CfP: 23rd High Performance Computing Symposium

September 5th, 2014

The 23rd High Performance Computing Symposium (April 12-15, 2015 in Alexandria, VA, USA) is devoted to the impact of high performance computing and communications on computer simulations. Topics of interest include:

  • GPU for general purpose computations (GPGPU)
  • Hybrid system modeling and simulation
  • Tools and environments for coupling parallel codes
  • Parallel algorithms and architectures
  • High performance software tools

Submission deadline for full papers: November 22, 2014. More information can be found at

Accelerated Combinatorial Optimization using Graphics Processing Units and C++ AMP

August 20th, 2014


In the course of less than a decade, Graphics Processing Units (GPUs) have evolved from narrowly scoped application specific accelerators to general-purpose parallel machines capable of accommodating an ever-growing set of algorithms. At the same time, programming GPUs appears to have become trapped around an attractor characterised by ad-hoc practices, non-portable implementations and inexact, uninformative performance reporting. The purpose of this paper is two-fold, on one hand pursuing an in-depth look at GPU hardware and its characteristics, and on the other demonstrating that portable, generic, mathematically grounded programming of these machines is possible and desirable. An agent-based meta-heuristic, the Max-Min Ant System (MMAS), provides the context. The major contributions brought about by this article are the following: (1) an optimal, portable, generic-algorithm based MMAS implementation is derived; (2) an in-depth analysis of AMD’s Graphics Core Next (GCN) GPU and the C++ AMP programming model is supplied; (3) a more robust approach to performance reporting is presented; (4) novel techniques for raising the abstraction level without sacrificing performance are employed. This represents the first implementation of an algorithm from the Ant Colony Optimisation (ACO) family using C++ AMP, whilst at the same time being one of the first uses of the latter programming environment.

(A. Voicu: “Accelerated Combinatorial Optimization using Graphics Processing Units and C++ AMP ”. International Journal of Computer Applications 100(6):21-30, August 2014. [DOI])

Call for Contributions: GPU algorithms for image processing and computer vision

July 22nd, 2014

“GPU Algorithms for Image Processing and Computer Vision”, to be published by Springer, will contain a collection of articles on fundamental image processing and computer vision methods adapted for Graphics Processing Units (GPUs). In recent years, substantial efforts were undertaken to adapt many such algorithms for massively-parallel GPU-based systems. The book is envisioned as a consolidation of such work into a single volume covering widely used methods and techniques. Each chapter will be written by authors working on a specific group of methods. It will provide mathematical background, parallel algorithm, and implementation details leading to reusable, adaptable, and scalable code fragments. The book will serve as a GPU implementation manual for many image processing and analysis algorithms providing valuable insights into parallelization strategies for GPUs as well as ready-to-use code fragments with a broad appeal to both developers and researchers interested in GPU computing. Read the rest of this entry »

On the Use of Remote GPUs and Low-Power Processors for the Acceleration of Scientific Applications

June 8th, 2014


Many current high-performance clusters include one or more GPUs per node in order to dramatically reduce application execution time, but the utilization of these accelerators is usually far below 100%. In this context, emote GPU virtualization can help to reduce acquisition costs as well as the overall energy consumption. In this paper, we investigate the potential overhead and bottlenecks of several “heterogeneous” scenarios consisting of client GPU-less nodes running CUDA applications and remote GPU-equipped server nodes providing access to NVIDIA hardware accelerators. The experimental evaluation is performed using three general-purpose multicore processors (Intel Xeon, Intel Atom and ARM Cortex A9), two graphics accelerators (NVIDIA GeForce GTX480 and NVIDIA Quadro M1000), and two relevant scientific applications (CUDASW++ and LAMMPS) arising in bioinformatics and molecular dynamics simulations.

(A. Castelló, J. Duato, R. Mayo, A. J. Peña, E. S. Quintana-Ortí, V. Roca, and F. Silla, “On the Use of Remote GPUs and Low-Power Processors for the Acceleration of Scientific Applications”. Fourth International Conference on Smart Grids, Green Communications and IT Energy-aware Technologies, ENERGY 2014, Chamonix (France), pp. 57–62, 20 – 24 April 2014. [PDF])

Improving Cache Locality for GPU-based Volume Rendering

June 8th, 2014


We present a cache-aware method for accelerating texture-based volume rendering on a graphics processing unit (GPU). Because a GPU has hierarchical architecture in terms of processing and memory units, cache optimization is important to maximize performance for memory-intensive applications. Our method localizes texture memory reference according to the location of the viewpoint and dynamically selects the width and height of thread blocks (TBs) so that each warp, which is a series of 32 threads processed simultaneously, can minimize memory access strides. We also incorporate transposed indexing of threads to perform TB-level cache optimization for specific viewpoints. Furthermore, we maximize TB size to exploit spatial locality with fewer resident TBs. For viewpoints with relatively large strides, we synchronize threads of the same TB at regular intervals to realize synchronous ray propagation. Experimental results indicate that our cache-aware method doubles the worst rendering performance compared to those provided by the CUDA and OpenCL software development kits.

(Yuki Sugimoto, Fumihiko Ino, and Kenichi Hagihara: “Improving Cache Locality for GPU-based Volume Rendering”. Parallel Computing 40(5/6): 59-69, May 2014. [DOI])

CfP: GPU in High Energy Physics 2014

June 3rd, 2014

The conference focuses on the application of GPUs in High Energy Physics (HEP), expanding on the trend of previous workshops on the topic and pointing to establishing a recurrent series. The emerging paradigm of the use of graphic processors as powerful accelerators in data- and computation-intensive applications found fertile ground in the computing challenges of the HEP community and is currently object of active investigations. This follows a long established trend which sees the increased use of cheap off-the-shelf commercial units to achieve unprecedented performances in parallel data processing, thus leveraging on a very strong commitment of hardware producers to the huge market of computer graphics and games. These hardware advances comes together with the continuous development of proprietary and free software to expose the raw computing power of GPUs for general-purpose applications and scientific computing in particular. All different applications of massively parallel computing in HEP will be addressed, from computational speed-ups in online and offline data selection and analysis to hard real-time applications in low-level triggering, to MonteCarlo simulations for lattice QCD. Both current activities and plans for foreseen experiments and projects will be discussed, together with perspectives on the evolution of the hardware and software.

The conference is held in Pisa (Italy), 10.9.2014 – 12.9.2014. More information:

BROCCOLI: Software for fast fMRI analysis on many-core CPUs and GPUs

May 27th, 2014


Analysis of functional magnetic resonance imaging (fMRI) data is becoming ever more computationally demanding as temporal and spatial resolutions improve, and large, publicly available data sets proliferate. Moreover, methodological improvements in the neuroimaging pipeline, such as non-linear spatial normalization, non-parametric permutation tests and Bayesian Markov Chain Monte Carlo approaches, can dramatically increase the computational burden. Despite these challenges, there do not yet exist any fMRI software packages which leverage inexpensive and powerful GPUs to perform these analyses. Here, we therefore present BROCCOLI, a free software package written in OpenCL that can be used for parallel analysis of fMRI data on a large variety of hardware configurations. BROCCOLI has, for example, been tested with an Intel CPU, an Nvidia GPU, and an AMD GPU. These tests show that parallel processing of fMRI data can lead to significantly faster analysis pipelines. This speedup can be achieved on relatively standard hardware, but further speed improvements require only a modest investment in GPU hardware. BROCCOLI (running on a GPU) can perform non-linear spatial normalization to a 1 mm3 brain template in 4–6 s, and run a second level permutation test with 10,000 permutations in about a minute. These non-parametric tests are generally more robust than their parametric counterparts, and can also enable more sophisticated analyses by estimating complicated null distributions. Additionally, BROCCOLI includes support for Bayesian first-level fMRI analysis using a Gibbs sampler. The new software is freely available under GNU GPL3 and can be downloaded from github:

(A. Eklund, P. Dufort, M. Villani and S. LaConte: “BROCCOLI: Software for fast fMRI analysis on many-core CPUs and GPUs”. Front. Neuroinform. 8:24, 2014. [DOI])

Master’s thesis: Parallel Computing for Digital Signal Processing on Mobile Device GPUs

May 27th, 2014

This master’s thesis by Markus Konrad analyzes the potentials of GPGPU on mobile devices such as smartphones or tablets. The question was, if and how the GPU on such devices can be used to speed up certain algorithms especially in the fields of image processing. GPU computing technologies such as OpenCL, OpenGL shaders, and Android RenderScript are assessed in the thesis. The abstract reads as follows:

This thesis studies how certain popular algorithms in the field of image and audio processing can be accelerated on mobile devices by means of parallel execution on their graphics processing unit (GPU). Several technologies with which this can be achieved are compared in terms of possible performance improvements, hardware and software support, as well as limitations of their programming model and functionality. The results of this research are applied in a practical project, consisting of performance improvements for marker detection in an Augmented Reality application for mobile devices.

The PDF is available for download and the source-code for some Android application prototypes is published on github.

Comparative Study of Frequent Itemset Mining Techniques on Graphics Processor

May 5th, 2014


Frequent itemset mining (FIM) is a core area for many data mining applications as association rules computation, clustering and correlations, which has been comprehensively studied over the last decades. Furthermore, databases are becoming gradually larger, thus requiring a higher computing power to mine them in reasonable time. At the same time, the improvements in high performance computing platforms are transforming them into massively parallel environments equipped with multi-core processors, such as GPUs. Hence, fully operating these systems to perform itemset mining poses as a challenging and critical problems that addressed by various researcher. We present survey of multi-core and GPU accelerated parallelization of the FIM algorithms.

(Dharmesh Bhalodiya and Chhaya patel:  “Comparative Study of Frequent Itemset Mining Techniques on Graphics Processor”. International Journal of Engineering Research and Applications 4(4):159-163, April 2014. [PDF])

Multi-GPU Implementation of the Minimum Volume Simplex Analysis Algorithm for Hyperspectral Unmixing

April 29th, 2014

Abstract :

Spectral unmixing is an important task in remotely sensed hyperspectral data exploitation. The linear mixture model has been widely used to unmix hyperspectral images by identifying a set of pure spectral signatures, called endmembers, and estimating their respective abundances in each pixel of the scene. Several algorithms have been proposed in the recent literature to automatically identify endmembers, even if the original hyperspectral scene does not contain any pure signatures. A popular strategy for endmember identification in highly mixed hyperspectral scenes has been the minimum volume simplex analysis (MVSA), known to be a computationally very expensive algorithm. This algorithm calculates the minimum volume enclosing simplex, as opposed to other algorithms that perform maximum simplex volume analysis (MSVA). The high computational complexity of MVSA, together with its very high memory requirements, has limited its adoption in the hyperspectral imaging community. In this paper we develop several optimizations to the MVSA algorithm. The main computational task of MVSA is the solution of a quadratic optimization problem with equality and inequality constraints, with the inequality constraints being in the order of the number of pixels multiplied by the number of endmembers. As a result, storing and computing the inequality constraint matrix is highly inefficient. The first optimization presented in this paper uses algebra operations in order to reduce the memory requirements of the algorithm. In the second optimization, we use graphics processing units (GPUs) to effectively solve (in parallel) the quadratic optimization problem involved in the computation of MVSA. In the third optimization, we extend the single GPU implementation to a multi-GPU one, developing a hybrid strategy that distributes the computation while taking advantage of GPU accelerators at each node. The presented optimizations are tested in different analysis scenarios (using both synthetic and real hyperspectral data) and shown to provide state-of-the-art results from the viewpoint of unmixing accuracy and computational performance. The speedup achieved using the full GPU cluster compared to the CPU implementation in tenfold in a real hyperspectral image.

(A. Agathos, J. Li, D. Petcu and A. Plaza: “Multi-GPU Implementation of the Minimum Volume Simplex Analysis Algorithm for Hyperspectral Unmixing”. IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing, accepted for publication , 2014. [PDF] )

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