Autonomic power and performance management for computing systems

With the increased complexity of platforms, the growing demand of applications and data centers’ servers sprawl, power consumption is reaching unsustainable limits. The need to improved power management is becoming essential for many reasons including reduced power consumption & cooling, improved density, reliability & compliance with environmental standards. This paper presents a theoretical framework and methodology for autonomic power and performance management in e-business data centers. We optimize for power and performance (performance-per-watt) at each level of the hierarchy while maintaining scalability. We adopt mathematically-rigorous optimization approach to minimize power while meeting performance constraints. Our experimental results show around 72% savings in power while maintaining performance as compared to static power management techniques and 69.8% additional savings with both global and local optimizations.

Fast VMM-based overlay networking for bridging the cloud and high performance computing

A collection of virtual machines (VMs) interconnected with an overlay network with a layer 2 abstraction has proven to be a powerful, unifying abstraction for adaptive distributed and parallel computing on loosely-coupled environments. It is now feasible to allow VMs hosting high performance computing (HPC) applications to seamlessly bridge distributed cloud resources and tightly-coupled supercomputing and cluster resources. However, to achieve the application performance that the tightly-coupled resources are capable of, it is important that the overlay network not introduce significant overhead relative to the native hardware, which is not the case for current user-level tools, including our own existing VNET/U system. In response, we describe the design, implementation, and evaluation of a virtual networking system that has negligible latency and bandwidth overheads in 1–10 Gbps networks. Our system, VNET/P, is directly embedded into our publicly available Palacios virtual machine monitor (VMM). VNET/P achieves native performance on 1 Gbps Ethernet networks and very high performance on 10 Gbps Ethernet networks. The NAS benchmarks generally achieve over 95 % of their native performance on both 1 and 10 Gbps. We have further demonstrated that VNET/P can operate successfully over more specialized tightly-coupled networks, such as Infiniband and Cray Gemini. Our results suggest it is feasible to extend a software-based overlay network designed for computing at wide-area scales into tightly-coupled environments.     

Job co-allocation strategies for multiple high performance computing clusters

To more effectively use a network of high performance computing clusters, allocating multi-process jobs across multiple connected clusters becomes an attractive possibility. This allocation process entails dividing the processes of a job among several clusters, which we refer to as co-allocation. Co-allocation offers the possibility of more efficient use of computer resources, reduced turn-around time and computations using numbers of processes larger than processes on any single cluster. In order to realize these possibilities, effective co-allocation, ultimately, depends on the inter-cluster communication cost. In this paper, we introduce a scalable co-allocation strategy called the Maximum Bandwidth Adjacent cluster Set (MBAS) strategy. The strategy makes use of two thresholds to control allocation: one to control the limit on bandwidth on usable inter-cluster communication links and another to control how jobs are split. A simulator that can simulate the dynamic behavior of jobs running across multiple clusters was developed and used to examine the performance of the MBAS co-allocation strategy. Our results indicate that by adjusting the thresholds for link level control and chunk size control in splitting jobs, the MBAS co-allocation strategy can significantly improve both user satisfaction and system utilization.     

Using priced timed automaton to analyse the energy consumption in cloud computing environment

According to the fact that cloud servers have different energy consumption on different running states, as well as the energy waste problem caused by the mismatching between cloud servers and cloud tasks, we carry out researches on the energy optimal method achieved by a priced timed automaton for the cloud computing center in this paper. The priced timed automaton is used to model the running behaviors of the cloud computing system. After introducing the matching matrix of cloud tasks and cloud resources as well as the power matrix of the running states of cloud servers, we design a generation algorithm for the cloud system automaton based on the generation rules and reduction rules given ahead. Then, we propose another algorithm to settle the minimum path energy consumption problem in the cloud system automaton, therefore obtaining an energy optimal solution and an energy optimal value for the cloud system. A case study and repeated experimental analyses manifest that our method is effective and feasible.     

Yabi: An online research environment for grid,high performance and cloud computing

Background  

There is a significant demand for creating pipelines or workflows in the life science discipline that chain a number of discrete compute and data intensive analysis tasks into sophisticated analysis procedures. This need has led to the development of general as well as domain-specific workflow environments that are either complex desktop applications or Internet-based applications. Complexities can arise when configuring these applications in heterogeneous compute and storage environments if the execution and data access models are not designed appropriately. These complexities manifest themselves through limited access to available HPC resources, significant overhead required to configure tools and inability for users to simply manage files across heterogenous HPC storage infrastructure.     

Searching for SNPs with cloud computing

As DNA sequencing outpaces improvements in computer speed, there is a critical need to accelerate tasks like alignment and SNP calling. Crossbow is a cloud-computing software tool that combines the aligner Bowtie and the SNP caller SOAPsnp. Executing in parallel using Hadoop, Crossbow analyzes data comprising 38-fold coverage of the human genome in three hours using a 320-CPU cluster rented from a cloud computing service for about $85. Crossbow is available from .     

The case for cloud computing in genome informatics

With DNA sequencing now getting cheaper more quickly than data storage or computation, the time may have come for genome informatics to migrate to the cloud.     

Adaptive Combiner for MapReduce on cloud computing

MapReduce is a programming model to process a massive amount of data on cloud computing. MapReduce processes data in two phases and needs to transfer intermediate data among computers between phases. MapReduce allows programmers to aggregate intermediate data with a function named combiner before transferring it. By leaving programmers the choice of using a combiner, MapReduce has a risk of performance degradation because aggregating intermediate data benefits some applications but harms others. Now, MapReduce can work with our proposal named the Adaptive Combiner for MapReduce (ACMR) to automatically, smartly, and trainer for getting a better performance without any interference of programmers. In experiments on seven applications, MapReduce can utilize ACMR to get the performance comparable to the system that is optimal for an application.     

Use of cloud computing in biomedicine

Nowadays, biomedicine is characterised by a growing need for processing of large amounts of data in real time. This leads to new requirements for information and communication technologies (ICT). Cloud computing offers a solution to these requirements and provides many advantages, such as cost savings, elasticity and scalability of using ICT. The aim of this paper is to explore the concept of cloud computing and the related use of this concept in the area of biomedicine. Authors offer a comprehensive analysis of the implementation of the cloud computing approach in biomedical research, decomposed into infrastructure, platform and service layer, and a recommendation for processing large amounts of data in biomedicine. Firstly, the paper describes the appropriate forms and technological solutions of cloud computing. Secondly, the high-end computing paradigm of cloud computing aspects is analysed. Finally, the potential and current use of applications in scientific research of this technology in biomedicine is discussed.     

Virtualizing high-end GPGPUs on ARM clusters for the next generation of high performance cloud computing

High performance cloud computing is behind the scene powering “the next big thing” as the mainstream accelerator for innovation in many areas. We describe here how to accelerate inexpensive ARM-based computing nodes with high-end GPGPUs hosted on x86_64 machines using the GVirtuS general-purpose virtualization service. We draw the vision of a possible next generation computing clusters characterized by highly heterogeneous parallelism heading to a lower electric power demanding, less heat producing and more environmental friendliness. Preliminary but promising performance data suggest that this solution could be considered as part of the foundations of the next generation of high performance cloud computing components.     

Managing overloaded hosts for energy-efficiency in cloud data centers

Cluster Computing - Traditional data centers are shifted toward the cloud computing paradigm. These data centers support the increasing demand for computational and data storage that consumes a...     

Greedy replica exchange algorithm for heterogeneous computing grids

Replica exchange molecular dynamics (REMD) has become a valuable tool in studying complex biomolecular systems. However, its application on distributed computing grids is limited by the heterogeneity of this environment. In this study, we propose a REMD implementation referred to as greedy REMD (gREMD) suitable for computations on heterogeneous grids. To decentralize replica management, gREMD utilizes a precomputed schedule of exchange attempts between temperatures. Our comparison of gREMD against standard REMD suggests four main conclusions. First, gREMD accelerates grid REMD simulations by as much as 40 %. Second, gREMD increases CPU utilization rates in grid REMD by up to 60 %. Third, we argue that gREMD is expected to maintain approximately constant CPU utilization rates and simulation wall-clock times with the increase in the number of replicas. Finally, we show that gREMD correctly implements the REMD algorithm and reproduces the conformational ensemble of a short peptide sampled in our previous standard REMD simulations. We believe that gREMD can find its place in large-scale REMD simulations on heterogeneous computing grids.

Open image in new window

Graphical Abstract Standard replica exchange molecular dynamics (REMD) typically requires all replicas to complete prior to initiation of the replica exchange protocol. Greedy REMD decentralizes this process and therefore only requires a replica and its predetermined exchange partner to have finished simulations prior to initiating replica exchange. Because greedy REMD reduces the idle time associated with replica exchange tasks, it becomes particularly well suited for performing REMD on heterogeneous distributed computing environments.

     

Design a cloud storage platform for pervasive computing environments

An increasing number of personal electronic handheld devices (e.g., SmartPhone, netbook, MID and etc.), which make up the personal pervasive computing environments, are playing an important role in our daily lives. Data storage and sharing is difficult for these devices due to the data inflation and the natural limitations of mobile devices, such as the limited storage space and the limited computing capability. Since the emerging cloud storage solutions can provide reliable and unlimited storage, they satisfy to the requirement of pervasive computing very well. Thus we designed a new cloud storage platform which includes a series of shadow storage services to address these new data management challenges in pervasive computing environments, which called as “SmartBox”. In SmartBox, each device is associated its shadow storage with a unique account, and the shadow storage acts as backup center as well as personal repository when the device is connected. To facilitate file navigation, all datasets in shadow storage are organized based on file attributes which support the users to seek files by semantic queries. We implemented a prototype of SmartBox focusing on pervasive environments being made up of Internet accessible devices. Experimental results with the deployments confirm the efficacy of shadow storage services in SmartBox.     

A hierarchical method for molecular docking using cloud computing

Discovering small molecules that interact with protein targets will be a key part of future drug discovery efforts. Molecular docking of drug-like molecules is likely to be valuable in this field; however, the great number of such molecules makes the potential size of this task enormous. In this paper, a method to screen small molecular databases using cloud computing is proposed. This method is called the hierarchical method for molecular docking and can be completed in a relatively short period of time. In this method, the optimization of molecular docking is divided into two subproblems based on the different effects on the protein–ligand interaction energy. An adaptive genetic algorithm is developed to solve the optimization problem and a new docking program (FlexGAsDock) based on the hierarchical docking method has been developed. The implementation of docking on a cloud computing platform is then discussed. The docking results show that this method can be conveniently used for the efficient molecular design of drugs.