BarrierPoint: sampled simulation of multi-threaded applications

Sampling is a well-known technique to speed up architectural simulation of long-running workloads while maintaining accurate performance predictions. A number of sampling techniques have recently been developed that extend well- known single-threaded techniques to allow sampled simulation of multi-threaded applications. Unfortunately, prior work is limited to non-synchronizing applications (e.g., server throughput workloads); requires the functional simulation of the entire application using a detailed cache hierarchy which limits the overall simulation speedup potential; leads to different units of work across different processor architectures which complicates performance analysis; or, requires massive machine resources to achieve reasonable simulation speedups. In this work, we propose BarrierPoint, a sampling methodology to accelerate simulation by leveraging globally synchronizing barriers in multi-threaded applications. BarrierPoint collects microarchitecture-independent code and data signatures to determine the most representative inter-barrier regions, called barrierpoints. BarrierPoint estimates total application execution time (and other performance metrics of interest) through detailed simulation of these barrierpoints only, leading to substantial simulation speedups. Barrierpoints can be simulated in parallel, use fewer simulation resources, and define fixed units of work to be used in performance comparisons across processor architectures. Our evaluation of BarrierPoint using NPB and Parsec benchmarks reports average simulation speedups of 24.7x (and up to 866.6x) with an average simulation error of 0.9% and 2.9% at most. On average, BarrierPoint reduces the number of simulation machine resources needed by 78x

Computing Petaflops over Terabytes of Data: The Case of Genome-Wide Association Studies

In many scientific and engineering applications, one has to solve not one but a sequence of instances of the same problem. Often times, the problems in the sequence are linked in a way that allows intermediate results to be reused. A characteristic example for this class of applications is given by the Genome-Wide Association Studies (GWAS), a widely spread tool in computational biology. GWAS entails the solution of up to trillions ($10^{12}$) of correlated generalized least-squares problems, posing a daunting challenge: the performance of petaflops ($10^{15}$ floating-point operations) over terabytes of data. In this paper, we design an algorithm for performing GWAS on multi-core architectures. This is accomplished in three steps. First, we show how to exploit the relation among successive problems, thus reducing the overall computational complexity. Then, through an analysis of the required data transfers, we identify how to eliminate any overhead due to input/output operations. Finally, we study how to decompose computation into tasks to be distributed among the available cores, to attain high performance and scalability. With our algorithm, a GWAS that currently requires the use of a supercomputer may now be performed in matter of hours on a single multi-core node. The discussion centers around the methodology to develop the algorithm rather than the specific application. We believe the paper contributes valuable guidelines of general applicability for computational scientists on how to develop and optimize numerical algorithms

Decreasing time consumption of microscopy image segmentation through parallel processing on the GPU

The computational performance of graphical processing units (GPUs) has improved significantly. Achieving speedup factors of more than 50x compared to single-threaded CPU execution are not uncommon due to parallel processing. This makes their use for high throughput microscopy image analysis very appealing. Unfortunately, GPU programming is not straightforward and requires a lot of programming skills and effort. Additionally, the attainable speedup factor is hard to predict, since it depends on the type of algorithm, input data and the way in which the algorithm is implemented. In this paper, we identify the characteristic algorithm and data-dependent properties that significantly relate to the achievable GPU speedup. We find that the overall GPU speedup depends on three major factors: (1) the coarse-grained parallelism of the algorithm, (2) the size of the data and (3) the computation/memory transfer ratio. This is illustrated on two types of well-known segmentation methods that are extensively used in microscopy image analysis: SLIC superpixels and high-level geometric active contours. In particular, we find that our used geometric active contour segmentation algorithm is very suitable for parallel processing, resulting in acceleration factors of 50x for 0.1 megapixel images and 100x for 10 megapixel images

Design and Implementation of an Extensible Variable Resolution Bathymetric Estimator

For grid-based bathymetric estimation techniques, determining the right resolution at which to work is essential. Appropriate grid resolution can be related, roughly, to data density and thence to sonar characteristics, survey methodology, and depth. It is therefore variable in almost all survey scenarios, and methods of addressing this problem can have enormous impact on the correctness and efficiency of computational schemes of this kind. This paper describes the design and implementation of a bathymetric depth estimation algorithm that attempts to address this problem by combining the computational efficiency of locally regular grids with piecewise-variable estimation resolution to provide a single logical data structure and associated algorithms that can adjust to local data conditions, change resolution where required to best support the data, and operate over essentially arbitrarily large areas as a single unit. The algorithm, which is in part a development of CUBE, is modular and extensible, and is structured as a client-server application to support different implementation modalities. The algorithm is called “CUBE with Hierarchical Resolution Techniques”, or CHRT

A fast multipole method for stellar dynamics

The approximate computation of all gravitational forces between $N$ interacting particles via the fast multipole method (FMM) can be made as accurate as direct summation, but requires less than $\mathcal{O}(N)$ operations. FMM groups particles into spatially bounded cells and uses cell-cell interactions to approximate the force at any position within the sink cell by a Taylor expansion obtained from the multipole expansion of the source cell. By employing a novel estimate for the errors incurred in this process, I minimise the computational effort required for a given accuracy and obtain a well-behaved distribution of force errors. For relative force errors of $\sim10^{-7}$, the computational costs exhibit an empirical scaling of $\propto N^{0.87}$. My implementation (running on a 16 core node) out-performs a GPU-based direct summation with comparable force errors for $N\gtrsim10^5$.Comment: 21 pages, 15 figures, accepted for publication in Journal for Computational Astrophysics and Cosmolog

Throughput Scaling Of Convolution For Error-Tolerant Multimedia Applications

Convolution and cross-correlation are the basis of filtering and pattern or template matching in multimedia signal processing. We propose two throughput scaling options for any one-dimensional convolution kernel in programmable processors by adjusting the imprecision (distortion) of computation. Our approach is based on scalar quantization, followed by two forms of tight packing in floating-point (one of which is proposed in this paper) that allow for concurrent calculation of multiple results. We illustrate how our approach can operate as an optional pre- and post-processing layer for off-the-shelf optimized convolution routines. This is useful for multimedia applications that are tolerant to processing imprecision and for cases where the input signals are inherently noisy (error tolerant multimedia applications). Indicative experimental results with a digital music matching system and an MPEG-7 audio descriptor system demonstrate that the proposed approach offers up to 175% increase in processing throughput against optimized (full-precision) convolution with virtually no effect in the accuracy of the results. Based on marginal statistics of the input data, it is also shown how the throughput and distortion can be adjusted per input block of samples under constraints on the signal-to-noise ratio against the full-precision convolution.Comment: IEEE Trans. on Multimedia, 201