Accelerating NBODY6 with Graphics Processing Units

We describe the use of Graphics Processing Units (GPUs) for speeding up the code NBODY6 which is widely used for direct $N$-body simulations. Over the years, the $N^2$ nature of the direct force calculation has proved a barrier for extending the particle number. Following an early introduction of force polynomials and individual time-steps, the calculation cost was first reduced by the introduction of a neighbour scheme. After a decade of GRAPE computers which speeded up the force calculation further, we are now in the era of GPUs where relatively small hardware systems are highly cost-effective. A significant gain in efficiency is achieved by employing the GPU to obtain the so-called regular force which typically involves some 99 percent of the particles, while the remaining local forces are evaluated on the host. However, the latter operation is performed up to 20 times more frequently and may still account for a significant cost. This effort is reduced by parallel SSE/AVX procedures where each interaction term is calculated using mainly single precision. We also discuss further strategies connected with coordinate and velocity prediction required by the integration scheme. This leaves hard binaries and multiple close encounters which are treated by several regularization methods. The present nbody6-GPU code is well balanced for simulations in the particle range $10^4-2 \times 10^5$ for a dual GPU system attached to a standard PC.Comment: 8 pages, 3 figures, 2 tables, MNRAS accepte

GLB: Lifeline-based Global Load Balancing library in X10

We present GLB, a programming model and an associated implementation that can handle a wide range of irregular paral- lel programming problems running over large-scale distributed systems. GLB is applicable both to problems that are easily load-balanced via static scheduling and to problems that are hard to statically load balance. GLB hides the intricate syn- chronizations (e.g., inter-node communication, initialization and startup, load balancing, termination and result collection) from the users. GLB internally uses a version of the lifeline graph based work-stealing algorithm proposed by Saraswat et al. Users of GLB are simply required to write several pieces of sequential code that comply with the GLB interface. GLB then schedules and orchestrates the parallel execution of the code correctly and efficiently at scale. We have applied GLB to two representative benchmarks: Betweenness Centrality (BC) and Unbalanced Tree Search (UTS). Among them, BC can be statically load-balanced whereas UTS cannot. In either case, GLB scales well-- achieving nearly linear speedup on different computer architectures (Power, Blue Gene/Q, and K) -- up to 16K cores

Performance Characterization of Multi-threaded Graph Processing Applications on Intel Many-Integrated-Core Architecture

Intel Xeon Phi many-integrated-core (MIC) architectures usher in a new era of terascale integration. Among emerging killer applications, parallel graph processing has been a critical technique to analyze connected data. In this paper, we empirically evaluate various computing platforms including an Intel Xeon E5 CPU, a Nvidia Geforce GTX1070 GPU and an Xeon Phi 7210 processor codenamed Knights Landing (KNL) in the domain of parallel graph processing. We show that the KNL gains encouraging performance when processing graphs, so that it can become a promising solution to accelerating multi-threaded graph applications. We further characterize the impact of KNL architectural enhancements on the performance of a state-of-the art graph framework.We have four key observations: 1 Different graph applications require distinctive numbers of threads to reach the peak performance. For the same application, various datasets need even different numbers of threads to achieve the best performance. 2 Only a few graph applications benefit from the high bandwidth MCDRAM, while others favor the low latency DDR4 DRAM. 3 Vector processing units executing AVX512 SIMD instructions on KNLs are underutilized when running the state-of-the-art graph framework. 4 The sub-NUMA cache clustering mode offering the lowest local memory access latency hurts the performance of graph benchmarks that are lack of NUMA awareness. At last, We suggest future works including system auto-tuning tools and graph framework optimizations to fully exploit the potential of KNL for parallel graph processing.Comment: published as L. Jiang, L. Chen and J. Qiu, "Performance Characterization of Multi-threaded Graph Processing Applications on Many-Integrated-Core Architecture," 2018 IEEE International Symposium on Performance Analysis of Systems and Software (ISPASS), Belfast, United Kingdom, 2018, pp. 199-20

NBODY6++GPU: Ready for the gravitational million-body problem

Accurate direct $N$-body simulations help to obtain detailed information about the dynamical evolution of star clusters. They also enable comparisons with analytical models and Fokker-Planck or Monte-Carlo methods. NBODY6 is a well-known direct $N$-body code for star clusters, and NBODY6++ is the extended version designed for large particle number simulations by supercomputers. We present NBODY6++GPU, an optimized version of NBODY6++ with hybrid parallelization methods (MPI, GPU, OpenMP, and AVX/SSE) to accelerate large direct $N$-body simulations, and in particular to solve the million-body problem. We discuss the new features of the NBODY6++GPU code, benchmarks, as well as the first results from a simulation of a realistic globular cluster initially containing a million particles. For million-body simulations, NBODY6++GPU is $400-2000$ times faster than NBODY6 with 320 CPU cores and 32 NVIDIA K20X GPUs. With this computing cluster specification, the simulations of million-body globular clusters including $5\%$ primordial binaries require about an hour per half-mass crossing time.Comment: 13 pages, 9 figures, 3 table

MPI-Vector-IO: Parallel I/O and Partitioning for Geospatial Vector Data

In recent times, geospatial datasets are growing in terms of size, complexity and heterogeneity. High performance systems are needed to analyze such data to produce actionable insights in an efficient manner. For polygonal a.k.a vector datasets, operations such as I/O, data partitioning, communication, and load balancing becomes challenging in a cluster environment. In this work, we present MPI-Vector-IO 1 , a parallel I/O library that we have designed using MPI-IO specifically for partitioning and reading irregular vector data formats such as Well Known Text. It makes MPI aware of spatial data, spatial primitives and provides support for spatial data types embedded within collective computation and communication using MPI message-passing library. These abstractions along with parallel I/O support are useful for parallel Geographic Information System (GIS) application development on HPC platforms

Gunrock: GPU Graph Analytics

For large-scale graph analytics on the GPU, the irregularity of data access and control flow, and the complexity of programming GPUs, have presented two significant challenges to developing a programmable high-performance graph library. "Gunrock", our graph-processing system designed specifically for the GPU, uses a high-level, bulk-synchronous, data-centric abstraction focused on operations on a vertex or edge frontier. Gunrock achieves a balance between performance and expressiveness by coupling high performance GPU computing primitives and optimization strategies with a high-level programming model that allows programmers to quickly develop new graph primitives with small code size and minimal GPU programming knowledge. We characterize the performance of various optimization strategies and evaluate Gunrock's overall performance on different GPU architectures on a wide range of graph primitives that span from traversal-based algorithms and ranking algorithms, to triangle counting and bipartite-graph-based algorithms. The results show that on a single GPU, Gunrock has on average at least an order of magnitude speedup over Boost and PowerGraph, comparable performance to the fastest GPU hardwired primitives and CPU shared-memory graph libraries such as Ligra and Galois, and better performance than any other GPU high-level graph library.Comment: 52 pages, invited paper to ACM Transactions on Parallel Computing (TOPC), an extended version of PPoPP'16 paper "Gunrock: A High-Performance Graph Processing Library on the GPU

Taking advantage of hybrid systems for sparse direct solvers via task-based runtimes

The ongoing hardware evolution exhibits an escalation in the number, as well as in the heterogeneity, of computing resources. The pressure to maintain reasonable levels of performance and portability forces application developers to leave the traditional programming paradigms and explore alternative solutions. PaStiX is a parallel sparse direct solver, based on a dynamic scheduler for modern hierarchical manycore architectures. In this paper, we study the benefits and limits of replacing the highly specialized internal scheduler of the PaStiX solver with two generic runtime systems: PaRSEC and StarPU. The tasks graph of the factorization step is made available to the two runtimes, providing them the opportunity to process and optimize its traversal in order to maximize the algorithm efficiency for the targeted hardware platform. A comparative study of the performance of the PaStiX solver on top of its native internal scheduler, PaRSEC, and StarPU frameworks, on different execution environments, is performed. The analysis highlights that these generic task-based runtimes achieve comparable results to the application-optimized embedded scheduler on homogeneous platforms. Furthermore, they are able to significantly speed up the solver on heterogeneous environments by taking advantage of the accelerators while hiding the complexity of their efficient manipulation from the programmer.Comment: Heterogeneity in Computing Workshop (2014