High-throughput Binding Affinity Calculations at Extreme Scales

Resistance to chemotherapy and molecularly targeted therapies is a major factor in limiting the effectiveness of cancer treatment. In many cases, resistance can be linked to genetic changes in target proteins, either pre-existing or evolutionarily selected during treatment. Key to overcoming this challenge is an understanding of the molecular determinants of drug binding. Using multi-stage pipelines of molecular simulations we can gain insights into the binding free energy and the residence time of a ligand, which can inform both stratified and personal treatment regimes and drug development. To support the scalable, adaptive and automated calculation of the binding free energy on high-performance computing resources, we introduce the High- throughput Binding Affinity Calculator (HTBAC). HTBAC uses a building block approach in order to attain both workflow flexibility and performance. We demonstrate close to perfect weak scaling to hundreds of concurrent multi-stage binding affinity calculation pipelines. This permits a rapid time-to-solution that is essentially invariant of the calculation protocol, size of candidate ligands and number of ensemble simulations. As such, HTBAC advances the state of the art of binding affinity calculations and protocols

Optimizing egalitarian performance in the side-effects model of colocation for data center resource management

In data centers, up to dozens of tasks are colocated on a single physical machine. Machines are used more efficiently, but tasks' performance deteriorates, as colocated tasks compete for shared resources. As tasks are heterogeneous, the resulting performance dependencies are complex. In our previous work [18] we proposed a new combinatorial optimization model that uses two parameters of a task - its size and its type - to characterize how a task influences the performance of other tasks allocated to the same machine. In this paper, we study the egalitarian optimization goal: maximizing the worst-off performance. This problem generalizes the classic makespan minimization on multiple processors (P||Cmax). We prove that polynomially-solvable variants of multiprocessor scheduling are NP-hard and hard to approximate when the number of types is not constant. For a constant number of types, we propose a PTAS, a fast approximation algorithm, and a series of heuristics. We simulate the algorithms on instances derived from a trace of one of Google clusters. Algorithms aware of jobs' types lead to better performance compared with algorithms solving P||Cmax. The notion of type enables us to model degeneration of performance caused by using standard combinatorial optimization methods. Types add a layer of additional complexity. However, our results - approximation algorithms and good average-case performance - show that types can be handled efficiently.Comment: Author's version of a paper published in Euro-Par 2017 Proceedings, extends the published paper with addtional results and proof

Resource management in heterogeneous computing systems with tasks of varying importance

2014 Summer.The problem of efficiently assigning tasks to machines in heterogeneous computing environments where different tasks can have different levels of importance (or value) to the computing system is a challenging one. The goal of this work is to study this problem in a variety of environments. One part of the study considers a computing system and its corresponding workload based on the expectations for future environments of Department of Energy and Department of Defense interest. We design heuristics to maximize a performance metric created using utility functions. We also create a framework to analyze the trade-offs between performance and energy consumption. We design techniques to maximize performance in a dynamic environment that has a constraint on the energy consumption. Another part of the study explores environments that have uncertainty in the availability of the compute resources. For this part, we design heuristics and compare their performance in different types of environments

EQUAL: Energy and QoS Aware Resource Allocation Approach for Clouds

The popularity of cloud computing is increasing by leaps and bounds. To cope with resource demands of increasing number of cloud users, the cloud market players establish large sized data centers. The huge energy consumption by the data centers and liability of fulfilling Quality of Service (QoS) requirements of the end users have made resource allocation a challenging task. In this paper, energy and QoS aware resource allocation approach which employs Antlion optimization for allocation of resources to virtual machines (VMs) is proposed. It can operate in three modes, namely power aware, performance aware, and balanced mode. The proposed approach enhances energy efficiency of the cloud infrastructure by improving the utilization of resources while fulfilling QoS requirements of the end users. The proposed approach is implemented in CloudSim. The simulation results have shown improvement in QoS and energy efficiency of the cloud

Thirty Years of Machine Learning: The Road to Pareto-Optimal Wireless Networks

Future wireless networks have a substantial potential in terms of supporting a broad range of complex compelling applications both in military and civilian fields, where the users are able to enjoy high-rate, low-latency, low-cost and reliable information services. Achieving this ambitious goal requires new radio techniques for adaptive learning and intelligent decision making because of the complex heterogeneous nature of the network structures and wireless services. Machine learning (ML) algorithms have great success in supporting big data analytics, efficient parameter estimation and interactive decision making. Hence, in this article, we review the thirty-year history of ML by elaborating on supervised learning, unsupervised learning, reinforcement learning and deep learning. Furthermore, we investigate their employment in the compelling applications of wireless networks, including heterogeneous networks (HetNets), cognitive radios (CR), Internet of things (IoT), machine to machine networks (M2M), and so on. This article aims for assisting the readers in clarifying the motivation and methodology of the various ML algorithms, so as to invoke them for hitherto unexplored services as well as scenarios of future wireless networks.Comment: 46 pages, 22 fig