Dataset Information

Scaling read aligners to hundreds of threads on general-purpose processors.

ABSTRACT:

Motivation

General-purpose processors can now contain many dozens of processor cores and support hundreds of simultaneous threads of execution. To make best use of these threads, genomics software must contend with new and subtle computer architecture issues. We discuss some of these and propose methods for improving thread scaling in tools that analyze each read independently, such as read aligners.

Results

We implement these methods in new versions of Bowtie, Bowtie 2 and HISAT. We greatly improve thread scaling in many scenarios, including on the recent Intel Xeon Phi architecture. We also highlight how bottlenecks are exacerbated by variable-record-length file formats like FASTQ and suggest changes that enable superior scaling.

Availability and implementation

Experiments for this study: https://github.com/BenLangmead/bowtie-scaling.

Bowtie

http://bowtie-bio.sourceforge.net.

Bowtie 2

http://bowtie-bio.sourceforge.net/bowtie2.

Hisat

http://www.ccb.jhu.edu/software/hisat.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Langmead B

PROVIDER: S-EPMC6361242 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Scaling read aligners to hundreds of threads on general-purpose processors.

Langmead Ben B Wilks Christopher C Antonescu Valentin V Charles Rone R

Bioinformatics (Oxford, England) 20190201 3

<h4>Motivation</h4>General-purpose processors can now contain many dozens of processor cores and support hundreds of simultaneous threads of execution. To make best use of these threads, genomics software must contend with new and subtle computer architecture issues. We discuss some of these and propose methods for improving thread scaling in tools that analyze each read independently, such as read aligners.<h4>Results</h4>We implement these methods in new versions of Bowtie, Bowtie 2 and HISAT. ...[more]

PMID: 30020410

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Project description:Conspectus There is need in the molecular simulation community to develop new quantum mechanical (QM) methods that can be routinely applied to the simulation of large molecular systems in complex, heterogeneous condensed phase environments. Although conventional methods, such as the hybrid quantum mechanical/molecular mechanical (QM/MM) method, are adequate for many problems, there remain other applications that demand a fully quantum mechanical approach. QM methods are generally required in applications that involve changes in electronic structure, such as when chemical bond formation or cleavage occurs, when molecules respond to one another through polarization or charge transfer, or when matter interacts with electromagnetic fields. A full QM treatment, rather than QM/MM, is necessary when these features present themselves over a wide spatial range that, in some cases, may span the entire system. Specific examples include the study of catalytic events that involve delocalized changes in chemical bonds, charge transfer, or extensive polarization of the macromolecular environment; drug discovery applications, where the wide range of nonstandard residues and protonation states are challenging to model with purely empirical MM force fields; and the interpretation of spectroscopic observables. Unfortunately, the enormous computational cost of conventional QM methods limit their practical application to small systems. Linear-scaling electronic structure methods (LSQMs) make possible the calculation of large systems but are still too computationally intensive to be applied with the degree of configurational sampling often required to make meaningful comparison with experiment. In this work, we present advances in the development of a quantum mechanical force field (QMFF) suitable for application to biological macromolecules and condensed phase simulations. QMFFs leverage the benefits provided by the LSQM and QM/MM approaches to produce a fully QM method that is able to simultaneously achieve very high accuracy and efficiency. The efficiency of the QMFF is made possible by partitioning the system into fragments and self-consistently solving for the fragment-localized molecular orbitals in the presence of the other fragment's electron densities. Unlike a LSQM, the QMFF introduces empirical parameters that are tuned to obtain very accurate intermolecular forces. The speed and accuracy of our QMFF is demonstrated through a series of examples ranging from small molecule clusters to condensed phase simulation, and applications to drug docking and protein-protein interactions. In these examples, comparisons are made to conventional molecular mechanical models, semiempirical methods, ab initio Hamiltonians, and a hybrid QM/MM method. The comparisons demonstrate the superior accuracy of our QMFF relative to the other models; nonetheless, we stress that the overarching role of QMFFs is not to supplant these established computational methods for problems where their use is appropriate. The role of QMFFs within the toolbox of multiscale modeling methods is to extend the range of applications to include problems that demand a fully quantum mechanical treatment of a large system with extensive configurational sampling.

Dataset Information

Scaling read aligners to hundreds of threads on general-purpose processors.

Motivation

Results

Availability and implementation

Bowtie

Bowtie 2

Hisat

Supplementary information

Publications

Scaling read aligners to hundreds of threads on general-purpose processors.

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