The Grid and Cloud User Support Environment (gUSE) enables users convenient and easy access to grid and cloud infrastructures by providing a general purpose, workflow-oriented graphical user interface to create and run workflows on various Distributed Computing Infrastructures (DCIs). Its arrangements for creating and modifying existing workflows are, however, non-intuitive and cumbersome due to the technologies and architecture employed by gUSE. In this paper, we outline the first integrated web-based workflow editor for gUSE with the aim of improving the user experience for those with industrial data workflows and the wider gUSE community. We report initial assessments of the editor's utility based on users' feedback. We argue that combining access to diverse scalable resources with improved workflow creation tools is important for all big data applications and research infrastructures.
While Galaxy is widely used, especially by the biomedical community, the data management capabilities are quite restricted for large data and necessitate data transfers between single jobs of a workflow to the server hosting the back-end of Galaxy. However, Galaxy can map to the highly parallelized enactments of Swift @cite_13 . Another workflow system well established in the biomedical community is Taverna but the workflow canvas is only available as a workbench. The workflows can be shared via the social website myExperiment @cite_14 .
@cite_14 @cite_13
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The Galaxy science portal is a popular gateway to data analysis and computational tools for a broad range of life sciences communities. While Galaxy enables users to overcome the complexities of integrating diverse tools into unified workflows, it has only limited capabilities to execute those tools on the parallel and often distributed high-performance resources that the life sciences fields increasingly requires. We outline here an approach to meet this pressing requirement with the Swift parallel scripting language and its distributed runtime system. Swift's model of computation - implicitly parallel functional dataflow - is an elemental abstraction to which the core computing model of Galaxy maps very closely. We describe an integration between Galaxy and Swift that is transforming Galaxy into a much more powerful science gateway, retaining its user-friendly nature while extending its power to execute highly scalable workflows on diverse parallel environments. Accessing and analyzing the exponentially expanding genomic sequence and functional data pose a challenge for biomedical researchers. Here we describe an interactive system, Galaxy, that combines the power of existing genome annotation databases with a simple Web portal to enable users to search remote resources, combine data from independent queries, and visualize the results. The heart of Galaxy is a flexible history system that stores the queries from each user; performs operations such as intersections, unions, and subtractions; and links to other computational tools. Galaxy can be accessed at http: g2.bx.psu.edu. Increased reliance on computational approaches in the life sciences has revealed grave concerns about how accessible and reproducible computation-reliant results truly are. Galaxy http: usegalaxy.org, an open web-based platform for genomic research, addresses these problems. Galaxy automatically tracks and manages data provenance and provides support for capturing the context and intent of computational methods. Galaxy Pages are interactive, web-based documents that provide users with a medium to communicate a complete computational analysis. As next-generation sequencing becomes an indispensible tool for biomedical research, it is crucial to provide analysis solutions that are usable and cost effective for biomedical researchers. Galaxy Cloud addresses this by combining the accessible Galaxy interface with automated management of cloud computing resources. Unlike purpose-built solutions, Galaxy allows users either to use existing tested best practices in the form of workflows or to construct their own analyses for novel tasks. Galaxy Cloud instances are owned and controlled entirely by the user who created them and can be used effectively in secure private clouds. Thus, Galaxy Cloud provides a solution that retains user control and privacy, makes complex analysis accessible and enables the use of practically limitless on-demand computing resources. Abstract Fast and simple access to computing resources for in-silico experiments and processing of large amounts of data have become crucial factors for researchers in the bioinformatics and biomedical domains. Cloud computing offers the possibility of accessing computing resources for a flexible amount of time and with varying requirements. We discuss how a full cloud stack ranging from Infrastructure-as-a-Service (IaaS) via Platform-as-a-Service (PaaS) to Software-as-a-Service (SaaS) can be built on open source technologies including the integration of high-throughput data transfers in all service types. Based on the scaling capabilities provided by the tools used on the IaaS level we devise a strategy to build a dynamically scaling PaaS offering for building and running workflows using Galaxy. Finally, applications — available as SaaS offerings — for two distinct use cases from the bioinformatics and biomedical domains are presented to demonstrate the feasibility and performance of our solution. We discuss here a parallel implementation of the visualisation of data from a galaxy formation simulation within the Triana problem-solving environment. The visualisation is a test case for our prototype Triana Grid software using a decentralized peer-to-peer approach. The Triana distributed environment is middleware independent and designed in such a way as to make it easily extensible by users of the system. This novel approach is usable both within a peer-to-peer framework, using JXTA, and within service oriented architectures, such as OGSA, by the use of a Grid application toolkit (GAT) interface. Furthermore, Triana has a pluggable architecture that allows the middleware independent representations of distributed task-graphs to be written in several popular formats. This facilitates the use of the mechanism within other disparate systems. Galaxy-formation simulation codes generate data that represent a series of particles in three dimensions and their associate properties as snapshots in time. An important aspect of these types of calculation is the visualization of time sequence data. The user of the code would like to visualize this data as an animation in two dimensions with the ability to vary the point of view, project that particular two dimensional slice and re-run the animation. The recalculation of the projection can be computed in parallel resulting in a considerable speedup. Capturing an enclosing volume of moving subjects and organs using fast individual image slice acquisition has shown promise in dealing with motion artefacts. Motion between slice acquisitions results in spatial inconsistencies that can be resolved by slice-to-volume reconstruction (SVR) methods to provide high quality 3D image data. Existing algorithms are, however, typically very slow, specialised to specific applications and rely on approximations, which impedes their potential clinical use. In this paper, we present a fast multi-GPU accelerated framework for slice-to-volume reconstruction. It is based on optimised 2D 3D registration, super-resolution with automatic outlier rejection and an additional (optional) intensity bias correction. We introduce a novel and fully automatic procedure for selecting the image stack with least motion to serve as an initial registration target. We evaluate the proposed method using artificial motion corrupted phantom data as well as clinical data, including tracked freehand ultrasound of the liver and fet al Magnetic Resonance Imaging. We achieve speed-up factors greater than 30 compared to a single CPU system and greater than 10 compared to currently available state-of-the-art multi-core CPU methods. We ensure high reconstruction accuracy by exact computation of the point-spread function for every input data point, which has not previously been possible due to computational limitations. Our framework and its implementation is scalable for available computational infrastructures and tests show a speed-up factor of 1.70 for each additional GPU. This paves the way for the online application of image based reconstruction methods during clinical examinations. The source code for the proposed approach is publicly available. To fully tap into the potential of heterogeneous machines composed of multicore processors and multiple accelerators, simple offloading approaches in which the main trunk of the application runs on regular cores while only specific parts are offloaded on accelerators are not sufficient. The real challenge is to build systems where the application would permanently spread across the entire machine, that is, where parallel tasks would be dynamically scheduled over the full set of available processing units. To face this challenge, we previously proposed StarPU, a runtime system capable of scheduling tasks over multicore machines equipped with GPU accelerators. StarPU uses a software virtual shared memory (VSM) that provides a highlevel programming interface and automates data transfers between processing units so as to enable a dynamic scheduling of tasks. We now present how we have extended StarPU to minimize the cost of transfers between processing units in order to efficiently cope with multi-GPU hardware configurations. To this end, our runtime system implements data prefetching based on asynchronous data transfers, and uses data transfer cost prediction to influence the decisions taken by the task scheduler. We demonstrate the relevance of our approach by benchmarking two parallel numerical algorithms using our runtime system. We obtain significant speedups and high efficiency over multicore machines equipped with multiple accelerators. We also evaluate the behaviour of these applications over clusters featuring multiple GPUs per node, showing how our runtime system can combine with MPI. Most high-performance, scientific libraries have adopted hybrid parallelization schemes - such as the popular MPI+OpenMP hybridization - to benefit from the capacities of modern distributed-memory machines. While these approaches have shown to achieve high performance, they require a lot of effort to design and maintain sophisticated synchronization communication strategies. On the other hand, task-based programming paradigms aim at delegating this burden to a runtime system for maximizing productivity. In this article, we assess the potential of task-based fast multipole methods (FMM) on clusters of multicore processors. We propose both a hybrid MPI+task FMM parallelization and a pure task-based parallelization where the MPI communications are implicitly handled by the runtime system. The latter approach yields a very compact code following a sequential task-based programming model. We show that task-based approaches can compete with a hybrid MPI+OpenMP highly optimized code and that furthermore the compact task-based scheme fully matches the performance of the sophisticated, hybrid MPI+task version, ensuring performance while maximizing productivity. We illustrate our discussion with the ScalFMM FMM library and the StarPU runtime system. Scalable management and self-organizational capabilities areemerging as central requirements for a generation of large-scale,highly dynamic, distributed applications. We have developed anentirely new distributed information management system calledAstrolabe. Astrolabe collects large-scale system state, permittingrapid updates and providing on-the-fly attribute aggregation. Thislatter capability permits an application to locate a resource, andalso offers a scalable way to track system state as it evolves overtime. The combination of features makes it possible to solve a widevariety of management and self-configuration problems. This paperdescribes the design of the system with a focus upon itsscalability. After describing the Astrolabe service, we presentexamples of the use of Astrolabe for locating resources,publish-subscribe, and distributed synchronization in largesystems. Astrolabe is implemented using a peer-to-peer protocol,and uses a restricted form of mobile code based on the SQL querylanguage for aggregation. This protocol gives rise to a novelconsistency model. Astrolabe addresses several securityconsiderations using a built-in PKI. The scalability of the systemis evaluated using both simulation and experiments; these confirmthat Astrolabe could scale to thousands and perhaps millions ofnodes, with information propagation delays in the tens of seconds. Cloud computing is gaining tremendous momentum in both academia and industry. In this context, we define the term "Cloud Workflow" as the specification, execution and provenance tracking of large-scale scientific workflows, as well as the management of data and computing resources to support the execution of large-scale scientific workflows in the Cloud. In this paper, we first analyze the gap between these two complementary technologies, and what it means to bring Clouds and workflows together. Then, we present the key challenges in supporting Cloud workflows, and present our reference framework for scientific workflow management in the Cloud. Last we present our experience in integrating a scientific workflow management system-Swift into the Cloud. We discuss the performance of cluster provisioning within the OpenNebula Cloud platform, the Eucalyptus Cloud platform and Amazon EC2, and we demonstrate the capability and efficiency of the integration using a NASA MODIS image processing workflow and the Montage image mosaic workflow.Note to practitioners. Scientific workflow management plays a very important role for scientific computing and application coordination, while Cloud computing offers scalability and resource on-demand. We devise autonomous methods to integrate scientific workflow management systems with Cloud platforms and also provision resources for large scale workflows, which can facilitate scientists to easily manage their workflows in the Cloud, and take advantage of large scale Cloud resources. There are a few integration options and many challenges in the process, and the experience we gain will help researchers in migrating their workflow management systems and workflow applications into the Cloud. We analyze the major challenges of running scientific workflows on the Cloud.We propose a reference framework to standardize the integration.The implementation experience proves that the framework is feasible and extendible.Cluster-recycling mechanism can improve the resource provisioning efficiency. SUMMARY This paper presents a number of algorithms to run the fast multipole method (FMM) on NVIDIA CUDA-capable graphical processing units (GPUs) (Nvidia Corporation, Sta. Clara, CA, USA). The FMM is a class of methods to compute pairwise interactions between N particles for a given error tolerance and with computational cost of O(N). The methods described in the paper are applicable to any FMMs in which the multipole-to-local (M2L) operator is a dense matrix and the matrix is precomputed. This is the case for example in the black-box fast multipole method (bbFMM), which is a variant of the FMM that can handle large class of kernels. This example will be used in our benchmarks. In the FMM, two operators represent most of the computational cost, and an optimal implementation typically tries to balance those two operators. One is the nearby interaction calculation (direct sum calculation, line 29 in Listing 1), and the other is the M2L operation. We focus on the M2L. By combining multiple M2L operations and reordering the primitive loops of the M2L so that CUDA threads can reuse or share common data, these approaches reduce the movement of data in the GPU. Because memory bandwidth is the primary bottleneck of these methods, significant performance improvements are realized. Four M2L schemes are detailed and analyzed in the case of a uniform tree. The four schemes are tested and compared with an optimized, OpenMP parallelized, multi-core CPU code. We consider high and low precision calculations by varying the number of Chebyshev nodes used in the bbFMM. The accuracy of the GPU codes is found to be satisfactory and achieved performance over 200 Gflop s on one NVIDIA Tesla C1060 GPU (Nvidia Corporation, Sta. Clara, CA, USA). This was compared against two quad-core Intel Xeon E5345 processors (Intel Corporation, Sta. Clara, CA, USA) running at 2.33 GHz, for a combined peak performance of 149 Gflop s for single precision. For the low FMM accuracy case, the observed performance of the CPU code was 37 Gflop s, whereas for the high FMM accuracy case, the performance was about 8.5 Gflop s, most likely because of a higher frequency of cache misses. We also present benchmarks on an NVIDIA C2050 GPU (a Fermi processor)(Nvidia Corporation, Sta. Clara, CA, USA) in single and double precision. Copyright © 2011 John Wiley & Sons, Ltd. There has been an increased growth in a number of applications that naturally generate large volumes of uncertain data. By the advent of such applications, the support of advanced analysis queries such as the skyline and its variant operators for big uncertain data has become important. In this paper, we propose the effective parallel algorithms using MapReduce to process the probabilistic skyline queries for uncertain data modeled by both discrete and continuous models. We present three filtering methods to identify probabilistic non-skyline objects in advance. We next develop a single MapReduce phase algorithm PS-QP-MR by utilizing space partitioning based on a variant of quadtrees to distribute the instances of objects effectively and the enhanced algorithm PS-QPF-MR by applying the three filtering methods additionally. We also propose the workload balancing technique to balance the workload of reduce functions based on the number of machines available. Finally, we present the brute-force algorithms PS-BR-MR and PS-BRF-MR with partitioning randomly and applying the filtering methods. In our experiments, we demonstrate the efficiency and scalability of PS-QPF-MR compared to the other algorithms. The performance of single image super-resolution has achieved significant improvement by utilizing deep convolutional neural networks (CNNs). The features in deep CNN contain different types of information which make different contributions to image reconstruction. However, most CNN-based models lack discriminative ability for different types of information and deal with them equally, which results in the representational capacity of the models being limited. On the other hand, as the depth of neural networks grows, the long-term information coming from preceding layers is easy to be weaken or lost in late layers, which is adverse to super-resolving image. To capture more informative features and maintain long-term information for image super-resolution, we propose a channel-wise and spatial feature modulation (CSFM) network in which a sequence of feature-modulation memory (FMM) modules is cascaded with a densely connected structure to transform low-resolution features to high informative features. In each FMM module, we construct a set of channel-wise and spatial attention residual (CSAR) blocks and stack them in a chain structure to dynamically modulate multi-level features in a global-and-local manner. This feature modulation strategy enables the high contribution information to be enhanced and the redundant information to be suppressed. Meanwhile, for long-term information persistence, a gated fusion (GF) node is attached at the end of the FMM module to adaptively fuse hierarchical features and distill more effective information via the dense skip connections and the gating mechanism. Extensive quantitative and qualitative evaluations on benchmark datasets illustrate the superiority of our proposed method over the state-of-the-art methods. Abstract : In this paper, we analyze seven MapReduce workload traces from production clusters at Facebook and at Cloudera customers in e-commerce, telecommunications media, and retail. Cumulatively, these traces comprise over a year's worth of data logged from over 5000 machines, and contain over two million jobs that perform 1.6 exabytes of I O. Key observations include input data forms up to 77 of all bytes, 90 of jobs access KB to GB sized files that make up less than 16 of stored bytes, up to 60 of jobs re-access data that has been touched within the past 6 hours, peak-to-median job submission rates are 9:1 or greater, an average of 68 of all compute time is spent in map, task-seconds-per-byte is a key metric for balancing compute and data bandwidth task durations range from seconds to hours, and five out of seven workloads contain map-only jobs. We have also deployed a public workload repository with workload replay tools so that the researchers can systematically assess design priorities and compare performance across diverse MapReduce workloads. Life sciences research is based on individuals, often with diverse skills, assembled into research groups. These groups use their specialist expertise to address scientific problems. The in silico experiments undertaken by these research groups can be represented as workflows involving the co-ordinated use of analysis programs and information repositories that may be globally distributed. With regards to Grid computing, the requirements relate to the sharing of analysis and information resources rather than sharing computational power. The myGrid project has developed the Taverna Workbench for the composition and execution of workflows for the life sciences community. This experience paper describes lessons learnt during the development of Taverna. A common theme is the importance of understanding how workflows fit into the scientists' experimental context. The lessons reflect an evolving understanding of life scientists' requirements on a workflow environment, which is relevant to other areas of data intensive and exploratory science. Copyright © 2005 John Wiley & Sons, Ltd. Scientific workflows are increasingly containerised, which requires rethinking central processing unit (CPU) sharing policies to accommodate different workload types. However, container engines running scientific workflows struggle to share the CPU fairly, as workload characteristics are not taken into account. This paper proposes a sharing policy called the Adaptive Completely Fair Scheduling policy (adCFS), which considers the future state of CPU usage and proactively shares CPU cycles between various containers based on their corresponding workload metrics (e.g., CPU usage, task runtime, #tasks). adCFS estimates the weight of workload characteristics and redistributes the CPU based on the corresponding weights. The Markov chain model is used to predict CPU state use, and the adCFS policy is triggered to dynamically allocate containers to the proper CPU portions. Experimental results show enhanced container CPU response time for those containers that run heavy and large jobs: these display 12 faster response time compared with the default CFS (Completely Fair Scheduler). adCFS therefore enhances CFS by considering workload metrics, which leads to the CPU being shared fairly when it is fully used. In this paper we present the results of parallelizing two life sciences applications, Markov random fields-based (MRF) liver segmentation and HMMER's Viterbi algorithm, using GPUs. We relate our experiences in porting both applications to the GPU as well as the techniques and optimizations that are most beneficial. The unique characteristics of both algorithms are demonstrated by implementations on an NVIDIA 8800 GTX Ultra using the CUDA programming environment. We test multiple enhancements in our GPU kernels in order to demonstrate the effectiveness of each strategy. Our optimized MRF kernel achieves over 130× speedup, and our hmmsearch implementation achieves up to 38× speedup. We show that the differences in speedup between MRF and hmmsearch is due primarily to the frequency at which the hmmsearch must read from the GPU's DRAM. Recent research efforts in the fields of data stream processing and data stream management systems (DSMSs) show the increasing importance of processing data streams, e. g., in the e-science domain. Together with the advent of peer-to-peer (P2P) networks and grid computing, this leads to the necessity of developing new techniques for distributing and processing continuous queries over data streams in such networks. In this paper, we present a novel approach for optimizing the integration, distribution, and execution of newly registered continuous queries over data streams in grid-based P2P networks. We introduce Windowed XQuery (WXQuery), our XQuery-based subscription language for continuous queries over XML data streams supporting window-based operators. Concentrating on filtering and window-based aggregation, we present our stream sharing algorithms as well as experimental evaluation results from the astrophysics application domain to assess our approach. As the prevalence of social media and GPS-enabled devices, a massive amount of geo-textual data has been generated in a stream fashion, leading to a variety of applications such as location-based recommendation and information dissemination. In this paper, we investigate a novel real-time top-k monitoring problem over sliding window of streaming data; that is, we continuously maintain the top-k most relevant geo-textual messages (e.g., geo-tagged tweets) for a large number of spatial-keyword subscriptions (e.g., registered users interested in local events) simultaneously. To provide the most recent information under controllable memory cost, sliding window model is employed on the streaming geo-textual data. To the best of our knowledge, this is the first work to study top-k spatial-keyword publish subscribe over sliding window. A novel system, called Skype (Top-k Spatial-keyword Publish Subscribe), is proposed in this paper. In Skype, to continuously maintain top-k results for massive subscriptions, we devise a novel indexing structure upon subscriptions such that each incoming message can be immediately delivered on its arrival. Moreover, to reduce the expensive top-k re-evaluation cost triggered by message expiration, we develop a novel cost-based k-skyband technique to reduce the number of re-evaluations in a cost-effective way. Extensive experiments verify the great efficiency and effectiveness of our proposed techniques.