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The trend towards highly parallel multi-processing is ubiquitous in all modern computer architectures, ranging from handheld devices to large-scale HPC systems; yet many applications are struggling to fully utilise the multiple levels of…

Supervised learning of Convolutional Neural Networks (CNNs), also known as supervised Deep Learning, is a computationally demanding process. To find the most suitable parameters of a network for a given application, numerous training…

Correlation Power Analysis (CPA) is a type of power analysis based side channel attack that can be used to derive the secret key of encryption algorithms including DES (Data Encryption Standard) and AES (Advanced Encryption Standard). A…

Discovering causal relationships from observational data is a crucial problem and it has applications in many research areas. The PC algorithm is the state-of-the-art constraint based method for causal discovery. However, runtime of the PC…

The introduction of Intel(R) Xeon Phi(TM) coprocessors opened up new possibilities in development of highly parallel applications. The familiarity and flexibility of the architecture together with compiler support integrated into the Intel…

Background: We describe an informatics framework for researchers and clinical investigators to efficiently perform parameter sensitivity analysis and auto-tuning for algorithms that segment and classify image features in a large dataset of…

Today, one of the main challenges for high-performance computing systems is to improve their performance by keeping energy consumption at acceptable levels. In this context, a consolidated strategy consists of using accelerators such as…

The discrete wavelet transform can be found at the heart of many image-processing algorithms. Until now, the transform on general-purpose processors (CPUs) was mostly computed using a separable lifting scheme. As the lifting scheme consists…

Principal component analysis (PCA) is a statistical technique commonly used in multivariate data analysis. However, PCA can be difficult to interpret and explain since the principal components (PCs) are linear combinations of the original…

Three dimensional particle-in-cell laser-plasma simulation is an important area of computational physics. Solving state-of-the-art problems requires large-scale simulation on a supercomputer using specialized codes. A growing demand in…

With multi-core processors a ubiquitous building block of modern supercomputers, it is now past time to enable applications to embrace these developments in processor design. To achieve exascale performance, applications will need ways of…

The surge in availability of genomic data holds promise for enabling determination of genetic causes of observed individual traits, with applications to problems such as discovery of the genetic roots of phenotypes, be they molecular…

We examine the Xeon Phi, which is based on Intel's Many Integrated Cores architecture, for its suitability to run the FDK algorithm--the most commonly used algorithm to perform the 3D image reconstruction in cone-beam computed tomography.…

We have extended the Falkon lightweight task execution framework to make loosely coupled programming on petascale systems a practical and useful programming model. This work studies and measures the performance factors involved in applying…

The implicit 2D3V particle-in-cell (PIC) code developed to study the interaction of ultrashort pulse lasers with matter [G. M. Petrov and J. Davis, Computer Phys. Comm. 179, 868 (2008); Phys. Plasmas 18, 073102 (2011)] has been parallelized…

We introduce the pCI software package for high-precision atomic structure calculations. The standard method of calculation is based on the configuration interaction (CI) method to describe valence correlations, but can be extended to attain…

Efficient and consistent string processing is critical in the exponentially growing genomic data era. Locally Consistent Parsing (LCP) addresses this need by partitioning an input genome string into short, exactly matching substrings (e.g.,…

The Adapteva Epiphany many-core architecture comprises a 2D tiled mesh Network-on-Chip (NoC) of low-power RISC cores with minimal uncore functionality. It offers high computational energy efficiency for both integer and floating point…

The Preconditioned Conjugate Gradient (PCG) method is widely used for solving linear systems of equations with sparse matrices. A recent version of PCG, Pipelined PCG, eliminates the dependencies in the computations of the PCG algorithm so…

The increasing number of processing elements and decreas- ing memory to core ratio in modern high-performance platforms makes efficient strong scaling a key requirement for numerical algorithms. In order to achieve efficient scalability on…