Distributed-Memory Breadth-First Search on Massive Graphs

This chapter studies the problem of traversing large graphs using the breadth-first search order on distributed-memory supercomputers. We consider both the traditional level-synchronous top-down algorithm as well as the recently discovered direction optimizing algorithm. We analyze the performance and scalability trade-offs in using different local data structures such as CSR and DCSC, enabling in-node multithreading, and graph decompositions such as 1D and 2D decomposition.Comment: arXiv admin note: text overlap with arXiv:1104.451

Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS

GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest supercomputers in the world. Here, we describe some of the ways we have been able to realize this through the use of parallelization on all levels, combined with a constant focus on absolute performance. Release 4.6 of GROMACS uses SIMD acceleration on a wide range of architectures, GPU offloading acceleration, and both OpenMP and MPI parallelism within and between nodes, respectively. The recent work on acceleration made it necessary to revisit the fundamental algorithms of molecular simulation, including the concept of neighborsearching, and we discuss the present and future challenges we see for exascale simulation - in particular a very fine-grained task parallelism. We also discuss the software management, code peer review and continuous integration testing required for a project of this complexity.Comment: EASC 2014 conference proceedin

Managing Communication Latency-Hiding at Runtime for Parallel Programming Languages and Libraries

This work introduces a runtime model for managing communication with support for latency-hiding. The model enables non-computer science researchers to exploit communication latency-hiding techniques seamlessly. For compiled languages, it is often possible to create efficient schedules for communication, but this is not the case for interpreted languages. By maintaining data dependencies between scheduled operations, it is possible to aggressively initiate communication and lazily evaluate tasks to allow maximal time for the communication to finish before entering a wait state. We implement a heuristic of this model in DistNumPy, an auto-parallelizing version of numerical Python that allows sequential NumPy programs to run on distributed memory architectures. Furthermore, we present performance comparisons for eight benchmarks with and without automatic latency-hiding. The results shows that our model reduces the time spent on waiting for communication as much as 27 times, from a maximum of 54% to only 2% of the total execution time, in a stencil application.Comment: PREPRIN

HERO: Heterogeneous Embedded Research Platform for Exploring RISC-V Manycore Accelerators on FPGA

Heterogeneous embedded systems on chip (HESoCs) co-integrate a standard host processor with programmable manycore accelerators (PMCAs) to combine general-purpose computing with domain-specific, efficient processing capabilities. While leading companies successfully advance their HESoC products, research lags behind due to the challenges of building a prototyping platform that unites an industry-standard host processor with an open research PMCA architecture. In this work we introduce HERO, an FPGA-based research platform that combines a PMCA composed of clusters of RISC-V cores, implemented as soft cores on an FPGA fabric, with a hard ARM Cortex-A multicore host processor. The PMCA architecture mapped on the FPGA is silicon-proven, scalable, configurable, and fully modifiable. HERO includes a complete software stack that consists of a heterogeneous cross-compilation toolchain with support for OpenMP accelerator programming, a Linux driver, and runtime libraries for both host and PMCA. HERO is designed to facilitate rapid exploration on all software and hardware layers: run-time behavior can be accurately analyzed by tracing events, and modifications can be validated through fully automated hard ware and software builds and executed tests. We demonstrate the usefulness of HERO by means of case studies from our research