Optimizing the MapReduce Framework on Intel Xeon Phi Coprocessor

With the ease-of-programming, flexibility and yet efficiency, MapReduce has become one of the most popular frameworks for building big-data applications. MapReduce was originally designed for distributed-computing, and has been extended to various architectures, e,g, multi-core CPUs, GPUs and FPGAs. In this work, we focus on optimizing the MapReduce framework on Xeon Phi, which is the latest product released by Intel based on the Many Integrated Core Architecture. To the best of our knowledge, this is the first work to optimize the MapReduce framework on the Xeon Phi. In our work, we utilize advanced features of the Xeon Phi to achieve high performance. In order to take advantage of the SIMD vector processing units, we propose a vectorization friendly technique for the map phase to assist the auto-vectorization as well as develop SIMD hash computation algorithms. Furthermore, we utilize MIMD hyper-threading to pipeline the map and reduce to improve the resource utilization. We also eliminate multiple local arrays but use low cost atomic operations on the global array for some applications, which can improve the thread scalability and data locality due to the coherent L2 caches. Finally, for a given application, our framework can either automatically detect suitable techniques to apply or provide guideline for users at compilation time. We conduct comprehensive experiments to benchmark the Xeon Phi and compare our optimized MapReduce framework with a state-of-the-art multi-core based MapReduce framework (Phoenix++). By evaluating six real-world applications, the experimental results show that our optimized framework is 1.2X to 38X faster than Phoenix++ for various applications on the Xeon Phi

Computing Platforms for Big Biological Data Analytics: Perspectives and Challenges.

The last decade has witnessed an explosion in the amount of available biological sequence data, due to the rapid progress of high-throughput sequencing projects. However, the biological data amount is becoming so great that traditional data analysis platforms and methods can no longer meet the need to rapidly perform data analysis tasks in life sciences. As a result, both biologists and computer scientists are facing the challenge of gaining a profound insight into the deepest biological functions from big biological data. This in turn requires massive computational resources. Therefore, high performance computing (HPC) platforms are highly needed as well as efficient and scalable algorithms that can take advantage of these platforms. In this paper, we survey the state-of-the-art HPC platforms for big biological data analytics. We first list the characteristics of big biological data and popular computing platforms. Then we provide a taxonomy of different biological data analysis applications and a survey of the way they have been mapped onto various computing platforms. After that, we present a case study to compare the efficiency of different computing platforms for handling the classical biological sequence alignment problem. At last we discuss the open issues in big biological data analytics

Multiple pattern matching for network security applications: Acceleration through vectorization (pre-print version)

As both new network attacks emerge and network traffic increases in volume, the need to perform network traffic inspection at high rates is ever increasing. The core of many security applications that inspect network traffic (such as Network Intrusion Detection) is pattern matching. At the same time, pattern matching is a major performance bottleneck for those applications: indeed, it is shown to contribute to more than 70% of the total running time of Intrusion Detection Systems. Although numerous efficient approaches to this problem have been proposed on custom hardware, it is challenging for pattern matching algorithms to gain benefit from the advances in commodity hardware. This becomes even more relevant with the adoption of Network Function Virtualization, that moves network services, such as Network Intrusion Detection, to the cloud, where scaling on commodity hardware is key for performance. In this paper, we tackle the problem of pattern matching and show how to leverage the architecture features found in commodity platforms. We present efficient algorithmic designs that achieve good cache locality and make use of modern vectorization techniques to utilize data parallelism within each core. We first identify properties of pattern matching that make it fit for vectorization and show how to use them in the algorithmic design. Second, we build on an earlier, cache-aware algorithmic design and show how we apply cache-locality combined with SIMD gather instructions to pattern matching. Third, we complement our algorithms with an analytical model that predicts their performance and that can be used to easily evaluate alternative designs. We evaluate our algorithmic design with open data sets of real-world network traffic: Our results on two different platforms, Haswell and Xeon-Phi, show a speedup of 1.8x and 3.6x, respectively, over Direct Filter Classification (DFC), a recently proposed algorithm by Choi et al. for pattern matching exploiting cache locality, and a speedup of more than 2.3x over Aho–Corasick, a widely used algorithm in today\u27s Intrusion Detection Systems. Finally, we utilize highly parallel hardware platforms, evaluate the scalability of our algorithms and compare it to parallel implementations of DFC and Aho–Corasick, achieving processing throughput of up to 45Gbps and close to 2 times higher throughput than Aho–Corasick

Analytical Query Execution Optimized for all Layers of Modern Hardware

Analytical database queries are at the core of business intelligence and decision support. To analyze the vast amounts of data available today, query execution needs to be orders of magnitude faster. Hardware advances have made a profound impact on database design and implementation. The large main memory capacity allows queries to execute exclusively in memory and shifts the bottleneck from disk access to memory bandwidth. In the new setting, to optimize query performance, databases must be aware of an unprecedented multitude of complicated hardware features. This thesis focuses on the design and implementation of highly efficient database systems by optimizing analytical query execution for all layers of modern hardware. The hardware layers include the network across multiple machines, main memory and the NUMA interconnection across multiple processors, the multiple levels of caches across multiple processor cores, and the execution pipeline within each core. For the network layer, we introduce a distributed join algorithm that minimizes the network traffic. For the memory hierarchy, we describe partitioning variants aware to the dynamics of the CPU caches and the NUMA interconnection. To improve the memory access rate of linear scans, we optimize lightweight compression variants and evaluate their trade-offs. To accelerate query execution within the core pipeline, we introduce advanced SIMD vectorization techniques generalizable across multiple operators. We evaluate our algorithms and techniques on both mainstream hardware and on many-integrated-core platforms, and combine our techniques in a new query engine design that can better utilize the features of many-core CPUs. In the era of hardware becoming increasingly parallel and datasets consistently growing in size, this thesis can serve as a compass for developing hardware-conscious databases with truly high-performance analytical query execution

Multiple Pattern Matching for Network Security Applications: Acceleration through Vectorization

Pattern matching is a key building block of Intrusion Detection Systems and firewalls, which are deployed nowadays on commodity systems from laptops to massive web servers in the cloud. In fact, pattern matching is one of their most computationally intensive parts and a bottleneck to their performance. In Network Intrusion Detection, for example, pattern matching algorithms handle thousands of patterns and contribute to more than 70% of the total running time of the system.In this paper, we introduce efficient algorithmic designs for multiple pattern matching which (a) ensure cache locality and (b) utilize modern SIMD instructions. We first identify properties of pattern matching that make it fit for vectorization and show how to use them in the algorithmic design. Second, we build on an earlier, cache-aware algorithmic design and we show how cache-locality combined with SIMD gather instructions, introduced in 2013 to Intel\u27s family of processors, can be applied to pattern matching. We evaluate our algorithmic design with open data sets of real-world network traffic:Our results on two different platforms, Haswell and Xeon-Phi, show a speedup of 1.8x and 3.6x, respectively, over Direct Filter Classification (DFC), a recently proposed algorithm by Choi et al. for pattern matching exploiting cache locality, and a speedup of more than 2.3x over Aho-Corasick, a widely used algorithm in today\u27s Intrusion Detection Systems

Hardware-Aware Algorithm Designs for Efficient Parallel and Distributed Processing

The introduction and widespread adoption of the Internet of Things, together with emerging new industrial applications, bring new requirements in data processing. Specifically, the need for timely processing of data that arrives at high rates creates a challenge for the traditional cloud computing paradigm, where data collected at various sources is sent to the cloud for processing. As an approach to this challenge, processing algorithms and infrastructure are distributed from the cloud to multiple tiers of computing, closer to the sources of data. This creates a wide range of devices for algorithms to be deployed on and software designs to adapt to.In this thesis, we investigate how hardware-aware algorithm designs on a variety of platforms lead to algorithm implementations that efficiently utilize the underlying resources. We design, implement and evaluate new techniques for representative applications that involve the whole spectrum of devices, from resource-constrained sensors in the field, to highly parallel servers. At each tier of processing capability, we identify key architectural features that are relevant for applications and propose designs that make use of these features to achieve high-rate, timely and energy-efficient processing.In the first part of the thesis, we focus on high-end servers and utilize two main approaches to achieve high throughput processing: vectorization and thread parallelism. We employ vectorization for the case of pattern matching algorithms used in security applications. We show that re-thinking the design of algorithms to better utilize the resources available in the platforms they are deployed on, such as vector processing units, can bring significant speedups in processing throughout. We then show how thread-aware data distribution and proper inter-thread synchronization allow scalability, especially for the problem of high-rate network traffic monitoring. We design a parallelization scheme for sketch-based algorithms that summarize traffic information, which allows them to handle incoming data at high rates and be able to answer queries on that data efficiently, without overheads.In the second part of the thesis, we target the intermediate tier of computing devices and focus on the typical examples of hardware that is found there. We show how single-board computers with embedded accelerators can be used to handle the computationally heavy part of applications and showcase it specifically for pattern matching for security-related processing. We further identify key hardware features that affect the performance of pattern matching algorithms on such devices, present a co-evaluation framework to compare algorithms, and design a new algorithm that efficiently utilizes the hardware features.In the last part of the thesis, we shift the focus to the low-power, resource-constrained tier of processing devices. We target wireless sensor networks and study distributed data processing algorithms where the processing happens on the same devices that generate the data. Specifically, we focus on a continuous monitoring algorithm (geometric monitoring) that aims to minimize communication between nodes. By deploying that algorithm in action, under realistic environments, we demonstrate that the interplay between the network protocol and the application plays an important role in this layer of devices. Based on that observation, we co-design a continuous monitoring application with a modern network stack and augment it further with an in-network aggregation technique. In this way, we show that awareness of the underlying network stack is important to realize the full potential of the continuous monitoring algorithm.The techniques and solutions presented in this thesis contribute to better utilization of hardware characteristics, across a wide spectrum of platforms. We employ these techniques on problems that are representative examples of current and upcoming applications and contribute with an outlook of emerging possibilities that can build on the results of the thesis

The Tag Filter Architecture: An energy-efficient cache and directory design

[EN] Power consumption in current high-performance chip multiprocessors (CMPs) has become a major design concern that aggravates with the current trend of increasing the core count. A significant fraction of the total power budget is consumed by on-chip caches which are usually deployed with a high associativity degree (even L1 caches are being implemented with eight ways) to enhance the system performance. On a cache access, each way in the corresponding set is accessed in parallel, which is costly in terms of energy. On the other hand, coherence protocols also must implement efficient directory caches that scale in terms of power consumption. Most of the state-of-the-art techniques that reduce the energy consumption of directories are at the cost of performance, which may become unacceptable for high-performance CMPs. In this paper, we propose an energy-efficient architectural design that can be effectively applied to any kind of cache memory. The proposed approach, called the Tag Filter (TF) Architecture, filters the ways accessed in the target cache set, and just a few ways are searched in the tag and data arrays. This allows the approach to reduce the dynamic energy consumption of caches without hurting their access time. For this purpose, the proposed architecture holds the XX least significant bits of each tag in a small auxiliary X-bit-wide array. These bits are used to filter the ways where the least significant bits of the tag do not match with the bits in the X-bit array. Experimental results show that, on average, the TF Architecture reduces the dynamic power consumption across the studied applications up to 74.9%74.9%, 85.9%85.9%, and 84.5%84.5% when applied to L1 caches, L2 caches, and directory caches, respectively.This work has been jointly supported by MINECO and European Commission (FEDER funds) under the project TIN2015-66972-C5-1-R/3-R and by Fundación Séneca, Agencia de Ciencia y Tecnología de la Región de Murcia under the project Jóvenes Líderes en Investigación 18956/JLI/13.Valls, J.; Ros Bardisa, A.; Gómez Requena, ME.; Sahuquillo Borrás, J. (2017). The Tag Filter Architecture: An energy-efficient cache and directory design. Journal of Parallel and Distributed Computing. 100:193-202. https://doi.org/10.1016/j.jpdc.2016.04.016S19320210