Parallelization of dynamic programming recurrences in computational biology

The rapid growth of biosequence databases over the last decade has led to a performance bottleneck in the applications analyzing them. In particular, over the last five years DNA sequencing capacity of next-generation sequencers has been doubling every six months as costs have plummeted. The data produced by these sequencers is overwhelming traditional compute systems. We believe that in the future compute performance, not sequencing, will become the bottleneck in advancing genome science. In this work, we investigate novel computing platforms to accelerate dynamic programming algorithms, which are popular in bioinformatics workloads. We study algorithm-specific hardware architectures that exploit fine-grained parallelism in dynamic programming kernels using field-programmable gate arrays: FPGAs). We advocate a high-level synthesis approach, using the recurrence equation abstraction to represent dynamic programming and polyhedral analysis to exploit parallelism. We suggest a novel technique within the polyhedral model to optimize for throughput by pipelining independent computations on an array. This design technique improves on the state of the art, which builds latency-optimal arrays. We also suggest a method to dynamically switch between a family of designs using FPGA reconfiguration to achieve a significant performance boost. We have used polyhedral methods to parallelize the Nussinov RNA folding algorithm to build a family of accelerators that can trade resources for parallelism and are between 15-130x faster than a modern dual core CPU implementation. A Zuker RNA folding accelerator we built on a single workstation with four Xilinx Virtex 4 FPGAs outperforms 198 3 GHz Intel Core 2 Duo processors. Furthermore, our design running on a single FPGA is an order of magnitude faster than competing implementations on similar-generation FPGAs and graphics processors. Our work is a step toward the goal of automated synthesis of hardware accelerators for dynamic programming algorithms

Obtaining performance and programmability using reconfigurable hardware for media processing

Thesis (Ph. D.)--Massachusetts Institute of Technology, School of Architecture and Planning, Program in Media Arts and Sciences, 2002.Includes bibliographical references (p. 127-132).An imperative requirement in the design of a reconfigurable computing system or in the development of a new application on such a system is performance gains. However, such developments suffer from long-and-difficult programming process, hard-to-predict performance gains, and limited scope of applications. To address these problems, we need to understand reconfigurable hardware's capabilities and limitations, its performance advantages and disadvantages, re-think reconfigurable system architectures, and develop new tools to explore its utility. We begin by examining performance contributors at the system level. We identify those from general-purpose and those from dedicated components. We propose an architecture by integrating reconfigurable hardware within the general-purpose framework. This is to avoid and minimize dedicated hardware and organization for programmability. We analyze reconfigurable logic architectures and their performance limitations. This analysis leads to a theory that reconfigurable logic can never be clocked faster than a fixed-logic design based on the same fabrication technology. Though highly unpredictable, we can obtain a quick upper bound estimate on the clock speed based on a few parameters. We also analyze microprocessor architectures and establish an analytical performance model. We use this model to estimate performance bounds using very little information on task properties. These bounds help us to detect potential memory-bound tasks. For a compute-bound task, we compare its performance upper bound with the upper bound on reconfigurable clock speed to further rule out unlikely speedup candidates.(cont.) These performance estimates require very few parameters, and can be quickly obtained without writing software or hardware codes. They can be integrated with design tools as front end tools to explore speedup opportunities without costly trials. We believe this will broaden the applicability of reconfigurable computing.by Ling-Pei Kung.Ph.D

Tools for efficient Deep Learning

In the era of Deep Learning (DL), there is a fast-growing demand for building and deploying Deep Neural Networks (DNNs) on various platforms. This thesis proposes five tools to address the challenges for designing DNNs that are efficient in time, in resources and in power consumption. We first present Aegis and SPGC to address the challenges in improving the memory efficiency of DL training and inference. Aegis makes mixed precision training (MPT) stabler by layer-wise gradient scaling. Empirical experiments show that Aegis can improve MPT accuracy by at most 4\%. SPGC focuses on structured pruning: replacing standard convolution with group convolution (GConv) to avoid irregular sparsity. SPGC formulates GConv pruning as a channel permutation problem and proposes a novel heuristic polynomial-time algorithm. Common DNNs pruned by SPGC have maximally 1\% higher accuracy than prior work. This thesis also addresses the challenges lying in the gap between DNN descriptions and executables by Polygeist for software and POLSCA for hardware. Many novel techniques, e.g. statement splitting and memory partitioning, are explored and used to expand polyhedral optimisation. Polygeist can speed up software execution in sequential and parallel by 2.53 and 9.47 times on Polybench/C. POLSCA achieves 1.5 times speedup over hardware designs directly generated from high-level synthesis on Polybench/C. Moreover, this thesis presents Deacon, a framework that generates FPGA-based DNN accelerators of streaming architectures with advanced pipelining techniques to address the challenges from heterogeneous convolution and residual connections. Deacon provides fine-grained pipelining, graph-level optimisation, and heuristic exploration by graph colouring. Compared with prior designs, Deacon shows resource/power consumption efficiency improvement of 1.2x/3.5x for MobileNets and 1.0x/2.8x for SqueezeNets. All these tools are open source, some of which have already gained public engagement. We believe they can make efficient deep learning applications easier to build and deploy.Open Acces

Cross-Layer Automated Hardware Design for Accuracy-Configurable Approximate Computing

Approximate Computing trades off computation accuracy against performance or energy efficiency. It is a design paradigm that arose in the last decade as an answer to diminishing returns from Dennard\u27s scaling and a shift in the prominent workloads. A range of modern workloads, categorized mainly as recognition, mining, and synthesis, features an inherent tolerance to approximations. Their characteristics, such as redundancies in their input data and robust-to-noise algorithms, allow them to produce outputs of acceptable quality, despite an approximation in some of their computations. Approximate Computing leverages the application tolerance by relaxing the exactness in computation towards primary design goals of increasing performance or improving energy efficiency. Existing techniques span across the abstraction layers of computer systems where cross-layer techniques are shown to offer a larger design space and yield higher savings. Currently, the majority of the existing work aims at meeting a single accuracy. The extent of approximation tolerance, however, significantly varies with a change in input characteristics and applications. In this dissertation, methods and implementations are presented for cross-layer and automated design of accuracy-configurable Approximate Computing to maximally exploit the performance and energy benefits. In particular, this dissertation addresses the following challenges and introduces novel contributions: A main Approximate Computing category in hardware is to scale either voltage or frequency beyond the safe limits for power or performance benefits, respectively. The rationale is that timing errors would be gradual and for an initial range tolerable. This scaling enables a fine-grain accuracy-configurability by varying the timing error occurrence. However, conventional synthesis tools aim at meeting a single delay for all paths within the circuit. Subsequently, with voltage or frequency scaling, either all paths succeed, or a large number of paths fail simultaneously, with a steep increase in error rate and magnitude. This dissertation presents an automated method for minimizing path delays by individually constraining the primary outputs of combinational circuits. As a result, it reduces the number of failing paths and makes the timing errors significantly more gradual, and also rarer and smaller on average. Additionally, it reveals that delays can be significantly reduced towards the least significant bit (LSB) and allows operating at a higher frequency when small operands are computed. Precision scaling, i.e., reducing the representation of data and its accuracy is widely used in multiple abstraction layers in Approximate Computing. Reducing data precision also reduces the transistor toggles, and therefore the dynamic power consumption. Application and architecture level precision scaling results in using only LSBs of the circuit. Arithmetic circuits often have less complexity and logic depth in LSBs compared to most significant bits (MSB). To take advantage of this circuit property, a delay-altering synthesis methodology is proposed. The method finds energy-optimal delay values under configurable precision usage and assigns them to primary outputs used for different precisions. Thereby, it enables dynamic frequency-precision scalable circuits for energy efficiency. Within the hardware architecture, it is possible to instantiate multiple units with the same functionality with different fixed approximation levels, where each block benefits from having fewer transistors and also synthesis relaxations. These blocks can be selected dynamically and thus allow to configure the accuracy during runtime. Instantiating such approximate blocks can be a lower dynamic power but higher area and leakage cost alternative to the current state-of-the-art gating mechanisms which switch off a group of paths in the circuit to reduce the toggling activity. Jointly, instantiating multiple blocks and gating mechanisms produce a large design space of accuracy-configurable hardware, where energy-optimal solutions require a cross-layer search in architecture and circuit levels. To that end, an approximate hardware synthesis methodology is proposed with joint optimizations in architecture and circuit for dynamic accuracy scaling, and thereby it enables energy vs. area trade-offs

Characterization and Avoidance of Critical Pipeline Structures in Aggressive Superscalar Processors

In recent years, with only small fractions of modern processors now accessible in a single cycle, computer architects constantly fight against propagation issues across the die. Unfortunately this trend continues to shift inward, and now the even most internal features of the pipeline are designed around communication, not computation. To address the inward creep of this constraint, this work focuses on the characterization of communication within the pipeline itself, architectural techniques to avoid it when possible, and layout co-design for early detection of problems. I present work in creating a novel detection tool for common case operand movement which can rapidly characterize an applications dataflow patterns. The results produced are suitable for exploitation as a small number of patterns can describe a significant portion of modern applications. Work on dynamic dependence collapsing takes the observations from the pattern results and shows how certain groups of operations can be dynamically grouped, avoiding unnecessary communication between individual instructions. This technique also amplifies the efficiency of pipeline data structures such as the reorder buffer, increasing both IPC and frequency. I also identify the same sets of collapsible instructions at compile time, producing the same benefits with minimal hardware complexity. This technique is also done in a backward compatible manner as the groups are exposed by simple reordering of the binarys instructions. I present aggressive pipelining approaches for these resources which avoids the critical timing often presumed necessary in aggressive superscalar processors. As these structures are designed for the worst case, pipelining them can produce greater frequency benefit than IPC loss. I also use the observation that the dynamic issue order for instructions in aggressive superscalar processors is predictable. Thus, a hardware mechanism is introduced for caching the wakeup order for groups of instructions efficiently. These wakeup vectors are then used to speculatively schedule instructions, avoiding the dynamic scheduling when it is not necessary. Finally, I present a novel approach to fast and high-quality chip layout. By allowing architects to quickly evaluate what if scenarios during early high-level design, chip designs are less likely to encounter implementation problems later in the process.Ph.D.Committee Chair: Scott Wills; Committee Member: David Schimmel; Committee Member: Gabriel Loh; Committee Member: Hsien-Hsin Lee; Committee Member: Yorai Ward

Cycle-accurate multicore performance models on FPGAs

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2011.Cataloged from PDF version of thesis.Includes bibliographical references (p. 159-165).The goal of this project is to improve computer architecture by accelerating cycle-accurate performance modeling of multicore processors using FPGAs. Contributions include a distributed technique controlling simulation on a highly-parallel substrate, hardware design techniques to reduce development effort, and a specific framework for modeling shared-memory multicore processors paired with realistic On-Chip Networks.by Michael Pellauer.Ph.D

Proceedings of the 21st Conference on Formal Methods in Computer-Aided Design – FMCAD 2021

The Conference on Formal Methods in Computer-Aided Design (FMCAD) is an annual conference on the theory and applications of formal methods in hardware and system verification. FMCAD provides a leading forum to researchers in academia and industry for presenting and discussing groundbreaking methods, technologies, theoretical results, and tools for reasoning formally about computing systems. FMCAD covers formal aspects of computer-aided system design including verification, specification, synthesis, and testing

Integrated support for Adaptivity and Fault-tolerance in MPSoCs

The technology improvement and the adoption of more and more complex applications in consumer electronics are forcing a rapid increase in the complexity of multiprocessor systems on chip (MPSoCs). Following this trend, MPSoCs are becoming increasingly dynamic and adaptive, for several reasons. One of these is that applications are getting intrinsically dynamic. Another reason is that the workload on emerging MPSoCs cannot be predicted because modern systems are open to new incoming applications at run-time. A third reason which calls for adaptivity is the decreasing component reliability associated with technology scaling. Components below the 32-nm node are more inclined to temporal or even permanent faults. In case of a malfunctioning system component, the rest of the system is supposed to take over its tasks. Thus, the system adaptivity goal shall influence several de- sign decisions, that have been listed below: 1) The applications should be specified such that system adaptivity can be easily supported. To this end, we consider Polyhedral Process Networks (PPNs) as model of computation to specify applications. PPNs are composed by concurrent and autonomous processes that communicate between each other using bounded FIFO channels. Moreover, in PPNs the control is completely distributed, as well as the memories. This represents a good match with the emerging MPSoC architectures, in which processing elements and memories are usually distributed. Most importantly, the simple operational semantics of PPNs allows for an easy adoption of system adaptivity mechanisms. 2) The hardware platform should guarantee the flexibility that adaptivity mechanisms require. Networks-on-Chip (NoCs) are emerging communication infrastructures for MPSoCs that, among many other advantages, allow for system adaptivity. This is because NoCs are generic, since the same platformcan be used to run different applications, or to run the same application with different mapping of processes. However, there is a mismatch between the generic structure of the NoCs and the semantics of the PPN model. Therefore, in this thesis we investigate and propose several communication approaches to overcome this mismatch. 3) The system must be able to change the process mapping at run-time, using process migration. To this end, a process migration mechanism has been proposed and evaluated. This mechanism takes into account specific requirements of the embedded domain such as predictability and efficiency. To face the problem of graceful degradation of the system, we enriched the MADNESS NoC platform by adding fault tolerance support at both software and hardware level. The proposed process migration mechanism can be exploited to cope with permanent faults by migrating the processes running on the faulty processing element. A fast heuristic is used to determine the new mapping of the processes to tiles. The experimental results prove that the overhead in terms of execution time, due to the execution time of the remapping heuristic, together with the actual process migration, is almost negligible compared to the execution time of the whole application. This means that the proposed approach allows the system to change its performance metrics and to react to faults without a substantial impact on the user experience