Search Results (35)

The demand for high-performance computing (HPC) continues to grow, driven by its critical role in advancing innovations in the rapidly evolving field of artificial intelligence. HPC has now entered the era of exascale supercomputers, introducing significant challenges related to sustainability. Balancing HPC performance with environmental sustainability presents a complex, multi-objective optimization problem. To the best of the author’s knowledge, no recent comprehensive investigation has explored the interplay between supercomputer performance and sustainability over a five-year period. This paper addresses this gap by examining the balance between these two aspects over a five-year period. This study collects and analyzes multi-year data on supercomputer performance and energy efficiency. The findings indicate that supercomputers pursuing higher performance often face challenges in maintaining top sustainability, while those focusing on sustainability tend to face challenges in achieving top performance. The analysis reveals that both the performance and power consumption of supercomputers have been rapidly increasing over the last five years. The findings also reveal that the performance of the most computationally powerful supercomputers is directly proportional to power consumption. The energy efficiency gains achieved by some top-performing supercomputers become challenging to maintain in the pursuit of higher performance. The findings of this study highlight the ongoing race toward zettascale supercomputers. This study can provide policymakers, researchers, and technologists with foundational evidence for rethinking supercomputing in the era of artificial intelligence. Full article

The emergence of exascale computing systems presents both opportunities and challenges in scientific computing, particularly for complex mathematical models requiring high-performance implementations. This paper addresses these challenges in the context of biomedical applications, specifically focusing on tumor angiogenesis modeling. We present a parallel implementation for solving a system of partial differential equations that describe the dynamics of tumor-induced blood vessel formation. Our approach leverages the Julia programming language and its CUDA capabilities, combining a high-level paradigm with efficient GPU acceleration. The implementation incorporates advanced optimization strategies for memory management and kernel organization, demonstrating significant performance improvements for large-scale simulations while maintaining numerical accuracy. Experimental results confirm the performance gains and reliability of the proposed parallel implementation. Full article

The growing adoption of supercomputers across various scientific disciplines, particularly by researchers without a background in computer science, has intensified the demand for parallel applications. These applications are typically developed using a combination of programming models within languages such as C, C++, and Fortran. However, modern multi-core processors and accelerators necessitate fine-grained control to achieve effective parallelism, complicating the development process. To address this, developers commonly utilize high-level programming models such as Open Multi-Processing (OpenMP), Open Accelerators (OpenACCs), Message Passing Interface (MPI), and Compute Unified Device Architecture (CUDA). These models may be used independently or combined into dual- or tri-model applications to leverage their complementary strengths. However, integrating multiple models introduces subtle and difficult-to-detect runtime errors such as data races, deadlocks, and livelocks that often elude conventional compilers. This complexity is exacerbated in applications that simultaneously incorporate MPI, OpenMP, and CUDA, where the origin of runtime errors, whether from individual models, user logic, or their interactions, becomes ambiguous. Moreover, existing tools are inadequate for detecting such errors in tri-model applications, leaving a critical gap in development support. To address this gap, the present study introduces a static analysis tool designed specifically for tri-model applications combining MPI, OpenMP, and CUDA in C++-based environments. The tool analyzes source code to identify both actual and potential runtime errors prior to execution. Central to this approach is the introduction of error dependency graphs, a novel mechanism for systematically representing and analyzing error correlations in hybrid applications. By offering both error classification and comprehensive static detection, the proposed tool enhances error visibility and reduces manual testing effort. This contributes significantly to the development of more robust parallel applications for high-performance computing (HPC) and future exascale systems. Full article

Advancements in computing platform deployment have acted as both push and pull elements for the advancement of engineering design and scientific knowledge. Historically, improvements in computing platforms were mostly dependent on simultaneous developments in hardware, software, architecture, and algorithms (a process known as co-design), which raised the performance of computational models. But, there are many obstacles to using the Exascale Computing Era sophisticated computing platforms effectively. These include but are not limited to massive parallelism, effective exploitation, and high complexity in programming, such as heterogeneous computing facilities. So, now is the time to create new algorithms that are more resilient, energy-aware, and able to address the demands of increasing data locality and achieve much higher concurrency through high levels of scalability and granularity. In this context, some methods, such as those based on hierarchical matrices (HMs), have been declared among the most promising in the use of new computing resources precisely because of their strongly hierarchical nature. This work aims to start to assess the advantages, and limits, of the use of HMs in operations such as the evaluation of matrix polynomials, which are crucial, for example, in a Graph Convolutional Deep Neural Network (GC-DNN) context. A case study from the GCNN context provides some insights into the effectiveness, in terms of accuracy, of the employment of HMs. Full article

The current paradigm of low-T combustion and autoignition of hydrocarbons is based on the sequential two-step oxygenation of fuel radicals. The key chain-branching occurs when the second oxygenation adduct (OOQOOH) is isomerized releasing an OH radical and a key ketohydroperoxide (KHP) intermediate. The subsequent homolytic dissociation of relatively weak O–O bonds in KHP generates two more radicals in the oxidation chain leading to ignition. Based on the recently introduced intramolecular “catalytic hydrogen atom transfer” mechanism (J. Phys. Chem. 2024, 128, 2169), abbreviated here as I-CHAT, we have identified a novel unimolecular decomposition channel for KHPs to form their classical isomers—enol hydroperoxides (EHP). The uncertainty in the contribution of enols is typically due to the high computed barriers for conventional (“direct”) keto–enol tautomerization. Remarkably, the I-CHAT dramatically reduces such barriers. The novel mechanism can be regarded as an intramolecular version of the intermolecular relay transfer of H-atoms mediated by an external molecule following the general classification of such processes (Catal. Rev.-Sci. Eng. 2014, 56, 403). Here, we present a detailed mechanistic and kinetic analysis of the I-CHAT-facilitated pathways applied to n-hexane, n-heptane, and n-pentane models as prototype molecules for gasoline, diesel, and hybrid rocket fuels. We particularly examined the formation kinetics and subsequent dissociation of the γ-enol-hydroperoxide isomer of the most abundant pentane-derived isomer γ-C5-KHP observed experimentally. To gain molecular-level insight into the I-CHAT catalysis, we have also explored the role of the internal catalyst moieties using truncated models. All applied models demonstrated a significant reduction in the isomerization barriers, primarily due to the decreased ring strain in transition states. In addition, the longer-range and sequential H-migration processes were also identified and illustrated via a combined double keto–enol conversion of heptane-2,6-diketo-4-hydroperoxide as a potential chain-branching model. To assess the possible impact of the I-CHAT channels on global fuel combustion characteristics, we performed a detailed kinetic analysis of the isomerization and decomposition of γ-C5-KHP comparing I-CHAT with key alternative reactions—direct dissociation and Korcek channels. Calculated rate parameters were implemented into a modified version of the n-pentane kinetic model developed earlier using RMG automated model generation tools (ACS Omega, 2023, 8, 4908). Simulations of ignition delay times revealed the significant effect of the new pathways, suggesting an important role of the I-CHAT pathways in the low-T combustion of large alkanes. Full article

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. Full article

Three-dimensional (3D) bioprinting belongs to the wide family of additive manufacturing techniques and employs cell-laden biomaterials. In particular, these materials, named “bioink”, are based on cytocompatible hydrogel compositions. To be printable, a bioink must have certain characteristics before, during, and after the printing process. These characteristics include achievable structural resolution, shape fidelity, and cell survival. In previous centuries, scientists have created mathematical models to understand how physical systems function. Only recently, with the quick progress of computational capabilities, high-fidelity and high-efficiency “computational simulation” tools have been developed based on such models and used as a proxy for real-world learning. Computational science, or “in silico” experimentation, is the term for this novel strategy that supplements pure theory and experiment. Moreover, a certain level of complexity characterizes the architecture of contemporary powerful computational resources, known as high-performance computing (HPC) resources, also due to the great heterogeneity of its structure. Lately, scientists and engineers have begun to develop and use computational models more extensively to also better understand the bioprinting process, rather than solely relying on experimental research, due to the large number of possible combinations of geometrical parameters and material properties, as well as the abundance of available bioprinting methods. This requires a new effort in designing and implementing computational tools capable of efficiently and effectively exploiting the potential of new HPC computing systems available in the Exascale Era. The final goal of this work is to offer an overview of the models, methods, and techniques that can be used for “in silico” experimentation of the physicochemical processes underlying the process of 3D bioprinting of cell-laden materials thanks to the use of up-to-date HPC resources. Full article

Today, various applications in different domains increasingly rely on high-performance computing (HPC) to accomplish computations swiftly. Integrating one or more programming models alongside the used programming language enhances system parallelism, thereby improving its performance. However, this integration can introduce runtime errors such as race conditions, deadlocks, or livelocks. Some of these errors may go undetected using conventional testing techniques, necessitating the exploration of additional methods for enhanced reliability. Formal methods, such as temporal logic, can be useful for detecting runtime errors since they have been widely used in real-time systems. Additionally, many software systems must adhere to temporal properties to ensure correct functionality. Temporal logics indeed serve as a formal frame that takes into account the temporal aspect when describing changes in elements or states over time. This paper proposes a temporal-logic-based testing tool utilizing instrumentation techniques designed for a dual-level programming model, namely, Message Passing Interface (MPI) and Open Multi-Processing (OpenMP), integrated with the C++ programming language. After a comprehensive study of temporal logic types, we found and proved that linear temporal logic is well suited as the foundation for our tool. Notably, while the tool is currently in development, our approach is poised to effectively address the highlighted examples of runtime errors by the proposed solution. This paper thoroughly explores various types and operators of temporal logic to inform the design of the testing tool based on temporal properties, aiming for a robust and reliable system. Full article

Earth system models (ESMs) are a common tool for estimating local and global greenhouse gas emissions under current and projected future conditions. Efforts are underway to expand the representation of wetlands in the Energy Exascale Earth System Model (E3SM) Land Model (ELM) by resolving the simultaneous contributions to greenhouse gas fluxes from multiple, different, sub-grid-scale patch-types, representing different eco-hydrological patches within a wetland. However, for this effort to be effective, it should be coupled with the detection and mapping of within-wetland eco-hydrological patches in real-world wetlands, providing models with corresponding information about vegetation cover. In this short communication, we describe the application of a recently developed NDVI-based method for within-wetland vegetation classification on a coastal wetland in Louisiana and the use of the resulting yearly vegetation cover as input for ELM simulations. Processed Harmonized Landsat and Sentinel-2 (HLS) datasets were used to drive the sub-grid composition of simulated wetland vegetation each year, thus tracking the spatial heterogeneity of wetlands at sufficient spatial and temporal resolutions and providing necessary input for improving the estimation of methane emissions from wetlands. Our results show that including NDVI-based classification in an ELM reduced the uncertainty in predicted methane flux by decreasing the model’s RMSE when compared to Eddy Covariance measurements, while a minimal bias was introduced due to the resampling technique involved in processing HLS data. Our study shows promising results in integrating the remote sensing-based classification of within-wetland vegetation cover into earth system models, while improving their performances toward more accurate predictions of important greenhouse gas emissions. Full article

The numerical study of relativistic magnetohydrodynamics (MHD) plays a crucial role in high-energy astrophysics but unfortunately is computationally demanding, given the complex physics involved (high Lorentz factor flows, extreme magnetization, and curved spacetimes near compact objects) and the large variety of spatial scales needed to resolve turbulent motions. A great benefit comes from the porting of existing codes running on standard processors to GPU-based platforms. However, this usually requires a drastic rewriting of the original code, the use of specific languages like CUDA, and a complex analysis of data management and optimization of parallel processes. Here, we describe the porting of the ECHO code for special and general relativistic MHD to accelerated devices, simply based on native Fortran language built-in constructs, especially do concurrent loops, few OpenACC directives, and straightforward data management provided by the Unified Memory option of NVIDIA compilers. Thanks to these very minor modifications to the original code, the new version of ECHO runs at least 16 times faster on GPU platforms as compared to CPU-based ones. The chosen benchmark is the 3D propagation of a relativistic MHD Alfvén wave, for which strong and weak scaling tests performed on the LEONARDO pre-exascale supercomputer at CINECA are provided (using up to 256 nodes corresponding to 1024 GPUs, and over 14 billion cells). Finally, an example of high-resolution relativistic MHD Alfvénic turbulence simulation is shown, demonstrating the potential for astrophysical plasmas of the new GPU-based version of ECHO. Full article

Exponential advances in computational power have fueled advances in many disciplines, and biology is no exception. High-Performance Computing (HPC) is gaining traction as one of the essential tools in scientific research. Further advances to exascale capabilities will necessitate more energy-efficient hardware. In this article, we present our efforts to improve the efficiency of genome assembly on ARM-based HPC systems. We use vectorization to optimize the popular genome assembly pipeline of minimap2, miniasm, and Racon. We compare different implementations using the Scalable Vector Extension (SVE) instruction set architecture and evaluate their performance in different aspects. Additionally, we compare the performance of autovectorization to hand-tuned code with intrinsics. Lastly, we present the design of a CPU dispatcher included in the Racon consensus module that enables the automatic selection of the fastest instruction set supported by the utilized CPU. Our findings provide a promising direction for further optimization of genome assembly on ARM-based HPC systems. Full article

As the development of high-performance computing (HPC) is growing, exascale computing is on the horizon. Therefore, it is imperative to develop parallel systems, such as graphics processing units (GPUs) and programming models, that can effectively utilise the powerful processing resources of exascale computing. A tri-level programming model comprising message passing interface (MPI), compute unified device architecture (CUDA), and open multi-processing (OpenMP) models may significantly enhance the parallelism, performance, productivity, and programmability of the heterogeneous architecture. However, the use of multiple programming models often leads to unexpected errors and behaviours during run-time. It is also difficult to detect such errors in high-level parallel programming languages. Therefore, this present study proposes a parallel hybrid testing tool that employs both static and dynamic testing techniques to address this issue. The proposed tool was designed to identify the run-time errors of C++ and MPI + OpenMP + CUDA systems by analysing the source code during run-time, thereby optimising the testing process and ensuring comprehensive error detection. The proposed tool was able to identify and categorise the run-time errors of tri-level programming models. This highlights the need for a parallel testing tool that is specifically designed for tri-level MPI + OpenMP + CUDA programming models. As contemporary parallel testing tools cannot, at present, be used to test software applications produced using tri-level MPI + OpenMP + CUDA programming models, this present study proposes the architecture of a parallel testing tool to detect run-time errors in tri-level MPI + OpenMP + CUDA programming models. Full article

Passive permeation of cellular membranes is a key feature of many therapeutics. The relevance of passive permeability spans all biological systems as they all employ biomembranes for compartmentalization. A variety of computational techniques are currently utilized and under active development to facilitate the characterization of passive permeability. These methods include lipophilicity relations, molecular dynamics simulations, and machine learning, which vary in accuracy, complexity, and computational cost. This review briefly introduces the underlying theories, such as the prominent inhomogeneous solubility diffusion model, and covers a number of recent applications. Various machine-learning applications, which have demonstrated good potential for high-volume, data-driven permeability predictions, are also discussed. Due to the confluence of novel computational methods and next-generation exascale computers, we anticipate an exciting future for computationally driven permeability predictions. Full article

In this study, we investigated the changing characteristics of climatic scale (monthly) tropical extreme precipitation in warming climates using the Energy Exascale Earth System Model (E3SM). The results are from Atmospheric Model Intercomparison Project (AMIP)-type simulations driven by (a) a control experiment with the present-day sea surface temperature (SST) and CO₂ concentration, (b) P4K, the same as in (a) but with a uniform increase of 4K in the SST globally, and (c) the same as in (a), but with an imposed SST and CO₂ concentration from the outputs of the coupled E3SM forced by a 4xCO₂ concentration. We found that as the surface warmed under P4K and 4xCO₂, both convective and stratiform rain increased. Importantly, there was an increasing fractional contribution of stratiform rain as a function of the precipitation intensity, with the most extreme but rare events occurring preferentially over land more than the ocean, and more so under 4xCO₂ than P4K. Extreme precipitation was facilitated by increased precipitation efficiency, reflecting accelerated rates of recycling of precipitation cloud water (both liquid and ice phases) in regions with colder anvil cloud tops. Changes in the vertical profiles of clouds, condensation heating, and vertical motions indicate increasing precipitation–cloud–circulation organization from the control and P4K to 4xCO₂. The results suggest that large-scale ocean warming, that is, P4K, was the primary cause contributing to an organization structure resembling the well-known mesoscale convective system (MCS), with increased extreme precipitation on shorter (hourly to daily) time scales. Additional 4xCO₂ atmospheric radiative heating and dynamically consistent anomalous SST further amplified the MCS organization under P4K. Analyses of the surface moist static energy distribution show that increases in the surface moisture (temperature) under P4K and 4xCO₂ was the key driver leading to enhanced convective instability over tropical ocean (land). However, a fast and large increase in the land surface temperature and lack of available local moisture resulted in a strong reduction in the land surface relative humidity, reflecting severe drying and enhanced convective inhibition (CIN). It is argued that very extreme and rare “record-breaking” precipitation events found over land under P4K, and more so under 4xCO₂, are likely due to the delayed onset of deep convection, that is, the longer the suppression of deep convection by CIN, the more severe the extreme precipitation when it eventually occurs, due to the release of a large amount of stored surplus convective available potential energy in the lower troposphere during prolonged CIN. Full article

Matrix multiplication is ubiquitous in high-performance applications. It will be a significant part of exascale workloads where power is a big concern. This work experimentally studied the power efficiency of three matrix multiplication algorithms: the definition-based, Strassen’s divide-and-conquer, and an optimized divide-and-conquer. The study used reliable on-chip integrated voltage regulators for measuring the power. Interactions with memory, mainly cache misses, were thoroughly investigated. The main result was that the optimized divide-and-conquer algorithm, which is the most time-efficient, was also the most power-efficient, but only for cases that fit in the cache. It consumed drastically less overall energy than the other two methods, regardless of placement in memory. For matrix sizes that caused a spill to the main memory, the definition-based algorithm consumes less power than the divide-and-conquer ones at a high total energy cost. The findings from this study may be of interest when cutting power usage is more vital than running for the shortest possible time or least amount of energy. Full article