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Writing efficient software for heterogeneous architectures equipped with modern accelerator devices presents a serious challenge to programmer productivity, creating a need for powerful performance-analysis tools to adequately support the software development process. To guide the design of such tools, we describe typical patterns of inefficient runtime behavior that may adversely affect the performance...
General-Purpose Graphics Processing Units (GPGPUs) are promising parallel platforms for high performance computing. The CUDA (Compute Unified Device Architecture) programming model provides improved programmability for general computing on GPGPUs. However, its unique execution model and memory model still pose significant challenges for developers of efficient GPGPU code. This paper proposes a new...
This paper describes a multi-threaded parallel design and implementation of the Smith-Waterman (SW) algorithm on graphic processing units (GPUs) with NVIDIA corporation's Compute Unified Device Architecture (CUDA). Central to this is a divide and conquer approach which divides the computation of a whole pairwise sequence alignment matrix into multiple sub-matrices (or parallelograms) each running...
Multicore architectures have established themselves as the new generation of computer architectures. As part of the one core to many cores evolution, memory access mechanisms have advanced rapidly. Several new memory access mechanisms have been implemented in many modern commodity multicore architectures. By specifying how processing cores access shared memory, memory access mechanisms directly influence...
Graphics processing units (GPUs) have evolved over the past few years from dedicated graphics rendering devices to powerful parallel processors, outperforming traditional central processing units (CPUs) in many areas of scientific computing. The use of GPUs as processing elements was very limited until recently, when the concept of general-purpose computing on graphics processing units (GPGPU) was...
This paper describes a multi-threaded parallel design and implementation of the Smith-Waterman (SM) algorithm on compute unified device architecture (CUDA)-compatible graphic processing units (GPUs). A novel technique has been put forward to solve the restriction on the length of the query sequence in previous GPU implementations of the Smith-Waterman algorithm. The main reasons behind this limitation...
The Smith Waterman algorithm for sequence alignment is one of the main tools of bioinformatics. It is used for sequence similarity searches and alignment of similar sequences. The high end graphical processing unit (GPU), used for processing graphics on desktop computers, deliver computational capabilities exceeding those of CPUs by an order of magnitude. Recently these capabilities became accessible...
This paper describes a design and implementation of the Smith-Waterman algorithm accelerated on the graphics processing unit (GPU). Our method is implemented using compute unified device architecture (CUDA), which is available on the nVIDIA GPU. The method efficiently uses on-chip shared memory to reduce the data amount being transferred between off-chip memory and processing elements in the GPU....
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