Supercomputer Research Articles

Efficient I/O Performance-Focused Scheduling in High-Performance Computing

High-performance computing (HPC) systems are becoming increasingly important as contemporary exascale applications with demand extensive computational and data processing capability. To optimize these systems, efficient scheduling of HPC applications is important. In particular, because I/O is a shared resource among applications and is becoming more important due to the emergence of big data, it is possible to improve performance by considering the architecture of HPC systems and scheduling jobs based on I/O resource requirements. In this paper, we propose a scheduling scheme that prioritizes HPC applications based on their I/O requirements. To accomplish this, our scheme analyzes the IOPS of scheduled applications by examining their execution history. Then, it schedules the applications at pre-configured intervals based on their expected IOPS to maximize the available IOPS across the entire system. Compared to the existing first-come first-served (FCFS) algorithm, experimental results using real-world HPC log data show that our scheme reduces total execution time by 305 h and decreases costs by USD 53 when scheduling 10,000 jobs utilizing public cloud resources.

Embankment Breach Simulation and Inundation Mapping Leveraging High-Performance Computing for Enhanced Flood Risk Prediction and Assessment

Abstract. Embankment breaches represent significant hazards to communities and infrastructure, precipitating catastrophic flood occurrences. The precise prediction of floods and understanding the scope of inundation stemming from embankment failures are imperative for effective disaster preparedness and response. This research delves into a case study on simulating embankment breaches to evaluate the extent of flooding. Leveraging advanced hydrodynamic models validated through high-performance computing (HPC) systems, and integrating real-time data assimilation, we aim to improve accuracy in flood forecasting. The study endeavours to bolster flood risk management by furnishing detailed inundation maps and insights into embankment breach dynamics, thereby facilitating enhanced preparedness and response strategies. Our findings reveal that simulations conducted on multicore processors offer superior performance compared to single-core setups, yielding enhanced result accuracy and providing administrators with increased lead time. It unlocks high-resolution simulations for intricate basin details, explores a wider range of flood scenarios quickly, and allows for efficient ensemble modelling to assess model uncertainty. Through HPC utilization, we can harness high-resolution digital elevation models (DEMs) for 2D-hydrodynamic modelling, enabling rapid assessment of water spread resulting from embankment breaches within a mere 20-minute timeframe, a significant improvement from the previous 3–4 hours duration.

Artificial photoelectric synaptic devices with ferroelectric diode effect for high-performance neuromorphic computing

Artificial photoelectric synaptic devices with ferroelectric diode effect for high-performance neuromorphic computing

Overview of High-Performance Computing And It’s Current Trend in India

This is an era of High-Performance Computing abbreviated as HPC. HPC evolved due to increase in demand of Processing speed. It is a hybrid technology that continuously changes its colors, so it is hard to define it in static words. However, if we still persist to define it the effort leads to a definition as below – “HPC is a branch of computer science that concentrates on combining the power of computing devices, networking infrastructure and storage systems using parallel hardware, networking and software technology that utilizes human expertise to gain optimized and sustained performance for solving scientific, engineering, big data and research problems including grand challenges like computer modeling, simulations and analysis of data.

Construction of Akushsky Core Functions Without Critical Cores

The residue number system is widely used in cryptography, digital signal processing, image processing systems, and other areas where high-performance computing is required. One of the main tools used in the residue number system is the Akushsky core function. However, its use is limited due to the existence of so-called critical cores. This study aims to develop Akushsky core functions that effectively eliminate the occurrence of critical cores, thereby enhancing their applicability in real-world scenarios. We introduce a fundamental approach to critical core detection that reduces the average time for critical core detection by 99.48% compared to the brute force algorithm. The results of our analysis indicate not only a substantial improvement in the speed of core detection but also an enhancement in the overall performance of systems utilizing the Akushsky core function. Our findings provide important insights into optimizing residue number systems and encourage further exploration into advanced computational techniques within this domain.

TOLEDO: enhancing Maestro GUI for non-expert users to perform massive MD simulations

Classical Molecular Dynamics (MD) simulates the dynamical evolution of biological systems at the atomic level. Using MD in conjunction with high-performance computing (HPC) architectures, we can evaluate the possible interactions between a ligand library against one protein target to find a drug that can influence a protein target to cure a disease. Simultaneously, we can also obtain information about their dynamic evolution. One of the primary software packages for MD simulations is Desmond, which employs Maestro for the setup, execution, and analysis of MD through a graphical user interface (GUI), which is suitable even for non-expert users. However, using the GUI, users can typically run only one short (less than 1000 ns) MD each time. Our work aims to create a method/protocol to run several MD simulations simultaneously on a remote HPC cluster within Maestro-Desmond. In this work, we provide TOLEDO (Throughput Optimization of Ligand-Protein Systems Exploration through Dynamics simulation in Optimized HPC systems) to overcome such limitations and run several MD simulations simultaneously. The best feature of TOLEDO is its independence from the usual time constraints of many clusters, with storage space being the only limitation. To run TOLEDO, we prepare/set up the protein-ligand complex before running MD via Maestro GUI. Next, we run the main TOLEDO script for several MD simulations on a supercomputer. When TOLEDO finishes, users obtain reports and graphics. The obtained results are easily interpretable. In essence, TOLEDO significantly enhances MD throughput beyond the capabilities of the Maestro GUI.

ExaWorks software development kit: a robust and scalable collection of interoperable workflows technologies

Scientific discovery increasingly requires executing heterogeneous scientific workflows on high-performance computing (HPC) platforms. Heterogeneous workflows contain different types of tasks (e.g., simulation, analysis, and learning) that need to be mapped, scheduled, and launched on different computing. That requires a software stack that enables users to code their workflows and automate resource management and workflow execution. Currently, there are many workflow technologies with diverse levels of robustness and capabilities, and users face difficult choices of software that can effectively and efficiently support their use cases on HPC machines, especially when considering the latest exascale platforms. We contributed to addressing this issue by developing the ExaWorks Software Development Kit (SDK). The SDK is a curated collection of workflow technologies engineered following current best practices and specifically designed to work on HPC platforms. We present our experience with (1) curating those technologies, (2) integrating them to provide users with new capabilities, (3) developing a continuous integration platform to test the SDK on DOE HPC platforms, (4) designing a dashboard to publish the results of those tests, and (5) devising an innovative documentation platform to help users to use those technologies. Our experience details the requirements and the best practices needed to curate workflow technologies, and it also serves as a blueprint for the capabilities and services that DOE will have to offer to support a variety of scientific heterogeneous workflows on the newly available exascale HPC platforms.

Research on Low-Power Digital Integrated Circuit Technology

In today’s diverse and rapidly developing field of low-power technologies, various industries are actively applying these advanced technologies to practical production in order to reduce energy consumption and mitigate environmental pollution. Based on this core concept, this article delves into and compares the principles, advantages, and disadvantages of the low-power technology of passive tag chips with the representative low-power technologies of dual-power and crossed-zero clocking, as well as their respective application areas. Specifically, the article conducts a detailed comparative analysis of the low-power technology of passive tag chips versus dual-power and crossed-zero clocking technologies from three perspectives: power consumption, design approach, and practical application. Through in-depth research, it was found that the low-power technology of passive tag chips holds significant advantages in the logistics industry, making it particularly well-suited for this field; meanwhile, dual-power and crossed-zero clocking technologies perform better in high-performance computing, making them more appropriate for such an application environment.

RISC-V Leads the Future: Evolution and Outlook of CPU Architecture

This essay mainly talked the development of CPU and some instruction set architecture based on RISCV. CPU is known as the Central Processing Unit, the main appliment is RISCV, Also the ARM architecture is characterized by a focus on the balance between low power consumption and high performance. Then X86, its significant advantage is its complex instruction set and excellent performance, so it can handle complex computational tasks. We also explore the Pipeline technology, it is a widely used parallel processing technology today. The design principle is to divide complex, multilevel combinational logic circuits into multiple levels. Then, we find some experiment data to explore our conclusion. We find that each has its own advantages and is better suited to different scenarios. In terms of performance, x86 offers superior capabilities but consumes more power, making it ideal for high-performance computing and server applications. ARM, on the other hand, excels in power efficiency and finds its primary use in mobile devices and embedded systems. RISC-V, known for its flexibility, allows for a balance between performance and power consumption based on specific requirements, making it suitable for highly customizable applications, IoT devices, and emerging high-performance computing markets. The advantages of each architecture in different fields depend on the specific application environment and demands placed on them.

A Comprehensive of CPU and GPU Performance and Applications in Autonomous Vehicles

The rapid advancement of autonomous vehicle technology over the past decade has significantly increased the complexity of intelligent transportation systems. This need is clearly reflected in the requirements for high-performance computing in autonomous vehicles — a requirement that artificial intelligence, machine learning and big data analytic have all come to meet through their integration. We need the CPU and GPU power to handle processing in real-time data, sensor fusion and decision-making. We investigate how the CPU and GPU perform in an autonomous driving scenario, concluding that these tasks are complementary to one another describing where each can be best used within a heterogeneous computing architecture. The research delves into how these computing chips can be best used under the demand for real-time processing, reliability and efficiency. The study is to better understand the techniques for improving CPU-GPU collaboration, and applies these new findings on performance-intensive tasks like image recognition or track construction. The technical part involves conducting driving scenarios in the real world on three different types of CPU and several GPU, with key metrics such as processing latency, power consumption and accuracy. The actual experimental results show the advantages of GPU parallel computing and deep learning, while CPU still has a good advantage in multi-tasking ability and logical calculation. The results are important for the implementation of future autonomous driving systems, highlighting heterogeneous computing architectures as a means to optimize and support safe, effective vehicle operations.

Co-designing ab initio electronic structure methods on a RISC-V vector architecture

Ab initio electronic structure applications are among the most widely used in High-Performance Computing (HPC), and the eigenvalue problem is often their main computational bottleneck. This article presents our initial efforts in porting these codes to a RISC-V prototype platform leveraging a wide Vector Processing Unit (VPU). Our software tester is based on a mini-app extracted from the ELPA eigensolver library. The user-space emulator Vehave and a RISC-V vector architecture implemented on an FPGA were tested. Metrics from both systems and different vectorisation strategies were extracted, ranging from the simplest and most portable one (using autovectorisation and assisting this by fusing loops in the code) to the more complex one (using intrinsics). We observed a progressive reduction in the number of vectorised instructions, executed instructions and computing cycles with the different methodologies, which will lead to a substantial speed-up in the calculations. The obtained outcomes are crucial in advancing the porting of computational materials and molecular science codes to (post)-exascale architectures using RISC-V-based technologies fully developed within the EU. Our evaluation also provides valuable feedback for hardware designers, engineers and compiler developers, making this use case pivotal for co-design efforts.

On a Simplified Approach to Achieve Parallel Performance and Portability Across CPU and GPU Architectures

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.

Self-Powered Dye-Sensitized Solar-Cell-Based Synaptic Devices for Multi-Scale Time-Series Data Processing in Physical Reservoir Computing.

Physical reservoir computing (PRC) using synaptic devices has attracted attention as a promising edge artificial intelligence device. To handle time-series data on various time scales, it is necessary to fabricate devices with the desired time scale. In this study, we fabricated a dye-sensitized solar-cell-based synaptic device with controllable time constants by changing the light intensity. This device showed synaptic features, such as paired-pulse facilitation and paired-pulse depression, in response to light intensity. Moreover, we found that the high computational performance of the time-series data processing task was achieved by changing the light intensity, even when the input pulse width was varied. In addition, the fabricated device can be used for motion recognition tasks. This study paves the way for realizing multiple time-scale PRC.

Data ecosystem using smart home technology to support healthy aging

Abstract Background Smart home technology has been widely used to mitigate the challenges that population aging brings. However, the lack of a centralized data ecosystem has prevented these technologies from realizing their full potential. This project aimed to construct a data ecosystem compatible with smart home sensors to monitor healthcare for seniors, improving their quality of life. Methods The infrastructure was constructed using a user-centered design approach, allowing smart devices such as motion, temperature sensors to operate independently and communicate through a Wi-Fi mesh network. API technology provides a reliable channel for real-time data collection. To ensure data privacy and security, extracted data is hosted in a cloud environment that provides comprehensive data protection, and cloud computing is utilized for high-performance computation tasks. Analytical models such as Machine Learning can be implemented to recognize indoor activities, achieving the goal of remote monitoring. Results This data ecosystem advances in privacy and security, interoperability, accessibility, and data-sharing. Unified authentication mechanism ensures data is transmitted among heterogeneous devices with minimal vulnerability. Additionally, the common communication protocol provides the foundation of interoperability between devices. With unobtrusive devices, inhabitants are not burdened with operation, ensuring their accessibility and improving their user experience. Lastly, the data is exchanged in a standardized JSON data format, enabling efficient data-sharing board data integration. Conclusions This project developed a data ecosystem based on existing smart home environments. The ecosystem is compatible with smart devices that families already have, effectively reducing additional healthcare costs. Implications of this study include helping health policy and decision makers to adopt more smart home ecosystems to keep older people healthy at home. Key messages • Study constructed a data ecosystem compatible with smart home sensors, achieving remote monitoring of indoor activities and improving the quality of life for seniors. • The developed ecosystem offers promotion in privacy and security, interoperability, accessibility, and efficient data-sharing, reducing healthcare costs.

Toward a Dynamic Allocation Strategy for Deadline‐Oriented Resource and Job Management in HPC Systems

ABSTRACTAs high‐performance computing (HPC) becomes a tool used in many different workflows, quality of service (QoS) becomes increasingly important. In many cases, this includes the reliable execution of an HPC job and the generation of the results by a certain deadline. The resource and job management system (RJMS) or simply RMS is responsible for receiving the job requests and executing the jobs with a deadline‐oriented policy to support the workflows. In this article, we evaluate how well static resource management policies cope with deadline‐constrained HPC jobs and explore two variations of a dynamic policy in this context. As the Hilbert curve‐based approach used by the SLURM workload manager represents the state‐of‐the‐art in production environments, it was selected as one of the static allocation strategies. The Manhattan median approach as a second allocation strategy was introduced as a research work that aims to minimize the communication overhead of the parallel programs by providing compact partitions more than the Hilbert curve approach. In contrast to the static partitions provided by the Hilbert curve approach and the Manhattan median approach, the leak approach focuses on supporting dynamic runtime behavior of the jobs and assigning nodes of the HPC system on demand at runtime. Since the contiguous leak version also relies on a compact set of nodes, the noncontiguous leak can provide additional nodes at a greater distance from the nodes already used by the job. Our preliminary results clearly show that a dynamic policy is needed to meet the requirements of a modern deadline‐oriented RMS scenario.

Shrinkage estimation of gene interaction networks in single-cell RNA sequencing data

BackgroundGene interaction networks are graphs in which nodes represent genes and edges represent functional interactions between them. These interactions can be at multiple levels, for instance, gene regulation, protein-protein interaction, or metabolic pathways. To analyse gene interaction networks at a large scale, gene co-expression network analysis is often applied on high-throughput gene expression data such as RNA sequencing data. With the advance in sequencing technology, expression of genes can be measured in individual cells. Single-cell RNA sequencing (scRNAseq) provides insights of cellular development, differentiation and characteristics at the transcriptomic level. High sparsity and high-dimensional data structures pose challenges in scRNAseq data analysis.ResultsIn this study, a sparse inverse covariance matrix estimation framework for scRNAseq data is developed to capture direct functional interactions between genes. Comparative analyses highlight high performance and fast computation of Stein-type shrinkage in high-dimensional data using simulated scRNAseq data. Data transformation approaches also show improvement in performance of shrinkage methods in non-Gaussian distributed data. Zero-inflated modelling of scRNAseq data based on a negative binomial distribution enhances shrinkage performance in zero-inflated data without interference on non zero-inflated count data.ConclusionThe proposed framework broadens application of graphical model in scRNAseq analysis with flexibility in sparsity of count data resulting from dropout events, high performance, and fast computational time. Implementation of the framework is in a reproducible Snakemake workflow https://github.com/calathea24/ZINBGraphicalModel and R package ZINBStein https://github.com/calathea24/ZINBStein.

Dynamic hybrid parallel computing of the Ray Model for solving underwater acoustic fields in vast sea

Utilizing acoustic information for search route planning will greatly increase the success rate of searching for underwater targets, which requires rapid computing of numerous underwater acoustic fields. The efficiency of traditional computing methods is too low to meet the requirements of rapid applications. In this paper, a underwater multi-acoustic fields computing model is developed based on ray theory, and multi-level hybrid parallel computing strategies are designed based on the model characteristics, and a dynamic scheduling optimization algorithm at process level is introduced to solve the load imbalance problem. All parallel computing strategies are tested in Tianhe-II High Performance Computer (HPC) system, and the tests show that: 1. compared with the serial version, hybrid parallel computing strategy provides a Speedup of 75.7 under 240 cores; 2. after the introduction of the dynamic scheduling optimization algorithm, the speed of solving the underwater acoustic fields is further increased by 28.99% under the same computing resources, and the Speedup reaches 97.67; 3. the optimal combination of process/thread parameter on the Tianhe-II HPC system is given as 3/8, and the final Speedup reaches 112.13.

A Nonlinear Approach in the Quantification of Numerical Uncertainty by High-Order Methods for Compressible Turbulence with Shocks

This is a comprehensive overview on our research work to link interdisciplinary modeling and simulation techniques to improve the predictability and reliability simulations (PARs) of compressible turbulence with shock waves for general audiences who are not familiar with our nonlinear approach. This focused nonlinear approach is to integrate our “nonlinear dynamical approach” with our “newly developed high order entropy-conserving, momentum-conserving and kinetic energy-preserving methods” in the quantification of numerical uncertainty in highly nonlinear flow simulations. The central issue is that the solution space of discrete genuinely nonlinear systems is much larger than that of the corresponding genuinely nonlinear continuous systems, thus obtaining numerical solutions that might not be solutions of the continuous systems. Traditional uncertainty quantification (UQ) approaches in numerical simulations commonly employ linearized analysis that might not provide the true behavior of genuinely nonlinear physical fluid flows. Due to the rapid development of high-performance computing, the last two decades have been an era when computation is ahead of analysis and when very large-scale practical computations are increasingly used in poorly understood multiscale data-limited complex nonlinear physical problems and non-traditional fields. This is compounded by the fact that the numerical schemes used in production computational fluid dynamics (CFD) computer codes often do not take into consideration the genuinely nonlinear behavior of numerical methods for more realistic modeling and simulations. Often, the numerical methods used might have been developed for weakly nonlinear flow or different flow types other than the flow being investigated. In addition, some of these methods are not discretely physics-preserving (structure-preserving); this includes but is not limited to entropy-conserving, momentum-conserving and kinetic energy-preserving methods. Employing theories of nonlinear dynamics to guide the construction of more appropriate, stable and accurate numerical methods could help, e.g., (a) delineate solutions of the discretized counterparts but not solutions of the governing equations; (b) prevent numerical chaos or numerical “turbulence” leading to FALSE predication of transition to turbulence; (c) provide more reliable numerical simulations of nonlinear fluid dynamical systems, especially by direct numerical simulations (DNS), large eddy simulations (LES) and implicit large eddy simulations (ILES) simulations; and (d) prevent incorrect computed shock speeds for problems containing stiff nonlinear source terms, if present. For computation intensive turbulent flows, the desirable methods should also be efficient and exhibit scalable parallelism for current high-performance computing. Selected numerical examples to illustrate the genuinely nonlinear behavior of numerical methods and our integrated approach to improve PARs are included.

The hydromechanical coupled numerical method in pseudo-3D axisymmetric domain with cracks extension and coalescence applies to the decompression failure problem

The stress-strain state of the saturated porous media determines the behavior of fracturing, which defines the efficiency of developing tight oil, shale, coalbed, and thermal energy fields. Therefore, reliable hydromechanical coupled simulations with destruction reconstruction are critical.The proposed innovative simulator has a strong interrelation between fluid flow and rock deformation of porous media and realizes a fully coupled pseudo-transient numerical method by high-performance computing (HPC) tools. To increase the detail of the results in the problem, a finite difference numerical algorithm was implemented in the axisymmetric cylindrical domain, which reduces from three to two dimensions without loss of precision. Highly efficient parallelization using CUDA on the GPU computes meshes of up to one billion cells, allowing the simulation of a total core sample to sub-micrometer resolution in an appropriate time. The algorithm has been validated to find the exact solution to the cylinder problem. The proposed model accounts for cracks propagation with their coalescence within a single computational static grid, which keeps timing close to the continuous model.This comprehensive implementation enables solving industrial problems, such as modeling core sample damage during rapid decompression. High-resolution simulations help reconstruct fracture propagation, analyze the initial stress state, and identify critical damage factors. The comparison with the exact solution to the cylinder problem confirmed the reliability of the algorithm. The calculation results show a strong dependence of decompression failure on the coalescence and elongation of cracks, influenced significantly by the rock's cohesion. Microcracks length and distribution play a decisive role in the decompressive destruction behavior of the rock sample. For the first time, the simulations demonstrated the decompressive destruction of a core sample during an uncontrolled, rapid core retrieval operation.

A comprehensive quantitative lifecycle cost and environmental impact analysis model for computing infrastructure

This paper presents a comprehensive quantitative model for quantitative assessment of the lifecycle costs and environmental impacts of computing infrastructure, with a focus on internet data centers (IDCs) and high-performance computing (HPC) facilities. The key innovation lies in the integration of interdisciplinary cost evaluation and carbon emission methods for the establishment of this quantitative model. This framework, which outlines key cost components and carbon emission factors, enables the calculation of total costs, electricity expenses, and greenhouse gas emissions throughout the lifecycle of infrastructure. With IDCs as a case study, the research clarifies the intricate cost structure associated with equipment procurement, energy usage, land acquisition, and operational expenses. This paper provides an in-depth understanding of the cost structure and environmental impact of computing infrastructure in support of sustainable decision-making in its development.•Based on established cost estimation methods, such as Lifecycle Cost Analysis (LCCA) and the Analogous Estimating Method, this study examines costs across construction and operation phases.•The Emission Factor Method is used to quantify environmental impact, emphasizing the significance of regional energy mix and power usage effectiveness (PUE).