high performance computing on graphics processing units: hgpu.org

Traditionally, we usually utilize the method of shotgun to cut a DNA sequence into pieces and we have to reconstruct the original DNA sequence from the pieces, those are widely used method for DNA assembly. Emerging DNA sequence technologies open up more opportunities for molecular biology. This paper introduce a new method to improve the […]

In this paper, we present an all-core implementation of Burrows Wheeler Compression algorithm that exploits all computing resources on a system. Our focus is to provide significant benefit to everyday users on common end-to-end applications by exploiting the parallelism of multiple CPU cores and many-core GPU on their machines. The all-core framework is suitable for […]

Dataflow execution engines such as MapReduce, DryadLINQ and PTask have enjoyed success because they simplify development for a class of important parallel applications. Expressing the computation as a dataflow graph allows the runtime, and not the programmer, to own problems such as synchronization, data movement and scheduling – leveraging dynamic information to inform strategy and […]

We propose an efficient first order primal-dual method for solving variational problems with nonconvex regularization such as TV^q. It is based on the recent idea in [1] to reformulate an existing primal-dual algorithm for convex optimization using Moreau’s identity. A systematic comparison to recent state of the art algorithms for nonconvex optimization (iteratively reweighted l1 […]

The paper presents a highly efficient way of simulating the dynamic behavior of deformable objects by means of the finite element method (FEM) with computations performed on Graphics Processing Units (GPU). The presented implementation reduces bottlenecks related to memory accesses by grouping the necessary data per node pairs, in contrast to the classical way done […]

Multi-thread architectures are the current trends for both PCs (multi-core CPUs and GPUs) and game consoles such as the Microsoft Xbox 360 and Sony Playstation 3. GPUs (Graphics Processing Units) have evolved into extremely powerful and flexible processors, allowing its use for processing different data. This advantage can be used in game development to optimize […]

Graphics processing units (GPUs) are important components of modern computing devices for not only graphics rendering, but also efficient parallel computations. However, their security problems are ignored despite their importance and popularity. In this paper, we first perform an in-depth security analysis on GPUs to detect security vulnerabilities. We observe that contemporary, widely-used GPUs, both […]

GPU programmers suffer from programmer-managed GPU memory because both performance and programmability heavily depend on GPU memory allocation and CPUGPU data transfer mechanisms. To improve performance and programmability, programmers should be able to place only the data frequently accessed by GPU on GPU memory while overlapping CPU-GPU data transfers and GPU executions as much as […]

Based on Intel’s Many Integrated Core (MIC) architecture, Intel Xeon Phi is one of the few truly many-core CPUs – featuring around 60 fairly powerful cores, two levels of caches, and graphic memory, all interconnected by a very fast ring. Given its promised ease-of-use and high performance, we took Xeon Phi out for a test […]

Nowadays, the advancements in internet technology are increasing by leaps and bounds. This has lead to the increase in threats by attackers, consequently compromising system security. Intrusion detection systems (IDS) provide an intelligent way to provide capable system security. Traditionally, IDS’s have been designed using several statistical based methods such as classification algorithms or artificial […]

Relativistic hydrodynamics became a very useful tool in high-energy physics after Landau’s application of this theory for explaining data on proton-proton collisions. It’s later application to heavy ion collisions has been very successful in modeling apparent collective behaviour of hot matter produced in such collisions. This work is a part of an effort of the […]

One of the fundamental issues in computer science is ordering a list of items. Although there is a huge number of sorting algorithms, sorting problem has attracted a great deal of research; because efficient sorting is important to optimize the use of other algorithms. Sorting algorithms have been studied extensively since past three decades. Their […]