Study of Parallel Programming Models on Computer Clusters with Accelerators

In order to reach exascale computing capability, accelerators have become a crucial part in developing supercomputers. This work examines the potential of two latest acceleration technologies, Intel Many Integrated Core (MIC) Architecture and Graphics Processing Units (GPUs). This thesis applies three benchmarks under 3 different configurations, MPI+CPU, MPI+GPU, and MPI+MIC. The benchmarks include intensely communicating application, loosely communicating application, and embarrassingly parallel application. This thesis also carries out a detailed study on the scalability and performance of MIC processors under two programming models, i.e., offload model and native model, on the Beacon computer cluster. According to different benchmarks, the results demonstrate different performance and scalability between GPU and MIC. (1) For embarrassingly parallel case, GPU-based parallel implementation on Keeneland computer cluster has a better performance than other accelerators. However, MIC-based parallel implementation shows a better scalability than the implementation on GPU. The performances of native model and offload model on MIC are very close. (2) For loosely communicating case, the performances on GPU and MIC are very close. The MIC-based parallel implementation still demonstrates a strong scalability when using 120 MIC processors in computation. (3) For the intensely communicating case, the MPI implementations on CPUs and GPUs both have a strong scalability. GPUs can consistently outperform other accelerators. However, the MIC-based implementation cannot scale quite well. The performance of different models on MIC is different from the performance of embarrassingly parallel case. Native model can consistently outperform the offload model by ~10 times. And there is not much performance gain when allocating more MIC processors. The increase of communication cost will offset the performance gain from the reduced workload on each MIC core. This work also tests the performance capabilities and scalability by changing the number of threads on each MIC card form 10 to 60. When using different number of threads for the intensely communicating case, it shows different capabilities of the MIC based offload model. The scalability can hold when the number of threads increases from 10 to 30, and the computation time reduces with a smaller rate from 30 threads to 50 threads. When using 60 threads, the computation time will increase. The reason is that the communication overhead will offset the performance gain when 60 threads are deployed on a single MIC card

Map Generation from Large Scale Incomplete and Inaccurate Data Labels

Accurately and globally mapping human infrastructure is an important and challenging task with applications in routing, regulation compliance monitoring, and natural disaster response management etc.. In this paper we present progress in developing an algorithmic pipeline and distributed compute system that automates the process of map creation using high resolution aerial images. Unlike previous studies, most of which use datasets that are available only in a few cities across the world, we utilizes publicly available imagery and map data, both of which cover the contiguous United States (CONUS). We approach the technical challenge of inaccurate and incomplete training data adopting state-of-the-art convolutional neural network architectures such as the U-Net and the CycleGAN to incrementally generate maps with increasingly more accurate and more complete labels of man-made infrastructure such as roads and houses. Since scaling the mapping task to CONUS calls for parallelization, we then adopted an asynchronous distributed stochastic parallel gradient descent training scheme to distribute the computational workload onto a cluster of GPUs with nearly linear speed-up.Comment: This paper is accepted by KDD 202

Faster inference from state space models via GPU computing

Funding: C.F.-J. is funded via a doctoral scholarship from the University of St Andrews, School of Mathematics and Statistics.Inexpensive Graphics Processing Units (GPUs) offer the potential to greatly speed up computation by employing their massively parallel architecture to perform arithmetic operations more efficiently. Population dynamics models are important tools in ecology and conservation. Modern Bayesian approaches allow biologically realistic models to be constructed and fitted to multiple data sources in an integrated modelling framework based on a class of statistical models called state space models. However, model fitting is often slow, requiring hours to weeks of computation. We demonstrate the benefits of GPU computing using a model for the population dynamics of British grey seals, fitted with a particle Markov chain Monte Carlo algorithm. Speed-ups of two orders of magnitude were obtained for estimations of the log-likelihood, compared to a traditional ‘CPU-only’ implementation, allowing for an accurate method of inference to be used where this was previously too computationally expensive to be viable. GPU computing has enormous potential, but one barrier to further adoption is a steep learning curve, due to GPUs' unique hardware architecture. We provide a detailed description of hardware and software setup, and our case study provides a template for other similar applications. We also provide a detailed tutorial-style description of GPU hardware architectures, and examples of important GPU-specific programming practices.Publisher PDFPeer reviewe

SkewEngine: enhancing performance of intensive calculations on regular meshes

In various applications such as hyperspectral data manipulation, MRI data exploration, or viewshed identification in digital elevation models, performing arithmetic operations on each point of a data mesh that involves other points can lead to computationally intractable problems. This paper presents SkewEngine, a tool designed to improve the performance of intensive calculations on regular 2-D data meshes, such as images, multispectral data volumes, or digital elevation models. SkewEngine addresses this problem by reorganizing the mesh in memory according to a preferred spatial direction, enabling more efficient execution of intensive calculations. It is demonstrated that SkewEngine offers significant speed improvements for various test cases, suggesting its usefulness in a broader range of applications requiring intensive data processing on regular meshes.Funding for open access charge: Universidad de Málaga/CBUA. This work has been fnanced by the Spanish Ministry of Science and Technology through the National Plan project PID2022-136575OB-I00, by the Andalusian Government and FEDER funds through the UMA20-FEDERJA-127 project, and by the University of Malaga (PIE22-099). We also thank the Supercomputing and Bioinformatics Service of the University of Malaga and the Spanish Supercomputing Network for facilitating access to the Picasso and Loginexa Supercomputers