GPU acceleration for statistical gene classification

The use of Bioinformatic tools in routine clinical diagnostics is still facing a number of issues. The more complex and advanced bioinformatic tools become, the more performance is required by the computing platforms. Unfortunately, the cost of parallel computing platforms is usually prohibitive for both public and small private medical practices. This paper presents a successful experience in using the parallel processing capabilities of Graphical Processing Units (GPU) to speed up bioinformatic tasks such as statistical classification of gene expression profiles. The results show that using open source CUDA programming libraries allows to obtain a significant increase in performances and therefore to shorten the gap between advanced bioinformatic tools and real medical practic

Recent Advances in Graph Partitioning

We survey recent trends in practical algorithms for balanced graph partitioning together with applications and future research directions

Parallelizing the QUDA Library for Multi-GPU Calculations in Lattice Quantum Chromodynamics

Graphics Processing Units (GPUs) are having a transformational effect on numerical lattice quantum chromodynamics (LQCD) calculations of importance in nuclear and particle physics. The QUDA library provides a package of mixed precision sparse matrix linear solvers for LQCD applications, supporting single GPUs based on NVIDIA's Compute Unified Device Architecture (CUDA). This library, interfaced to the QDP++/Chroma framework for LQCD calculations, is currently in production use on the "9g" cluster at the Jefferson Laboratory, enabling unprecedented price/performance for a range of problems in LQCD. Nevertheless, memory constraints on current GPU devices limit the problem sizes that can be tackled. In this contribution we describe the parallelization of the QUDA library onto multiple GPUs using MPI, including strategies for the overlapping of communication and computation. We report on both weak and strong scaling for up to 32 GPUs interconnected by InfiniBand, on which we sustain in excess of 4 Tflops.Comment: 11 pages, 7 figures, to appear in the Proceedings of Supercomputing 2010 (submitted April 12, 2010

Comparing Performance and Portability between CUDA and SYCL for Protein Database Search on NVIDIA, AMD, and Intel GPUs

The heterogeneous computing paradigm has led to the need for portable and efficient programming solutions that can leverage the capabilities of various hardware devices, such as NVIDIA, Intel, and AMD GPUs. This study evaluates the portability and performance of the SYCL and CUDA languages for one fundamental bioinformatics application (Smith-Waterman protein database search) across different GPU architectures, considering single and multi-GPU configurations from different vendors. The experimental work showed that, while both CUDA and SYCL versions achieve similar performance on NVIDIA devices, the latter demonstrated remarkable code portability to other GPU architectures, such as AMD and Intel. Furthermore, the architectural efficiency rates achieved on these devices were superior in 3 of the 4 cases tested. This brief study highlights the potential of SYCL as a viable solution for achieving both performance and portability in the heterogeneous computing ecosystem.Comment: This article was accepted for publication in 2023 IEEE 35th International Symposium on Computer Architecture and High Performance Computing (SBAC-PAD

High-throughput fuzzy clustering on heterogeneous architectures

[EN] The Internet of Things (IoT) is pushing the next economic revolution in which the main players are data and immediacy. IoT is increasingly producing large amounts of data that are now classified as "dark data'' because most are created but never analyzed. The efficient analysis of this data deluge is becoming mandatory in order to transform it into meaningful information. Among the techniques available for this purpose, clustering techniques, which classify different patterns into groups, have proven to be very useful for obtaining knowledge from the data. However, clustering algorithms are computationally hard, especially when it comes to large data sets and, therefore, they require the most powerful computing platforms on the market. In this paper, we investigate coarse and fine grain parallelization strategies in Intel and Nvidia architectures of fuzzy minimals (FM) algorithm; a fuzzy clustering technique that has shown very good results in the literature. We provide an in-depth performance analysis of the FM's main bottlenecks, reporting a speed-up factor of up to 40x compared to the sequential counterpart version.This work was partially supported by the Fundacion Seneca del Centro de Coordinacion de la Investigacion de la Region de Murcia under Project 20813/PI/18, and by Spanish Ministry of Science, Innovation and Universities under grants TIN2016-78799-P (AEI/FEDER, UE), RTI2018-096384-B-I00, RTI2018-098156-B-C53 and RTC-2017-6389-5.Cebrian, JM.; Imbernón, B.; Soto, J.; García, JM.; Cecilia-Canales, JM. (2020). High-throughput fuzzy clustering on heterogeneous architectures. Future Generation Computer Systems. 106:401-411. https://doi.org/10.1016/j.future.2020.01.022S401411106Waldrop, M. M. (2016). The chips are down for Moore’s law. Nature, 530(7589), 144-147. doi:10.1038/530144aCecilia, J. M., Timon, I., Soto, J., Santa, J., Pereniguez, F., & Munoz, A. (2018). High-Throughput Infrastructure for Advanced ITS Services: A Case Study on Air Pollution Monitoring. IEEE Transactions on Intelligent Transportation Systems, 19(7), 2246-2257. doi:10.1109/tits.2018.2816741Singh, D., & Reddy, C. K. (2014). A survey on platforms for big data analytics. Journal of Big Data, 2(1). doi:10.1186/s40537-014-0008-6Stephens, N., Biles, S., Boettcher, M., Eapen, J., Eyole, M., Gabrielli, G., … Walker, P. (2017). The ARM Scalable Vector Extension. IEEE Micro, 37(2), 26-39. doi:10.1109/mm.2017.35Wright, S. A. (2019). Performance Modeling, Benchmarking and Simulation of High Performance Computing Systems. Future Generation Computer Systems, 92, 900-902. doi:10.1016/j.future.2018.11.020Jain, A. K., Murty, M. N., & Flynn, P. J. (1999). Data clustering. ACM Computing Surveys, 31(3), 264-323. doi:10.1145/331499.331504Lee, J., Hong, B., Jung, S., & Chang, V. (2018). Clustering learning model of CCTV image pattern for producing road hazard meteorological information. Future Generation Computer Systems, 86, 1338-1350. doi:10.1016/j.future.2018.03.022Pérez-Garrido, A., Girón-Rodríguez, F., Bueno-Crespo, A., Soto, J., Pérez-Sánchez, H., & Helguera, A. M. (2017). Fuzzy clustering as rational partition method for QSAR. Chemometrics and Intelligent Laboratory Systems, 166, 1-6. doi:10.1016/j.chemolab.2017.04.006H.S. Nagesh, S. Goil, A. Choudhary, A scalable parallel subspace clustering algorithm for massive data sets, in: Proceedings 2000 International Conference on Parallel Processing, 2000, pp. 477–484.Bezdek, J. C., Ehrlich, R., & Full, W. (1984). FCM: The fuzzy c-means clustering algorithm. Computers & Geosciences, 10(2-3), 191-203. doi:10.1016/0098-3004(84)90020-7Havens, T. C., Bezdek, J. C., Leckie, C., Hall, L. O., & Palaniswami, M. (2012). Fuzzy c-Means Algorithms for Very Large Data. IEEE Transactions on Fuzzy Systems, 20(6), 1130-1146. doi:10.1109/tfuzz.2012.2201485Flores-Sintas, A., Cadenas, J., & Martin, F. (1998). A local geometrical properties application to fuzzy clustering. Fuzzy Sets and Systems, 100(1-3), 245-256. doi:10.1016/s0165-0114(97)00038-9Soto, J., Flores-Sintas, A., & Palarea-Albaladejo, J. (2008). Improving probabilities in a fuzzy clustering partition. Fuzzy Sets and Systems, 159(4), 406-421. doi:10.1016/j.fss.2007.08.016Timón, I., Soto, J., Pérez-Sánchez, H., & Cecilia, J. M. (2016). Parallel implementation of fuzzy minimals clustering algorithm. Expert Systems with Applications, 48, 35-41. doi:10.1016/j.eswa.2015.11.011Flores-Sintas, A., M. Cadenas, J., & Martin, F. (2001). Detecting homogeneous groups in clustering using the Euclidean distance. Fuzzy Sets and Systems, 120(2), 213-225. doi:10.1016/s0165-0114(99)00110-4Wang, H., Potluri, S., Luo, M., Singh, A. K., Sur, S., & Panda, D. K. (2011). MVAPICH2-GPU: optimized GPU to GPU communication for InfiniBand clusters. Computer Science - Research and Development, 26(3-4), 257-266. doi:10.1007/s00450-011-0171-3Kaltofen, E., & Villard, G. (2005). On the complexity of computing determinants. computational complexity, 13(3-4), 91-130. doi:10.1007/s00037-004-0185-3Johnson, S. C. (1967). Hierarchical clustering schemes. Psychometrika, 32(3), 241-254. doi:10.1007/bf02289588Saxena, A., Prasad, M., Gupta, A., Bharill, N., Patel, O. P., Tiwari, A., … Lin, C.-T. (2017). A review of clustering techniques and developments. Neurocomputing, 267, 664-681. doi:10.1016/j.neucom.2017.06.053Woodley, A., Tang, L.-X., Geva, S., Nayak, R., & Chappell, T. (2019). Parallel K-Tree: A multicore, multinode solution to extreme clustering. Future Generation Computer Systems, 99, 333-345. doi:10.1016/j.future.2018.09.038Kwedlo, W., & Czochanski, P. J. (2019). A Hybrid MPI/OpenMP Parallelization of $K$ -Means Algorithms Accelerated Using the Triangle Inequality. IEEE Access, 7, 42280-42297. doi:10.1109/access.2019.2907885Li, Y., Zhao, K., Chu, X., & Liu, J. (2013). Speeding up k-Means algorithm by GPUs. Journal of Computer and System Sciences, 79(2), 216-229. doi:10.1016/j.jcss.2012.05.004Saveetha, V., & Sophia, S. (2018). Optimal Tabu K-Means Clustering Using Massively Parallel Architecture. Journal of Circuits, Systems and Computers, 27(13), 1850199. doi:10.1142/s0218126618501992Djenouri, Y., Djenouri, D., Belhadi, A., & Cano, A. (2019). Exploiting GPU and cluster parallelism in single scan frequent itemset mining. Information Sciences, 496, 363-377. doi:10.1016/j.ins.2018.07.020Krawczyk, B. (2016). GPU-Accelerated Extreme Learning Machines for Imbalanced Data Streams with Concept Drift. Procedia Computer Science, 80, 1692-1701. doi:10.1016/j.procs.2016.05.509Fang, Y., Chen, Q., & Xiong, N. (2019). A multi-factor monitoring fault tolerance model based on a GPU cluster for big data processing. 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A performance focused, development friendly and model aided parallelization strategy for scientific applications

The amelioration of high performance computing platforms has provided unprecedented computing power with the evolution of multi-core CPUs, massively parallel architectures such as General Purpose Graphics Processing Units (GPGPUs) and Many Integrated Core (MIC) architectures such as Intel\u27s Xeon phi coprocessor. However, it is a great challenge to leverage capabilities of such advanced supercomputing hardware, as it requires efficient and effective parallelization of scientific applications. This task is difficult mainly due to complexity of scientific algorithms coupled with the variety of available hardware and disparate programming models. To address the aforementioned challenges, this thesis presents a parallelization strategy to accelerate scientific applications that maximizes the opportunities of achieving speedup while minimizing the development efforts. Parallelization is a three step process (1) choose a compatible combination of architecture and parallel programming language, (2) translate base code/algorithm to a parallel language and (3) optimize and tune the application. In this research, a quantitative comparison of run time for various implementations of k-means algorithm, is used to establish that native languages (OpenMP, MPI, CUDA) perform better on respective architectures as opposed to vendor-neutral languages such as OpenCL. A qualitative model is used to select an optimal architecture for a given application by aligning the capabilities of accelerators with characteristics of the application. Once the optimal architecture is chosen, the corresponding native language is employed. This approach provides the best performance with reasonable accuracy (78%) of predicting a fitting combination, while eliminating the need for exploring different architectures individually. It reduces the required development efforts considerably as the application need not be re-written in multiple languages. The focus can be solely on optimization and tuning to achieve the best performance on available architectures with minimized investment in terms of cost and efforts. To verify the prediction accuracy of the qualitative model, the OpenDwarfs benchmark suite, which implements the Berkeley\u27s dwarfs in OpenCL, is used. A dwarf is an algorithmic method that captures a pattern of computation and communication. For the purpose of this research, the focus is on 9 application from various algorithmic domains that cover the seven dwarfs of symbolic computation, which were identified by Phillip Colella, as omnipresent in scientific and engineering applications. To validate the parallelization strategy collectively, a case study is undertaken. This case study involves parallelization of the Lower Upper Decomposition for the Gaussian Elimination algorithm from the linear algebra domain, using conventional trial and error methods as well as the proposed \u27Architecture First, Language Later\u27\u27 strategy. The development efforts incurred are contrasted for both methods. The aforesaid proposed strategy is observed to reduce the development efforts by an average of 50%

Parallelization Strategies for Graph-Code-Based Similarity Search

The volume of multimedia assets in collections is growing exponentially, and the retrieval of information is becoming more complex. The indexing and retrieval of multimedia content is generally implemented by employing feature graphs. Feature graphs contain semantic information on multimedia assets. Machine learning can produce detailed semantic information on multimedia assets, reflected in a high volume of nodes and edges in the feature graphs. While increasing the effectiveness of the information retrieval results, the high level of detail and also the growing collections increase the processing time. Addressing this problem, Multimedia Feature Graphs (MMFGs) and Graph Codes (GCs) have been proven to be fast and effective structures for information retrieval. However, the huge volume of data requires more processing time. As Graph Code algorithms were designed to be parallelizable, different paths of parallelization can be employed to prove or evaluate the scalability options of Graph Code processing. These include horizontal and vertical scaling with the use of Graphic Processing Units (GPUs), Multicore Central Processing Units (CPUs), and distributed computing. In this paper, we show how different parallelization strategies based on Graph Codes can be combined to provide a significant improvement in efficiency. Our modeling work shows excellent scalability with a theoretical speedup of 16,711 on a top-of-the-line Nvidia H100 GPU with 16,896 cores. Our experiments with a mediocre GPU show that a speedup of 225 can be achieved and give credence to the theoretical speedup. Thus, Graph Codes provide fast and effective multimedia indexing and retrieval, even in billion-scale use cases