Characterizing and Accelerating Bioinformatics Workloads on Modern Microarchitectures

Bioinformatics, the use of computer techniques to analyze biological data, has been a particularly active research field in the last two decades. Advances in this field have contributed to the collection of enormous amounts of data, and the sheer amount of available data has started to overtake the processing capability possible with current computer systems. Clearly, computer architects need to have a better understanding of how bioinformatics applications work and what kind of architectural techniques could be used to accelerate these important scientific workloads on future processors. In this dissertation, we develop a bioinformatic benchmark suite and provide a detailed characterization of these applications in common use today from a computer architect's point of view. We analyze a wide range of detailed execution characteristics including instruction mix, IPC measurements, L1 and L2 cache misses on a real architecture; and proceed to analyze the workloads' memory access characteristics. We then concentrate on accelerating a particularly computationally intensive bioinformatics workload on the novel Cell Broadband Engine multiprocessor architecture. The HMMER workload is used for protein profile searching using hidden Markov models, and most of its execution time is spent running the Viterbi algorithm. We parallelize and partition the HMMER application to implement it on the Cell Broadband Engine. In order to run the Viterbi algorithm on the 256KB local stores of the Cell BE synergistic processing units (SPEs), we present a method to develop a fast SIMD implementation of the Viterbi algorithm that reduces the storage requirements significantly. Our HMMER implementation for the Cell BE architecture, Cell-HMMER, exploits the multiple levels of parallelism inherent in this application, and can run protein profile searches up to 27.98 times faster than a modern dual-core x86 microprocessor

Automatic generation of synthetic workloads for multicore systems

textWhen designing a computer system, benchmark programs are used with cycle accurate performance/power simulators and HDL level simulators to evaluate novel architectural enhancements, perform design space exploration, understand the worst-case power characteristics of various designs and find performance bottlenecks. This research effort is directed towards automatically generating synthetic benchmarks to tackle three design challenges: 1) For most of the simulation related purposes, full runs of modern real world parallel applications like the PARSEC, SPLASH suites cannot be used as they take machine weeks of time on cycle accurate and HDL level simulators incurring a prohibitively large time cost 2) The second design challenge is that, some of these real world applications are intellectual property and cannot be shared with processor vendors for design studies 3) The most significant problem in the design stage is the complexity involved in fixing the maximum power consumption of a multicore design, called the Thermal Design Power (TDP). In an effort towards fixing this maximum power consumption of a system at the most optimal point, designers are used to hand-crafting possible code snippets called power viruses. But, this process of trying to manually write such maximum power consuming code snippets is very tedious. All of these aforementioned challenges has lead to the resurrection of synthetic benchmarks in the recent past, serving as a promising solution to all the challenges. During the design stage of a multicore system, availability of a framework to automatically generate system-level synthetic benchmarks for multicore systems will greatly simplify the design process and result in more confident design decisions. The key idea behind such an adaptable benchmark synthesis framework is to identify the key characteristics of real world parallel applications that affect the performance and power consumption of a real program and create synthetic executable programs by varying the values for these characteristics. Firstly, with such a framework, one can generate miniaturized synthetic clones for large target (current and futuristic) parallel applications enabling an architect to use them with slow low-level simulation models (e.g., RTL models in VHDL/Verilog) and helps in tailoring designs to the targeted applications. These synthetic benchmark clones can be distributed to architects and designers even if the original applications are intellectual property, when they are not publicly available. Lastly, such a framework can be used to automatically create maximum power consuming code snippets to be able to help in fixing the TDP, heat sinks, cooling system and other power related features of the system. The workload cloning framework built using the proposed synthetic benchmark generation methodology is evaluated to show its superiority over the existing cloning methodologies for single-core systems by generating miniaturized clones for CPU2006 and ImplantBench workloads with only an average error of 2.9% in performance for up to five orders of magnitude of simulation speedup. The correlation coefficient predicting the sensitivity to design changes is 0.95 and 0.98 for performance and power consumption. The proposed framework is evaluated by cloning parallel applications implemented based on p-threads and OpenMP in the PARSEC benchmark suite. The average error in predicting performance is 4.87% and that of power consumption is 2.73%. The correlation coefficient predicting the sensitivity to design changes is 0.92 for performance. The efficacy of the proposed synthetic benchmark generation framework for power virus generation is evaluation on SPARC, Alpha and x86 ISAs using full system simulators and also using real hardware. The results show that the power viruses generated for single-core systems consume 14-41% more power compared to MPrime on SPARC ISA. Similarly, the power viruses generated for multicore systems consume 45-98%, 40-89% and 41-56% more power than PARSEC workloads, running multiple copies of MPrime and multithreaded SPECjbb respectively.Electrical and Computer Engineerin

DAMOV: A New Methodology and Benchmark Suite for Evaluating Data Movement Bottlenecks

Data movement between the CPU and main memory is a first-order obstacle against improving performance, scalability, and energy efficiency in modern systems. Computer systems employ a range of techniques to reduce overheads tied to data movement, spanning from traditional mechanisms (e.g., deep multi-level cache hierarchies, aggressive hardware prefetchers) to emerging techniques such as Near-Data Processing (NDP), where some computation is moved close to memory. Our goal is to methodically identify potential sources of data movement over a broad set of applications and to comprehensively compare traditional compute-centric data movement mitigation techniques to more memory-centric techniques, thereby developing a rigorous understanding of the best techniques to mitigate each source of data movement. With this goal in mind, we perform the first large-scale characterization of a wide variety of applications, across a wide range of application domains, to identify fundamental program properties that lead to data movement to/from main memory. We develop the first systematic methodology to classify applications based on the sources contributing to data movement bottlenecks. From our large-scale characterization of 77K functions across 345 applications, we select 144 functions to form the first open-source benchmark suite (DAMOV) for main memory data movement studies. We select a diverse range of functions that (1) represent different types of data movement bottlenecks, and (2) come from a wide range of application domains. Using NDP as a case study, we identify new insights about the different data movement bottlenecks and use these insights to determine the most suitable data movement mitigation mechanism for a particular application. We open-source DAMOV and the complete source code for our new characterization methodology at https://github.com/CMU-SAFARI/DAMOV.Comment: Our open source software is available at https://github.com/CMU-SAFARI/DAMO

Domain Specific Computing in Tightly-Coupled Heterogeneous Systems

Over the past several decades, researchers and programmers across many disciplines have relied on Moores law and Dennard scaling for increases in compute capability in modern processors. However, recent data suggest that the number of transistors per square inch on integrated circuits is losing pace with Moores laws projection due to the breakdown of Dennard scaling at smaller semiconductor process nodes. This has signaled the beginning of a new “golden age in computer architecture” in which the paradigm will be shifted from improving traditional processor performance for general tasks to architecting hardware that executes a class of applications in a high-performing manner. This shift will be paved, in part, by making compute systems more heterogeneous and investigating domain specific architectures. However, the notion of domain specific architectures raises many research questions. Specifically, what constitutes a domain? How does one architect hardware for a specific domain? In this dissertation, we present our work towards domain specific computing. We start by constructing a guiding definition for our target domain and then creating a benchmark suite of applications based on our domain definition. We then use quantitative metrics from the literature to characterize our domain in order to gain insights regarding what would be most beneficial in hardware targeted specifically for the domain. From the characterization, we learn that data movement is a particularly salient aspect of our domain. Motivated by this fact, we evaluate our target platform, the Intel HARPv2 CPU+FPGA system, for architecting domain specific hardware through a portability and performance evaluation. To guide the creation of domain specific hardware for this platform, we create a novel tool to quantify spatial and temporal locality. We apply this tool to our benchmark suite and use the generated outputs as features to an unsupervised clustering algorithm. We posit that the resulting clusters represent sub-domains within our originally specified domain; specifically, these clusters inform whether a kernel of computation should be designed as a widely vectorized or deeply pipelined compute unit. Using the lessons learned from the domain characterization and hardware platform evaluation, we outline our process of designing hardware for our domain, and empirically verify that our prediction regarding a wide or deep kernel implementation is correct

Analytical cost metrics: days of future past

2019 Summer.Includes bibliographical references.Future exascale high-performance computing (HPC) systems are expected to be increasingly heterogeneous, consisting of several multi-core CPUs and a large number of accelerators, special-purpose hardware that will increase the computing power of the system in a very energy-efficient way. Specialized, energy-efficient accelerators are also an important component in many diverse systems beyond HPC: gaming machines, general purpose workstations, tablets, phones and other media devices. With Moore's law driving the evolution of hardware platforms towards exascale, the dominant performance metric (time efficiency) has now expanded to also incorporate power/energy efficiency. This work builds analytical cost models for cost metrics such as time, energy, memory access, and silicon area. These models are used to predict the performance of applications, for performance tuning, and chip design. The idea is to work with domain specific accelerators where analytical cost models can be accurately used for performance optimization. The performance optimization problems are formulated as mathematical optimization problems. This work explores the analytical cost modeling and mathematical optimization approach in a few ways. For stencil applications and GPU architectures, the analytical cost models are developed for execution time as well as energy. The models are used for performance tuning over existing architectures, and are coupled with silicon area models of GPU architectures to generate highly efficient architecture configurations. For matrix chain products, analytical closed form solutions for off-chip data movement are built and used to minimize the total data movement cost of a minimum op count tree

Software for Exascale Computing - SPPEXA 2016-2019

This open access book summarizes the research done and results obtained in the second funding phase of the Priority Program 1648 "Software for Exascale Computing" (SPPEXA) of the German Research Foundation (DFG) presented at the SPPEXA Symposium in Dresden during October 21-23, 2019. In that respect, it both represents a continuation of Vol. 113 in Springer’s series Lecture Notes in Computational Science and Engineering, the corresponding report of SPPEXA’s first funding phase, and provides an overview of SPPEXA’s contributions towards exascale computing in today's sumpercomputer technology. The individual chapters address one or more of the research directions (1) computational algorithms, (2) system software, (3) application software, (4) data management and exploration, (5) programming, and (6) software tools. The book has an interdisciplinary appeal: scholars from computational sub-fields in computer science, mathematics, physics, or engineering will find it of particular interest