puffin¶

Summary

Source: https://github.com/UKFELs/Puffin

Path: /software/puffin/<version>/

Documentation: https://github.com/UKFELs/Puffin/blob/master/doc/manual.pdf (2018)

Citations: LT Campbell and BWJ McNeil, Physics of Plasmas 19, 093119 (2012) IPAC 2018

Puffin (Parallel Unaveraged Fel INtegrator) simulates a Free Electron Laser (FEL). Puffin is a massively parallel numerical solver for an unaveraged, 3D FEL system of equations, and is written in Fortran 90, using MPI and OpenMP.

Using puffin¶

Simply load the corresponding module:

module load maxwell puffin
which puffin
   /software/puffin/1.9.0.2/bin/puffin 

# the module also defines some environment variables to simplify the commands. Simply unset if disturbing:
OMPI_MCA_pml=ucx
OMPI_MCA_opal_warn_on_missing_libcuda=0
UCX_LOG_LEVEL=error

Running puffin batch-jobs on Maxwell¶

puffin is a hybrid OPENMP/MPI application. As it turns out, performance is best when using a small number of MPI processes (4) in favor of OPENMP threads.

A sample batch script:

#!/bin/bash 
#SBATCH --partition=upex
#SBATCH --time=4-00:00:00
#SBATCH --nodes=4
#SBATCH --constraint='[7542|Gold-6140|Gold-6240]'
#SBATCH --output=puffin-%j.out
#SBATCH --job-name=puffin
unset LD_PRELOAD
source /etc/profile.d/modules.sh

module load maxwell puffin

mpirun -N 4 puffin puffin.in