Search Results (250)

The traditional finite element program is executed on the CPU; however, it is challenging for the CPU to compute the ultra-large scale finite element model. In this paper, we present a set of efficient algorithms based on GPU acceleration technology for the dynamic response of fluid-saturated porous media, named PNAM, encompassing the assembly of the global matrix and the iterative solution of equations. In the assembly part, the CSR storage format of the global matrix is directly obtained from the element matrix. For data with two million degrees of freedom, it merely takes approximately 1 s to generate all the data of global matrices, which is significantly superior to the CPU version. Regarding the iterative solution of equations, a novel algorithm based on the CUDA kernel function is proposed. For a data set with two million degrees of freedom, it takes only about 0.05 s to compute an iterative step and transfer the data to the CPU. The program is designed to calculate either in single or double precision. The change in precision has little impact on the assembly of the global matrix, but the calculation time of double precision is generally 1.5 to 2 times that of single precision in the iterative solution part for a model with 2 million degrees of freedom. PNAM has high computational efficiency and great compatibility, which can be used to solve not only saturated fluid problems but also a variety of other problems. Full article

Estimating ego-motion in autonomous vehicles is critical for tasks such as localization, navigation, obstacle avoidance, and so on. While traditional methods often rely on direct pose estimation or AI-based approaches, these can be computationally intensive, especially for small, incremental movements typically observed between consecutive frames. In this work, we propose a brute-force-based ego-motion estimation algorithm that takes advantage of the constraints of autonomous vehicles, which are assumed to have only three degrees of freedom (x, y, and yaw). Our approach is based on a genetic algorithm to efficiently explore potential vehicle movements. By generating an initial seed of random motion candidates and iteratively mutating and selecting the best-performing individuals, we minimize the cost function that measures image similarity between frames. Furthermore, we implement the algorithm using CUDA to exploit parallel processing, significantly improving computational speed. Experimental results demonstrate that our approach achieves accurate ego-motion estimation with high efficiency, making it suitable for real-time autonomous vehicle applications. Full article

Fast charge/discharge scheduling of battery storage systems is essential in microgrids to effectively balance variable renewable energy sources, meet fluctuating demand, and maintain grid stability. To achieve this, parallel processing is employed, allowing batteries to respond instantly to dynamic conditions. By managing the complexity, high data volume, and rapid decision-making requirements in real time, parallel processing ensures that the microgrid operates with stability, efficiency, and safety. With the application of deep reinforcement learning (DRL) in scheduling algorithm design, the demand for computational power has further increased significantly. To address this challenge, we propose a Ray-based parallel framework to accelerate the development of fast charge/discharge scheduling for battery storage systems in microgrids. We demonstrate how to implement a real-world scheduling problem in the framework. We focused on minimizing power losses and reducing the ramping rate of net loads by leveraging the Asynchronous Advantage Actor Critic (A3C) algorithms and the features of the Ray cluster for real-time decision making. Multiple instances of OpenDSS were executed concurrently, with each instance simulating a distinct environment and efficiently processing input data. Additionally, Numba CUDA was utilized to facilitate GPU acceleration of shared memory, significantly enhancing the performance of the computationally intensive reward function in A3C. The proposed framework enhanced scheduling performance, enabling efficient energy management in complex, dynamic microgrid environments. Full article

Simultaneous Localization and Mapping (SLAM) algorithms are crucial for enabling agents to estimate their position in unknown environments. In autonomous navigation systems, these algorithms need to operate in real-time on devices with limited resources, emphasizing the importance of reducing complexity and ensuring efficient performance. While SLAM solutions aim at ensuring accurate and timely localization and mapping, one of their main limitations is their computational complexity. In this scenario, particle filter-based approaches such as FastSLAM 2.0 can significantly benefit from parallel programming due to their modular construction. The parallelization process involves identifying the parameters affecting the computational complexity in order to distribute the computation among single multiprocessors as efficiently as possible. However, the computational complexity of methodologies such as FastSLAM 2.0 can depend on multiple parameters whose values may, in turn, depend on each specific use case scenario ( ingi.e., the context), leading to multiple possible parallelization designs. Furthermore, the features of the hardware architecture in use can significantly influence the performance in terms of latency. Therefore, the selection of the optimal parallelization modality still needs to be empirically determined. This may involve redesigning the parallel algorithm depending on the context and the hardware architecture. In this paper, we propose a CUDA-based adaptable design for FastSLAM 2.0 on GPU, in combination with an evaluation methodology that enables the assessment of the optimal parallelization modality based on the context and the hardware architecture without the need for the creation of separate designs. The proposed implementation includes the parallelization of all the functional blocks of the FastSLAM 2.0 pipeline. Additionally, we contribute a parallelized design of the data association step through the Joint Compatibility Branch and Bound (JCBB) method. Multiple resampling algorithms are also included to accommodate the needs of a wide variety of navigation scenarios. Full article

Background/Objectives: Progressive Supranuclear Palsy (PSP) is a tauopathy showing a marked symptoms overlap with Parkinson’s Disease (PD). PSP pathology suggests that tau protein might represent a valuable biomarker to distinguish between the two diseases. Here, we investigated the presence and diagnostic value of six different tau species (total tau, 4R-tau isoform, tau aggregates, p-tau202, p-tau231 and p-tau396) in serum from 13 PSP and 13 PD patients and 12 healthy controls (HCs). Methods: ELISA commercial kits were employed to assess all the tau species except for t-tau, which was assessed by a single molecule array (SIMOA)-based commercial kit. Possible correlations between tau species and biological and clinical features of our cohorts were also evaluated. Results: Among the six tau species tested, only p-tau396 was detectable in serum. Concentration of p-tau396 was significantly higher in both PSP and PD groups compared to HC, but PSP and PD patients showed largely overlapping values. Moreover, serum concentration of p-tau396 strongly correlated with disease severity in PSP and not in PD. Conclusions: Overall, we identified serum p-tau396 as the most expressed phosphorylated tau species in serum and as a potential tool for assessing PSP clinical staging. Moreover, we demonstrated that other p-tau species may be present at too low concentrations in serum to be detected by ELISA, suggesting that future work should focus on other biological matrices. Full article

This study examines various algorithms for computing the convex hull of a set of n points in a d-dimensional space. Convex hulls are fundamental in computational geometry and are applied in computer graphics, pattern recognition, and computational biology. Such convex hulls can also be useful in symmetry problems. For instance, when points are arranged symmetrically, the convex hull is also likely to be symmetrically shaped, which can be useful for object recognition in computer vision or pattern recognition. The focus is primarily on two-dimensional algorithms, including well-known methods like Gift Wrapping, Graham Scan, Divide and Conquer, QuickHull, TORCH, Kirkpatrick–Sediel, and Chan’s algorithms. These algorithms vary in terms of time complexity and scalability to higher dimensions. This study is extended to three-dimensional convex hull algorithms, such as NAW, randomized insertion, and parallelized versions, such as CudaHull and CudaChain. This study aimed to elucidate the operational principles, step-by-step procedures, and comparative time complexities of each algorithm. The implementation in Python facilitates a detailed comparison of the algorithmic performance through stepwise analysis and graphical outputs. The ultimate goal is to provide insights into the strengths and weaknesses of each algorithm under various scenarios, thereby offering a comprehensive guide for practical implementation. Full article

The Winograd algorithm reduces the computational complexity of convolutional neural networks (CNNs) by minimizing the number of multiplications required for convolutions, making it particularly suitable for resource-constrained edge devices. Concurrently, most edge hardware accelerators utilize 8-bit integer arithmetic to enhance energy efficiency and reduce inference latency, requiring the quantization of CNNs before deployment. Combining Winograd-based convolution with quantization offers the potential for both performance acceleration and reduced energy consumption. However, prior research has identified significant challenges in this combination, particularly due to numerical instability and substantial accuracy degradation caused by the transformations required in the Winograd domain, making the two techniques incompatible on edge hardware. In this work, we describe our latest training scheme, which addresses these challenges, enabling the successful integration of Winograd-accelerated convolution with low-precision quantization while maintaining high task-related accuracy. Our approach mitigates the numerical instability typically introduced during the transformation, ensuring compatibility between the two techniques. Additionally, we extend our work by presenting a custom-optimized CUDA implementation of quantized Winograd convolution for NVIDIA edge GPUs. This implementation takes full advantage of the proposed training scheme, achieving both high computational efficiency and accuracy, making it a compelling solution for edge-based AI applications. Our training approach enables significant MAC reduction with minimal impact on prediction quality. Furthermore, our hardware results demonstrate up to a 3.4× latency reduction for specific layers, and a 1.44× overall reduction in latency for the entire DeepLabV3 model, compared to the standard implementation. Full article

In this paper, we consider the finite difference approximation for a one-dimensional mathematical model of heat conduction in a three-layered solid with interfacial conditions for temperature and heat flux between the layers. The finite difference scheme is unconditionally stable, convergent, and equivalent to the solution of two linear algebraic systems. We evaluate various methods for solving the involved linear systems by analyzing direct and iterative solvers, including GPU-accelerated approaches using CuPy and PyCUDA. We evaluate performance and scalability and contribute to advancing computational techniques for modeling complex physical processes accurately and efficiently. Full article

We introduce <tt>ssc-cdi</tt>, an open-source software package from the Sirius Scientific Computing family, designed for memory-efficient, single-node multi-GPU ptychography reconstruction. <tt>ssc-cdi</tt> offers a range of reconstruction engines in Python version 3.9.2 and C++/CUDA. It aims at developing local expertise and customized solutions to meet the specific needs of beamlines and user community of the Brazilian Synchrotron Light Laboratory (LNLS). We demonstrate ptychographic reconstruction of beamline data and present benchmarks for the package. Results show that <tt>ssc-cdi</tt> effectively handles extreme datasets typical of modern X-ray facilities without significantly compromising performance, offering a complementary approach to well-established packages of the community and serving as a robust tool for high-resolution imaging applications. Full article

Efficiently simulating solid mechanics is vital across various engineering applications. As constitutive models grow more complex and simulations scale up in size, harnessing the capabilities of modern computer architectures has become essential for achieving timely results. This paper presents advancements in running parallel simulations of solid mechanics on multi-core CPUs and GPUs using a single-code implementation. This portability is made possible by the C++ matrix and array (MATAR) library, which interfaces with the C++ Kokkos library, enabling the selection of fine-grained parallelism backends (e.g., CUDA, HIP, OpenMP, pthreads, etc.) at compile time. MATAR simplifies the transition from Fortran to C++ and Kokkos, making it easier to modernize legacy solid mechanics codes. We applied this approach to modernize a suite of constitutive models and to demonstrate substantial performance improvements across different computer architectures. This paper includes comparative performance studies using multi-core CPUs along with AMD and NVIDIA GPUs. Results are presented using a hypoelastic–plastic model, a crystal plasticity model, and the viscoplastic self-consistent generalized material model (VPSC-GMM). The results underscore the potential of using the MATAR library and modern computer architectures to accelerate solid mechanics simulations. Full article

Background/Objectives: The current research examines the accuracy of α-synuclein in RBCs as a diagnostic biomarker for PD and PSP, despite their distinct molecular etiologies. Methods: We used ELISA to measure total, oligomeric, and p129-α-synuclein levels in erythrocytes from 8 PSP patients, 19 PD patients, and 18 healthy controls (HCs). The classification performances of RBC α-synuclein levels were investigated by receiver operator characteristic (ROC) curve. We also evaluated a possible correlation between RBC α-synuclein level and the biological and clinical features of our cohorts. Results: RBC total α-synuclein was higher in PSP patients compared to both PD patients and HCs, achieving good classification performance (AUC: 0.853) in distinguishing PSP patients from PD patients, with a sensitivity of 100% and a specificity of 70.6%; moreover, the levels of this biomarker positively correlated with disease severity in PSP group. Regarding oligomeric α-synuclein and p129-α-synuclein, the latter was slightly increased in RBCs from PSP patients compared to HCs, but no correlations were detected. Conclusions: Although these findings need to be confirmed in larger studies, our pilot work suggests that RBC total α-synuclein may represent a potential molecular biomarker for the differential diagnosis and clinical staging of PSP. Full article

Theano, TensorFlow, Keras, Torch, PyTorch, and other software frameworks have remarkably stimulated the popularity of deep learning (DL). Apart from all the good they achieve, the danger of such frameworks is that they unintentionally spur a black-box attitude. Some practitioners play around with building blocks offered by frameworks and rely on them, having a superficial understanding of the internal mechanics. This paper constitutes a concise tutorial that elucidates the flows of signals and gradients in deep neural networks, enabling readers to successfully implement a deep network from scratch. By “from scratch”, we mean with access to a programming language and numerical libraries but without any components that hide DL computations underneath. To achieve this goal, the following five topics need to be well understood: (1) automatic differentiation, (2) the initialization of weights, (3) learning algorithms, (4) regularization, and (5) the organization of computations. We cover all of these topics in the paper. From a tutorial perspective, the key contributions include the following: (a) proposition of R and S operators for tensors—rashape and stack, respectively—that facilitate algebraic notation of computations involved in convolutional, pooling, and flattening layers; (b) a Python project named hmdl (“home-made deep learning”); and (c) consistent notation across all mathematical contexts involved. The hmdl project serves as a practical example of implementation and a reference. It was built using NumPy and Numba modules with JIT and CUDA amenities applied. In the experimental section, we compare hmdl implementation to Keras (backed with TensorFlow). Finally, we point out the consistency of the two in terms of convergence and accuracy, and we observe the superiority of the latter in terms of efficiency. Full article

Clinical differentiation of progressive supranuclear palsy (PSP) from Parkinson’s disease (PD) is challenging due to overlapping phenotypes and late onset of PSP specific symptoms, highlighting the need for easily assessable biomarkers. We used proximity elongation assay (PEA) to analyze 460 proteins in serum samples from 46 PD, 30 PSP patients, and 24 healthy controls. ANCOVA was used to identify the most promising proteins and machine learning (ML) XGBoost and random forest algorithms to assess their classification performance. Promising proteins were also quantified by ELISA. Moreover, correlations between serum biomarkers and biological and clinical features were investigated. We identified five proteins (TFF3, CPB1, OPG, CNTN1, TIMP4) showing different levels between PSP and PD, which achieved good performance (AUC: 0.892) when combined by ML. On the other hand, when the three most significant biomarkers (TFF3, CPB1 and OPG) were analyzed by ELISA, there was no difference between groups. Serum levels of TFF3 positively correlated with age in all subjects’ groups, while for OPG and CPB1 such a correlation occurred in PSP patients only. Moreover, CPB1 positively correlated with disease severity in PD, while no correlations were observed in the PSP group. Overall, we identified CPB1 correlating with PD severity, which may support clinical staging of PD. In addition, our results showing discrepancy between PEA and ELISA technology suggest that caution should be used when translating proteomic findings into clinical practice. Full article

This paper presents software advances to easily exploit computer architectures consisting of a multi-core CPU and CPU+GPU to accelerate diverse types of high-performance computing (HPC) applications using a single code implementation. The paper describes and demonstrates the performance of the open-source C++ matrix and array (MATAR) library that uniquely offers: (1) a straightforward syntax for programming productivity, (2) usable data structures for data-oriented programming (DOP) for performance, and (3) a simple interface to the open-source C++ Kokkos library for portability and memory management across CPUs and GPUs. The portability across architectures with a single code implementation is achieved by automatically switching between diverse fine-grained parallelism backends (e.g., CUDA, HIP, OpenMP, pthreads, etc.) at compile time. The MATAR library solves many longstanding challenges associated with easily writing software that can run in parallel on any computer architecture. This work benefits projects seeking to write new C++ codes while also addressing the challenges of quickly making existing Fortran codes performant and portable over modern computer architectures with minimal syntactical changes from Fortran to C++. We demonstrate the feasibility of readily writing new C++ codes and modernizing existing codes with MATAR to be performant, parallel, and portable across diverse computer architectures. Full article

Arable land loss has become a critical issue in China because of rapid urbanization, industrial expansion, and unsustainable agricultural practices. While previous studies have explored the factors contributing to this loss, they often fall short in addressing the challenges of spatial heterogeneity and large-scale dataset analysis. This research introduces an innovative approach to geographically weighted regression (GWR) for assessing arable land loss in China, effectively addressing these challenges. Focusing on Chongqing, Guizhou, and Yunnan Provinces over the past two decades, it examines spatial autocorrelation with R-squared values exceeding 0.6 and residuals. Eight factors, including environmental elements (rain, evaporation, slope, digital elevation model) and human activities (distance to city, distance to roads, population, GDP), were analyzed. By visualizing and analyzing R² spatial patterns, the results reveal a clear spatial agglomeration distribution, primarily in urban areas with industries, highly urbanized cities, and flat terrains near rivers, influenced by GDP, population, rain, and slope. The novelty of this study is that it significantly enhances GWR computational capabilities for handling extensive datasets by utilizing Compute Unified Device Architecture (CUDA) on a high-performance GPU cloud server. Simultaneously, it conducts comprehensive analyses of the GWR model’s local results through visualization and spatial autocorrelation tools, enhancing the interpretability of the GWR model. Through spatial clustering analysis of local results, this study enables targeted exploration of factors influencing arable land changes in various temporal and spatial dimensions while also evaluating the reliability of the model results. Full article