EpochSims

EpochSims is a helper tool for job submission and data analysis on High Performance Computing (HPC) systems, specifically designed for the epoch, particle-in-cell code plasma physics simulations.

Folder Structure

configs: used to define environment variables and experiment configurations.
decks: contains input decks. Each subdirectory within decks corresponds to a different experiment. Within these subdirectories, you will find decks with slight variations.
analysis: Contains animation and your jupyter notebook. It is not synced by git.

Usage

Initial configuration

Change environment variables in configs/base_config.py

Submit running job

Add a new experiment configuration to configs/metadata.json
Create a subdirectory <experiment_name> within decks
Write a deck file <deck_name>.deck under decks/<experiment_name> directory

Submit the job using submit_job.py

python submit_job.py -e <experiment_name> -d <deck_name> -n <num_nodes> -t <num_tasks_per_node> -l <time_limit>

Run post processing job

2D simulation

Default quantities and plotting parameters associated with them quantities are defined in animate_2d.py and configs/metadata.py. Change them if you want

Run animation jobs using animate_2d.py

python animate_2d.py <sim_id_1> <sim_id_2> ...

It is recommended to encapsulate it with a slurm script and submit using sbatch

#!/bin/bash
#SBATCH --time=01:00:00
#SBATCH --nodes=1 --ntasks-per-node=40
#SBATCH --job-name=animate_2d
#SBATCH --account=PAS0035
#SBATCH --output=/users/PAS2137/wang15032/EpochSims/temp/animate_2d_%j.out
#PBS -m abe


python animate_2d.py 1e21_on_target_w_preplasma_20240521 1e21_off_target_w_preplasma_20240521 5e21_on_target_w_preplasma_20240521 5e21_off_target_w_preplasma_20240521

Use sbatch to submit it

sbatch <path_to_your_job>