A Parallel Mesh-Adaptive Framework for Hyperbolic Conservation Laws

We report on the development of a computational framework for the parallel, mesh-adaptive solution of systems of hyperbolic conservation laws like the time-dependent Euler equations in compressible gas dynamics or Magneto-Hydrodynamics (MHD) and similar models in plasma physics. Local mesh refinement is realized by the recursive bisection of grid blocks along each spatial dimension, implemented numerical schemes include standard finite-differences as well as shock-capturing central schemes, both in connection with Runge-Kutta type integrators. Parallel execution is achieved through a configurable hybrid of POSIX-multi-threading and MPI-distribution with dynamic load balancing. One- two- and three-dimensional test computations for the Euler equations have been carried out and show good parallel scaling behavior. The Racoon framework is currently used to study the formation of singularities in plasmas and fluids.Comment: late submissio

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

Efficient Irregular Wavefront Propagation Algorithms on Hybrid CPU-GPU Machines

In this paper, we address the problem of efficient execution of a computation pattern, referred to here as the irregular wavefront propagation pattern (IWPP), on hybrid systems with multiple CPUs and GPUs. The IWPP is common in several image processing operations. In the IWPP, data elements in the wavefront propagate waves to their neighboring elements on a grid if a propagation condition is satisfied. Elements receiving the propagated waves become part of the wavefront. This pattern results in irregular data accesses and computations. We develop and evaluate strategies for efficient computation and propagation of wavefronts using a multi-level queue structure. This queue structure improves the utilization of fast memories in a GPU and reduces synchronization overheads. We also develop a tile-based parallelization strategy to support execution on multiple CPUs and GPUs. We evaluate our approaches on a state-of-the-art GPU accelerated machine (equipped with 3 GPUs and 2 multicore CPUs) using the IWPP implementations of two widely used image processing operations: morphological reconstruction and euclidean distance transform. Our results show significant performance improvements on GPUs. The use of multiple CPUs and GPUs cooperatively attains speedups of 50x and 85x with respect to single core CPU executions for morphological reconstruction and euclidean distance transform, respectively.Comment: 37 pages, 16 figure

An Efficient OpenMP Loop Scheduler for Irregular Applications on Large-Scale NUMA Machines

International audienceNowadays shared memory HPC platforms expose a large number of cores organized in a hierarchical way. Parallel application programmers strug- gle to express more and more fine-grain parallelism and to ensure locality on such NUMA platforms. Independent loops stand as a natural source of paral- lelism. Parallel environments like OpenMP provide ways of parallelizing them efficiently, but the achieved performance is closely related to the choice of pa- rameters like the granularity of work or the loop scheduler. Considering that both can depend on the target computer, the input data and the loop workload, the application programmer most of the time fails at designing both portable and ef- ficient implementations. We propose in this paper a new OpenMP loop scheduler, called adaptive, that dynamically adapts the granularity of work considering the underlying system state. Our scheduler is able to perform dynamic load balancing while taking memory affinity into account on NUMA architectures. Results show that adaptive outperforms state-of-the-art OpenMP loop schedulers on memory- bound irregular applications, while obtaining performance comparable to static on parallel loops with a regular workload

Unleashing Fine-Grained Parallelism on Embedded Many-Core Accelerators with Lightweight OpenMP Tasking

In recent years, programmable many-core accelerators (PMCAs) have been introduced in embedded systems to satisfy stringent performance/Watt requirements. This has increased the urge for programming models capable of effectively leveraging hundreds to thousands of processors. Task-based parallelism has the potential to provide such capabilities, offering high-level abstractions to outline abundant and irregular parallelism in embedded applications. However, efficiently supporting this programming paradigm on embedded PMCAs is challenging, due to the large time and space overheads it introduces. In this paper we describe a lightweight OpenMP tasking runtime environment (RTE) design for a state-of-the-art embedded PMCA, the Kalray MPPA 256. We provide an exhaustive characterization of the costs of our RTE, considering both synthetic workload and real programs, and we compare to several other tasking RTEs. Experimental results confirm that our solution achieves near-ideal parallelization speedups for tasks as small as 5K cycles, and an average speedup of 12 × for real benchmarks, which is 60% higher than what we observe with the original Kalray OpenMP implementation

RELEASE: A High-level Paradigm for Reliable Large-scale Server Software

Erlang is a functional language with a much-emulated model for building reliable distributed systems. This paper outlines the RELEASE project, and describes the progress in the first six months. The project aim is to scale the Erlang’s radical concurrency-oriented programming paradigm to build reliable general-purpose software, such as server-based systems, on massively parallel machines. Currently Erlang has inherently scalable computation and reliability models, but in practice scalability is constrained by aspects of the language and virtual machine. We are working at three levels to address these challenges: evolving the Erlang virtual machine so that it can work effectively on large scale multicore systems; evolving the language to Scalable Distributed (SD) Erlang; developing a scalable Erlang infrastructure to integrate multiple, heterogeneous clusters. We are also developing state of the art tools that allow programmers to understand the behaviour of massively parallel SD Erlang programs. We will demonstrate the effectiveness of the RELEASE approach using demonstrators and two large case studies on a Blue Gene

RELEASE: A High-level Paradigm for Reliable Large-scale Server Software

Erlang is a functional language with a much-emulated model for building reliable distributed systems. This paper outlines the RELEASE project, and describes the progress in the rst six months. The project aim is to scale the Erlang's radical concurrency-oriented programming paradigm to build reliable general-purpose software, such as server-based systems, on massively parallel machines. Currently Erlang has inherently scalable computation and reliability models, but in practice scalability is constrained by aspects of the language and virtual machine. We are working at three levels to address these challenges: evolving the Erlang virtual machine so that it can work effectively on large scale multicore systems; evolving the language to Scalable Distributed (SD) Erlang; developing a scalable Erlang infrastructure to integrate multiple, heterogeneous clusters. We are also developing state of the art tools that allow programmers to understand the behaviour of massively parallel SD Erlang programs. We will demonstrate the e ectiveness of the RELEASE approach using demonstrators and two large case studies on a Blue Gene

Preparing sparse solvers for exascale computing.

Sparse solvers provide essential functionality for a wide variety of scientific applications. Highly parallel sparse solvers are essential for continuing advances in high-fidelity, multi-physics and multi-scale simulations, especially as we target exascale platforms. This paper describes the challenges, strategies and progress of the US Department of Energy Exascale Computing project towards providing sparse solvers for exascale computing platforms. We address the demands of systems with thousands of high-performance node devices where exposing concurrency, hiding latency and creating alternative algorithms become essential. The efforts described here are works in progress, highlighting current success and upcoming challenges. This article is part of a discussion meeting issue 'Numerical algorithms for high-performance computational science'