RAxML-Cell: Parallel Phylogenetic Tree Inference on the Cell Broadband Engine

Phylogenetic tree reconstruction is one of the grand challenge problems in Bioinformatics. The search for a best-scoring tree with 50 organisms, under a reasonable optimality criterion, creates a topological search space which is as large as the number of atoms in the universe. Computational phylogeny is challenging even for the most powerful supercomputers. It is also an ideal candidate for benchmarking emerging multiprocessor architectures, because it exhibits various levels of fine and coarse-grain parallelism. In this paper, we present the porting, optimization, and evaluation of RAxML on the Cell Broadband Engine. RAxML is a provably efficient, hill climbing algorithm for computing phylogenetic trees based on the Maximum Likelihood (ML) method. The algorithm uses an embarrassingly parallel search method, which also exhibits data-level parallelism and control parallelism in the computation of the likelihood functions. We present the optimization of one of the currently fastest tree search algorithms, on a real Cell blade prototype. We also investigate problems and present solutions pertaining to the optimization of floating point code, control flow, communication, scheduling, and multi-level parallelization on the Cell

Maximizing multithreaded multicore architectures through thread migrations

Heterogeneity in general-purpose workloads often end up in non optimal per-thread hardware resource usage. The current trend towards multicore architectures, containing several multithreaded cores, increases the need of a complexity-effective way to expose the heterogeneity in general-purpose workloads to the underlying hardware, in order to obtain all the potential performance of these architectures. In this paper we present the Heterogeneity-Aware Dynamic Thread Migrator (hDTM), a novel complexity-effective hardware mechanism that exposes the heterogeneity in software to the hardware, also enabling the hardware to react to the dynamic behavior variations in the running applications. By means of core-to-core thread migrations, the hDTM mechanism strives to perform the desired behavior transparently to the Operating System. As an example of the general-purpose hDTM concept presented in this paper, we describe a naive hDTM implementation for a Power5-like processor and provide results on the benefits of the proposed mechanism. Our results indicate that even this simple hDTM implementation is able to get close to hDTM’s goal, not only avoiding losses due to bad thread-to-core assignments (up to a 25%) but also going beyond the best static thread-to-core assignment upper limit.Postprint (published version

Using MCD-DVS for dynamic thermal management performance improvement

With chip temperature being a major hurdle in microprocessor design, techniques to recover the performance loss due to thermal emergency mechanisms are crucial in order to sustain performance growth. Many techniques for power reduction in the past and some on thermal management more recently have contributed to alleviate this problem. Probably the most important thermal control technique is dynamic voltage and frequency scaling (DVS) which allows for almost cubic reduction in power with worst-case performance penalty only linear. So far, DVS techniques for temperature control have been studied at the chip level. Finer grain DVS is feasible if a globally-asynchronous locally-synchronous (GALS) design style is employed. GALS, also known as multiple-clock domain (MCD), allows for an independent voltage and frequency control for each one of the clock domains that are part of the chip. There are several studies on DVS for GALS that aim to improve energy and power efficiency but not temperature. This paper proposes and analyses the usage of DVS at the domain level to control temperature in a clustered MCD microarchitecture with the goal of improving the performance of applications that do not meet the thermal constraints imposed by the designers.Peer ReviewedPostprint (published version

Dynamic Multigrain Parallelization on the Cell Broadband Engine

This paper addresses the problem of orchestrating and scheduling parallelism at multiple levels of granularity on heterogeneous multicore processors. We present policies and mechanisms for adaptive exploitation and scheduling of multiple layers of parallelism on the Cell Broadband Engine. Our policies combine event-driven task scheduling with malleable loop-level parallelism, which is exposed from the runtime system whenever task-level parallelism leaves cores idle. We present a runtime system for scheduling applications with layered parallelism on Cell and investigate its potential with RAxML, a computational biology application which infers large phylogenetic trees, using the Maximum Likelihood (ML) method. Our experiments show that the Cell benefits significantly from dynamic parallelization methods, that selectively exploit the layers of parallelism in the system, in response to workload characteristics. Our runtime environment outperforms naive parallelization and scheduling based on MPI and Linux by up to a factor of 2.6. We are able to execute RAxML on one Cell four times faster than on a dual-processor system with Hyperthreaded Xeon processors, and 5--10\% faster than on a single-processor system with a dual-core, quad-thread IBM Power5 processor

Mixed-mode multicore reliability

Future processors are expected to observe increasing rates of hardware faults. Using Dual-Modular Redundancy (DMR), two cores of a multicore can be loosely coupled to redundantly execute a single software thread, providing very high coverage from many difference sources of faults. This reliability, however, comes at a high price in terms of per-thread IPC and overall system throughput. We make the observation that a user may want to run both applications requiring high reliability, such as financial software, and more fault tolerant applications requiring high performance, such as media or web software, on the same machine at the same time. Yet a traditional DMR system must fully operate in redundant mode whenever any application requires high reliability. This paper proposes a Mixed-Mode Multicore (MMM), which enables most applications, including the system software, to run with high reliability in DMR mode, while applications that need high performance can avoid the penalty of DMR. Though conceptually simple, two key challenges arise: 1) care must be taken to protect reliable applications from any faults occurring to applications running in high performance mode, and 2) the desire to execute additional independent software threads for a performance application complicates the scheduling of computation to cores. After solving these issues, an MMM is shown to improve overall system performance, compared to a traditional DMR system, by approximately 2X when one reliable and one performance application are concurrently executing

Exploring New Search Algorithms and Hardware for Phylogenetics: RAxML Meets the IBM Cell

Phylogenetic inference is considered to be one of the grand challenges in Bioinformatics due to the immense computational requirements. RAxML is currently among the fastest and most accurate programs for phylogenetic tree inference under the Maximum Likelihood (ML) criterion. First, we introduce new tree search heuristics that accelerate RAxML by a factor of 2.43 while returning equally good trees. The performance of the new search algorithm has been assessed on 18 real-world datasets comprising 148 up to 4,843 DNA sequences. We then present the implementation, optimization, and evaluation of RAxML on the IBM Cell Broadband Engine. We address the problems and provide solutions pertaining to the optimization of floating point code, control flow, communication, and scheduling of multi-level parallelism on the Cel

A Detailed Analysis of Contemporary ARM and x86 Architectures

RISC vs. CISC wars raged in the 1980s when chip area and processor design complexity were the primary constraints and desktops and servers exclusively dominated the computing landscape. Today, energy and power are the primary design constraints and the computing landscape is significantly different: growth in tablets and smartphones running ARM (a RISC ISA) is surpassing that of desktops and laptops running x86 (a CISC ISA). Further, the traditionally low-power ARM ISA is entering the high-performance server market, while the traditionally high-performance x86 ISA is entering the mobile low-power device market. Thus, the question of whether ISA plays an intrinsic role in performance or energy efficiency is becoming important, and we seek to answer this question through a detailed measurement based study on real hardware running real applications. We analyze measurements on the ARM Cortex-A8 and Cortex-A9 and Intel Atom and Sandybridge i7 microprocessors over workloads spanning mobile, desktop, and server computing. Our methodical investigation demonstrates the role of ISA in modern microprocessors? performance and energy efficiency. We find that ARM and x86 processors are simply engineering design points optimized for different levels of performance, and there is nothing fundamentally more energy efficient in one ISA class or the other. The ISA being RISC or CISC seems irrelevant