SWAPHI: Smith-Waterman Protein Database Search on Xeon Phi Coprocessors

The maximal sensitivity of the Smith-Waterman (SW) algorithm has enabled its wide use in biological sequence database search. Unfortunately, the high sensitivity comes at the expense of quadratic time complexity, which makes the algorithm computationally demanding for big databases. In this paper, we present SWAPHI, the first parallelized algorithm employing Xeon Phi coprocessors to accelerate SW protein database search. SWAPHI is designed based on the scale-and-vectorize approach, i.e. it boosts alignment speed by effectively utilizing both the coarse-grained parallelism from the many co-processing cores (scale) and the fine-grained parallelism from the 512-bit wide single instruction, multiple data (SIMD) vectors within each core (vectorize). By searching against the large UniProtKB/TrEMBL protein database, SWAPHI achieves a performance of up to 58.8 billion cell updates per second (GCUPS) on one coprocessor and up to 228.4 GCUPS on four coprocessors. Furthermore, it demonstrates good parallel scalability on varying number of coprocessors, and is also superior to both SWIPE on 16 high-end CPU cores and BLAST+ on 8 cores when using four coprocessors, with the maximum speedup of 1.52 and 1.86, respectively. SWAPHI is written in C++ language (with a set of SIMD intrinsics), and is freely available at http://swaphi.sourceforge.net.Comment: A short version of this paper has been accepted by the IEEE ASAP 2014 conferenc

Breadth First Search Vectorization on the Intel Xeon Phi

Breadth First Search (BFS) is a building block for graph algorithms and has recently been used for large scale analysis of information in a variety of applications including social networks, graph databases and web searching. Due to its importance, a number of different parallel programming models and architectures have been exploited to optimize the BFS. However, due to the irregular memory access patterns and the unstructured nature of the large graphs, its efficient parallelization is a challenge. The Xeon Phi is a massively parallel architecture available as an off-the-shelf accelerator, which includes a powerful 512 bit vector unit with optimized scatter and gather functions. Given its potential benefits, work related to graph traversing on this architecture is an active area of research. We present a set of experiments in which we explore architectural features of the Xeon Phi and how best to exploit them in a top-down BFS algorithm but the techniques can be applied to the current state-of-the-art hybrid, top-down plus bottom-up, algorithms. We focus on the exploitation of the vector unit by developing an improved highly vectorized OpenMP parallel algorithm, using vector intrinsics, and understanding the use of data alignment and prefetching. In addition, we investigate the impact of hyperthreading and thread affinity on performance, a topic that appears under researched in the literature. As a result, we achieve what we believe is the fastest published top-down BFS algorithm on the version of Xeon Phi used in our experiments. The vectorized BFS top-down source code presented in this paper can be available on request as free-to-use software

Extreme Scale De Novo Metagenome Assembly

Metagenome assembly is the process of transforming a set of short, overlapping, and potentially erroneous DNA segments from environmental samples into the accurate representation of the underlying microbiomes's genomes. State-of-the-art tools require big shared memory machines and cannot handle contemporary metagenome datasets that exceed Terabytes in size. In this paper, we introduce the MetaHipMer pipeline, a high-quality and high-performance metagenome assembler that employs an iterative de Bruijn graph approach. MetaHipMer leverages a specialized scaffolding algorithm that produces long scaffolds and accommodates the idiosyncrasies of metagenomes. MetaHipMer is end-to-end parallelized using the Unified Parallel C language and therefore can run seamlessly on shared and distributed-memory systems. Experimental results show that MetaHipMer matches or outperforms the state-of-the-art tools in terms of accuracy. Moreover, MetaHipMer scales efficiently to large concurrencies and is able to assemble previously intractable grand challenge metagenomes. We demonstrate the unprecedented capability of MetaHipMer by computing the first full assembly of the Twitchell Wetlands dataset, consisting of 7.5 billion reads - size 2.6 TBytes.Comment: Accepted to SC1

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

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

High Performance Biological Pairwise Sequence Alignment: FPGA versus GPU versus Cell BE versus GPP

This paper explores the pros and cons of reconfigurable computing in the form of FPGAs for high performance efficient computing. In particular, the paper presents the results of a comparative study between three different acceleration technologies, namely, Field Programmable Gate Arrays (FPGAs), Graphics Processor Units (GPUs), and IBM’s Cell Broadband Engine (Cell BE), in the design and implementation of the widely-used Smith-Waterman pairwise sequence alignment algorithm, with general purpose processors as a base reference implementation. Comparison criteria include speed, energy consumption, and purchase and development costs. The study shows that FPGAs largely outperform all other implementation platforms on performance per watt criterion and perform better than all other platforms on performance per dollar criterion, although by a much smaller margin. Cell BE and GPU come second and third, respectively, on both performance per watt and performance per dollar criteria. In general, in order to outperform other technologies on performance per dollar criterion (using currently available hardware and development tools), FPGAs need to achieve at least two orders of magnitude speed-up compared to general-purpose processors and one order of magnitude speed-up compared to domain-specific technologies such as GPUs

Coupling SIMD and SIMT Architectures to Boost Performance of a Phylogeny-aware Alignment Kernel

Background: Aligning short DNA reads to a reference sequence alignment is a prerequisite for detecting their biological origin and analyzing them in a phylogenetic context. With the PaPaRa tool we introduced a dedicated dynamic programming algorithm for simultaneously aligning short reads to reference alignments and corresponding evolutionary reference trees. The algorithm aligns short reads to phylogenetic profiles that correspond to the branches of such a reference tree. The algorithm needs to perform an immense number of pairwise alignments. Therefore, we explore vector intrinsics and GPUs to accelerate the PaPaRa alignment kernel. Results: We optimized and parallelized PaPaRa on CPUs and GPUs. Via SSE 4.1 SIMD (Single Instruction, Multiple Data) intrinsics for x86 SIMD architectures and multi-threading, we obtained a 9-fold acceleration on a single core as well as linear speedups with respect to the number of cores. The peak CPU performance amounts to 18.1 GCUPS (Giga Cell Updates per Second) using all four physical cores on an Intel i7 2600 CPU running at 3.4 GHz. The average CPU performance (averaged over all test runs) is 12.33 GCUPS. We also used OpenCL to execute PaPaRa on a GPU SIMT (Single Instruction, Multiple Threads) architecture. A NVIDIA GeForce 560 GPU delivered peak and average performance of 22.1 and 18.4 GCUPS respectively. Finally, we combined the SIMD and SIMT implementations into a hybrid CPU-GPU system that achieved an accumulated peak performance of 33.8 GCUPS. Conclusions: This accelerated version of PaPaRa (available at www.exelixis-lab.org/software.html) provides a significant performance improvement that allows for analyzing larger datasets in less time. We observe that state-of-the-art SIMD and SIMT architectures deliver comparable performance for this dynamic programming kernel when the “competing programmer approach” is deployed. Finally, we show that overall performance can be substantially increased by designing a hybrid CPU-GPU system with appropriate load distribution mechanisms