A Taxonomy of Data Grids for Distributed Data Sharing, Management and Processing

Data Grids have been adopted as the platform for scientific communities that need to share, access, transport, process and manage large data collections distributed worldwide. They combine high-end computing technologies with high-performance networking and wide-area storage management techniques. In this paper, we discuss the key concepts behind Data Grids and compare them with other data sharing and distribution paradigms such as content delivery networks, peer-to-peer networks and distributed databases. We then provide comprehensive taxonomies that cover various aspects of architecture, data transportation, data replication and resource allocation and scheduling. Finally, we map the proposed taxonomy to various Data Grid systems not only to validate the taxonomy but also to identify areas for future exploration. Through this taxonomy, we aim to categorise existing systems to better understand their goals and their methodology. This would help evaluate their applicability for solving similar problems. This taxonomy also provides a "gap analysis" of this area through which researchers can potentially identify new issues for investigation. Finally, we hope that the proposed taxonomy and mapping also helps to provide an easy way for new practitioners to understand this complex area of research.Comment: 46 pages, 16 figures, Technical Repor

Efficient replica-exchange across distributed production infrastructure

Replica-Exchange (RE) methods represent a class of algorithms that involve a large number of loosely-coupled ensembles and are used to understand physical phenomena -- ranging from protein folding dynamics to binding affinity calculations. We develop a framework for RE that supports different replica pairing and coordination mechanisms, that can use a wide range of production cyberinfrastructure concurrently. Additionally, our framework uses a flexible pilot-job implementation, which enables effective resource allocation for multiple replicas. We characterize the performance of two different RE algorithms - synchronous and asynchronous - at unprecedented scales on production distributed infrastructure (Teragrid and LONI). The synchronous RE algorithm is implemented with a centralized master, while the asynchronous RE algorithm is implemented with both centralized and decentralized replica management schemes. We evaluate the performance of the different algorithms and implementations when we scale-up the number of replicas (up to 256) on a single machine and when we scale-out across 2 and 4 machines. Both the synchronous and asynchronous algorithms perform similarly when the number of replicas is small. But as the number of replicas increase, in the synchronous RE, the synchronization cost increases the total time to completion. In the centralized asynchronous RE, the cost of managing many replicas in a centralized manner increases the time to completion but not as much as in the synchronous RE. The decentralized asynchronous RE scales much better with increasing number of replicas. When scaled-out across many machines, the performance of synchronous RE depends on whether the machines are homogeneous or heterogeneous. A heterogeneous infrastructure means increased synchronization costs. We also run tests to see if one of the algorithms is better suited to achieve more crosswalks and temperature mixing -- better sampling

Asynchronous Teams and Tasks in a Message Passing Environment

As the discipline of scientific computing grows, so too does the "skills gap" between the increasingly complex scientific applications and the efficient algorithms required. Increasing demand for computational power on the march towards exascale requires innovative approaches. Closing the skills gap avoids the many pitfalls that lead to poor utilisation of resources and wasted investment. This thesis tackles two challenges: asynchronous algorithms for parallel computing and fault tolerance. First I present a novel asynchronous task invocation methodology for Discontinuous Galerkin codes called enclave tasking. The approach modifies the parallel ordering of tasks that allows for efficient scaling on dynamic meshes up to 756 cores. It ensures high levels of concurrency and intermixes tasks of different computational properties. Critical tasks along domain boundaries are prioritised for an overlap of computation and communication. The second contribution is the teaMPI library, forming teams of MPI processes exchanging consistency data through an asynchronous "heartbeat". In contrast to previous approaches, teaMPI operates fully asynchronously with reduced overhead. It is also capable of detecting individually slow or failing ranks and inconsistent data among replicas. Finally I provide an outlook into how asynchronous teams using enclave tasking can be combined into an advanced team-based diffusive load balancing scheme. Both concepts are integrated into and contribute towards the ExaHyPE project, a next generation code that solves hyperbolic equation systems on dynamically adaptive cartesian grids

Distributed computing practice for large-scale science and engineering applications

It is generally accepted that the ability to develop large-scale distributed applications has lagged seriously behind other developments in cyberinfrastructure. In this paper, we provide insight into how such applications have been developed and an understanding of why developing applications for distributed infrastructure is hard. Our approach is unique in the sense that it is centered around half a dozen existing scientific applications; we posit that these scientific applications are representative of the characteristics, requirements, as well as the challenges of the bulk of current distributed applications on production cyberinfrastructure (such as the US TeraGrid). We provide a novel and comprehensive analysis of such distributed scientific applications. Specifically, we survey existing models and methods for large-scale distributed applications and identify commonalities, recurring structures, patterns and abstractions. We find that there are many ad hoc solutions employed to develop and execute distributed applications, which result in a lack of generality and the inability of distributed applications to be extensible and independent of infrastructure details. In our analysis, we introduce the notion of application vectors: a novel way of understanding the structure of distributed applications. Important contributions of this paper include identifying patterns that are derived from a wide range of real distributed applications, as well as an integrated approach to analyzing applications, programming systems and patterns, resulting in the ability to provide a critical assessment of the current practice of developing, deploying and executing distributed applications. Gaps and omissions in the state of the art are identified, and directions for future research are outlined

Scalable and Reliable Sparse Data Computation on Emergent High Performance Computing Systems

Heterogeneous systems with both CPUs and GPUs have become important system architectures in emergent High Performance Computing (HPC) systems. Heterogeneous systems must address both performance-scalability and power-scalability in the presence of failures. Aggressive power reduction pushes hardware to its operating limit and increases the failure rate. Resilience allows programs to progress when subjected to faults and is an integral component of large-scale systems, but incurs significant time and energy overhead. The future exascale systems are expected to have higher power consumption with higher fault rates. Sparse data computation is the fundamental kernel in many scientific applications. It is suitable for the studies of scalability and resilience on heterogeneous systems due to its computational characteristics. To deliver the promised performance within the given power budget, heterogeneous computing mandates a deep understanding of the interplay between scalability and resilience. Managing scalability and resilience is challenging in heterogeneous systems, due to the heterogeneous compute capability, power consumption, and varying failure rates between CPUs and GPUs. Scalability and resilience have been traditionally studied in isolation, and optimizing one typically detrimentally impacts the other. While prior works have been proved successful in optimizing scalability and resilience on CPU-based homogeneous systems, simply extending current approaches to heterogeneous systems results in suboptimal performance-scalability and/or power-scalability. To address the above multiple research challenges, we propose novel resilience and energy-efficiency technologies to optimize scalability and resilience for sparse data computation on heterogeneous systems with CPUs and GPUs. First, we present generalized analytical and experimental methods to analyze and quantify the time and energy costs of various recovery schemes, and develop and prototype performance optimization and power management strategies to improve scalability for sparse linear solvers. Our results quantitatively reveal that each resilience scheme has its own advantages depending on the fault rate, system size, and power budget, and the forward recovery can further benefit from our performance and power optimizations for large-scale computing. Second, we design a novel resilience technique that relaxes the requirement of synchronization and identicalness for processes, and allows them to run in heterogeneous resources with power reduction. Our results show a significant reduction in energy for unmodified programs in various fault situations compared to exact replication techniques. Third, we propose a novel distributed sparse tensor decomposition that utilizes an asynchronous RDMA-based approach with OpenSHMEM to improve scalability on large-scale systems and prove that our method works well in heterogeneous systems. Our results show our irregularity-aware workload partition and balanced-asynchronous algorithms are scalable and outperform the state-of-the-art distributed implementations. We demonstrate that understanding different bottlenecks for various types of tensors plays critical roles in improving scalability

Inclusion of Enclosed Hydration Effects in the Binding Free Energy Estimation of Dopamine D3 Receptor Complexes

Confined hydration and conformational flexibility are some of the challenges encountered for the rational design of selective antagonists of G-protein coupled receptors. We present a set of C3-substituted (-)-stepholidine derivatives as potent binders of the dopamine D3 receptor. The compounds are characterized biochemically, as well as by computer modeling using a novel molecular dynamics-based alchemical binding free energy approach which incorporates the effect of the displacement of enclosed water molecules from the binding site. The free energy of displacement of specific hydration sites is obtained using the Hydration Site Analysis method with explicit solvation. This work underscores the critical role of confined hydration and conformational reorganization in the molecular recognition mechanism of dopamine receptors and illustrates the potential of binding free energy models to represent these key phenomena.Comment: This is the first report of using enclosed hydration in estimating binding free energies of protein-ligand complexes using implicit solvatio

Data Management in the APPA System

International audienceCombining Grid and P2P technologies can be exploited to provide high-level data sharing in large-scale distributed environments. However, this combination must deal with two hard problems: the scale of the network and the dynamic behavior of the nodes. In this paper, we present our solution in APPA (Atlas Peer-to-Peer Architecture), a data management system with high-level services for building large-scale distributed applications. We focus on data availability and data discovery which are two main requirements for implementing large-scale Grids. We have validated APPA's services through a combination of experimentation over Grid5000, which is a very large Grid experimental platform, and simulation using SimJava. The results show very good performance in terms of communication cost and response time

Large-scale Data Analysis and Deep Learning Using Distributed Cyberinfrastructures and High Performance Computing

Data in many research fields continues to grow in both size and complexity. For instance, recent technological advances have caused an increased throughput in data in various biological-related endeavors, such as DNA sequencing, molecular simulations, and medical imaging. In addition, the variance in the types of data (textual, signal, image, etc.) adds an additional complexity in analyzing the data. As such, there is a need for uniquely developed applications that cater towards the type of data. Several considerations must be made when attempting to create a tool for a particular dataset. First, we must consider the type of algorithm required for analyzing the data. Next, since the size and complexity of the data imposes high computation and memory requirements, it is important to select a proper hardware environment on which to build the application. By carefully both developing the algorithm and selecting the hardware, we can provide an effective environment in which to analyze huge amounts of highly complex data in a large-scale manner. In this dissertation, I go into detail regarding my applications using big data and deep learning techniques to analyze complex and large data. I investigate how big data frameworks, such as Hadoop, can be applied to problems such as large-scale molecular dynamics simulations. Following this, many popular deep learning frameworks are evaluated and compared to find those that suit certain hardware setups and deep learning models. Then, we explore an application of deep learning to a biomedical problem, namely ADHD diagnosis from fMRI data. Lastly, I demonstrate a framework for real-time and fine-grained vehicle detection and classification. With each of these works in this dissertation, a unique large-scale analysis algorithm or deep learning model is implemented that caters towards the problem and leverages specialized computing resources