On Designing Multicore-aware Simulators for Biological Systems

The stochastic simulation of biological systems is an increasingly popular technique in bioinformatics. It often is an enlightening technique, which may however result in being computational expensive. We discuss the main opportunities to speed it up on multi-core platforms, which pose new challenges for parallelisation techniques. These opportunities are developed in two general families of solutions involving both the single simulation and a bulk of independent simulations (either replicas of derived from parameter sweep). Proposed solutions are tested on the parallelisation of the CWC simulator (Calculus of Wrapped Compartments) that is carried out according to proposed solutions by way of the FastFlow programming framework making possible fast development and efficient execution on multi-cores.Comment: 19 pages + cover pag

Single-Board-Computer Clusters for Cloudlet Computing in Internet of Things

The number of connected sensors and devices is expected to increase to billions in the near future. However, centralised cloud-computing data centres present various challenges to meet the requirements inherent to Internet of Things (IoT) workloads, such as low latency, high throughput and bandwidth constraints. Edge computing is becoming the standard computing paradigm for latency-sensitive real-time IoT workloads, since it addresses the aforementioned limitations related to centralised cloud-computing models. Such a paradigm relies on bringing computation close to the source of data, which presents serious operational challenges for large-scale cloud-computing providers. In this work, we present an architecture composed of low-cost Single-Board-Computer clusters near to data sources, and centralised cloud-computing data centres. The proposed cost-efficient model may be employed as an alternative to fog computing to meet real-time IoT workload requirements while keeping scalability. We include an extensive empirical analysis to assess the suitability of single-board-computer clusters as cost-effective edge-computing micro data centres. Additionally, we compare the proposed architecture with traditional cloudlet and cloud architectures, and evaluate them through extensive simulation. We finally show that acquisition costs can be drastically reduced while keeping performance levels in data-intensive IoT use cases.Ministerio de Economía y Competitividad TIN2017-82113-C2-1-RMinisterio de Economía y Competitividad RTI2018-098062-A-I00European Union’s Horizon 2020 No. 754489Science Foundation Ireland grant 13/RC/209

LEGaTO: first steps towards energy-efficient toolset for heterogeneous computing

LEGaTO is a three-year EU H2020 project which started in December 2017. The LEGaTO project will leverage task-based programming models to provide a software ecosystem for Made-in-Europe heterogeneous hardware composed of CPUs, GPUs, FPGAs and dataflow engines. The aim is to attain one order of magnitude energy savings from the edge to the converged cloud/HPC.Peer ReviewedPostprint (author's final draft