BEAGLE 3:Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics

© 2019 The Author(s). BEAGLE is a high-performance likelihood-calculation library for phylogenetic inference. The BEAGLE library defines a simple, but flexible, application programming interface (API), and includes a collection of efficient implementations for calculation under a variety of evolutionary models on different hardware devices. The library has been integrated into recent versions of popular phylogenetics software packages including BEAST and MrBayes and has been widely used across a diverse range of evolutionary studies. Here, we present BEAGLE 3 with new parallel implementations, increased performance for challenging data sets, improved scalability, and better usability. We have added new OpenCL and central processing unit-threaded implementations to the library, allowing the effective utilization of a wider range of modern hardware. Further, we have extended the API and library to support concurrent computation of independent partial likelihood arrays, for increased performance of nucleotide-model analyses with greater flexibility of data partitioning. For better scalability and usability, we have improved how phylogenetic software packages use BEAGLE in multi-GPU (graphics processing unit) and cluster environments, and introduced an automated method to select the fastest device given the data set, evolutionary model, and hardware. For application developers who wish to integrate the library, we also have developed an online tutorial. To evaluate the effect of the improvements, we ran a variety of benchmarks on state-of-the-art hardware. For a partitioned exemplar analysis, we observe run-time performance improvements as high as 5.9-fold over our previous GPU implementation. BEAGLE 3 is free, open-source software licensed under the Lesser GPL and available at https://beagle-dev.github.io

Reducing energy demand: a review of issues, challenges and approaches

Most commentators expect improved energy efficiency and reduced energy demand to provide the dominant contribution to tackling global climate change. But at the global level, the correlation between increased wealth and increased energy consumption is very strong and the impact of policies to reduce energy demand is both limited and contested. Different academic disciplines approach energy demand reduction in different ways: emphasising some mechanisms and neglecting others, being more or less optimistic about the potential for reducing energy demand and providing insights that are more or less useful for policymakers. This article provides an overview of the main issues and challenges associated with energy demand reduction, summarises how this challenge is ‘framed’ by key academic disciplines, indicates how these can provide complementary insights for policymakers and argues that a ‘sociotechnical’ perspective can provide a deeper understanding of the nature of this challenge and the processes through which it can be achieved. The article integrates ideas from the natural sciences, economics, psychology, innovation studies and sociology but does not give equal weight to each. It argues that reducing energy demand will prove more difficult than is commonly assumed and current approaches will be insufficient to deliver the transformation required

Impact of Scottish smoke-free legislation on smoking quit attempts and prevalence

<p><b>Objectives:</b> In Scotland, legislation was implemented in March 2006 prohibiting smoking in all wholly or partially enclosed public spaces. We investigated the impact on attempts to quit smoking and smoking prevalence.</p> <p><b>Methods:</b> We performed time series models using Box-Jenkins autoregressive integrated moving averages (ARIMA) on monthly data on the gross ingredient cost of all nicotine replacement therapy (NRT) prescribed in Scotland in 2003–2009, and quarterly data on self-reported smoking prevalence between January 1999 and September 2010 from the Scottish Household Survey.</p> <p><b>Results:</b> NRT prescription costs were significantly higher than expected over the three months prior to implementation of the legislation. Prescription costs peaked at £1.3 million in March 2006; £292,005.9 (95% CI £260,402.3, £323,609, p<0.001) higher than the monthly norm. Following implementation of the legislation, costs fell exponentially by around 26% per month (95% CI 17%, 35%, p<0.001). Twelve months following implementation, the costs were not significantly different to monthly norms. Smoking prevalence fell by 8.0% overall, from 31.3% in January 1999 to 23.7% in July–September 2010. In the quarter prior to implementation of the legislation, smoking prevalence fell by 1.7% (95% CI 2.4%, 1.0%, p<0.001) more than expected from the underlying trend.</p> <p><b>Conclusions:</b> Quit attempts increased in the three months leading up to Scotland's smoke-free legislation, resulting in a fall in smoking prevalence. However, neither has been sustained suggesting the need for additional tobacco control measures and ongoing support.</p&gt

BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics

Phylogenetic inference is fundamental to our understanding of most aspects of the origin and evolution of life, and in recent years, there has been a concentration of interest in statistical approaches such as Bayesian inference and maximum likelihood estimation. Yet, for large data sets and realistic or interesting models of evolution, these approaches remain computationally demanding. High-throughput sequencing can yield data for thousands of taxa, but scaling to such problems using serial computing often necessitates the use of nonstatistical or approximate approaches. The recent emergence of graphics processing units (GPUs) provides an opportunity to leverage their excellent floating-point computational performance to accelerate statistical phylogenetic inference. A specialized library for phylogenetic calculation would allow existing software packages to make more effective use of available computer hardware, including GPUs. Adoption of a common library would also make it easier for other emerging computing architectures, such as field programmable gate arrays, to be used in the future. We present BEAGLE, an application programming interface (API) and library for high-performance statistical phylogenetic inference. The API provides a uniform interface for performing phylogenetic likelihood calculations on a variety of compute hardware platforms. The library includes a set of efficient implementations and can currently exploit hardware including GPUs using NVIDIA CUDA, central processing units (CPUs) with Streaming SIMD Extensions and related processor supplementary instruction sets, and multicore CPUs via OpenMP. To demonstrate the advantages of a common API, we have incorporated the library into several popular phylogenetic software packages. The BEAGLE library is free open source software licensed under the Lesser GPL and available from http://beagle-lib.googlecode.com. An example client program is available as public domain software.This work was supported by the National Science Foundation [grant numbers DBI-0755048, DEB-0732920, DEB-1036448, DMS-0931642, EF-0331495, EF-0905606, EF-0949453]; the National Institutes of Health [grant numbers R01-HG006139, R01-GM037841, R01-GM078985, R01-GM086887, R01-NS063897]; the Biotechnology and Biological Sciences Research Council [grant number BB/H011285/1]; the Wellcome Trust [grant number WT092807MA]; and Google Summer of Code

Determination of neutrino mass hierarchy by 21 cm line and CMB B-mode polarization observations

We focus on the ongoing and future observations for both the 21 cm line and the CMB B-mode polarization produced by a CMB lensing, and study their sensitivities to the effective number of neutrino species, the total neutrino mass, and the neutrino mass hierarchy. We find that combining the CMB observations with future square kilometer arrays optimized for 21 cm line such as Omniscope can determine the neutrino mass hierarchy at 2 sigma. We also show that a more feasible combination of Planck + POLARBEAR and SKA can strongly improve errors of the bounds on the total neutrino mass and the effective number of neutrino species to be Delta Sigma m_nu ~ 0.12 eV and Delta N_nu ~ 0.38 at 2 sigma.Comment: 10 pages, 3 figures, to appear in Phys. Lett.

Toxoplasma and coxiella infection and psychiatric morbidity: A retrospective cohort analysis

BACKGROUND: It has been suggested that infection with Toxoplasma gondii is associated with slow reaction and poor concentration, whilst infection with Coxiella burnetii may lead to persistent symptoms of fatigue. METHODS: 425 farmers completed the Revised Clinical Interview Schedule (CIS-R) by computer between March and July 1999 to assess psychiatric morbidity. Samples of venous blood had been previously collected and seroprevalence of T. gondii and C. burnetii was assessed. RESULTS: 45% of the cohort were seropositive for T. gondii and 31% were positive for C. burnetii. Infection with either agent was not associated with symptoms reflecting clinically relevant levels of concentration difficulties, fatigue, depression, depressive ideas or overall psychiatric morbidity. CONCLUSIONS: We do not provide any evidence that infection with Toxoplasma gondii or Coxiella burnetii is associated with neuropsychiatric morbidity, in particular with symptoms of poor concentration or fatigue. However, this is a relatively healthy cohort with few individuals reporting neuropsychiatric morbidity and therefore the statistical power to test the study hypotheses is limited

Spectroscopic binaries among Hipparcos M giants III. The eccentricity-period diagram and mass-transfer signatures

This paper is the third one in a series devoted to studying the properties of binaries involving M giants. We use a new set of orbits to construct the first (e-logP) diagram of an extensive sample of M giant binaries, to obtain their mass-function distribution, and to derive evolutionary constraints for this class of binaries and related systems. The orbital properties of binaries involving M giants were analysed and compared with those of related families of binaries (K giants, post-AGB stars, barium stars, Tc-poor S stars). The orbital elements of post-AGB stars and M giants are not different, which may very indicate that, for the considered sample of post-AGB binaries, the post-AGB star left the AGB at quite an early stage (M4 or so). Neither are the orbital elements of post-mass-transfer binaries like barium stars very different from those of M giants, suggesting that the mass transfer did not alter the orbital elements much, contrary to current belief. Finally, we show that binary systems with e < 0.4 log P - 1 (with periods expressed in days) are predominantly post-mass-transfer systems, because (i) the vast majority of barium and S systems match this condition, and (ii) these systems have companion masses peaking around 0.6 solar mass, as expected for white dwarfs. The latter property has been shown to hold as well for open-cluster binaries involving K giants, for which a lower bound on the companion mass may easily be set.Comment: 14 pages, 12 figures, accepted for publication in A&A, language editing changes onl