An FPGA implementation of an investigative many-core processor, Fynbos : in support of a Fortran autoparallelising software pipeline

Includes bibliographical references.In light of the power, memory, ILP, and utilisation walls facing the computing industry, this work examines the hypothetical many-core approach to finding greater compute performance and efficiency. In order to achieve greater efficiency in an environment in which Moore’s law continues but TDP has been capped, a means of deriving performance from dark and dim silicon is needed. The many-core hypothesis is one approach to exploiting these available transistors efficiently. As understood in this work, it involves trading in hardware control complexity for hundreds to thousands of parallel simple processing elements, and operating at a clock speed sufficiently low as to allow the efficiency gains of near threshold voltage operation. Performance is there- fore dependant on exploiting a new degree of fine-grained parallelism such as is currently only found in GPGPUs, but in a manner that is not as restrictive in application domain range. While removing the complex control hardware of traditional CPUs provides space for more arithmetic hardware, a basic level of control is still required. For a number of reasons this work chooses to replace this control largely with static scheduling. This pushes the burden of control primarily to the software and specifically the compiler, rather not to the programmer or to an application specific means of control simplification. An existing legacy tool chain capable of autoparallelising sequential Fortran code to the degree of parallelism necessary for many-core exists. This work implements a many-core architecture to match it. Prototyping the design on an FPGA, it is possible to examine the real world performance of the compiler-architecture system to a greater degree than simulation only would allow. Comparing theoretical peak performance and real performance in a case study application, the system is found to be more efficient than any other reviewed, but to also significantly under perform relative to current competing architectures. This failing is apportioned to taking the need for simple hardware too far, and an inability to implement static scheduling mitigating tactics due to lack of support for such in the compiler

Research And Application Of Parallel Computing Algorithms For Statistical Phylogenetic Inference

Estimating the evolutionary history of organisms, phylogenetic inference, is a critical step in many analyses involving biological sequence data such as DNA. The likelihood calculations at the heart of the most effective methods for statistical phylogenetic analyses are extremely computationally intensive, and hence these analyses become a bottleneck in many studies. Recent progress in computer hardware, specifically the increase in pervasiveness of highly parallel, many-core processors has created opportunities for new approaches to computationally intensive methods, such as those in phylogenetic inference. We have developed an open source library, BEAGLE, which uses parallel computing methods to greatly accelerate statistical phylogenetic inference, for both maximum likelihood and Bayesian approaches. BEAGLE defines a uniform application programming interface and includes a collection of efficient implementations that use NVIDIA CUDA, OpenCL, and C++ threading frameworks for evaluating likelihoods under a wide variety of evolutionary models, on GPUs as well as on multi-core CPUs. BEAGLE employs a number of different parallelization techniques for phylogenetic inference, at different granularity levels and for distinct processor architectures. On CUDA and OpenCL devices, the library enables concurrent computation of site likelihoods, data subsets, and independent subtrees. The general design features of the library also provide a model for software development using parallel computing frameworks that is applicable to other domains. BEAGLE has been integrated with some of the leading programs in the field, such as MrBayes and BEAST, and is used in a diverse range of evolutionary studies, including those of disease causing viruses. The library can provide significant performance gains, with the exact increase in performance depending on the specific properties of the data set, evolutionary model, and hardware. In general, nucleotide analyses are accelerated on the order of 10-fold and codon analyses on the order of 100-fold

Proceedings of the 5th International Workshop on Reconfigurable Communication-centric Systems on Chip 2010 - ReCoSoC\u2710 - May 17-19, 2010 Karlsruhe, Germany. (KIT Scientific Reports ; 7551)

ReCoSoC is intended to be a periodic annual meeting to expose and discuss gathered expertise as well as state of the art research around SoC related topics through plenary invited papers and posters. The workshop aims to provide a prospective view of tomorrow\u27s challenges in the multibillion transistor era, taking into account the emerging techniques and architectures exploring the synergy between flexible on-chip communication and system reconfigurability

Parallel and Distributed Computing

The 14 chapters presented in this book cover a wide variety of representative works ranging from hardware design to application development. Particularly, the topics that are addressed are programmable and reconfigurable devices and systems, dependability of GPUs (General Purpose Units), network topologies, cache coherence protocols, resource allocation, scheduling algorithms, peertopeer networks, largescale network simulation, and parallel routines and algorithms. In this way, the articles included in this book constitute an excellent reference for engineers and researchers who have particular interests in each of these topics in parallel and distributed computing

3rd Many-core Applications Research Community (MARC) Symposium. (KIT Scientific Reports ; 7598)

This manuscript includes recent scientific work regarding the Intel Single Chip Cloud computer and describes approaches for novel approaches for programming and run-time organization

Memory abstractions for parallel programming

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2012.Cataloged from PDF version of thesis.Includes bibliographical references (p. 156-163).A memory abstraction is an abstraction layer between the program execution and the memory that provides a different "view" of a memory location depending on the execution context in which the memory access is made. Properly designed memory abstractions help ease the task of parallel programming by mitigating the complexity of synchronization or admitting more efficient use of resources. This dissertation describes five memory abstractions for parallel programming: (i) cactus stacks that interoperate with linear stacks, (ii) efficient reducers, (iii) reducer arrays, (iv) ownershipaware transactions, and (v) location-based memory fences. To demonstrate the utility of memory abstractions, my collaborators and I developed Cilk-M, a dynamically multithreaded concurrency platform which embodies the first three memory abstractions. Many dynamic multithreaded concurrency platforms incorporate cactus stacks to support multiple stack views for all the active children simultaneously. The use of cactus stacks, albeit essential, forces concurrency platforms to trade off between performance, memory consumption, and interoperability with serial code due to its incompatibility with linear stacks. This dissertation proposes a new strategy to build a cactus stack using thread-local memory mapping (or TLMM), which enables Cilk-M to satisfy all three criteria simultaneously. A reducer hyperobject allows different branches of a dynamic multithreaded program to maintain coordinated local views of the same nonlocal variable. With reducers, one can use nonlocal variables in a parallel computation without restructuring the code or introducing races. This dissertation introduces memory-mapped reducers, which admits a much more efficient access compared to existing implementations. When used in large quantity, reducers incur unnecessarily high overhead in execution time and space consumption. This dissertation describes support for reducer arrays, which offers the same functionality as an array of reducers with significantly less overhead. Transactional memory is a high-level synchronization mechanism, designed to be easier to use and more composable than fine-grain locking. This dissertation presents ownership-aware transactions, the first transactional memory design that provides provable safety guarantees for "opennested" transactions. On architectures that implement memory models weaker than sequential consistency, programs communicating via shared memory must employ memory-fences to ensure correct execution. This dissertation examines the concept of location-based memoryfences, which unlike traditional memory fences, incurs latency only when synchronization is necessary.by I-Ting Angelina Lee.Ph.D

Efficient Communication and Synchronization on Manycore Processors

The increased number of cores integrated on a chip has brought about a number of challenges. Concerns about the scalability of cache coherence protocols have urged both researchers and practitioners to explore alternative programming models, where cache coherence is not a given. Message passing, traditionally used in distributed systems, has surfaced as an appealing alternative to shared memory, commonly used in multiprocessor systems. In this thesis, we study how basic communication and synchronization primitives on manycore processors can be improved, with an accent on taking advantage of message passing. We do this in two different contexts: (i) message passing is the only means of communication and (ii) it coexists with traditional cache-coherent shared memory. In the first part of the thesis, we analytically and experimentally study collective communication on a message-passing manycore processor. First, we devise broadcast algorithms for the Intel SCC, an experimental manycore platform without coherent caches. Our ideas are captured by OC-Bcast (on-chip broadcast), a tree-based broadcast algorithm. Two versions of OC-Bcast are presented: One for synchronous communication, suitable for use in high-performance libraries implementing the Message Passing Interface (MPI), and another for asynchronous communication, for use in distributed algorithms and general-purpose software. Both OC-Bcast flavors are based on one-sided communication and significantly outperform (by up to 3x) state-of-the-art two-sided algorithms. Next, we conceive an analytical communication model for the SCC. By expressing the latency and throughput of different broadcast algorithms through this model, we reveal that the advantage of OC-Bcast comes from greatly reducing the number of off-chip memory accesses on the critical path. The second part of the thesis focuses on lock-based synchronization. We start by introducing the concept of hybrid mutual exclusion algorithms, which rely both on cache-coherent shared memory and message passing. The hybrid algorithms we present, HybLock and HybComb, are shown to significantly outperform (by even 4x) their shared-memory-only counterparts, when used to implement concurrent counters, stacks and queues on a hybrid Tilera TILE-Gx processor. The advantage of our hybrid algorithms comes from the fact that their most critical parts rely on message passing, thereby avoiding the overhead of the cache coherence protocol. Still, we take advantage of shared memory, as shared state makes the implementation of certain mechanisms much more straightforward. Next, we try to profit from these insights even on processors without hardware support for message passing. Taking two classic x86 processors from Intel and AMD, we come up with cache-aware optimizations that improve the performance of executing contended critical sections by as much as 6x

Simulation Modelling of Distributed-Shared Memory Multiprocessors

Institute for Computing Systems ArchitectureDistributed shared memory (DSM) systems have been recognised as a compelling platform for parallel computing due to the programming advantages and scalability. DSM systems allow applications to access data in a logically shared address space by abstracting away the distinction of physical memory location. As the location of data is transparent, the sources of overhead caused by accessing the distant memories are difficult to analyse. This memory locality problem has been identified as crucial to DSM performance. Many researchers have investigated the problem using simulation as a tool for conducting experiments resulting in the progressive evolution of DSM systems. Nevertheless, both the diversity of architectural configurations and the rapid advance of DSM implementations impose constraints on simulation model designs in two issues: the limitation of the simulation framework on model extensibility and the lack of verification applicability during a simulation run causing the delay in verification process. This thesis studies simulation modelling techniques for memory locality analysis of various DSM systems implemented on top of a cluster of symmetric multiprocessors. The thesis presents a simulation technique to promote model extensibility and proposes a technique for verification applicability, called a Specification-based Parameter Model Interaction (SPMI). The proposed techniques have been implemented in a new interpretation-driven simulation called DSiMCLUSTER on top of a discrete event simulation (DES) engine known as HASE. Experiments have been conducted to determine which factors are most influential on the degree of locality and to determine the possibility to maximise the stability of performance. DSiMCLUSTER has been validated against a SunFire 15K server and has achieved similarity of cache miss results, an average of +-6% with the worst case less than 15% of difference. These results confirm that the techniques used in developing the DSiMCLUSTER can contribute ways to achieve both (a) a highly extensible simulation framework to keep up with the ongoing innovation of the DSM architecture, and (b) the verification applicability resulting in an efficient framework for memory analysis experiments on DSM architecture

Earth imaging with microsatellites: An investigation, design, implementation and in-orbit demonstration of electronic imaging systems for earth observation on-board low-cost microsatellites.

This research programme has studied the possibilities and difficulties of using 50 kg microsatellites to perform remote imaging of the Earth. The design constraints of these missions are quite different to those encountered in larger, conventional spacecraft. While the main attractions of microsatellites are low cost and fast response times, they present the following key limitations: Payload mass under 5 kg, Continuous payload power under 5 Watts, peak power up to 15 Watts, Narrow communications bandwidths (9.6 / 38.4 kbps), Attitude control to within 5°, No moving mechanics. The most significant factor is the limited attitude stability. Without sub-degree attitude control, conventional scanning imaging systems cannot preserve scene geometry, and are therefore poorly suited to current microsatellite capabilities. The foremost conclusion of this thesis is that electronic cameras, which capture entire scenes in a single operation, must be used to overcome the effects of the satellite's motion. The potential applications of electronic cameras, including microsatellite remote sensing, have erupted with the recent availability of high sensitivity field-array CCD (charge-coupled device) image sensors. The research programme has established suitable techniques and architectures necessary for CCD sensors, cameras and entire imaging systems to fulfil scientific/commercial remote sensing despite the difficult conditions on microsatellites. The author has refined these theories by designing, building and exploiting in-orbit five generations of electronic cameras. The major objective of meteorological scale imaging was conclusively demonstrated by the Earth imaging camera flown on the UoSAT-5 spacecraft in 1991. Improved cameras have since been carried by the KITSAT-1 (1992) and PoSAT-1 (1993) microsatellites. PoSAT-1 also flies a medium resolution camera (200 metres) which (despite complete success) has highlighted certain limitations of microsatellites for high resolution remote sensing. A reworked, and extensively modularised, design has been developed for the four camera systems deployed on the FASat-Alfa mission (1995). Based on the success of these missions, this thesis presents many recommendations for the design of microsatellite imaging systems. The novelty of this research programme has been the principle of designing practical camera systems to fit on an existing, highly restrictive, satellite platform, rather than conceiving a fictitious small satellite to support a high performance scanning imager. This pragmatic approach has resulted in the first incontestable demonstrations of the feasibility of remote sensing of the Earth from inexpensive microsatellites