Displacement"]
+}

experiments/configs/mini.json

@@ -4,11 +4,11 @@
   },
   "Application": "Cells",
   "Geometry": {
-    "blocksize": [20, 20, 20],
+    "blocksize": [40, 20, 20],
-    "blockcount": [2, 1, 1]
+    "blockcount": [1, 1, 1]
   },
   "Settings": {
-    "timesteps": 500,
+    "timesteps": 200,
     "randomseed": 42
   },
   "Filling": {
@@ -76,7 +76,7 @@
     },
     "dynamicecm": {
       "enabled": true,
-      "stepsPerMcs": 100,
+      "stepsPerMcs": 10,
       "pushSteps": 10,
       "pushWeight": 2,
       "ecmCellID": 0,

experiments/configs/small.json

@@ -8,7 +8,7 @@
     "blockcount": [1, 1, 1]
   },
   "Settings": {
-    "timesteps": 1,
+    "timesteps": 3,
     "randomseed": 42
   },
   "Filling": {

experiments/configs/spheroid/config.json

@@ -0,0 +1,116 @@
+{
+    "Comments": ["Celltype         Usage", "0                Not Used", "1-5             Solids for blood vessels / ECM", "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": [8, 8, 6],
+        "blocksize": [50, 50, 67]
+    },
+    "Settings": {
+        "randomseed": 0,
+        "timesteps": 100
+    },
+    "WriteActions": ["CellInfo"],
+    "Writers": {
+        "CellInfo": {
+            "field": "",
+            "groupsize": 0,
+            "steps": 1,
+            "writer": "CellInfo"
+        },
+        "ParallelVTK_Cells": {
+            "field": "cells",
+            "outputtype": "UInt32",
+            "printhints": false,
+            "steps": 1,
+            "writer": "ParallelVtkImage"
+        },
+        "ParallelVTK_Displacement": {
+            "writer": "ParallelVtkImage",
+            "outputtype": "Float32",
+            "field": "dynamicecm",
+            "components": [0, 1, 2],
+            "steps": 1
+        }
+    },
+    "Include": "config_filling_1.json"
+}

experiments/configs/spheroid/config_filling_1.json

@@ -0,0 +1,44 @@
+{
+    "DefineFunctions": [
+        "r_angle()=360*rnd()",
+        "r_size()=400*rnd()"
+    ],
+    "Filling": {
+        "cells": [
+            {
+                "_comment": "This is for the dynamic ECM",
+                "shape": "cube",
+                "box": [
+                  [0, 0, 0],
+                  [399, 399, 401]
+                ],
+                "value": 0,
+                "celltype": 0
+            },
+            {
+                "shape": "sphere",
+                "pattern": "voronoi",
+                "count": 5500,
+                "radius": 75,
+                "center": [
+                    200,
+                    200,
+                    200
+                ],
+                "box": [
+                    [
+                        110,
+                        110,
+                        110
+                    ],
+                    [
+                        290,
+                        290,
+                        290
+                    ]
+                ],
+                "celltype": 9
+            }
+        ]
+    }
+}

experiments/scripts/gen/strong.py

@@ -0,0 +1,77 @@
+import copy
+import json
+
+from dataclasses import dataclass
+from typing import Tuple
+
+@dataclass
+class Configuration:
+    nodes: int
+    tasks: int
+    gpus_per_node: int
+    blockcount: Tuple[int, int, int]
+    blocksize: Tuple[int, int, int]
+
+    def get_domain_size(self) -> int:
+        return self.blockcount[0] * self.blocksize[0] * self.blockcount[1] * self.blocksize[1] * self.blockcount[2] * self.blocksize[2]
+
+configurations = [
+    Configuration( 1,   12,   1, ( 1,  4, 3), (400, 100, 134)),
+    Configuration( 1,   24,   2, ( 2,  4, 3), (200, 100, 134)),
+    Configuration( 1,   48,   4, ( 4,  4, 3), (100, 100, 134)),
+    Configuration( 2,   96,   4, ( 4,  4, 6), (100, 100,  67)),
+    Configuration( 4,  192,   4, ( 4,  8, 6), (100,  50,  67)),
+    Configuration( 8,  384,   4, ( 8,  8, 6), ( 50,  50,  67)),
+    Configuration(16,  768,   4, ( 8, 16, 6), ( 50,  25,  67)),
+    Configuration(32, 1536,   4, (16, 16, 6), ( 25,  25,  67))
+]
+
+with open("templates/spheroid.json") as template_file:
+    template = json.load(template_file)
+
+for c in configurations:
+    print(c)
+    assert(c.get_domain_size() == configurations[0].get_domain_size())
+
+    nastja_config = copy.deepcopy(template)
+
+    nastja_config["Geometry"]["blockcount"] = c.blockcount
+    nastja_config["Geometry"]["blocksize"] = c.blocksize
+
+    label = f"{c.nodes:02}"
+
+    if c.gpus_per_node < 4:
+        label += f"g{c.gpus_per_node}"
+
+    with open(f"configs/measurements/strong/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=strong-{label}
+#SBATCH --account=hkf6
+#SBATCH --partition=booster
+#SBATCH --nodes={c.nodes}
+#SBATCH --ntasks={c.tasks}
+# Counted per node
+#SBATCH --gres=gpu:{c.gpus_per_node}
+#SBATCH --time=06:00:00
+#SBATCH --output=logs/strong-{label}-%A_%a.log
+#SBATCH --error=logs/strong-{label}-%A_%a.log
+#SBATCH --array=1-5
+
+SOURCE_DIR=/p/project/cellsinsilico/paulslustigebude
+OUTPUT_DIR="/p/scratch/cellsinsilico/paul/nastja-out/strong-{label}-${{SLURM_ARRAY_TASK_ID}}"
+
+echo "${{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/strong/spheroid_{c.nodes:02}.json" \\
+  -o "${{OUTPUT_DIR}}"
+"""
+
+    with open(f"batch/measurements/strong/strong-{label}", "w", encoding="utf8") as batch_config_file:
+        batch_config_file.write(batch_config)

experiments/templates/spheroid.json

@@ -0,0 +1,116 @@
+{
+    "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": [4, 4, 3],
+        "blocksize": [100, 100, 134]
+    },
+    "Settings": {
+        "randomseed": 0,
+        "timesteps": 100
+    },
+    "WriteActions": ["CellInfo"],
+    "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": "config_filling_1.json"
+}