In recent years, increased attention is being given to software quality assurance and protection. With considerable verification and protection schemes proposed and deployed, today’s software unfortunately still fails to be protected from cyberattacks, especially in the presence of insecure organization of heap metadata. In this paper, we aim to explore whether heap metadata could be corrupted and

Graphics processing units (GPUs) have a strong floating-point capability and a high memory bandwidth in data parallelism and have been widely used in high-performance computing (HPC). Compute unified device architecture (CUDA) is used as a parallel computing platform and programming model for the GPU to reduce the complexity of programming. The programmable GPUs are becoming popular in computational

Capturing mutation patterns of each individual influenza virus sequence is often challenging; in this paper, we demonstrated that using a binary encoding scheme coupled with dimension reduction technique, we were able to capture the intrinsic mutation pattern of the virus. Our approach looks at the variance between sequences instead of the commonly used p-distance or Hamming distance. We first convert

The QR factorization is one of the most important operations in dense linear algebra, offering a numerically stable method for solving linear systems of equations including overdetermined and underdetermined systems. Modern implementations of the QR factorization, such as the one in the LAPACK library, suffer from performance limitations due to the use of matrix–vector type operations in the phase

High-throughput sequencing (CHIP-Seq) data exhibit binding events with possible binding locations and their strengths, followed by interpretation of the locations of peaks. Recent methods tend to summarize all CHIP-Seq peaks detected within a limited up and down region of each gene into one real-valued score in order to quantify the probability of regulation in a region. Applying subspace clustering

In high-performance computing on distributed-memory systems, communication often represents a significant part of the overall execution time. The relative cost of communication will certainly continue to rise as compute-density growth follows the current technology and industry trends. Design of lower-communication alternatives to fundamental computational algorithms has become an important field of

Tackling computationally challenging problems with high efficiency often requires the combination of algorithmic innovation, advanced architecture, and thorough exploitation of parallelism. We demonstrate this synergy through synthetic aperture radar (SAR) via backprojection, an image reconstruction method that can require hundreds of TFLOPS. Computation cost is significantly reduced by our new algorithm

Text analysis tools are nowadays required to process increasingly large corpora which are often organized as small files (abstracts, news articles, etc.). Cloud computing offers a convenient, on-demand, pay-as-you-go computing environment for solving such problems. We investigate provisioning on the Amazon EC2 cloud from the user perspective, attempting to provide a scheduling strategy that is both

The development of grid and workflow technologies has enabled complex, loosely coupled scientific applications to be executed on distributed resources. Many of these applications consist of large numbers of short-duration tasks whose runtimes are heavily influenced by delays in the execution environment. Such applications often perform poorly on the grid because of the large scheduling overheads commonly

Scientific computing has entered a new era of scale and sharing with the arrival of cyberinfrastructure facilities for computational experimentation. A key emerging concept is scientific workflows, which provide a declarative representation of complex scientific applications that can be automatically managed and executed in distributed shared resources. In the coming decades, computational experimentation

With the recent advent of new heterogeneous computing architectures there is still a lack of parallel problem solving environments that can help scientists to use easily and efficiently hybrid supercomputers. Many scientific simulations that use structured grids to solve partial differential equations in fact rely on stencil computations. Stencil computations have become crucial in solving many challenging

The Partitioned Global Address Space (PGAS) model of Unified Parallel C (UPC) can help users express and manage application data locality on non-uniform memory access (NUMA) multi-core shared-memory systems to get good performance. First, we describe several UPC program optimization techniques that are important to achieving good performance on NUMA multi-core computers with examples and quantitative

Node level heterogeneous architectures have become attractive during the last decade for several reasons: compared to traditional symmetric CPUs, they offer high peak performance and are energy and/or cost efficient. With the increase of fine-grained parallelism in high-performance computing, as well as the introduction of parallelism in workstations, there is an acute need for a good overview and

We present a parallel implementation of an algorithm for calculating the two-point angular correlation function as applied in the field of computational cosmology. The algorithm has been specifically developed for a reconfigurable computer. Our implementation utilizes a microprocessor and two reconfigurable processors on a dual-MAP SRC-6 system. The two reconfigurable processors are used as two application-specific

The technical papers program for SC13 received 449 submissions of which 90 where selected for the program giving an acceptance rate of 20%. A rigorous peer review process, including author rebuttals and a 1.5 day face-to-face program committee meeting ensured that selected papers were the very best in our field. One of the tasks at the face-to-face meeting was also to select finalists for the best

In the area of network performance and discovery, network tomography focuses on reconstructing network properties using only end-to-end measurements at the application layer. One challenging problem in network tomography is reconstructing available bandwidth along all links during multiple source/multiple destination transmissions. The traditional measurement procedures used for bandwidth tomography

The Computational Fluid Dynamics code OVERFLOW includes as one of its solver options an algorithm which is a fairly small piece of code but which accounts for a significant portion of the total computational time. This paper studies some of the issues in accelerating this piece of code by using a Graphics Processing Unit (GPU). The algorithm needs to be modified to be suitable for a GPU and attention

This article has no abstract.

This paper describes and evaluates a scalable and efficient resilience scheme based on the concept of containment domains. Containment domains are a programming construct that enable applications to express resilience needs and to interact with the system to tune and specialize error detection, state preservation and restoration, and recovery schemes. Containment domains have weak transactional semantics

High performance computing (HPC) systems use checkpoint-restart to tolerate failures. Typically, applications store their states in checkpoints on a parallel file system (PFS). As applications scale up, checkpoint-restart incurs high overheads due to contention for PFS resources. The high overheads force large-scale applications to reduce checkpoint frequency, which means more compute time is lost

The safety of dikes in The Netherlands, located in the delta of the rivers Rhine, Meuse and Scheldt, has been the subject of debate for more than ten years. The safety (or flood risk) of a particular area may depend on the safety of other areas. This is referred to as effects of river system behaviour on flood risk (quantified as the estimated number of casualties and economic damage). A computational

An approach for incorporating embedded simulation and analysis capabilities in complex simulation codes through template-based generic programming is presented. This approach relies on templating and operator overloading within the C++ language to transform a given calculation into one that can compute a variety of additional quantities that are necessary for many state-of-the-art simulation and analysis

Although there are a lot of robust and effective scientific libraries in Java, the utilization of these libraries in pure Java is difficult and cumbersome, especially for the average scientist that does not expertise in software development. We illustrate that ScalaLab presents an easier and productive MATLAB like front end. Also, the main strengths and weaknesses of the core Java libraries of ScalaLab

Large, complex scientific and engineering application code have a significant investment in computational kernels to implement their mathematical models. Porting these computational kernels to the collection of modern manycore accelerator devices is a major challenge in that these devices have diverse programming models, application programming interfaces (APIs), and performance requirements. The Kokkos

One of the challenges to achieving good performance on multicore architectures is the effective utilization of the underlying memory hierarchy. While this is an issue for single-core architectures, it is a critical problem for multicore chips. In this paper, we formulate the unified multicore model (UMM) to help understand the fundamental limits on cache performance on these architectures. The UMM

In this work we present a runtime threading system which provides an efficient substrate for fine-grain parallelism, suitable for deployment in multicore platforms. Its architecture encompasses a number of optimizations that make it particularly effective in managing a large number of threads and with low overheads. The runtime system has been integrated into an OpenMP implementation to allow for transparent

Breadth-First Search is an important kernel used by many graph-processing applications. In many of these emerging applications of BFS, such as analyzing social networks, the input graphs are low-diameter and scale-free. We propose a hybrid approach that is advantageous for low-diameter graphs, which combines a conventional top-down algorithm along with a novel bottom-up algorithm. The bottom-up algorithm

The widely used Message Passing Interface (MPI) is complex and rich. As a result, application developers require automated tools to avoid and to detect MPI programming errors. We present the Marmot Umpire Scalable Tool (MUST) that detects such errors with significantly increased scalability. We present improvements to our graph-based deadlock detection approach for MPI, which cover future MPI extensions

The enormous growth of biological sequence databases has caused bioinformatics to be rapidly moving towards a data-intensive, computational science. As a result, the computational power needed by bioinformatics applications is growing rapidly as well. The recent emergence of low cost parallel multicore accelerator technologies has made it possible to reduce execution times of many bioinformatics applications

Intrepid is a Trilinos package for advanced discretizations of Partial Differential Equations (PDEs). The package provides a comprehensive set of tools for local, cell-based construction of a wide range of numerical methods for PDEs. This paper describes the mathematical ideas and software design principles incorporated in the package. We also provide representative examples showcasing the use of Intrepid

PHASTA falls under the category of high-performance scientific computation codes designed for solving partial differential equations (PDEs). Its a massively parallel unstructured, implicit solver with particular emphasis on fluid dynamics (CFD) applications. More specifically, PHASTA is a parallel, hierarchic, adaptive, stabilized, transient analysis code that effectively employs advanced anisotropic

The IBM Cell Broadband Engine (BE) is a novel multi-core chip with the potential for the demanding floating point performance that is required for high-fidelity scientific simulations. However, data movement within the chip can be a major challenge to realizing the benefits of the peak floating point rates. In this paper, we present the results of implementing Sweep3D on the Cell/B.E. using an intra-chip

We introduce the Concurrent Collections (CnC) programming model. CnC supports flexible combinations of task and data parallelism while retaining determinism. CnC is implicitly parallel, with the user providing high-level operations along with semantic ordering constraints that together form a CnC graph. We formally describe the execution semantics of CnC and prove that the model guarantees deterministic

Reproducibility of an experiment is a commonly used metric to determine its validity. Within scientific computing, this can become difficult due to the accumulation of floating point rounding errors in the numerical computation, greatly reducing the accuracy of the computation. Matrix multiplication is particularly susceptible to these rounding errors which is why there exist so many solutions, ranging

This article has no abstract.

The Cell Broadband Engine architecture is a revolutionary processor architecture well suited for many scientific codes. This paper reports on an effort to implement several traditional high-performance scientific computing applications on the Cell Broadband Engine processor, including molecular dynamics, quantum chromodynamics and quantum chemistry codes. The paper discusses data and code restructuring

In this paper a method for execution programming of data-intensive applications is presented. The method is based on storage Quality of Service (SQoS) provisioning. SQoS provisioning uses the semantic based storage monitoring based on a storage resources model and a storage performance management. Test results show the gain for the execution time when using the QStorMan toolkit which implements the

We present Tpetra, a Trilinos package for parallel linear algebra primitives implementing the Petra object model. We describe Tpetra's design, based on generic programming via C++ templated types and template metaprogramming. We discuss some benefits of this approach in the context of scientific computing, with illustrations consisting of code and notable empirical results.

In this paper, we present the methodology for the introduction to scientific computing based on model-centered learning. We propose multiphase queueing systems as a basis for learning objects. We use Python and parallel programming for implementing the models and present the computer code and results of stochastic simulations.

In generic programming, software components are parameterized on types. When available, a static specialization mechanism allows selecting, for a given set of parameters, a more suitable version of a generic component than its primary version. The normal C++ template specialization mechanism is based on the type pattern of the parameters, which is not always the best way to guide the specialization

Accurate and timely prediction of weather phenomena, such as hurricanes and flash floods, require high-fidelity compute intensive simulations of multiple finer regions of interest within a coarse simulation domain. Current weather applications execute these nested simulations sequentially using all the available processors, which is sub-optimal due to their sub-linear scalability. In this work, we

This paper examines whether lossy compression can be used effectively in physics simulations as a possible strategy to combat the expected data-movement bottleneck in future high performance computing architectures. We show that, for the codes and simulations we tested, compression levels of 3–5X can be applied without causing significant changes to important physical quantities. Rather than applying

Locality of computation is key to obtaining high performance on a broad variety of parallel architectures and applications. It is moreover an essential component of strategies for energy-efficient computing. OpenMP is a widely available industry standard for shared memory programming. With the pervasive deployment of multi-core computers and the steady growth in core count, a productive programming

In this paper, we present a programming and runtime framework that enables the autonomic management of complex application workflows on hybrid computing infrastructures. The framework is designed to address system and application heterogeneity and dynamics to ensure that application objectives and constraints are satisfied. The need for such autonomic system and application management is becoming critical

Harnessing the power of multicore platforms is challenging due to the additional levels of parallelism present. In this paper we use the NAS Parallel Benchmarks to study three programming models, MPI, OpenMP and PGAS to understand their performance and memory usage characteristics on current multicore architectures. To understand these characteristics we use the Integrated Performance Monitoring tool

Matrix factorization (or often called decomposition) is a frequently used kernel in a large number of applications ranging from linear solvers to data clustering and machine learning. The central contribution of this paper is a thorough performance study of four popular matrix factorization techniques, namely, LU, Cholesky, QR and SVD on the STI Cell broadband engine. The paper explores algorithmic

A significant open issue in cloud computing is the real performance of the infrastructure. Few, if any, cloud providers or technologies offer quantitative performance guarantees. Regardless of the potential advantages of the cloud in comparison to enterprise-deployed applications, cloud infrastructures may ultimately fail if deployed applications cannot predictably meet behavioral requirements. In

Cell Superscalar's (CellSs) main goal is to provide a simple, flexible and easy programming approach for the Cell Broadband Engine (Cell/B.E.) that automatically exploits the inherent concurrency of the applications at a task level. The CellSs environment is based on a source-to-source compiler that translates annotated C or Fortran code and a runtime library tailored for the Cell/B.E. that takes care

Automatic tuning (auto-tuning) of software has emerged in recent years as a promising method that tries to automatically adapt the behaviour of a program to attain different performance objectives on a given computing system. This method is gaining momentum due to the increasing complexity of modern multicore-based hardware architectures. Many solutions to auto-tuning have been explored ranging from

Reverse-Time Migration (RTM) is a state-of-the-art technique in seismic acoustic imaging, because of the quality and integrity of the images it provides. Oil and gas companies trust RTM with crucial decisions on multi-million-dollar drilling investments. But RTM requires vastly more computational power than its predecessor techniques, and this has somewhat hindered its practical success. On the other

We have developed a new programming framework, called Sieve, to support parallel numerical partial differential equation(s) (PDE) algorithms operating over distributed meshes. We have also developed a reference implementation of Sieve in C++ as a library of generic algorithms operating on distributed containers conforming to the Sieve interface. Sieve makes instances of the incidence relation, or arrows

This article has no abstract.

For mobile multiprocessor applications, achieving high performance with low energy consumption is a challenging task. In order to help programmers to meet these design requirements, system development tools play an important role. In this paper, we describe one such development tool, ePRO-MP, which profiles and optimizes both performance and energy consumption of multi-threaded applications running

The ever-increasing scale of scientific data has become a significant challenge for researchers that rely on networks to interact with remote computing systems and transfer results to collaborators worldwide. Despite the availability of high-capacity connections, scientists struggle with inadequate cyberinfrastructure that cripples data transfer performance, and impedes scientific progress. The Science

Critical to the scalability of parallel adaptive simulations are parallel control functions including load balancing, reduced inter-process communication and optimal data decomposition. In distributed meshes, many mesh-based applications frequently access neighborhood information for computational purposes which must be transmitted efficiently to avoid parallel performance degradation when the neighbors

This article has no abstract.

Cloud computing, with its promise of virtually infinite resources, seems to suit well in solving resource greedy scientific computing problems. To study the effects of moving parallel scientific applications onto the cloud, we deployed several benchmark applications like matrix–vector operations and NAS parallel benchmarks, and DOUG (Domain decomposition On Unstructured Grids) on the cloud. DOUG is

The performance potential of the Cell/B.E., as well as its availability, have attracted a lot of attention from various high-performance computing (HPC) fields. While computation intensive kernels proved to be exceptionally well suited for running on the Cell, irregular data-intensive applications are usually considered as poor matches. In this paper, we present our complete solution for enabling such

The spectacular growth in the number of cores in current supercomputers poses design challenges for the development of performance analysis and tuning tools. To be effective, such analysis and tuning tools must be scalable and be able to manage the dynamic behaviour of parallel applications. In this work, we present ELASTIC, an environment for dynamic tuning of large-scale parallel applications. To

MueLu is a library within the Trilinos software project [An overview of Trilinos, Technical Report SAND2003-2927, Sandia National Laboratories, 2003] and provides a framework for parallel multigrid preconditioning methods for large sparse linear systems. While providing efficient implementations of modern multigrid methods based on smoothed aggregation and energy minimization concepts, MueLu is designed