Improving the scalability of parallel N-body applications with an event driven constraint based execution model

The scalability and efficiency of graph applications are significantly constrained by conventional systems and their supporting programming models. Technology trends like multicore, manycore, and heterogeneous system architectures are introducing further challenges and possibilities for emerging application domains such as graph applications. This paper explores the space of effective parallel execution of ephemeral graphs that are dynamically generated using the Barnes-Hut algorithm to exemplify dynamic workloads. The workloads are expressed using the semantics of an Exascale computing execution model called ParalleX. For comparison, results using conventional execution model semantics are also presented. We find improved load balancing during runtime and automatic parallelism discovery improving efficiency using the advanced semantics for Exascale computing.Comment: 11 figure

Learning from the Success of MPI

The Message Passing Interface (MPI) has been extremely successful as a portable way to program high-performance parallel computers. This success has occurred in spite of the view of many that message passing is difficult and that other approaches, including automatic parallelization and directive-based parallelism, are easier to use. This paper argues that MPI has succeeded because it addresses all of the important issues in providing a parallel programming model.Comment: 12 pages, 1 figur

The Parallelism Motifs of Genomic Data Analysis

Genomic data sets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share this data with the research community, but some of these genomic data analysis problems require large scale computational platforms to meet both the memory and computational requirements. These applications differ from scientific simulations that dominate the workload on high end parallel systems today and place different requirements on programming support, software libraries, and parallel architectural design. For example, they involve irregular communication patterns such as asynchronous updates to shared data structures. We consider several problems in high performance genomics analysis, including alignment, profiling, clustering, and assembly for both single genomes and metagenomes. We identify some of the common computational patterns or motifs that help inform parallelization strategies and compare our motifs to some of the established lists, arguing that at least two key patterns, sorting and hashing, are missing

The AXIOM software layers

AXIOM project aims at developing a heterogeneous computing board (SMP-FPGA).The Software Layers developed at the AXIOM project are explained.OmpSs provides an easy way to execute heterogeneous codes in multiple cores. People and objects will soon share the same digital network for information exchange in a world named as the age of the cyber-physical systems. The general expectation is that people and systems will interact in real-time. This poses pressure onto systems design to support increasing demands on computational power, while keeping a low power envelop. Additionally, modular scaling and easy programmability are also important to ensure these systems to become widespread. The whole set of expectations impose scientific and technological challenges that need to be properly addressed.The AXIOM project (Agile, eXtensible, fast I/O Module) will research new hardware/software architectures for cyber-physical systems to meet such expectations. The technical approach aims at solving fundamental problems to enable easy programmability of heterogeneous multi-core multi-board systems. AXIOM proposes the use of the task-based OmpSs programming model, leveraging low-level communication interfaces provided by the hardware. Modular scalability will be possible thanks to a fast interconnect embedded into each module. To this aim, an innovative ARM and FPGA-based board will be designed, with enhanced capabilities for interfacing with the physical world. Its effectiveness will be demonstrated with key scenarios such as Smart Video-Surveillance and Smart Living/Home (domotics).Peer ReviewedPostprint (author's final draft

A system’s approach to cache hierarchy-aware decomposition of data-parallel computations

Dissertação para obtenção do Grau de Mestre em Engenharia InformáticaThe architecture of nowadays’ processors is very complex, comprising several computational cores and an intricate hierarchy of cache memories. The latter, in particular, differ considerably between the many processors currently available in the market, resulting in a wide variety of configurations. Application development is typically oblivious of this complexity and diversity, taking only into consideration the number of available execution cores. This oblivion prevents such applications from fully harnessing the computing power available in these architectures. This problem has been recognized by the community, which has proposed languages and models to express and tune applications according to the underlying machine’s hierarchy. These, however, lack the desired abstraction level, forcing the programmer to have deep knowledge of computer architecture and parallel programming, in order to ensure performance portability across a wide range of architectures. Realizing these limitations, the goal of this thesis is to delegate these hierarchy-aware optimizations to the runtime system. Accordingly, the programmer’s responsibilities are confined to the definition of procedures for decomposing an application’s domain, into an arbitrary number of partitions. With this, the programmer has only to reason about the application’s data representation and manipulation. We prototyped our proposal on top of a Java parallel programming framework, and evaluated it from a performance perspective, against cache neglectful domain decompositions. The results demonstrate that our optimizations deliver significant speedups against decomposition strategies based solely on the number of execution cores, without requiring the programmer to reason about the machine’s hardware. These facts allow us to conclude that it is possible to obtain performance gains by transferring hierarchyaware optimizations concerns to the runtime system

Using shared-data localization to reduce the cost of inspector-execution in unified-parallel-C programs

Programs written in the Unified Parallel C (UPC) language can access any location of the entire local and remote address space via read/write operations. However, UPC programs that contain fine-grained shared accesses can exhibit performance degradation. One solution is to use the inspector-executor technique to coalesce fine-grained shared accesses to larger remote access operations. A straightforward implementation of the inspector executor transformation results in excessive instrumentation that hinders performance.; This paper addresses this issue and introduces various techniques that aim at reducing the generated instrumentation code: a shared-data localization transformation based on Constant-Stride Linear Memory Descriptors (CSLMADs) [S. Aarseth, Gravitational N-Body Simulations: Tools and Algorithms, Cambridge Monographs on Mathematical Physics, Cambridge University Press, 2003.], the inlining of data locality checks and the usage of an index vector to aggregate the data. Finally, the paper introduces a lightweight loop code motion transformation to privatize shared scalars that were propagated through the loop body.; A performance evaluation, using up to 2048 cores of a POWER 775, explores the impact of each optimization and characterizes the overheads of UPC programs. It also shows that the presented optimizations increase performance of UPC programs up to 1.8 x their UPC hand-optimized counterpart for applications with regular accesses and up to 6.3 x for applications with irregular accesses.Peer ReviewedPostprint (author's final draft

Late allocation and early release of physical registers

The register file is one of the critical components of current processors in terms of access time and power consumption. Among other things, the potential to exploit instruction-level parallelism is closely related to the size and number of ports of the register file. In conventional register renaming schemes, both register allocation and releasing are conservatively done, the former at the rename stage, before registers are loaded with values, and the latter at the commit stage of the instruction redefining the same register, once registers are not used any more. We introduce VP-LAER, a renaming scheme that allocates registers later and releases them earlier than conventional schemes. Specifically, physical registers are allocated at the end of the execution stage and released as soon as the processor realizes that there will be no further use of them. VP-LAER enhances register utilization, that is, the fraction of allocated registers having a value to be read in the future. Detailed cycle-level simulations show either a significant speedup for a given register file size or a reduction in the register file size for a given performance level, especially for floating-point codes, where the register file pressure is usually high.Peer ReviewedPostprint (published version

Towards a Parallel Hierarchical Adaptive Solver Tool

International audienceConstraint satisfaction and combinatorial optimization problems , even when modeled with efficient metaheurisics such as local search remain computationally very intensive. Solvers stand to benefit significantly from execution on parallel systems, which are increasingly available. The architectural diversity and complexity of the latter means that these systems pose ever greater challenges in order to be effectively used, both from the point of view of the modeling effort and from that of the degree of coverage of the available computing resources. In this article we discuss impositions and design issues for a framework to make efficient use of various parallel architectures

Topology-Aware and Dependence-Aware Scheduling and Memory Allocation for Task-Parallel Languages

International audienceWe present a joint scheduling and memory allocation algorithm for efficient execution of task-parallel programs on non-uniform memory architecture (NUMA) systems. Task and data placement decisions are based on a static description of the memory hierarchy and on runtime information about intertask communication. Existing locality-aware scheduling strategies for fine-grained tasks have strong limitations: they are specific to some class of machines or applications, they do not handle task dependences, they require manual program annotations, or they rely on fragile profiling schemes. By contrast, our solution makes no assumption on the structure of programs or on the layout of data in memory. Experimental results, based on the OpenStream language, show that locality of accesses to main memory of scientific applications can be increased significantly on a 64-core machine, resulting in a speedup of up to 1.63× compared to a state-of-the-art work-stealing scheduler