Add single block configs
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31
experiments/batch/cuda-singleblock
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31
experiments/batch/cuda-singleblock
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#!/usr/bin/env bash
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#SBATCH --job-name=cuda-singleblock
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# Forschergruppe Schug
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#SBATCH --account=hkf6
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# 48 Cores, 512GiB RAM, 4x NVIDIA A100 GPUs
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#SBATCH --partition=booster
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# Right now we're using a single node
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#SBATCH --nodes=1
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# Number of MPI processes
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#SBATCH --ntasks=1
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#SBATCH --cpus-per-task=1
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# For now, we are using a single GPU only
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#SBATCH --gres=gpu:1
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#SBATCH --time=01:00:00
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#SBATCH --output=logs/cuda-singleblock-%j.log
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#SBATCH --error=logs/cuda-singleblock-%j.log
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SOURCE_DIR=/p/project/cellsinsilico/paulslustigebude
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OUTPUT_DIR=/p/scratch/cellsinsilico/paul/nastja-out/cuda-singleblock
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mkdir -p "${OUTPUT_DIR}"
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source "${SOURCE_DIR}/activate-nastja-modules"
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# This is actually the default behavior for a single task anyways
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# However I'm leaving this here for documentation reasons
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export CUDA_VISIBLE_DEVICES=0
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srun "${SOURCE_DIR}/nastja/build-cuda/nastja" \
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-c "${SOURCE_DIR}/ma/experiments/configs/genesis-singleblock.json" \
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-o "${OUTPUT_DIR}"
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29
experiments/batch/ecm-debug
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29
experiments/batch/ecm-debug
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#!/usr/bin/env bash
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#SBATCH --job-name=ecm-debug
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# Forschergruppe Schug
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#SBATCH --account=hkf6
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# 48 Cores, 512GiB RAM, 4x NVIDIA A100 GPUs
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#SBATCH --partition=booster
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#SBATCH --nodes=1
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#SBATCH --ntasks=1
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#SBATCH --cpus-per-task=1
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# For now, we are using a single GPU only
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#SBATCH --gres=gpu:1
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#SBATCH --time=00:10:00
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#SBATCH --output=logs/ecm-debug-%j.log
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#SBATCH --error=logs/ecm-debug-%j.log
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SOURCE_DIR=/p/project/cellsinsilico/paulslustigebude
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OUTPUT_DIR=/p/scratch/cellsinsilico/paul/nastja-out/ecm-debug
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mkdir -p "${OUTPUT_DIR}"
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source "${SOURCE_DIR}/activate-nastja-modules"
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# This is actually the default behavior for a single task anyways
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# However I'm leaving this here for documentation reasons
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export CUDA_VISIBLE_DEVICES=0
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srun "${SOURCE_DIR}/nastja/build-cuda/nastja" \
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-c "${SOURCE_DIR}/ma/experiments/configs/ecm-debug.json" \
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-o "${OUTPUT_DIR}"
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26
experiments/batch/nocuda-singleblock
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26
experiments/batch/nocuda-singleblock
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#!/usr/bin/env bash
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#SBATCH --job-name=nocuda-singleblock
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# Forschergruppe Schug
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#SBATCH --account=hkf6
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# 48 Cores, 512GiB RAM, 4x NVIDIA A100 GPUs
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#SBATCH --partition=booster
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# Right now we're using a single node
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#SBATCH --nodes=1
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# Number of MPI processes
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#SBATCH --ntasks=1
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#SBATCH --cpus-per-task=1
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# For now, we are using a single GPU only
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#SBATCH --time=01:00:00
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#SBATCH --output=logs/nocuda-singleblock-%j.log
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#SBATCH --error=logs/nocuda-singleblock-%j.log
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SOURCE_DIR=/p/project/cellsinsilico/paulslustigebude
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OUTPUT_DIR=/p/scratch/cellsinsilico/paul/nastja-out/nocuda-singleblock
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mkdir -p "${OUTPUT_DIR}"
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source "${SOURCE_DIR}/activate-nastja-modules"
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srun "${SOURCE_DIR}/nastja/build-nocuda/nastja" \
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-c "${SOURCE_DIR}/ma/experiments/configs/genesis-singleblock.json" \
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-o "${OUTPUT_DIR}"
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88
experiments/configs/ecm-debug.json
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88
experiments/configs/ecm-debug.json
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{
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"#Testing": {
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"description": "Just dynamic ECM for debugging"
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},
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"Application": "Cells",
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"Geometry": {
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"blocksize": [5, 5, 5],
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"blockcount": [1, 1, 1]
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},
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"Settings": {
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"timesteps": 10,
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"randomseed": 42
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},
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"Filling": {
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"cells": [
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{
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"_comment": "This is for the dynamic ECM",
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"shape": "cube",
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"box": [
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[0, 0, 0],
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[4, 4, 4]
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],
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"value": 0,
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"celltype": 0
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}
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]
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},
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"CellsInSilico": {
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"liquid": 1,
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"adhesion": {
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"matrix": [
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[0, 0, 0, 0],
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[0, 0, 0, 0],
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[0, 0, 10, 5],
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[0, 0, 5, 5]
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]
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},
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"temperature": 15,
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"volume": {
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"default": [0, 0, 7000, 1000],
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"lambda": {
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"storage": "const",
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"value": 10
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}
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},
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"surface": {
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"default": [0, 0, 2500, 1000],
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"lambda": {
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"storage": "const",
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"value": 10
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}
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},
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"checkerboard": "00",
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"energyfunctions": ["Volume00", "Surface00", "Adhesion00", "DynamicECM00"],
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"dynamicecm": {
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"enabled": true,
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"stepsPerMcs": 1,
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"pushSteps": 1,
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"pushWeight": 2,
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"ecmCellID": 0,
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"deltat": 0.1,
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"eta": 0.25,
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"k0": 0.1,
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"k1": 0.1,
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"c": 4,
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"alpha": 2,
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"d": 0.3,
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"phi": 1,
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"lambda": 50
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}
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},
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"Writers": {
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"ParallelVTK_Cells": {
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"writer": "ParallelVtkImage",
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"outputtype": "UInt32",
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"field": "cells",
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"steps": 1
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},
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"ParallelVTK_Displacement": {
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"writer": "ParallelVtkImage",
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"outputtype": "Float32",
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"field": "dynamicecm",
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"components": [0, 1, 2],
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"steps": 1
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}
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},
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"WriteActions": ["ParallelVTK_Cells", "ParallelVTK_Displacement"]
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}
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131
experiments/configs/genesis-singleblock.json
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131
experiments/configs/genesis-singleblock.json
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{
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"#Testing": {
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"description": "Cellular Potts Model with dynamic ECM"
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},
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"Application": "Cells",
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"Geometry": {
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"blocksize": [80, 80, 80],
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"blockcount": [1, 1, 1]
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},
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"Settings": {
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"timesteps": 250,
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"randomseed": 42
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},
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"Filling": {
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"cells": [
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{
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"_comment": "This is for the dynamic ECM",
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"shape": "cube",
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"box": [
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[0, 0, 0],
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[79, 79, 79]
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],
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"value": 0,
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"celltype": 0
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},
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{
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"shape": "cube",
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"box": [
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[41, 35, 10],
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[45, 39, 15]
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],
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"celltype": 2
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},
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{
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"shape": "cube",
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"box": [
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[40, 15, 14],
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[47, 22, 20]
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],
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"celltype": 2
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},
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{
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"shape": "cube",
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"box": [
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[40, 20, 20],
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[47, 27, 26]
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],
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"celltype": 3
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},
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{
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"shape": "cube",
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"box": [
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[38, 20, 60],
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[45, 27, 66]
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],
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"celltype": 3
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}
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]
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},
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"CellsInSilico": {
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"liquid": 1,
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"adhesion": {
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"matrix": [
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[0, 0, 0, 0],
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[0, 0, 0, 0],
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[0, 0, 10, 5],
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[0, 0, 5, 5]
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]
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},
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"temperature": 15,
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"volume": {
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"default": {
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"storage": "const",
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"value": 2000
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},
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"lambda": {
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"storage": "const",
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"value": 10
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}
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},
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"surface": {
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"default": {
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"storage": "const",
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"value": 800
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},
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"lambda": {
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"storage": "const",
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"value": 10
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}
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},
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"cleaner": {
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"killdistance": 100
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},
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"checkerboard": "00",
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"energyfunctions": ["Volume00", "Surface00", "Adhesion00", "DynamicECM00"],
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"centerofmass": {
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"steps": 10
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},
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"dynamicecm": {
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"enabled": true,
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"stepsPerMcs": 100,
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"pushSteps": 10,
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"pushWeight": 2,
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"ecmCellID": 0,
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"deltat": 0.1,
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"eta": 0.25,
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"k0": 0.1,
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"k1": 0.1,
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"c": 4,
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"alpha": 2,
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"d": 0.3,
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"phi": 1
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}
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},
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"Writers": {
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"ParallelVTK_Cells": {
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"writer": "ParallelVtkImage",
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"outputtype": "UInt32",
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"field": "cells",
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"steps": 1
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},
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"ParallelVTK_Displacement": {
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"writer": "ParallelVtkImage",
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"outputtype": "Float32",
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"field": "dynamicecm",
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"components": [0, 1, 2],
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"steps": 1
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}
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},
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"WriteActions": ["ParallelVTK_Cells", "ParallelVTK_Displacement"]
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}
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