arXiv subjects

Katherine Yelick

Publications and source records attributed to Katherine Yelick.

30 records · Page 2Linked to original sources

arXiv2020

diBELLA: Distributed Long Read to Long Read Alignment

We present a parallel algorithm and scalable implementation for genome analysis, specifically the problem of finding overlaps and alignments for data from "third generation" long read sequencers. While long sequences of DNA offer enormous advantages for biological analysis and insight, current long read sequencing instruments have high error rates and therefore require different approaches to analysis than their short read counterparts. Our work focuses on an efficient distributed-memory parallelization of an accurate single-node algorithm for overlapping and aligning long reads. We achieve scalability of this irregular algorithm by addressing the competing issues of increasing parallelism, minimizing communication, constraining the memory footprint, and ensuring good load balance. The resulting application, diBELLA, is the first distributed memory overlapper and aligner specifically designed for long reads and parallel scalability. We describe and present analyses for high level design trade-offs and conduct an extensive empirical analysis that compares performance characteristics across state-of-the-art HPC systems as well as a commercial cloud architectures, highlighting the advantages of state-of-the-art network technologies.

cs.DC↗

arXiv2020

The Parallelism Motifs of Genomic Data Analysis

Genomic data sets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share this data with the research community, but some of these genomic data analysis problems require large scale computational platforms to meet both the memory and computational requirements. These applications differ from scientific simulations that dominate the workload on high end parallel systems today and place different requirements on programming support, software libraries, and parallel architectural design. For example, they involve irregular communication patterns such as asynchronous updates to shared data structures. We consider several problems in high performance genomics analysis, including alignment, profiling, clustering, and assembly for both single genomes and metagenomes. We identify some of the common computational patterns or motifs that help inform parallelization strategies and compare our motifs to some of the established lists, arguing that at least two key patterns, sorting and hashing, are missing.

cs.DC↗

arXiv2019

RDMA vs. RPC for Implementing Distributed Data Structures

Distributed data structures are key to implementing scalable applications for scientific simulations and data analysis. In this paper we look at two implementation styles for distributed data structures: remote direct memory access (RDMA) and remote procedure call (RPC). We focus on operations that require individual accesses to remote portions of a distributed data structure, e.g., accessing a hash table bucket or distributed queue, rather than global operations in which all processors collectively exchange information. We look at the trade-offs between the two styles through microbenchmarks and a performance model that approximates the cost of each. The RDMA operations have direct hardware support in the network and therefore lower latency and overhead, while the RPC operations are more expressive but higher cost and can suffer from lack of attentiveness from the remote side. We also run experiments to compare the real-world performance of RDMA- and RPC-based data structure operations with the predicted performance to evaluate the accuracy of our model, and show that while the model does not always precisely predict running time, it allows us to choose the best implementation in the examples shown. We believe this analysis will assist developers in designing data structures that will perform well on current network architectures, as well as network architects in providing better support for this class of distributed data structures.

cs.DC↗

arXiv2018

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.

cs.DC↗

arXiv2018

Communication-Avoiding Optimization Methods for Distributed Massive-Scale Sparse Inverse Covariance Estimation

Across a variety of scientific disciplines, sparse inverse covariance estimation is a popular tool for capturing the underlying dependency relationships in multivariate data. Unfortunately, most estimators are not scalable enough to handle the sizes of modern high-dimensional data sets (often on the order of terabytes), and assume Gaussian samples. To address these deficiencies, we introduce HP-CONCORD, a highly scalable optimization method for estimating a sparse inverse covariance matrix based on a regularized pseudolikelihood framework, without assuming Gaussianity. Our parallel proximal gradient method uses a novel communication-avoiding linear algebra algorithm and runs across a multi-node cluster with up to 1k nodes (24k cores), achieving parallel scalability on problems with up to ~819 billion parameters (1.28 million dimensions); even on a single node, HP-CONCORD demonstrates scalability, outperforming a state-of-the-art method. We also use HP-CONCORD to estimate the underlying dependency structure of the brain from fMRI data, and use the result to identify functional regions automatically. The results show good agreement with a clustering from the neuroscience literature.

stat.ML↗

arXiv2017

Advanced Cyberinfrastructure for Science, Engineering, and Public Policy

Progress in many domains increasingly benefits from our ability to view the systems through a computational lens, i.e., using computational abstractions of the domains; and our ability to acquire, share, integrate, and analyze disparate types of data. These advances would not be possible without the advanced data and computational cyberinfrastructure and tools for data capture, integration, analysis, modeling, and simulation. However, despite, and perhaps because of, advances in "big data" technologies for data acquisition, management and analytics, the other largely manual, and labor-intensive aspects of the decision making process, e.g., formulating questions, designing studies, organizing, curating, connecting, correlating and integrating crossdomain data, drawing inferences and interpreting results, have become the rate-limiting steps to progress. Advancing the capability and capacity for evidence-based improvements in science, engineering, and public policy requires support for (1) computational abstractions of the relevant domains coupled with computational methods and tools for their analysis, synthesis, simulation, visualization, sharing, and integration; (2) cognitive tools that leverage and extend the reach of human intellect, and partner with humans on all aspects of the activity; (3) nimble and trustworthy data cyber-infrastructures that connect, manage a variety of instruments, multiple interrelated data types and associated metadata, data representations, processes, protocols and workflows; and enforce applicable security and data access and use policies; and (4) organizational and social structures and processes for collaborative and coordinated activity across disciplinary and institutional boundaries.

cs.CY↗

arXiv2017

Extreme-Scale De Novo Genome Assembly

De novo whole genome assembly reconstructs genomic sequence from short, overlapping, and potentially erroneous DNA segments and is one of the most important computations in modern genomics. This work presents HipMER, a high-quality end-to-end de novo assembler designed for extreme scale analysis, via efficient parallelization of the Meraculous code. Genome assembly software has many components, each of which stresses different components of a computer system. This chapter explains the computational challenges involved in each step of the HipMer pipeline, the key distributed data structures, and communication costs in detail. We present performance results of assembling the human genome and the large hexaploid wheat genome on large supercomputers up to tens of thousands of cores.

cs.DC↗

arXiv2016

21st Century Computer Architecture

Because most technology and computer architecture innovations were (intentionally) invisible to higher layers, application and other software developers could reap the benefits of this progress without engaging in it. Higher performance has both made more computationally demanding applications feasible (e.g., virtual assistants, computer vision) and made less demanding applications easier to develop by enabling higher-level programming abstractions (e.g., scripting languages and reusable components). Improvements in computer system cost-effectiveness enabled value creation that could never have been imagined by the field's founders (e.g., distributed web search sufficiently inexpensive so as to be covered by advertising links). The wide benefits of computer performance growth are clear. Recently, Danowitz et al. apportioned computer performance growth roughly equally between technology and architecture, with architecture credited with ~80x improvement since 1985. As semiconductor technology approaches its "end-of-the-road" (see below), computer architecture will need to play an increasing role in enabling future ICT innovation. But instead of asking, "How can I make my chip run faster?," architects must now ask, "How can I enable the 21st century infrastructure, from sensors to clouds, adding value from performance to privacy, but without the benefit of near-perfect technology scaling?". The challenges are many, but with appropriate investment, opportunities abound. Underlying these opportunities is a common theme that future architecture innovations will require the engagement of and investments from innovators in other ICT layers.

cs.CY↗

arXiv2016

An Asynchronous Task-based Fan-Both Sparse Cholesky Solver

Systems of linear equations arise at the heart of many scientific and engineering applications. Many of these linear systems are sparse; i.e., most of the elements in the coefficient matrix are zero. Direct methods based on matrix factorizations are sometimes needed to ensure accurate solutions. For example, accurate solution of sparse linear systems is needed in shift-invert Lanczos to compute interior eigenvalues. The performance and resource usage of sparse matrix factorizations are critical to time-to-solution and maximum problem size solvable on a given platform. In many applications, the coefficient matrices are symmetric, and exploiting symmetry will reduce both the amount of work and storage cost required for factorization. When the factorization is performed on large-scale distributed memory platforms, communication cost is critical to the performance of the algorithm. At the same time, network topologies have become increasingly complex, so that modern platforms exhibit a high level of performance variability. This makes scheduling of computations an intricate and performance-critical task. In this paper, we investigate the use of an asynchronous task paradigm, one-sided communication and dynamic scheduling in implementing sparse Cholesky factorization (symPACK) on large-scale distributed memory platforms. Our solver symPACK relies on efficient and flexible communication primitives provided by the UPC++ library. Performance evaluation shows good scalability and that symPACK outperforms state-of-the-art parallel distributed memory factorization packages, validating our approach on practical cases.

cs.MS↗

arXiv2016

Accelerating Science: A Computing Research Agenda

The emergence of "big data" offers unprecedented opportunities for not only accelerating scientific advances but also enabling new modes of discovery. Scientific progress in many disciplines is increasingly enabled by our ability to examine natural phenomena through the computational lens, i.e., using algorithmic or information processing abstractions of the underlying processes; and our ability to acquire, share, integrate and analyze disparate types of data. However, there is a huge gap between our ability to acquire, store, and process data and our ability to make effective use of the data to advance discovery. Despite successful automation of routine aspects of data management and analytics, most elements of the scientific process currently require considerable human expertise and effort. Accelerating science to keep pace with the rate of data acquisition and data processing calls for the development of algorithmic or information processing abstractions, coupled with formal methods and tools for modeling and simulation of natural processes as well as major innovations in cognitive tools for scientists, i.e., computational tools that leverage and extend the reach of human intellect, and partner with humans on a broad range of tasks in scientific discovery (e.g., identifying, prioritizing formulating questions, designing, prioritizing and executing experiments designed to answer a chosen question, drawing inferences and evaluating the results, and formulating new questions, in a closed-loop fashion). This calls for concerted research agenda aimed at: Development, analysis, integration, sharing, and simulation of algorithmic or information processing abstractions of natural processes, coupled with formal methods and tools for their analyses and simulation; Innovations in cognitive tools that augment and extend human intellect and partner with humans in all aspects of science.

cs.CY↗

arXiv2015

On Holder-Brascamp-Lieb inequalities for torsion-free discrete Abelian groups

Hölder-Brascamp-Lieb inequalities provide upper bounds for a class of multilinear expressions, in terms of $L^p$ norms of the functions involved. They have been extensively studied for functions defined on Euclidean spaces. Bennett-Carbery-Christ-Tao have initiated the study of these inequalities for discrete Abelian groups and, in terms of suitable data, have characterized the set of all tuples of exponents for which such an inequality holds for specified data, as the convex polyhedron defined by a particular finite set of affine inequalities. In this paper we advance the theory of such inequalities for torsion-free discrete Abelian groups in three respects. The optimal constant in any such inequality is shown to equal $1$ whenever it is finite. An algorithm that computes the admissible polyhedron of exponents is developed. It is shown that nonetheless, existence of an algorithm that computes the full list of inequalities in the Bennett-Carbery-Christ-Tao description of the admissible polyhedron for all data, is equivalent to an affirmative solution of Hilbert's Tenth Problem over the rationals. That problem remains open. Applications to computer science will be explored in a forthcoming companion paper.

math.CA↗

arXiv2013

Communication lower bounds and optimal algorithms for programs that reference arrays -- Part 1

The movement of data (communication) between levels of a memory hierarchy, or between parallel processors on a network, can greatly dominate the cost of computation, so algorithms that minimize communication are of interest. Motivated by this, attainable lower bounds for the amount of communication required by algorithms were established by several groups for a variety of algorithms, including matrix computations. Prior work of Ballard-Demmel-Holtz-Schwartz relied on a geometric inequality of Loomis and Whitney for this purpose. In this paper the general theory of discrete multilinear Holder-Brascamp-Lieb (HBL) inequalities is used to establish communication lower bounds for a much wider class of algorithms. In some cases, algorithms are presented which attain these lower bounds. Several contributions are made to the theory of HBL inequalities proper. The optimal constant in such an inequality for torsion-free Abelian groups is shown to equal one whenever it is finite. Bennett-Carbery-Christ-Tao had characterized the tuples of exponents for which such an inequality is valid as the convex polyhedron defined by a certain finite list of inequalities. The problem of constructing an algorithm to decide whether a given inequality is on this list, is shown to be equivalent to Hilbert's Tenth Problem over the rationals, which remains open. Nonetheless, an algorithm which computes the polyhedron itself is constructed.

math.CA↗