Molecular dynamics recipes for genome research

Molecular dynamics (MD) simulation allows one to predict the time evolution of a system of interacting particles. It is widely used in physics, chemistry and biology to address specific questions about the structural properties and dynamical mechanisms of model systems. MD earned a great success in genome research, as it proved to be beneficial in sorting pathogenic from neutral genomic mutations. Considering their computational requirements, simulations are commonly performed on HPC computing devices, which are generally expensive and hard to administer. However, variables like the software tool used for modeling and simulation or the size of the molecule under investigation might make one hardware type or configuration more advantageous than another or even make the commodity hardware definitely suitable for MD studies. This work aims to shed lights on this aspect

Iso-energy-efficiency: An approach to power-constrained parallel computation

Future large scale high performance supercomputer systems require high energy efficiency to achieve exaflops computational power and beyond. Despite the need to understand energy efficiency in high-performance systems, there are few techniques to evaluate energy efficiency at scale. In this paper, we propose a system-level iso-energy-efficiency model to analyze, evaluate and predict energy-performance of data intensive parallel applications with various execution patterns running on large scale power-aware clusters. Our analytical model can help users explore the effects of machine and application dependent characteristics on system energy efficiency and isolate efficient ways to scale system parameters (e.g. processor count, CPU power/frequency, workload size and network bandwidth) to balance energy use and performance. We derive our iso-energy-efficiency model and apply it to the NAS Parallel Benchmarks on two power-aware clusters. Our results indicate that the model accurately predicts total system energy consumption within 5% error on average for parallel applications with various execution and communication patterns. We demonstrate effective use of the model for various application contexts and in scalability decision-making

Performance analysis of direct N-body algorithms for astrophysical simulations on distributed systems

We discuss the performance of direct summation codes used in the simulation of astrophysical stellar systems on highly distributed architectures. These codes compute the gravitational interaction among stars in an exact way and have an O(N^2) scaling with the number of particles. They can be applied to a variety of astrophysical problems, like the evolution of star clusters, the dynamics of black holes, the formation of planetary systems, and cosmological simulations. The simulation of realistic star clusters with sufficiently high accuracy cannot be performed on a single workstation but may be possible on parallel computers or grids. We have implemented two parallel schemes for a direct N-body code and we study their performance on general purpose parallel computers and large computational grids. We present the results of timing analyzes conducted on the different architectures and compare them with the predictions from theoretical models. We conclude that the simulation of star clusters with up to a million particles will be possible on large distributed computers in the next decade. Simulating entire galaxies however will in addition require new hybrid methods to speedup the calculation.Comment: 22 pages, 8 figures, accepted for publication in Parallel Computin

Machine Learning-Based Elastic Cloud Resource Provisioning in the Solvency II Framework

The Solvency II Directive (Directive 2009/138/EC) is a European Directive issued in November 2009 and effective from January 2016, which has been enacted by the European Union to regulate the insurance and reinsurance sector through the discipline of risk management. Solvency II requires European insurance companies to conduct consistent evaluation and continuous monitoring of risks—a process which is computationally complex and extremely resource-intensive. To this end, companies are required to equip themselves with adequate IT infrastructures, facing a significant outlay. In this paper we present the design and the development of a Machine Learning-based approach to transparently deploy on a cloud environment the most resource-intensive portion of the Solvency II-related computation. Our proposal targets DISAR®, a Solvency II-oriented system initially designed to work on a grid of conventional computers. We show how our solution allows to reduce the overall expenses associated with the computation, without hampering the privacy of the companies’ data (making it suitable for conventional public cloud environments), and allowing to meet the strict temporal requirements required by the Directive. Additionally, the system is organized as a self-optimizing loop, which allows to use information gathered from actual (useful) computations, thus requiring a shorter training phase. We present an experimental study conducted on Amazon EC2 to assess the validity and the efficiency of our proposal