Ebook: High-Performance Computing Using FPGAs

High-Performance Computing using FPGA covers the area of high performance reconfigurable computing (HPRC). This book provides an overview of architectures, tools and applications for High-Performance Reconfigurable Computing (HPRC). FPGAs offer very high I/O bandwidth and fine-grained, custom and flexible parallelism and with the ever-increasing computational needs coupled with the frequency/power wall, the increasing maturity and capabilities of FPGAs, and the advent of multicore processors which has caused the acceptance of parallel computational models. The Part on architectures will introduce different FPGA-based HPC platforms: attached co-processor HPRC architectures such as the CHREC’s Novo-G and EPCC’s Maxwell systems; tightly coupled HRPC architectures, e.g. the Convey hybrid-core computer; reconfigurably networked HPRC architectures, e.g. the QPACE system, and standalone HPRC architectures such as EPFL’s CONFETTI system. The Part on Tools will focus on high-level programming approaches for HPRC, with chapters on C-to-Gate tools (such as Impulse-C, AutoESL, Handel-C, MORA-C++); Graphical tools (MATLAB-Simulink, NI LabVIEW); Domain-specific languages, languages for heterogeneous computing(for example OpenCL, Microsoft’s Kiwi and Alchemy projects). The part on Applications will present case from several application domains where HPRC has been used successfully, such as Bioinformatics and Computational Biology; Financial Computing; Stencil computations; Information retrieval; Lattice QCD; Astrophysics simulations; Weather and climate modeling.

This book is concerned with the emerging field of High Performance Reconfigurable Computing (HPRC), which aims to harness the high performance and relative low power of reconfigurable hardware–in the form Field Programmable Gate Arrays (FPGAs)–in High Performance Computing (HPC) applications. It presents the latest developments in this field from applications, architecture, and tools and methodologies points of view. We hope that this work will form a reference for existing researchers in the field, and entice new researchers and developers to join the HPRC community.

The book includes:

• Thirteen application chapters which present the most important application areas tackled by high performance reconfigurable computers, namely: financial computing, bioinformatics and computational biology, data search and processing, stencil computation e.g. computational fluid dynamics and seismic modeling, cryptanalysis, astronomical N-body simulation, and circuit simulation.
• Seven architecture chapters which present both commercial and academic parallel FPGA architectures, low latency and high performance FPGA-based networks and memory architectures for parallel machines, and a high speed optical dynamic reconfiguration mechanism for HPRC.
• Five tools and methodologies chapters which address the important issue of productivity and high performance in HPRC. These include a study of precision and arithmetic issues in HPRC, comparative studies of C-based high level synthesis tools and RTL-based approaches, taxonomy of HPRC tools and a framework of their analysis, and an integrated hardware-software-application approach to HPRC.

This book is concerned with the emerging field of High Performance Reconfigurable Computing (HPRC), which aims to harness the high performance and relative low power of reconfigurable hardware–in the form Field Programmable Gate Arrays (FPGAs)–in High Performance Computing (HPC) applications. It presents the latest developments in this field from applications, architecture, and tools and methodologies points of view. We hope that this work will form a reference for existing researchers in the field, and entice new researchers and developers to join the HPRC community.

The book includes:

• Thirteen application chapters which present the most important application areas tackled by high performance reconfigurable computers, namely: financial computing, bioinformatics and computational biology, data search and processing, stencil computation e.g. computational fluid dynamics and seismic modeling, cryptanalysis, astronomical N-body simulation, and circuit simulation.
• Seven architecture chapters which present both commercial and academic parallel FPGA architectures, low latency and high performance FPGA-based networks and memory architectures for parallel machines, and a high speed optical dynamic reconfiguration mechanism for HPRC.
• Five tools and methodologies chapters which address the important issue of productivity and high performance in HPRC. These include a study of precision and arithmetic issues in HPRC, comparative studies of C-based high level synthesis tools and RTL-based approaches, taxonomy of HPRC tools and a framework of their analysis, and an integrated hardware-software-application approach to HPRC.

Content:
Front Matter....Pages i-xi
Front Matter....Pages 1-2
High-Performance Hardware Acceleration of Asset Simulations....Pages 3-32
Monte-Carlo Simulation-Based Financial Computing on the Maxwell FPGA Parallel Machine....Pages 33-80
Bioinformatics Applications on the FPGA-Based High-Performance Computer RIVYERA....Pages 81-103
FPGA-Accelerated Molecular Dynamics....Pages 105-135
FPGA-Based HPRC for Bioinformatics Applications....Pages 137-175
High-Performance Computing for Neuroinformatics Using FPGA....Pages 177-207
High-Performance FPGA-Accelerated Real-Time Search....Pages 209-244
High-Performance Data Processing Over N-ary Trees....Pages 245-277
FPGA-Based Systolic Computational-Memory Array for Scalable Stencil Computations....Pages 279-303
High Performance Implementation of RTM Seismic Modeling on FPGAs: Architecture, Arithmetic and Power Issues....Pages 305-334
High-Performance Cryptanalysis on RIVYERA and COPACOBANA Computing Systems....Pages 335-366
FPGA-Based HPRC Systems for Scientific Applications....Pages 367-387
Accelerating the SPICE Circuit Simulator Using an FPGA: A Case Study....Pages 389-427
Front Matter....Pages 429-429
The Convey Hybrid-Core Architecture....Pages 431-451
Low Cost High Performance Reconfigurable Computing....Pages 453-479
An FPGA-Based Supercomputer for Statistical Physics: The Weird Case of Janus....Pages 481-506
Accelerate Communication, not Computation!....Pages 507-542
High-Speed Torus Interconnect Using FPGAs....Pages 543-567
MEMSCALE: Re-architecting Memory Resources for Clusters....Pages 569-604
High-Performance Computing Based on High-Speed Dynamic Reconfiguration....Pages 605-627
Front Matter....Pages 629-629
Reconfigurable Arithmetic for High-Performance Computing....Pages 631-663
Acceleration of the Discrete Element Method: From RTL to C-Based Design....Pages 665-693
Optimising Euroben Kernels on Maxwell....Pages 695-718
Assessing Productivity of High-Level Design Methodologies for High-Performance Reconfigurable Computers....Pages 719-745
Maximum Performance Computing with Dataflow Engines....Pages 747-774
Back Matter....Pages 775-803

This book is concerned with the emerging field of High Performance Reconfigurable Computing (HPRC), which aims to harness the high performance and relative low power of reconfigurable hardware–in the form Field Programmable Gate Arrays (FPGAs)–in High Performance Computing (HPC) applications. It presents the latest developments in this field from applications, architecture, and tools and methodologies points of view. We hope that this work will form a reference for existing researchers in the field, and entice new researchers and developers to join the HPRC community.

The book includes:

• Thirteen application chapters which present the most important application areas tackled by high performance reconfigurable computers, namely: financial computing, bioinformatics and computational biology, data search and processing, stencil computation e.g. computational fluid dynamics and seismic modeling, cryptanalysis, astronomical N-body simulation, and circuit simulation.
• Seven architecture chapters which present both commercial and academic parallel FPGA architectures, low latency and high performance FPGA-based networks and memory architectures for parallel machines, and a high speed optical dynamic reconfiguration mechanism for HPRC.
• Five tools and methodologies chapters which address the important issue of productivity and high performance in HPRC. These include a study of precision and arithmetic issues in HPRC, comparative studies of C-based high level synthesis tools and RTL-based approaches, taxonomy of HPRC tools and a framework of their analysis, and an integrated hardware-software-application approach to HPRC.

Content:
Front Matter....Pages i-xi
Front Matter....Pages 1-2
High-Performance Hardware Acceleration of Asset Simulations....Pages 3-32
Monte-Carlo Simulation-Based Financial Computing on the Maxwell FPGA Parallel Machine....Pages 33-80
Bioinformatics Applications on the FPGA-Based High-Performance Computer RIVYERA....Pages 81-103
FPGA-Accelerated Molecular Dynamics....Pages 105-135
FPGA-Based HPRC for Bioinformatics Applications....Pages 137-175
High-Performance Computing for Neuroinformatics Using FPGA....Pages 177-207
High-Performance FPGA-Accelerated Real-Time Search....Pages 209-244
High-Performance Data Processing Over N-ary Trees....Pages 245-277
FPGA-Based Systolic Computational-Memory Array for Scalable Stencil Computations....Pages 279-303
High Performance Implementation of RTM Seismic Modeling on FPGAs: Architecture, Arithmetic and Power Issues....Pages 305-334
High-Performance Cryptanalysis on RIVYERA and COPACOBANA Computing Systems....Pages 335-366
FPGA-Based HPRC Systems for Scientific Applications....Pages 367-387
Accelerating the SPICE Circuit Simulator Using an FPGA: A Case Study....Pages 389-427
Front Matter....Pages 429-429
The Convey Hybrid-Core Architecture....Pages 431-451
Low Cost High Performance Reconfigurable Computing....Pages 453-479
An FPGA-Based Supercomputer for Statistical Physics: The Weird Case of Janus....Pages 481-506
Accelerate Communication, not Computation!....Pages 507-542
High-Speed Torus Interconnect Using FPGAs....Pages 543-567
MEMSCALE: Re-architecting Memory Resources for Clusters....Pages 569-604
High-Performance Computing Based on High-Speed Dynamic Reconfiguration....Pages 605-627
Front Matter....Pages 629-629
Reconfigurable Arithmetic for High-Performance Computing....Pages 631-663
Acceleration of the Discrete Element Method: From RTL to C-Based Design....Pages 665-693
Optimising Euroben Kernels on Maxwell....Pages 695-718
Assessing Productivity of High-Level Design Methodologies for High-Performance Reconfigurable Computers....Pages 719-745
Maximum Performance Computing with Dataflow Engines....Pages 747-774
Back Matter....Pages 775-803
....