Running EPOCH

Locally

1. git clone --recursive https://github.com/Warwick-Plasma/epoch.git
2. Install libraries
   1. (ON MAC) brew install open-mpi
   2. (LINUX) sudo apt install gfortran openmpi-bin openmpi-common libopenmpi-dev libgtk2.0-dev
3. Open one of the epoch folders
4. Modify the Makefile to do have the correct flags using gedit Makefile
5. Run command to compile: make COMPILER=gfortran MPIF90=mpif90 -j4
6. Copy over the wanted deck from the /epochxd/example_decks to a new folder with the deck inside renamed to input.deck
7. Finally run the simulation using mpirun -n 8 ./bin/epoch1d <<< /path/to/deck
8. To review *.sdf files there are two options:
   1. (Recommended) Install sdf_xarray: See https://github.com/PlasmaFAIR/sdf-xarray
   2. Building sdf_helper: Run pip install numpy matplotlib and setup tools

On Viking

1. cd scratch
2. git clone --recursive https://github.com/Warwick-Plasma/epoch.git
3. cd epoch/epoch2d
4. nano Makefile
5. [OPTIONAL] Remove the # at the start of the #DEFINES += $(D)PHOTONS for QED
6. module load OpenMPI/3.1.3-GCC-8.2.0-2.31.1
7. make COMPILER=gfortran --debug -j4
8. Create a new simulation folder for epoch mkdir test1
9. Copy an existing deck file over (e.g. example_decks/qed_rese.deck) cp example_decks/qed_rese.deck test1/input.deck. NOTE: deck must always be called input.deck
10. Navigate to the ~/scratch directory and create a jobscript using nano jobscript.sh and copy in the bash script attached at the bottom of this file. NOTE: Please change the user.email to be your normal username
11. Finally run sbatch jobscript.sh and wait for completion

#!/usr/bin/env bash

#SBATCH --job-name=muon_test_1
#SBATCH --ntasks=96
#SBATCH --partition=nodes
#SBATCH --time=02-00:00:00 # Time limit (DD-HH:MM:SS)
#SBATCH --account=pet-pic-2022
#SBATCH --output=%x-%j.log
#SBATCH [email protected]
#SBATCH --mail-type=ALL # Mail events (NONE, BEGIN, END, FAIL, ALL)

# Abort if any command fails
set -e

# Purge any previously loaded modules
module purge

# Load modules
module load OpenMPI/3.1.3-GCC-8.2.0-2.31.1

# Prestart
cd epoch/epoch2d
echo Working directory: `pwd`
echo Running job on host:
echo -e '\t'`hostname` at `date`'\n'

# Script initialisation
srun ~/scratch/epoch/epoch2d/bin/epoch2d <<< ~/scratch/epoch/epoch2d/test1

# Job completed
echo '\n'Job completed at `date`