Resource provisioning in Science Clouds: Requirements and challenges

Cloud computing has permeated into the information technology industry in the last few years, and it is emerging nowadays in scientific environments. Science user communities are demanding a broad range of computing power to satisfy the needs of high-performance applications, such as local clusters, high-performance computing systems, and computing grids. Different workloads are needed from different computational models, and the cloud is already considered as a promising paradigm. The scheduling and allocation of resources is always a challenging matter in any form of computation and clouds are not an exception. Science applications have unique features that differentiate their workloads, hence, their requirements have to be taken into consideration to be fulfilled when building a Science Cloud. This paper will discuss what are the main scheduling and resource allocation challenges for any Infrastructure as a Service provider supporting scientific applications

Unifying data and replica placement for data-intensive services in geographically distributed clouds

The increased reliance of data management applications on cloud computing technologies has rendered research in identifying solutions to the data placement problem to be of paramount importance. The objective of the classical data placement problem is to optimally partition, while also allowing for replication, the set of data-items into distributed data centers to minimize the overall network communication cost. Despite significant advancement in data placement research, replica placement has seldom been studied in unison with data placement. More specifically, most of the existing solutions employ a two-phase approach: 1) data placement, followed by 2) replication. Replication should however be seen as an integral part of data placement, and should be studied as a joint optimization problem with the latter. In this paper, we propose a unified paradigm of data placement, called CPR, which combines data placement and replication of data-intensive services into geographically distributed clouds as a joint optimization problem. Underneath CPR, lies an overlapping correlation clustering algorithm capable of assigning a data-item to multiple data centers, thereby enabling us to jointly solve data placement and replication. Experiments on a real-world trace-based online social network dataset show that CPR is effective and scalable. Empirically, it is approximate to 35% better in efficacy on the evaluated metrics, while being up to 8 times faster in execution time when compared to state-of-the-art techniques

UnifyDR: A Generic Framework for Unifying Data and Replica Placement

The advent of (big) data management applications operating at Cloud scale has led to extensive research on the data placement problem. The key objective of data placement is to obtain a partitioning (possibly allowing for replicas) of a set of data-items into distributed nodes that minimizes the overall network communication cost. Although replication is intrinsic to data placement, it has seldom been studied in combination with the latter. On the contrary, most of the existing solutions treat them as two independent problems, and employ a two-phase approach: (1) data placement, followed by (2) replica placement. We address this by proposing a new paradigm, CDR , with the objective of c ombining d ata and r eplica placement as a single joint optimization problem. Specifically, we study two variants of the CDR problem: (1) CDR-Single , where the objective is to minimize the communication cost alone, and (2) CDR-Multi , which performs a multi-objective optimization to also minimize traffic and storage costs. To unify data and replica placement, we propose a generic framework called UnifyDR , which leverages overlapping correlation clustering to assign a data-item to multiple nodes, thereby facilitating data and replica placement to be performed jointly. We establish the generic nature of UnifyDR by portraying its ability to address the CDR problem in two real-world use-cases, that of join-intensive online analytical processing (OLAP) queries and a location-based online social network (OSN) service. The effectiveness and scalability of UnifyDR are showcased by experiments performed on data generated using the TPC-DS benchmark and a trace of the Gowalla OSN for the OLAP queries and OSN service use-case, respectively. Empirically, the presented approach obtains an improvement of approximately 35% in terms of the evaluated metrics and a speed-up of 8 times in comparison to state-of-the-art techniques.This work was supported by the Agentschap Innoveren & Ondernemen (VLAIO) Strategic Fundamental Research (SBO) under Grant 150038 (DiSSeCt)

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

Optimization and Management of Large-scale Scientific Workflows in Heterogeneous Network Environments: From Theory to Practice

Next-generation computation-intensive scientific applications feature large-scale computing workflows of various structures, which can be modeled as simple as linear pipelines or as complex as Directed Acyclic Graphs (DAGs). Supporting such computing workflows and optimizing their end-to-end network performance are crucial to the success of scientific collaborations that require fast system response, smooth data flow, and reliable distributed operation.We construct analytical cost models and formulate a class of workflow mapping problems with different mapping objectives and network constraints. The difficulty of these mapping problems essentially arises from the topological matching nature in the spatial domain, which is further compounded by the resource sharing complicacy in the temporal dimension. We provide detailed computational complexity analysis and design optimal or heuristic algorithms with rigorous correctness proof or performance analysis. We decentralize the proposed mapping algorithms and also investigate these optimization problems in unreliable network environments for fault tolerance.To examine and evaluate the performance of the workflow mapping algorithms before actual deployment and implementation, we implement a simulation program that simulates the execution dynamics of distributed computing workflows. We also develop a scientific workflow automation and management platform based on an existing workflow engine for experimentations in real environments. The performance superiority of the proposed mapping solutions are illustrated by extensive simulation-based comparisons with existing algorithms and further verified by large-scale experiments on real-life scientific workflow applications through effective system implementation and deployment in real networks

Evaluating and Enabling Scalable High Performance Computing Workloads on Commercial Clouds

Performance, usability, and accessibility are critical components of high performance computing (HPC). Usability and performance are especially important to academic researchers as they generally have little time to learn a new technology and demand a certain type of performance in order to ensure the quality and quantity of their research results. We have observed that while not all workloads run well in the cloud, some workloads perform well. We have also observed that although commercial cloud adoption by industry has been growing at a rapid pace, its use by academic researchers has not grown as quickly. We aim to help close this gap and enable researchers to utilize the commercial cloud more efficiently and effectively. We present our results on architecting and benchmarking an HPC environment on Amazon Web Services (AWS) where we observe that there are particular types of applications that are and are not suited for the commercial cloud. Then, we present our results on architecting and building a provisioning and workflow management tool (PAW), where we developed an application that enables a user to launch an HPC environment in the cloud, execute a customizable workflow, and after the workflow has completed delete the HPC environment automatically. We then present our results on the scalability of PAW and the commercial cloud for compute intensive workloads by deploying a 1.1 million vCPU cluster. We then discuss our research into the feasibility of utilizing commercial cloud infrastructure to help tackle the large spikes and data-intensive characteristics of Transportation Cyberphysical Systems (TCPS) workloads. Then, we present our research in utilizing the commercial cloud for urgent HPC applications by deploying a 1.5 million vCPU cluster to process 211TB of traffic video data to be utilized by first responders during an evacuation situation. Lastly, we present the contributions and conclusions drawn from this work