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

Harnessing the Power of Many: Extensible Toolkit for Scalable Ensemble Applications

Many scientific problems require multiple distinct computational tasks to be executed in order to achieve a desired solution. We introduce the Ensemble Toolkit (EnTK) to address the challenges of scale, diversity and reliability they pose. We describe the design and implementation of EnTK, characterize its performance and integrate it with two distinct exemplar use cases: seismic inversion and adaptive analog ensembles. We perform nine experiments, characterizing EnTK overheads, strong and weak scalability, and the performance of two use case implementations, at scale and on production infrastructures. We show how EnTK meets the following general requirements: (i) implementing dedicated abstractions to support the description and execution of ensemble applications; (ii) support for execution on heterogeneous computing infrastructures; (iii) efficient scalability up to O(10^4) tasks; and (iv) fault tolerance. We discuss novel computational capabilities that EnTK enables and the scientific advantages arising thereof. We propose EnTK as an important addition to the suite of tools in support of production scientific computing

BrainFrame: A node-level heterogeneous accelerator platform for neuron simulations

Objective: The advent of High-Performance Computing (HPC) in recent years has led to its increasing use in brain study through computational models. The scale and complexity of such models are constantly increasing, leading to challenging computational requirements. Even though modern HPC platforms can often deal with such challenges, the vast diversity of the modeling field does not permit for a single acceleration (or homogeneous) platform to effectively address the complete array of modeling requirements. Approach: In this paper we propose and build BrainFrame, a heterogeneous acceleration platform, incorporating three distinct acceleration technologies, a Dataflow Engine, a Xeon Phi and a GP-GPU. The PyNN framework is also integrated into the platform. As a challenging proof of concept, we analyze the performance of BrainFrame on different instances of a state-of-the-art neuron model, modeling the Inferior- Olivary Nucleus using a biophysically-meaningful, extended Hodgkin-Huxley representation. The model instances take into account not only the neuronal- network dimensions but also different network-connectivity circumstances that can drastically change application workload characteristics. Main results: The synthetic approach of three HPC technologies demonstrated that BrainFrame is better able to cope with the modeling diversity encountered. Our performance analysis shows clearly that the model directly affect performance and all three technologies are required to cope with all the model use cases.Comment: 16 pages, 18 figures, 5 table

Metascheduling of HPC Jobs in Day-Ahead Electricity Markets

High performance grid computing is a key enabler of large scale collaborative computational science. With the promise of exascale computing, high performance grid systems are expected to incur electricity bills that grow super-linearly over time. In order to achieve cost effectiveness in these systems, it is essential for the scheduling algorithms to exploit electricity price variations, both in space and time, that are prevalent in the dynamic electricity price markets. In this paper, we present a metascheduling algorithm to optimize the placement of jobs in a compute grid which consumes electricity from the day-ahead wholesale market. We formulate the scheduling problem as a Minimum Cost Maximum Flow problem and leverage queue waiting time and electricity price predictions to accurately estimate the cost of job execution at a system. Using trace based simulation with real and synthetic workload traces, and real electricity price data sets, we demonstrate our approach on two currently operational grids, XSEDE and NorduGrid. Our experimental setup collectively constitute more than 433K processors spread across 58 compute systems in 17 geographically distributed locations. Experiments show that our approach simultaneously optimizes the total electricity cost and the average response time of the grid, without being unfair to users of the local batch systems.Comment: Appears in IEEE Transactions on Parallel and Distributed System

High-Throughput Computing on High-Performance Platforms: A Case Study

The computing systems used by LHC experiments has historically consisted of the federation of hundreds to thousands of distributed resources, ranging from small to mid-size resource. In spite of the impressive scale of the existing distributed computing solutions, the federation of small to mid-size resources will be insufficient to meet projected future demands. This paper is a case study of how the ATLAS experiment has embraced Titan---a DOE leadership facility in conjunction with traditional distributed high- throughput computing to reach sustained production scales of approximately 52M core-hours a years. The three main contributions of this paper are: (i) a critical evaluation of design and operational considerations to support the sustained, scalable and production usage of Titan; (ii) a preliminary characterization of a next generation executor for PanDA to support new workloads and advanced execution modes; and (iii) early lessons for how current and future experimental and observational systems can be integrated with production supercomputers and other platforms in a general and extensible manner

EPOBF: Energy Efficient Allocation of Virtual Machines in High Performance Computing Cloud

Cloud computing has become more popular in provision of computing resources under virtual machine (VM) abstraction for high performance computing (HPC) users to run their applications. A HPC cloud is such cloud computing environment. One of challenges of energy efficient resource allocation for VMs in HPC cloud is tradeoff between minimizing total energy consumption of physical machines (PMs) and satisfying Quality of Service (e.g. performance). On one hand, cloud providers want to maximize their profit by reducing the power cost (e.g. using the smallest number of running PMs). On the other hand, cloud customers (users) want highest performance for their applications. In this paper, we focus on the scenario that scheduler does not know global information about user jobs and user applications in the future. Users will request shortterm resources at fixed start times and non interrupted durations. We then propose a new allocation heuristic (named Energy-aware and Performance per watt oriented Bestfit (EPOBF)) that uses metric of performance per watt to choose which most energy-efficient PM for mapping each VM (e.g. maximum of MIPS per Watt). Using information from Feitelson's Parallel Workload Archive to model HPC jobs, we compare the proposed EPOBF to state of the art heuristics on heterogeneous PMs (each PM has multicore CPU). Simulations show that the EPOBF can reduce significant total energy consumption in comparison with state of the art allocation heuristics.Comment: 10 pages, in Procedings of International Conference on Advanced Computing and Applications, Journal of Science and Technology, Vietnamese Academy of Science and Technology, ISSN 0866-708X, Vol. 51, No. 4B, 201