From c7d4a50a851cf78536bf8d0a0306362296b73b55 Mon Sep 17 00:00:00 2001 From: Paul Brinkmeier Date: Wed, 13 Dec 2023 14:07:12 +0100 Subject: [PATCH] Add new batch files --- experiments/batch/build-cuda | 4 +- experiments/batch/build-nocuda | 4 +- experiments/batch/cuda | 32 ++++++++ experiments/batch/nocuda | 4 +- experiments/batch/nocuda-noecm | 26 ++++++ experiments/configs/genesis-noecm.json | 109 +++++++++++++++++++++++++ 6 files changed, 173 insertions(+), 6 deletions(-) create mode 100644 experiments/batch/cuda create mode 100644 experiments/batch/nocuda-noecm create mode 100644 experiments/configs/genesis-noecm.json diff --git a/experiments/batch/build-cuda b/experiments/batch/build-cuda index a178f3a..3b2f6cd 100644 --- a/experiments/batch/build-cuda +++ b/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 diff --git a/experiments/batch/build-nocuda b/experiments/batch/build-nocuda index 67ed26b..14158c5 100644 --- a/experiments/batch/build-nocuda +++ b/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 diff --git a/experiments/batch/cuda b/experiments/batch/cuda new file mode 100644 index 0000000..f404a30 --- /dev/null +++ b/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 "${OUTPUT_DIR}" diff --git a/experiments/batch/nocuda b/experiments/batch/nocuda index 882a0ed..0f35e8a 100644 --- a/experiments/batch/nocuda +++ b/experiments/batch/nocuda @@ -12,8 +12,8 @@ #SBATCH --ntasks-per-node=16 #SBATCH --cpus-per-task=1 #SBATCH --time=01:00:00 -#SBATCH --output=nocuda-%j.out -#SBATCH --error=nocuda-%j.err +#SBATCH --output=logs/nocuda-%j.log +#SBATCH --error=logs/nocuda-%j.log SOURCE_DIR=/p/project/cellsinsilico/paulslustigebude OUTPUT_DIR=/p/scratch/cellsinsilico/paul/nastja-out/nocuda diff --git a/experiments/batch/nocuda-noecm b/experiments/batch/nocuda-noecm new file mode 100644 index 0000000..055b128 --- /dev/null +++ b/experiments/batch/nocuda-noecm @@ -0,0 +1,26 @@ +#!/usr/bin/env bash + +#SBATCH --job-name=nocuda-noecm +# Forschergruppe Schug +#SBATCH --account=hkf6 +# 48 Cores, 512GiB RAM, 4x NVIDIA A100 GPUs +#SBATCH --partition=booster +# Right now we're using a single node +#SBATCH --nodes=1 +# Number of MPI processes +# TODO: Change the config and set to this the maximum of 48 +#SBATCH --ntasks-per-node=16 +#SBATCH --cpus-per-task=1 +#SBATCH --time=01:00:00 +#SBATCH --output=logs/nocuda-noecm-%j.log +#SBATCH --error=logs/nocuda-noecm-%j.log + +SOURCE_DIR=/p/project/cellsinsilico/paulslustigebude +OUTPUT_DIR=/p/scratch/cellsinsilico/paul/nastja-out/nocuda-noecm + +mkdir -p "${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}" diff --git a/experiments/configs/genesis-noecm.json b/experiments/configs/genesis-noecm.json new file mode 100644 index 0000000..4b2e542 --- /dev/null +++ b/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"] +}