No abstract

With the increasing popularity of the cloud computing model and rapid proliferation of cloud infrastructures there are increasing concerns about energy consumption and consequent impact of cloud computing as a contributor to global CO2 emissions. To date, little is known about how to incorporate energy consumption and CO2 concerns into cloud application development and deployment decision models. In this respect, this paper describes an eco-aware approach that relies on the definition, monitoring and utilization of energy and CO2 metrics combined with the use of innovative application scheduling and runtime adaptation techniques to optimize energy consumption and CO2 footprint of cloud applications as well as the underlying infrastructure. The eco-aware approach involves measuring or quantifying the energy consumption and CO2 at different levels of cloud computing, using that information to create scheduling and adaptation techniques that contribute towards reducing the energy consumption and CO2 emissions, and finally testing and validating the developed solutions in a multi-site cloud environment with the help of challenging case study applications. The experimental and validation results show the potential of the eco-aware approach to significantly reduce the CO2 footprint and consequent environmental impact of cloud applications.

Workflow management systems represent, manage, and execute multistep computational analyses and offer many benefits to bioinformaticians. They provide a common language for describing analysis workflows, contributing to reproducibility and to building libraries of reusable components. They can support both incremental build and re-entrancy—the ability to selectively re-execute parts of a workflow in the presence of additional inputs or changes in configuration and to resume execution from where a workflow previously stopped. Many workflow management systems enhance portability by supporting the use of containers, high-performance computing (HPC) systems, and clouds. Most importantly, workflow management systems allow bioinformaticians to delegate how their workflows are run to the workflow management system and its developers. This frees the bioinformaticians to focus on what these workflows should do, on their data analyses, and on their science. RiboViz is a package to extract biological insight from ribosome profiling data to help advance understanding of protein synthesis. At the heart of RiboViz is an analysis workflow, implemented in a Python script. To conform to best practices for scientific computing which recommend the use of build tools to automate workflows and to reuse code instead of rewriting it, the authors reimplemented this workflow within a workflow management system. To select a workflow management system, a rapid survey of available systems was undertaken, and candidates were shortlisted: Snakemake, cwltool, Toil, and Nextflow. Each candidate was evaluated by quickly prototyping a subset of the RiboViz workflow, and Nextflow was chosen. The selection process took 10 person-days, a small cost for the assurance that Nextflow satisfied the authors’ requirements. The use of prototyping can offer a low-cost way of making a more informed selection of software to use within projects, rather than relying solely upon reviews and recommendations by others.

No abstract

Sound synthesis using physical modeling, emulating systems of a complexity approaching and even exceeding that of real-world acoustic musical instruments, is becoming possible, thanks to recent theoretical developments in musical acoustics and algorithm design. Severe practical difficulties remain, both at the level of the raw computational resources required, and at the level of user control. An approach to the first difficulty is through the use of large-scale parallelization, and results for a variety of physical modeling systems are presented here. Any progress with regard to the second difficulty requires, necessarily, the experience and advice of professional musicians. A basic interface to a parallelized large-scale physical modeling synthesis system is presented here, accompanied by first-hand descriptions of the working methods of five composers, each of whom generated complete multichannel pieces using the system.