Particle-in-Cell Kinetic Simulation Software Center
The first publication based on the skeleton codes recently appeared in Physics of Plasmas:
R. Scott Hughes, Joseph Wang, Viktor K. Decyk, and S. Peter Gary, “Effects of
variations in electron thermal velocity on the whistler anisotropy instability: Particle-in-
cell simulations,” Physics of Plasmas 23, 042106 (2016). DOI: 10.1063/1.4945748
This work made used of the 2D darwin code mdpic2 and studied whistler wave instabilities for solar wind parameters.
Alessandro Fanfarillo and Damian Rouson from Italy have translated the PICKSC skeleton code ppic2 to utilize Coarray Fortran. Coarray Fortran enables a programmer to write parallel programs using a Partitioned Global Address Space (PGAS) scheme. It is part of the Fortran2008 standard and provides an alternative to the dominant Message-Passing Interface (MPI) paradigm.
The code ppic2_caf is available here on the PICKSC site.
Viktor Decyk has developed fully 3D versions of skeleton PIC codes illustrating the hybrid parallel algorithmic techniques for utilizing both OpenMP and MPI. These skeleton codes have recently been benchmarked on the Edison machine at NERSC.
For the electromagnetic code on a problem size of 1024^3 grids with 27 particles/cell, one can see good scaling up to nearly 100,000 cores, nearly the entire Edison machine. There are 10 FFTs per time step, and the particle time gives about 2 psec/particle/time step at 98,304 cores.
Electrostatic, electromagnetic, and Darwin versions are available. These codes may be accessed here on the OpenMP/MPI skeleton code subpage or at our GitHub repository for skeleton codes.
PICKSC’s PIC skeleton codes will be used as a case study for a tutorial on “live programming” at SC’15 in Austin, Texas on Nov 15.
For more details see: http://sc15.supercomputing.org/schedule/event_detail?evid=tut145
Henry Gardner is co-author of an advanced textbook on design patterns in scientific programming (book home page and Amazon link).
A new video has been produced that highlights activities at The Plasma Science and Technology Institute at UCLA. This Institute consists of affiliated laboratories and research groups that investigate fundamental questions related plasmas, and it includes the research activities performed by PICKSC scientists.
The areas of study include basic plasma physics, fusion research, space plasmas, laser-plasma interactions, advanced accelerators, novel radiation sources, and plasma-materials processing. Diverse programs encompass experimentation, theory, and computer simulation.
The video may be seen here.
Ben Swift, a Research Fellow in the School of Computer Science at the Australian National University, has been working on a project looking at run-time load balancing and optimisation of scientific simulations running on parallel computing architectures. He chose PICKSC’s Skeleton Codes as a basis for studying live programming workflow.
You can watch a video here: Live programming: bringing the HPC development workflow to life
More about Ben Swift may be found on his webpage.
We are pleased to announce the availability and full release of a hierarchy of skeleton codes.
Skeleton codes are bare-bones but fully functional PIC codes containing all the crucial elements but not the diagnostics and initial conditions typical of production codes. These are sometimes also called mini-apps. We are providing a hierarchy of skeleton PIC codes, from very basic serial codes for beginning students to very sophisticated codes with 3 levels of parallelism for HPC experts. The codes are designed for high performance, but not at the expense of code obscurity. They illustrate the use of a variety of parallel programming techniques, such as MPI, OpenMP, and CUDA, in both Fortran and C. For students new to parallel processing, we also provide some Tutorial and Quickstart codes.
If you like to register to receive regular software updates, please contact us.
UCLA graduate student Peicheng Yu, current PICKSC post-doc Xinlu Xu, and collaborators have been investigating the mitigation of the numerical Cerenkov instability (NCI) which occurs when a plasma drifts near the speed of light in a PIC code. In a series of papers (references below) they have developed a general theory as well as mitigation strategies for fully spectral (FFT based) and hybrid (FFT and finite difference) solvers. Recently they published an article in Communications in Computer Physics [1] and posted a new article on the arxiv: arXiv:1502.01376 [physics.comp-ph]. If you would like more information, please contact Mr. Peicheng Yu at tpc02@ucla.edu.
Expand for References:
PICKSC member Asher Davidson has recently published an article in the Journal of Computational Physics detailing the implementation of a quasi-3D algorithm into OSIRIS. Read moreFor many plasma physics problems, three-dimensional and kinetic effects are very important. However, such simulations are very computationally intensive. Fortunately, there is a class of problems for which there is nearly azimuthal symmetry and the dominant three-dimensional physics is captured by the inclusion of only a few azimuthal harmonics. Recently, it was proposed [1] to model one such problem, laser wakefield acceleration, by expanding the fields and currents in azimuthal harmonics and truncating the expansion. The complex amplitudes of the fundamental and first harmonic for the fields were solved on an r–z grid and a procedure for calculating the complex current amplitudes for each particle based on its motion in Cartesian geometry was presented using a Marder’s correction to maintain the validity of Gauss’s law. In this paper, we describe an implementation of this algorithm into OSIRIS using a rigorous charge conserving current deposition method to maintain the validity of Gauss’s law. We show that this algorithm is a hybrid method which uses a particles-in-cell description in r–z and a gridless description in ϕ. We include the ability to keep an arbitrary number of harmonics and higher order particle shapes. Examples for laser wakefield acceleration, plasma wakefield acceleration, and beam loading are also presented and directions for future work are discussed.