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. 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Enhancing the context-aware FOREX market simulation using a parallel elastic network model

[EN] Foreign exchange (FOREX) market is a decentralized global marketplace in which different participants, such as international banks, companies or investors, can buy, sell, exchange and speculate on currencies. This market is considered to be the largest financial market in the world in terms of trading volume. Indeed, the just-in-time price prediction for a currency pair exchange rate (e.g., EUR/USD) provides valuable information for companies and investors as they can take different actions to improve their business. The trading volume in the FOREX market is huge, disperses, in continuous operations (24 h except weekends), and the context significantly affects the exchange rates. This paper introduces a context-aware algorithm to model the behavior of the FOREX Market, called parallel elastic network model (PENM). This algorithm is inspired by natural procedures like the behavior of macromolecules in dissolution. The main results of this work include the possibility to represent the market evolution of up to 21 currency pair, being all connected, thus emulating the real-world FOREX market behavior. Moreover, because the computational needs required are highly costly as the number of currency pairs increases, a hybrid parallelization using several shared memory and message passing algorithms studied on distributed cluster is evaluated to achieve a high-throughput algorithm that answers the real-time constraints of the FOREX market. The PENM is also compared with a vector autoregressive (VAR) model using both a classical statistical measure and a profitability measure. Specifically, the results indicate that PENM outperforms VAR models in terms of quality, achieving up to 930xspeed-up factor compared to traditional R codes using in this field.This work was jointly supported by the Fundación Séneca (Agencia Regional de Ciencia y Tecnología, Región de Murcia) under Grant 20813/PI/18 and by the Spanish MEC and European Commission FEDER under Grants TIN2016-78799-P and TIN2016-80565-R (AEI/FEDER, UE).Contreras, AV.; Llanes, A.; Herrera, FJ.; Navarro, S.; López-Espin, JJ.; Cecilia-Canales, JM. (2020). Enhancing the context-aware FOREX market simulation using a parallel elastic network model. The Journal of Supercomputing. 76(3):2022-2038. https://doi.org/10.1007/s11227-019-02838-1S20222038763Bahrepour M, Akbarzadeh-T MR, Yaghoobi M, Naghibi-S MB (2011) An adaptive ordered fuzzy time series with application to FOREX. Expert Syst Appl 38(1):475–485Bank for International Settlements. https://www.bis.org/ . 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Towards Real-Time Detection and Tracking of Spatio-Temporal Features: Blob-Filaments in Fusion Plasma

A novel algorithm and implementation of real-time identification and tracking of blob-filaments in fusion reactor data is presented. Similar spatio-temporal features are important in many other applications, for example, ignition kernels in combustion and tumor cells in a medical image. This work presents an approach for extracting these features by dividing the overall task into three steps: local identification of feature cells, grouping feature cells into extended feature, and tracking movement of feature through overlapping in space. Through our extensive work in parallelization, we demonstrate that this approach can effectively make use of a large number of compute nodes to detect and track blob-filaments in real time in fusion plasma. On a set of 30GB fusion simulation data, we observed linear speedup on 1024 processes and completed blob detection in less than three milliseconds using Edison, a Cray XC30 system at NERSC.Comment: 14 pages, 40 figure

GSWO: A Programming Model for GPU-enabled Parallelization of Sliding Window Operations in Image Processing

Sliding Window Operations (SWOs) are widely used in image processing applications. They often have to be performed repeatedly across the target image, which can demand significant computing resources when processing large images with large windows. In applications in which real-time performance is essential, running these filters on a CPU often fails to deliver results within an acceptable timeframe. The emergence of sophisticated graphic processing units (GPUs) presents an opportunity to address this challenge. However, GPU programming requires a steep learning curve and is error-prone for novices, so the availability of a tool that can produce a GPU implementation automatically from the original CPU source code can provide an attractive means by which the GPU power can be harnessed effectively. This paper presents a GPUenabled programming model, called GSWO, which can assist GPU novices by converting their SWO-based image processing applications from the original C/C++ source code to CUDA code in a highly automated manner. This model includes a new set of simple SWO pragmas to generate GPU kernels and to support effective GPU memory management. We have implemented this programming model based on a CPU-to-GPU translator (C2GPU). Evaluations have been performed on a number of typical SWO image filters and applications. The experimental results show that the GSWO model is capable of efficiently accelerating these applications, with improved applicability and a speed-up of performance compared to several leading CPU-to- GPU source-to-source translators

Evaluation of Clustering Algorithms on GPU-Based Edge Computing Platforms

[EN] Internet of Things (IoT) is becoming a new socioeconomic revolution in which data and immediacy are the main ingredients. IoT generates large datasets on a daily basis but it is currently considered as "dark data", i.e., data generated but never analyzed. The efficient analysis of this data is mandatory to create intelligent applications for the next generation of IoT applications that benefits society. Artificial Intelligence (AI) techniques are very well suited to identifying hidden patterns and correlations in this data deluge. In particular, clustering algorithms are of the utmost importance for performing exploratory data analysis to identify a set (a.k.a., cluster) of similar objects. Clustering algorithms are computationally heavy workloads and require to be executed on high-performance computing clusters, especially to deal with large datasets. This execution on HPC infrastructures is an energy hungry procedure with additional issues, such as high-latency communications or privacy. Edge computing is a paradigm to enable light-weight computations at the edge of the network that has been proposed recently to solve these issues. In this paper, we provide an in-depth analysis of emergent edge computing architectures that include low-power Graphics Processing Units (GPUs) to speed-up these workloads. Our analysis includes performance and power consumption figures of the latest Nvidia's AGX Xavier to compare the energy-performance ratio of these low-cost platforms with a high-performance cloud-based counterpart version. Three different clustering algorithms (i.e., k-means, Fuzzy Minimals (FM), and Fuzzy C-Means (FCM)) are designed to be optimally executed on edge and cloud platforms, showing a speed-up factor of up to 11x for the GPU code compared to sequential counterpart versions in the edge platforms and energy savings of up to 150% between the edge computing and HPC platforms.This work has been partially supported by the Spanish Ministry of Science and Innovation, under the Ramon y Cajal Program (Grant No. RYC2018-025580-I) and under grants RTI2018-096384-B-I00, RTC-2017-6389-5 and RTC2019-007159-5 and by the Fundacion Seneca del Centro de Coordinacion de la Investigacion de la Region de Murcia under Project 20813/PI/18.Cecilia-Canales, JM.; Cano, J.; Morales-García, J.; Llanes, A.; Imbernón, B. (2020). Evaluation of Clustering Algorithms on GPU-Based Edge Computing Platforms. Sensors. 20(21):1-19. https://doi.org/10.3390/s20216335S1192021Gebauer, H., Fleisch, E., Lamprecht, C., & Wortmann, F. 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A survey on platforms for big data analytics. Journal of Big Data, 2(1). doi:10.1186/s40537-014-0008-6Khayyat, M., Elgendy, I. A., Muthanna, A., Alshahrani, A. S., Alharbi, S., & Koucheryavy, A. (2020). Advanced Deep Learning-Based Computational Offloading for Multilevel Vehicular Edge-Cloud Computing Networks. IEEE Access, 8, 137052-137062. doi:10.1109/access.2020.3011705Satyanarayanan, M. (2017). The Emergence of Edge Computing. Computer, 50(1), 30-39. doi:10.1109/mc.2017.9Capra, M., Peloso, R., Masera, G., Roch, M. R., & Martina, M. (2019). Edge Computing: A Survey On the Hardware Requirements in the Internet of Things World. Future Internet, 11(4), 100. doi:10.3390/fi11040100Lu, H., Gu, C., Luo, F., Ding, W., & Liu, X. (2020). Optimization of lightweight task offloading strategy for mobile edge computing based on deep reinforcement learning. Future Generation Computer Systems, 102, 847-861. doi:10.1016/j.future.2019.07.019Mimmack, G. M., Mason, S. J., & Galpin, J. S. (2001). 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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.2019.2907885Liu, B., He, S., He, D., Zhang, Y., & Guizani, M. (2019). A Spark-Based Parallel Fuzzy $c$ -Means Segmentation Algorithm for Agricultural Image Big Data. IEEE Access, 7, 42169-42180. doi:10.1109/access.2019.2907573Baydoun, M., Ghaziri, H., & Al-Husseini, M. (2018). CPU and GPU parallelized kernel K-means. The Journal of Supercomputing, 74(8), 3975-3998. doi:10.1007/s11227-018-2405-7Li, 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.2012.05.004Cuomo, S., De Angelis, V., Farina, G., Marcellino, L., & Toraldo, G. (2019). A GPU-accelerated parallel K-means algorithm. Computers & Electrical Engineering, 75, 262-274. doi:10.1016/j.compeleceng.2017.12.002Al-Ayyoub, M., Abu-Dalo, A. M., Jararweh, Y., Jarrah, M., & Sa’d, M. A. (2015). A GPU-based implementations of the fuzzy C-means algorithms for medical image segmentation. The Journal of Supercomputing, 71(8), 3149-3162. doi:10.1007/s11227-015-1431-yAit Ali, N., Cherradi, B., El Abbassi, A., Bouattane, O., & Youssfi, M. (2018). GPU fuzzy c-means algorithm implementations: performance analysis on medical image segmentation. Multimedia Tools and Applications, 77(16), 21221-21243. doi:10.1007/s11042-017-5589-6Timón, 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.2015.11.011Cebrian, J. M., Imbernón, B., Soto, J., García, J. M., & Cecilia, J. M. (2020). High-throughput fuzzy clustering on heterogeneous architectures. Future Generation Computer Systems, 106, 401-411. doi:10.1016/j.future.2020.01.022Cecilia, 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.2018.2816741Sriramakrishnan, P., Kalaiselvi, T., & Rajeswaran, R. (2019). Modified local ternary patterns technique for brain tumour segmentation and volume estimation from MRI multi-sequence scans with GPU CUDA machine. Biocybernetics and Biomedical Engineering, 39(2), 470-487. doi:10.1016/j.bbe.2019.02.002Fang, Y., Chen, Q., & Xiong, N. (2019). A multi-factor monitoring fault tolerance model based on a GPU cluster for big data processing. Information Sciences, 496, 300-316. doi:10.1016/j.ins.2018.04.053Rodriguez, M. Z., Comin, C. H., Casanova, D., Bruno, O. M., Amancio, D. R., Costa, L. da F., & Rodrigues, F. A. (2019). Clustering algorithms: A comparative approach. PLOS ONE, 14(1), e0210236. doi:10.1371/journal.pone.0210236Pandove, D., Goel, S., & Rani, R. (2018). Systematic Review of Clustering High-Dimensional and Large Datasets. ACM Transactions on Knowledge Discovery from Data, 12(2), 1-68. doi:10.1145/3132088Bezdek, 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)90020-7Soto, 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.2007.08.016Kolen, J. F., & Hutcheson, T. (2002). Reducing the time complexity of the fuzzy c-means algorithm. IEEE Transactions on Fuzzy Systems, 10(2), 263-267. doi:10.1109/91.99512

Accelerating Pattern Matching in Neuromorphic Text Recognition System Using Intel Xeon Phi Coprocessor

Neuromorphic computing systems refer to the computing architecture inspired by the working mechanism of human brains. The rapidly reducing cost and increasing performance of state-of-the-art computing hardware allows large-scale implementation of machine intelligence models with neuromorphic architectures and opens the opportunity for new applications. One such computing hardware is Intel Xeon Phi coprocessor, which delivers over a TeraFLOP of computing power with 61 integrated processing cores. How to efficiently harness such computing power to achieve real time decision and cognition is one of the key design considerations. This work presents an optimized implementation of Brain-State-in-a-Box (BSB) neural network model on the Xeon Phi coprocessor for pattern matching in the context of intelligent text recognition of noisy document images. From a scalability standpoint on a High Performance Computing (HPC) platform we show that efficient workload partitioning and resource management can double the performance of this many-core architecture for neuromorphic applications

The Scalability-Efficiency/Maintainability-Portability Trade-off in Simulation Software Engineering: Examples and a Preliminary Systematic Literature Review

Large-scale simulations play a central role in science and the industry. Several challenges occur when building simulation software, because simulations require complex software developed in a dynamic construction process. That is why simulation software engineering (SSE) is emerging lately as a research focus. The dichotomous trade-off between scalability and efficiency (SE) on the one hand and maintainability and portability (MP) on the other hand is one of the core challenges. We report on the SE/MP trade-off in the context of an ongoing systematic literature review (SLR). After characterizing the issue of the SE/MP trade-off using two examples from our own research, we (1) review the 33 identified articles that assess the trade-off, (2) summarize the proposed solutions for the trade-off, and (3) discuss the findings for SSE and future work. Overall, we see evidence for the SE/MP trade-off and first solution approaches. However, a strong empirical foundation has yet to be established; general quantitative metrics and methods supporting software developers in addressing the trade-off have to be developed. We foresee considerable future work in SSE across scientific communities.Comment: 9 pages, 2 figures. Accepted for presentation at the Fourth International Workshop on Software Engineering for High Performance Computing in Computational Science and Engineering (SEHPCCSE 2016

CAVASS: A Computer-Assisted Visualization and Analysis Software System

The Medical Image Processing Group at the University of Pennsylvania has been developing (and distributing with source code) medical image analysis and visualization software systems for a long period of time. Our most recent system, 3DVIEWNIX, was first released in 1993. Since that time, a number of significant advancements have taken place with regard to computer platforms and operating systems, networking capability, the rise of parallel processing standards, and the development of open-source toolkits. The development of CAVASS by our group is the next generation of 3DVIEWNIX. CAVASS will be freely available and open source, and it is integrated with toolkits such as Insight Toolkit and Visualization Toolkit. CAVASS runs on Windows, Unix, Linux, and Mac but shares a single code base. Rather than requiring expensive multiprocessor systems, it seamlessly provides for parallel processing via inexpensive clusters of work stations for more time-consuming algorithms. Most importantly, CAVASS is directed at the visualization, processing, and analysis of 3-dimensional and higher-dimensional medical imagery, so support for digital imaging and communication in medicine data and the efficient implementation of algorithms is given paramount importance

Parallel ant colony optimization for the training of cell signaling networks

[Abstract]: Acquiring a functional comprehension of the deregulation of cell signaling networks in disease allows progress in the development of new therapies and drugs. Computational models are becoming increasingly popular as a systematic tool to analyze the functioning of complex biochemical networks, such as those involved in cell signaling. CellNOpt is a framework to build predictive logic-based models of signaling pathways by training a prior knowledge network to biochemical data obtained from perturbation experiments. This training can be formulated as an optimization problem that can be solved using metaheuristics. However, the genetic algorithm used so far in CellNOpt presents limitations in terms of execution time and quality of solutions when applied to large instances. Thus, in order to overcome those issues, in this paper we propose the use of a method based on ant colony optimization, adapted to the problem at hand and parallelized using a hybrid approach. The performance of this novel method is illustrated with several challenging benchmark problems in the study of new therapies for liver cancer