Analyzing large-scale DNA Sequences on Multi-core Architectures

Rapid analysis of DNA sequences is important in preventing the evolution of different viruses and bacteria during an early phase, early diagnosis of genetic predispositions to certain diseases (cancer, cardiovascular diseases), and in DNA forensics. However, real-world DNA sequences may comprise several Gigabytes and the process of DNA analysis demands adequate computational resources to be completed within a reasonable time. In this paper we present a scalable approach for parallel DNA analysis that is based on Finite Automata, and which is suitable for analyzing very large DNA segments. We evaluate our approach for real-world DNA segments of mouse (2.7GB), cat (2.4GB), dog (2.4GB), chicken (1GB), human (3.2GB) and turkey (0.2GB). Experimental results on a dual-socket shared-memory system with 24 physical cores show speed-ups of up to 17.6x. Our approach is up to 3x faster than a pattern-based parallel approach that uses the RE2 library.Comment: The 18th IEEE International Conference on Computational Science and Engineering (CSE 2015), Porto, Portugal, 20 - 23 October 201

A fine-grain time-sharing Time Warp system

Although Parallel Discrete Event Simulation (PDES) platforms relying on the Time Warp (optimistic) synchronization protocol already allow for exploiting parallelism, several techniques have been proposed to further favor performance. Among them we can mention optimized approaches for state restore, as well as techniques for load balancing or (dynamically) controlling the speculation degree, the latter being specifically targeted at reducing the incidence of causality errors leading to waste of computation. However, in state of the art Time Warp systems, events’ processing is not preemptable, which may prevent the possibility to promptly react to the injection of higher priority (say lower timestamp) events. Delaying the processing of these events may, in turn, give rise to higher incidence of incorrect speculation. In this article we present the design and realization of a fine-grain time-sharing Time Warp system, to be run on multi-core Linux machines, which makes systematic use of event preemption in order to dynamically reassign the CPU to higher priority events/tasks. Our proposal is based on a truly dual mode execution, application vs platform, which includes a timer-interrupt based support for bringing control back to platform mode for possible CPU reassignment according to very fine grain periods. The latter facility is offered by an ad-hoc timer-interrupt management module for Linux, which we release, together with the overall time-sharing support, within the open source ROOT-Sim platform. An experimental assessment based on the classical PHOLD benchmark and two real world models is presented, which shows how our proposal effectively leads to the reduction of the incidence of causality errors, as compared to traditional Time Warp, especially when running with higher degrees of parallelism

Performance Characterization of Multi-threaded Graph Processing Applications on Intel Many-Integrated-Core Architecture

Intel Xeon Phi many-integrated-core (MIC) architectures usher in a new era of terascale integration. Among emerging killer applications, parallel graph processing has been a critical technique to analyze connected data. In this paper, we empirically evaluate various computing platforms including an Intel Xeon E5 CPU, a Nvidia Geforce GTX1070 GPU and an Xeon Phi 7210 processor codenamed Knights Landing (KNL) in the domain of parallel graph processing. We show that the KNL gains encouraging performance when processing graphs, so that it can become a promising solution to accelerating multi-threaded graph applications. We further characterize the impact of KNL architectural enhancements on the performance of a state-of-the art graph framework.We have four key observations: 1 Different graph applications require distinctive numbers of threads to reach the peak performance. For the same application, various datasets need even different numbers of threads to achieve the best performance. 2 Only a few graph applications benefit from the high bandwidth MCDRAM, while others favor the low latency DDR4 DRAM. 3 Vector processing units executing AVX512 SIMD instructions on KNLs are underutilized when running the state-of-the-art graph framework. 4 The sub-NUMA cache clustering mode offering the lowest local memory access latency hurts the performance of graph benchmarks that are lack of NUMA awareness. At last, We suggest future works including system auto-tuning tools and graph framework optimizations to fully exploit the potential of KNL for parallel graph processing.Comment: published as L. Jiang, L. Chen and J. Qiu, "Performance Characterization of Multi-threaded Graph Processing Applications on Many-Integrated-Core Architecture," 2018 IEEE International Symposium on Performance Analysis of Systems and Software (ISPASS), Belfast, United Kingdom, 2018, pp. 199-20

ILP and TLP in Shared Memory Applications: A Limit Study

The work in this dissertation explores the limits of Chip-multiprocessors (CMPs) with respect to shared-memory, multi-threaded benchmarks, which will help aid in identifying microarchitectural bottlenecks. This, in turn, will lead to more efficient CMP design. In the first part we introduce DotSim, a trace-driven toolkit designed to explore the limits of instruction and thread-level scaling and identify microarchitectural bottlenecks in multi-threaded applications. DotSim constructs an instruction-level Data Flow Graph (DFG) from each thread in multi-threaded applications, adjusting for inter-thread dependencies. The DFGs dynamically change depending on the microarchitectural constraints applied. Exploiting these DFGs allows for the easy extraction of the performance upper bound. We perform a case study on modeling the upper-bound performance limits of a processor microarchitecture modeled off a AMD Opteron. In the second part, we conduct a limit study simultaneously analyzing the two dominant forms of parallelism exploited by modern computer architectures: Instruction Level Parallelism (ILP) and Thread Level Parallelism (TLP). This study gives insight into the upper bounds of performance that future architectures can achieve. Furthermore, it identifies the bottlenecks of emerging workloads. To the best of our knowledge, our work is the first study that combines the two forms of parallelism into one study with modern applications. We evaluate the PARSEC multithreaded benchmark suite using DotSim. We make several contributions describing the high-level behavior of next-generation applications. For example, we show that these applications contain up to a factor of 929X more ILP than what is currently being extracted from real machines. We then show the effects of breaking the application into increasing numbers of threads (exploiting TLP), instruction window size, realistic branch prediction, realistic memory latency, and thread dependencies on exploitable ILP. Our examination shows that theses benchmarks differ vastly from one another. As a result, we expect that no single, homogeneous, micro-architecture will work optimally for all, arguing for reconfigurable, heterogeneous designs. In the third part of this thesis, we use our novel simulator DotSim to study the benefits of prefetching shared memory within critical sections. In this chapter we calculate the upper bound of performance under our given constraints. Our intent is to provide motivation for new techniques to exploit the potential benefits of reducing latency of shared memory among threads. We conduct an idealized workload characterization study focusing on the data that is truly shared among threads, using a simplified memory model. We explore the degree of shared memory criticality, and characterize the benefits of being able to use latency reducing techniques to reduce execution time and increase ILP. We find that on average true sharing among benchmarks is quite low compared to overall memory accesses on the critical path and overall program. We also find that truly shared memory between threads does not affect the critical path for the majority of benchmarks, and when it does the impact is less than 1%. Therefore, we conclude that it is not worth exploring latency reducing techniques of truly shared memory within critical sections

A Non-Blocking Priority Queue for the Pending Event Set

The large diffusion of shared-memory multi-core machines has impacted the way Parallel Discrete Event Simulation (PDES) engines are built. While they were originally conceived as data-partitioned platforms, where each thread is in charge of managing a subset of simulation objects, nowadays the trend is to shift towards share-everything settings. In this scenario, any thread can (in principle) take care of CPU-dispatching pending events bound to whichever simulation object, which helps to fully share the load across the available CPU-cores. Hence, a fundamental aspect to be tackled is to provide an efficient globally-shared pending events’ set from which multiple worker threads can concurrently extract events to be processed, and into which they can concurrently insert new produced events to be processed in the future. To cope with this aspect, we present the design and implementation of a concurrent non-blocking pending events’ set data structure, which can be seen as a variant of a classical calendar queue. Early experimental data collected with a synthetic stress test are reported, showing excellent scalability of our proposal on a machine equipped with 32 CPU-cores