A portable platform for accelerated PIC codes and its application to GPUs using OpenACC

We present a portable platform, called PIC_ENGINE, for accelerating Particle-In-Cell (PIC) codes on heterogeneous many-core architectures such as Graphic Processing Units (GPUs). The aim of this development is efficient simulations on future exascale systems by allowing different parallelization strategies depending on the application problem and the specific architecture. To this end, this platform contains the basic steps of the PIC algorithm and has been designed as a test bed for different algorithmic options and data structures. Among the architectures that this engine can explore, particular attention is given here to systems equipped with GPUs. The study demonstrates that our portable PIC implementation based on the OpenACC programming model can achieve performance closely matching theoretical predictions. Using the Cray XC30 system, Piz Daint, at the Swiss National Supercomputing Centre (CSCS), we show that PIC_ENGINE running on an NVIDIA Kepler K20X GPU can outperform the one on an Intel Sandybridge 8-core CPU by a factor of 3.4

Efficiency of linked cell algorithms

The linked cell list algorithm is an essential part of molecular simulation software, both molecular dynamics and Monte Carlo. Though it scales linearly with the number of particles, there has been a constant interest in increasing its efficiency, because a large part of CPU time is spent to identify the interacting particles. Several recent publications proposed improvements to the algorithm and investigated their efficiency by applying them to particular setups. In this publication we develop a general method to evaluate the efficiency of these algorithms, which is mostly independent of the parameters of the simulation, and test it for a number of linked cell list algorithms. We also propose a combination of linked cell reordering and interaction sorting that shows a good efficiency for a broad range of simulation setups.Comment: Submitted to Computer Physics Communications on 22 December 2009, still awaiting a referee repor

Platform Dependent Verification: On Engineering Verification Tools for 21st Century

The paper overviews recent developments in platform-dependent explicit-state LTL model checking.Comment: In Proceedings PDMC 2011, arXiv:1111.006

Even faster sorting of (not only) integers

In this paper we introduce RADULS2, the fastest parallel sorter based on radix algorithm. It is optimized to process huge amounts of data making use of modern multicore CPUs. The main novelties include: extremely optimized algorithm for handling tiny arrays (up to about a hundred of records) that could appear even billions times as subproblems to handle and improved processing of larger subarrays with better use of non-temporal memory stores

Defining Asymptotic Parallel Time Complexity of Data-dependent Algorithms

The scientific research community has reached a stage of maturity where its strong need for high-performance computing has diffused into also everyday life of engineering and industry algorithms. In efforts to satisfy this need, parallel computers provide an efficient and economical way to solve large-scale and/or time-constrained problems. As a consequence, the end-users of these systems have a vested interest in defining the asymptotic time complexity of parallel algorithms to predict their performance on a particular parallel computer. The asymptotic parallel time complexity of data-dependent algorithms depends on the number of processors, data size, and other parameters. Discovering the main other parameters is a challenging problem and the clue in obtaining a good estimate of performance order. Great examples of these types of applications are sorting algorithms, searching algorithms and solvers of the traveling salesman problem (TSP). This article encompasses all the knowledge discovery aspects to the problem of defining the asymptotic parallel time complexity of datadependent algorithms. The knowledge discovery methodology begins by designing a considerable number of experiments and measuring their execution times. Then, an interactive and iterative process explores data in search of patterns and/or relationships detecting some parameters that affect performance. Knowing the key parameters which characterise time complexity, it becomes possible to hypothesise to restart the process and to produce a subsequent improved time complexity model. Finally, the methodology predicts the performance order for new data sets on a particular parallel computer by replacing a numerical identification. As a case of study, a global pruning traveling salesman problem implementation (GP-TSP) has been chosen to analyze the influence of indeterminism in performance prediction of data-dependent parallel algorithms, and also to show the usefulness of the defined knowledge discovery methodology. The subsequent hypotheses generated to define the asymptotic parallel time complexity of the TSP were corroborated one by one. The experimental results confirm the expected capability of the proposed methodology; the predictions of performance time order were rather good comparing with real execution time (in the order of 85%)