Search

Summary: A memory cube network is an interconnection network composed of 3D stacked memories called memory cubes. By exploiting a packet switching, it can provide fast memory accesses to a large number of memory cubes. Although interconnection networks have been studied in many years for supercomputers and data centers, existing technologies are difficult to apply to memory cube networks. This is because the link length and the number of ports are limited, and hence the hop count increases. In this article, we propose a dual diagonal mesh (DDM), a layout‐oriented memory‐cube network. Furthermore, we propose the routing algorithm and the router architecture with bypassed pipelines for DDM. Our experimental results demonstrate that our routing and router architecture with bypassed pipelines reduces the memory access latency. We implement four router architectures and evaluate them with the traffic patterns derived from the NAS parallel benchmark. [ABSTRACT FROM AUTHOR]

Networks are designed to communicate, operate, and allocate tasks to respective commodities. Operating supercomputers became challenging, which was handled by the network design commonly known as hypercube, denoted by Q n . In a recent study, the hypercube networks were insufficient to hold supercomputers' parallel processors. Thus, variants of hypercubes were discovered to produce an alternative to the hypercube. A new variant of the hypercube, the fractal cubic network, can be used as the best alternative in the case of hypercubes. Our research investigates that the fractal cubic network is a rooted product of two graphs. We try to determine its domination and resolving domination parameters, which could be applied to resource location and broadcasting-related problems. [ABSTRACT FROM AUTHOR]

Recent advances in cloud computing, large language models, and deep learning have started a race to create massive High-Performance Computing (HPC) centers worldwide. These centers increase in energy consumption proportionally to their computing capabilities; for example, according to the top 500 organization, the HPC centers Frontier, Aurora, and Super Computer Fugaku report energy consumptions of 22,786 kW, 38,698 kW, and 29,899 kW, respectively. Currently, energy-aware scheduling is a topic of interest to many researchers. However, as far as we know, this work is the first approach considering the idle energy consumption by the HPC units and the possibility of turning off unused units entirely, driven by a quantitative objective function. We found that even when turning off unused machines, the objectives of makespan and energy consumption still conflict and, therefore, their multi-objective optimization nature. This work presents empirical results for AGEMOEA, AGEMOEA2, GWASFGA, MOCell, MOMBI, MOMBI2, NSGA2, and SMS-EMOA. The best-performing algorithm is MOCell for the 400 real scheduling problem tests. In contrast, the best-performing algorithm is GWASFGA for a small-instance synthetic testbed. [ABSTRACT FROM AUTHOR]

This project introduces a metric-driven strategy for enhancing real-time task planning within a mobile distributed system. The core design revolves around a realtime task planning algorithm that exploits consensus mechanisms among multiple nodes. By incorporating innovative real-time scheduling algorithms, validated on a supercomputer, the project establishes frameworks for simulating distributed mobile environments in real-time. This enables the execution of tasks in unpredictable contexts, ensuring adherence to stringent time constraints and empowering decision-making capabilities. The primary objective is to optimize task allocation in mobile distributed systems, including aerial nodes, thereby facilitating seamless data transfer while maintaining data integrity. The project builds upon the Fan task scheduler, integrating compensatory measures for online load distribution and optimization of message routes, effectively reducing communication latency in dynamic mobile environments. The contributions made aim to enhance real-time task allocation across diverse nodes, enabling the transfer of location and search data across networks without any data loss. This approach bears significant importance for the efficient management of tasks within dynamic scenarios. [ABSTRACT FROM AUTHOR]

Electronic structure calculations have the potential to predict key matter transformations for applications of strategic technological importance, from drug discovery to material science and catalysis. However, a predictive physicochemical characterization of these processes often requires accurate quantum chemical modeling of complex molecular systems with hundreds to thousands of atoms. Due to the computationally demanding nature of electronic structure calculations and the complexity of modern high-performance computing hardware, quantum chemistry software has historically failed to operate at such large molecular scales with accuracy and speed that are useful in practice. In this paper, novel algorithms and software are presented that enable extreme-scale quantum chemistry capabilities with particular emphasis on exascale calculations. This includes the development and application of the multi-Graphics Processing Unit (GPU) library LibCChem 2.0 as part of the General Atomic and Molecular Electronic Structure System package and of the standalone Extreme-scale Electronic Structure System (EXESS), designed from the ground up for scaling on thousands of GPUs to perform high-performance accurate quantum chemistry calculations at unprecedented speed and molecular scales. Among various results, we report that the EXESS implementation enables Hartree–Fock/cc-pVDZ plus RI-MP2/cc-pVDZ/cc-pVDZ-RIFIT calculations on an ionic liquid system with 623 016 electrons and 146 592 atoms in less than 45 min using 27 600 GPUs on the Summit supercomputer with a 94.6% parallel efficiency. [ABSTRACT FROM AUTHOR]

With the growing reliance of modern supercomputers on accelerator-based architecture such a graphics processing units (GPUs), the development and optimization of electronic structure methods to exploit these massively parallel resources has become a recent priority. While significant strides have been made in the development GPU accelerated, distributed memory algorithms for many modern electronic structure methods, the primary focus of GPU development for Gaussian basis atomic orbital methods has been for shared memory systems with only a handful of examples pursing massive parallelism. In the present work, we present a set of distributed memory algorithms for the evaluation of the Coulomb and exact exchange matrices for hybrid Kohn–Sham DFT with Gaussian basis sets via direct density-fitted (DF-J-Engine) and seminumerical (sn-K) methods, respectively. The absolute performance and strong scalability of the developed methods are demonstrated on systems ranging from a few hundred to over one thousand atoms using up to 128 NVIDIA A100 GPUs on the Perlmutter supercomputer. [ABSTRACT FROM AUTHOR]

As part of the US Department of Energy's Exascale Computing Project (ECP), Rice University has been refining its HPCToolkit performance tools to better support measurement and analysis of applications executing on exascale supercomputers. To efficiently collect performance measurements of GPU-accelerated applications, HPCToolkit employs novel non-blocking data structures to communicate performance measurements between tool threads and application threads. To attribute performance information in detail to source lines, loop nests, and inlined call chains, HPCToolkit performs parallel analysis of large CPU and GPU binaries involved in the execution of an exascale application to rapidly recover mappings between machine instructions and source code. To analyze terabytes of performance measurements gathered during executions at exascale, HPCToolkit employs distributed-memory parallelism, multithreading, sparse data structures, and out-of-core streaming analysis algorithms. To support interactive exploration of profiles up to terabytes in size, HPCToolkit's hpcviewer graphical user interface uses out-of-core methods to visualize performance data. The result of these efforts is that HPCToolkit now supports collection, analysis, and presentation of profiles and traces of GPU-accelerated applications at exascale. These improvements have enabled HPCToolkit to efficiently measure, analyze and explore terabytes of performance data for executions using as many as 64K MPI ranks and 64K GPU tiles on ORNL's Frontier supercomputer. HPCToolkit's support for measurement and analysis of GPU-accelerated applications has been employed to study a collection of open-science applications developed as part of ECP. This paper reports on these experiences, which provided insight into opportunities for tuning applications, strengths and weaknesses of HPCToolkit itself, as well as unexpected behaviors in executions at exascale. [ABSTRACT FROM AUTHOR]

The achievement of quantum computational advantage, also known as quantum supremacy, is a major milestone at which a quantum computer can solve a problem significantly faster than the world's most powerful classical computers. Two tasks, boson sampling and random quantum circuit sampling, have experimentally exhibited quantum advantages on photonic and superconducting platforms respectively. Classical benchmarking is essential, yet challenging, because these tasks are intractable for classical computers. This study reviews models, algorithms and large‐scale simulations of these two sampling tasks. These approaches continue to hold substantial significance for research in both current noisy intermediate‐scale quantum (NISQ) systems and future fault‐tolerant quantum computing. [ABSTRACT FROM AUTHOR]

Summary: NERSC's newest system, Perlmutter, features a 35 PB all‐flash Lustre file system built on HPE Cray ClusterStor E1000. We present its architecture, early performance figures, and performance considerations unique to this architecture. We demonstrate the performance of E1000 OSSes through low‐level Lustre tests that achieve over 90% of the theoretical bandwidth of the SSDs at the OST and LNet levels. We also show end‐to‐end performance for both traditional dimensions of I/O performance (peak bulk‐synchronous bandwidth) and nonoptimal workloads endemic to production computing (small, incoherent I/Os at random offsets) and compare them to NERSC's previous system, Cori, to illustrate that Perlmutter achieves the performance of a burst buffer and the resilience of a scratch file system. Finally, we discuss performance considerations unique to all‐flash Lustre and present ways in which users and HPC facilities can adjust their I/O patterns and operations to make optimal use of such architectures. [ABSTRACT FROM AUTHOR]

In this study, we develop new reverse engineering (RE) techniques to identify the organization of the synaptic inputs generating firing patterns of populations of neurons. We tested these techniques in silico to allow rigorous evaluation of their effectiveness, using remarkably extensive parameter searches enabled by massively-parallel computation on supercomputers. We chose spinal motoneurons as our target neural system, since motoneurons process all motor commands and have well-established input-output properties. One set of simulated motoneurons was driven by 300,000+ simulated combinations of excitatory, inhibitory, and neuromodulatory inputs. Our goal was to determine if these firing patterns had sufficient information to allow RE identification of the input combinations. Like other neural systems, the motoneuron input-output system is likely non-unique. This non-uniqueness could potentially limit this RE approach, as many input combinations can produce similar outputs. However, our simulations revealed that firing patterns contained sufficient information to sharply restrict the solution space. Thus, our RE approach successfully generated estimates of the actual simulated patterns of excitation, inhibition, and neuromodulation, with variances accounted for ranging from 75-90%. It was striking that nonlinearities induced in firing patterns by the neuromodulation inputs did not impede RE, but instead generated distinctive features in firing patterns that aided RE. These simulations demonstrate the potential of this form of RE analysis. It is likely that the ever-increasing capacity of supercomputers will allow increasingly accurate RE of neuron inputs from their firing patterns from many neural systems. [ABSTRACT FROM AUTHOR]

The InfiniBand (IB) interconnection technology is widely used in the networks of modern supercomputers and data centers. Among other advantages, the IB-based network devices allow for building multiple network topologies, and the IB control software (subnet manager) supports several routing engines suitable for the most common topologies. However, the implementation of some novel topologies in IB-based networks may be difficult if suitable routing algorithms are not supported, or if the IB switch or NIC architectures are not directly applicable for that topology. This work describes the implementation of the network topology known as KNS in a real HPC cluster using an IB network. As far as we know, this is the first implementation of this topology in an IB-based system. In more detail, we have implemented the KNS routing algorithm in the OpenSM software distribution of the subnet manager, and we have adapted the available IB-based switches to the particular structure of this topology. We have evaluated the correctness of our implementation through experiments in the real cluster, using well-known benchmarks. The obtained results, which match the expected performance for the KNS topology, show that this topology can be implemented in IB-based clusters as an alternative to other interconnection patterns. [ABSTRACT FROM AUTHOR]

The increasing trend of manycore processors makes multithreaded communication more important to avoid costly global synchronization among cores. One of the representative approaches that require multithreaded communication is the global task-based programming model. In the model, a program is divided into tasks, and tasks are asynchronously executed by each node, and independent thread-to-thread communications are expected. However, the Message passing interface (MPI) based approach is not efficient because of design issues. In this research, we design and implement the utofu transport layer in an abstracted communication library called Unified communication-X (UCX) for efficient remote direct memory access (RDMA) based multithreaded communication on Tofu Interconnect D. The evaluation results on Fugaku show that UCX can significantly improve the multithreaded performance over MPI, while maintaining portability between systems thanks to UCX. UCX shows about 32.8 times lower latency than Fujitsu MPI with 24 threads in the multithreaded pingpong benchmark and about 37.8 times higher update rate than Fujitsu MPI with 24 threads on 256 nodes in multithreaded GUPs benchmark. [ABSTRACT FROM AUTHOR]

The MFEM (Modular Finite Element Methods) library is a high-performance C++ library for finite element discretizations. MFEM supports numerous types of finite element methods and is the discretization engine powering many computational physics and engineering applications across a number of domains. This paper describes some of the recent research and development in MFEM, focusing on performance portability across leadership-class supercomputing facilities, including exascale supercomputers, as well as new capabilities and functionality, enabling a wider range of applications. Much of this work was undertaken as part of the Department of Energy's Exascale Computing Project (ECP) in collaboration with the Center for Efficient Exascale Discretizations (CEED). [ABSTRACT FROM AUTHOR]

Radiative transfer (RT) is a crucial ingredient for self-consistent modelling of numerous astrophysical phenomena across cosmic history. However, on-the-fly integration into radiation hydrodynamics (RHD) simulations is computationally demanding, particularly due to the stringent time-stepping conditions and increased dimensionality inherent in multifrequency collisionless Boltzmann physics. The emergence of exascale supercomputers, equipped with extensive CPU cores and GPU accelerators, offers new opportunities for enhancing RHD simulations. We present the first steps towards optimizing arepo - rt for such high-performance computing environments. We implement a novel node-to-node (n-to-n) communication strategy that utilizes shared memory to substitute intranode communication with direct memory access. Furthermore, combining multiple internode messages into a single message substantially enhances network bandwidth utilization and performance for large-scale simulations on modern supercomputers. The single-message n-to-n approach also improves performance on smaller scale machines with less optimized networks. Furthermore, by transitioning all RT-related calculations to GPUs, we achieve a significant computational speedup of around 15 for standard benchmarks compared to the original CPU implementation. As a case study, we perform cosmological RHD simulations of the Epoch of Reionization, employing a similar setup as the THESAN project. In this context, RT becomes sub-dominant such that even without modifying the core arepo codebase, there is an overall threefold improvement in efficiency. The advancements presented here have broad implications, potentially transforming the complexity and scalability of future simulations for a wide variety of astrophysical studies. Our work serves as a blueprint for porting similar simulation codes based on unstructured resolution elements to GPU-centric architectures. [ABSTRACT FROM AUTHOR]

Quantum computers promise to surpass the most powerful classical supercomputers in tackling critical practical problems, such as designing pharmaceuticals and fertilizers, optimizing supply chains and traffic, and enhancing machine learning. Since quantum computers operate fundamentally differently from classical ones, their emergence will give rise to a new evolutionary branch of statistical and data analytics methodologies. This review aims to provide an introduction to quantum computing accessible to statisticians and data scientists, equipping them with a comprehensive framework, the basic language, and building blocks of quantum algorithms, as well as an overview of existing quantum applications in statistics and data analysis. Our objective is to empower statisticians and data scientists to follow quantum computing literature relevant to their fields, collaborate with quantum algorithm designers, and ultimately drive the development of the next generation of statistical and data analytics tools. [ABSTRACT FROM AUTHOR]

Acceleration of the density-functional tight-binding (DFTB) method on single and multiple graphical processing units (GPUs) was accomplished using the MAGMA linear algebra library. Two major computational bottlenecks of DFTB ground-state calculations were addressed in our implementation: the Hamiltonian matrix diagonalization and the density matrix construction. The code was implemented and benchmarked on two different computer systems: (1) the SUMMIT IBM Power9 supercomputer at the Oak Ridge National Laboratory Leadership Computing Facility with 1–6 NVIDIA Volta V100 GPUs per computer node and (2) an in-house Intel Xeon computer with 1–2 NVIDIA Tesla P100 GPUs. The performance and parallel scalability were measured for three molecular models of 1-, 2-, and 3-dimensional chemical systems, represented by carbon nanotubes, covalent organic frameworks, and water clusters. [ABSTRACT FROM AUTHOR]

It is a challenging but key task to reduce the tritium inventory in EU-DEMO to levels that are acceptable for a nuclear regulator. As solution to this issue, a smart fuel cycle architecture is proposed based on the concept of Direct Internal Recycling (DIR), in which the Metal Foil Pump (MFP) will play an important role to separate the unburnt hydrogen isotopes coming from the divertor by exploiting the superpermeation phenomenon. In this study, we will present the assessment of the performance of the lower port of EU-DEMO after the integration of the MFP. For the first time, a thorough comparison of three different MFP (parallel long tubes, sandwich and halo) designs is performed regarding conductance for helium molecules, the pumping speed and the separation factor for deuterium molecules under different physical and geometric parameters. All simulations were carried out in supercomputer Marconi-Fusion with our in-house Test Particle Monte Carlo (TPMC) simulation code ProVac3D because the code had been parallelized with high efficiency. These results are essential for the development of a suitable MFP design in the vacuum-pumping train of EU-DEMO. [ABSTRACT FROM AUTHOR]

To address the challenge of finding new combination therapies against castration-sensitive prostate cancer, we introduce Vini, a computational tool that predicts the efficacy of drug combinations at the intracellular level by integrating data from the KEGG, DrugBank, Pubchem, Protein Data Bank, Uniprot, NCI-60 and COSMIC databases. Vini is a computational tool that predicts the efficacy of drugs and their combinations at the intracellular level. It addresses the problem comprehensively by considering all known target genes, proteins and small molecules and their mutual interactions involved in the onset and development of cancer. The results obtained point to new, previously unexplored combination therapies that could theoretically be promising candidates for the treatment of castration-sensitive prostate cancer and could prevent the inevitable progression of the cancer to the incurable castration-resistant stage. Furthermore, after analyzing the obtained triple combinations of drugs and their targets, the most common targets became clear: ALK, BCL-2, mTOR, DNA and androgen axis. These results may help to define future therapies against castration-sensitive prostate cancer. The use of the Vini computer model to explore therapeutic combinations represents an innovative approach in the search for effective treatments for castration-sensitive prostate cancer, which, if clinically validated, could potentially lead to new breakthrough therapies. [ABSTRACT FROM AUTHOR]

The increasing availability of machines relying on non-GPU architectures, such as ARM A64FX in high-performance computing, provides a set of interesting challenges to application developers. In addition to requiring code portability across different parallelization schemes, programs targeting these architectures have to be highly adaptable in terms of compute kernel sizes to accommodate different execution characteristics for various heterogeneous workloads. In this paper, we demonstrate an approach to write compute kernels using Kokko's abstraction layer to be executed on x86 and A64FX CPUs and NVIDIA GPUs. In addition to applying Kokkos as an abstraction over the execution of compute kernels on different heterogeneous execution environments, we show that the use of standard C++ constructs, as exposed by the HPX runtime system, enables platform portability based on the real-world Octo-Tiger astrophysics application. We report our experience with porting Octo-Tiger to the ARM A64FX architecture provided by Stony Brook's Ookami and Riken's Supercomputer Fugaku and compare the resulting performance with that achieved on well-established GPU-oriented HPC machines such as ORNL's Summit, NERSC's Perlmutter, and CSCS's Piz Daint systems. Octo-Tiger scaled well on Supercomputer Fugaku without any major code changes due to the abstraction levels provided by HPX and Kokkos. Adding vectorization support for ARM's SVE to Octo-Tiger was trivial thanks to using standard C++ interfaces. [ABSTRACT FROM AUTHOR]

Summary: Parallel I/O is a critical technique for moving data between compute and storage subsystems of supercomputers. With massive amounts of data produced or consumed by compute nodes, high‐performant parallel I/O is essential. I/O benchmarks play an important role in this process; however, there is a scarcity of I/O benchmarks representative of current workloads on HPC systems. Toward creating representative I/O kernels from real‐world applications, we have created h5bench , a set of I/O kernels that exercise hierarchical data format version 5 (HDF5) I/O on parallel file systems in numerous dimensions. Our focus on HDF5 is due to the parallel I/O library's heavy usage in various scientific applications running on supercomputing systems. The various tests benchmarked in the h5bench suite include I/O operations (read and write), data locality (arrays of basic data types and arrays of structures), array dimensionality (one‐dimensional arrays, two‐dimensional meshes, three‐dimensional cubes), I/O modes (synchronous and asynchronous). In this paper, we present the observed performance of h5bench executed along several of these dimensions on existing supercomputers (Cori and Summit) and pre‐exascale platforms (Perlmutter, Theta, and Polaris). h5bench measurements can be used to identify performance bottlenecks and their root causes and evaluate I/O optimizations. As the I/O patterns of h5bench are diverse and capture the I/O behaviors of various HPC applications, this study will be helpful to the broader supercomputing and I/O community. [ABSTRACT FROM AUTHOR]

Quantum computing as emerging technology raises high expectations to accelerate complicated calculations, superseding capabilities of presently available supercomputers and to provide a solution to the ever-increasing challenge of processing big amount of data. Besides theoretical promises, quantum computers have successfully been realized in experimental settings during the past few years, and can now also be accessed commercially. Given this availability of quantum computers, their application potential can be scrutinized. Promised to lead to disruptive changes in addressing and solving problems from the domains of simulation, optimization and machine learning, quantum computers have been researched in context of many application scenarios in industrial and academic setting in the recent years. However, it turns out that currently available quantum computers are still to small in size and limited in quality to fulfill the high hopes set in them at the moment. This review reflects on the current state of the technology coming from the perspective of the application, and indicates the developments required on hardware, software and algorithmic side to eventually make quantum computing beneficial for applications. [ABSTRACT FROM AUTHOR]

Ultra-sensitive sensors based on the resonant properties of whispering gallery modes (WGMs) can detect fractional changes in nanoscale environments down to the length and time scales of single molecules. However, it is challenging to isolate single-molecule signals from competing noise sources in experiments, such as thermal and mechanical sources of noise, and—at the most fundamental level—the shot noise limit of classical light. Additionally, in contrast to traditional bulk refractive index measurements, analyzing single-molecule signals is complicated by the localized nature of their interactions with nanoscale field gradients. This perspective discusses multifaceted solutions to these challenges, including the use of quantum light sources to boost the signal-to-noise ratio in experiments and leveraging the power of supercomputers to predict the electronic response of molecules to WGM optoplasmonic fields. We further discuss the role of machine learning in WGM sensing, including several advanced models that can predict molecular polarizability and solvent effects. These advancements in WGM spectroscopy and computational modeling can help to decipher the molecular mechanics of enzymes, enable studies of catalysis on the nanoscale, and probe the quantum nature of molecules. [ABSTRACT FROM AUTHOR]

Currently, research on the lattice Boltzmann method mainly focuses on its numerical simulation and applications, and there is an increasing demand for large-scale simulations in practical scenarios. In response to this situation, this study successfully implemented a large-scale heterogeneous parallel algorithm for the lattice Boltzmann method using OpenMP, MPI, Pthread, and OpenCL parallel technologies on the "Dongfang" supercomputer system. The accuracy and effectiveness of this algorithm were verified through the lid-driven cavity flow simulation. The paper focused on optimizing the algorithm in four aspects: Firstly, non-blocking communication was employed to overlap communication and computation, thereby improving parallel efficiency. Secondly, high-speed shared memory was utilized to enhance memory access performance and reduce latency. Thirdly, a balanced computation between the central processing unit and the accelerator was achieved through proper task partitioning and load-balancing strategies. Lastly, memory access efficiency was improved by adjusting the memory layout. Performance testing demonstrated that the optimized algorithm exhibited improved parallel efficiency and scalability, with computational performance that is 4 times greater than before optimization and 20 times that of a 32-core CPU. [ABSTRACT FROM AUTHOR]

Summary: The Oak Ridge Leadership Computing Facility (OLCF) has a long history of supporting and promoting GPU‐accelerated computing starting with the deployment of the Titan supercomputer in 2021 and continuing with the Summit supercomputer which has a theoretical peak performance of approximately 200 petaflops. Because the majority of Summit's computational power comes from its 27,972 GPUs, users must port their applications to one of the supported programming models in order to make efficient use of the system. To prepare the transition to Frontier, the OLCF's exascale supercomputer, users will need to adapt to an entirely new ecosystem which will include new hardware and software technologies. First, users will need to familiarize themselves with the AMD Radeon GPU architecture. Furthermore, users who have been previously relying on CUDA will need to transition to the Heterogeneous‐Computing Interface for Portability (HIP) or one of the other supported programming models (e.g., OpenMP, OpenACC). In this work, we describe our initial experiences and lessons learned in porting three applications or proxy apps currently running on Summit to the HPE/Cray ecosystem to leverage the compute power from AMD GPUs: minisweep, GenASiS, and Sparkler. Each one is representative of current production workloads utilized at the OLCF, different programming languages, and different programming models. [ABSTRACT FROM AUTHOR]

The ability to accurately predict when a job on a supercomputer will leave the queue and start to run is not only beneficial for providing insights to users, but can also help enable non‐traditional HPC workloads that are not necessarily suited to the batch queue style‐approach that is ubiquitous on production HPC machines. However there are numerous challenges in achieving such a prediction with high accuracy, not least because the queue's state can change rapidly and depend upon many factors. In this work, we explore a novel machine learning approach for predicting queue wait times, hypothesising that such a model can capture the complex behavior resulting from the queue policy and other interactions to generate accurate job start times. For ARCHER2 (HPE Cray EX), Cirrus (HPE 8600), and 4‐cabinet (HPE Cray EX) we explore how different machine learning approaches and techniques improve the accuracy of our predictions, comparing against the estimation generated by Slurm. By combining categorization and regression models, we demonstrate that our approach delivers the most accurate predictions across our machines of interest, with the result of this work being the ability to predict job start times within 1 min of the actual start time for around 65% of jobs on ARCHER2 and 4‐cabinet, and 76% of jobs on Cirrus. When compared against what Slurm can deliver, via the backfill plugin, this represents around 3.8 times better accuracy on ARCHER2 and 18 times better for Cirrus. Furthermore our approach can accurately predicting the start time for three quarters of all job within 10 min of the actual start time on ARCHER2 and 4‐cabinet, and for 90% of jobs on Cirrus. Whilst the initial driver of this work was to better facilitate non‐traditional, interactive and urgent, workloads on HPC machines, the insights gained can also be used to provide wider benefits to users, enrich existing batch queue systems, and inform supercomputing center policy also. [ABSTRACT FROM AUTHOR]

The development of new exascale supercomputers has dramatically increased the need for fast, high-performance networking technology. Efficient network topologies, such as Dragonfly+, have been introduced to meet the demands of data-intensive applications and to match the massive computing power of GPUs and accelerators. However, these supercomputers still face performance variability mainly caused by the network that affects system and application performance. This study comprehensively analyzes performance variability on a large-scale HPC system with Dragonfly+ network topology, focusing on factors such as communication patterns, message size, job placement locality, MPI collective algorithms, and overall system workload. The study also proposes an easy-to-measure metric for estimating network background traffic generated by other users, which can be used to estimate the performance of our job accurately. The insights gained from this study contribute to improving performance predictability, enhancing job placement policies and MPI algorithm selection, and optimizing resource management strategies in supercomputers. [ABSTRACT FROM AUTHOR]

The rapidly advancing fields of machine learning and mathematical modeling, greatly enhanced by the recent growth in artificial intelligence, are the focus of this special issue. This issue compiles extensively revised and improved versions of the top papers from the workshop on Mathematical Modeling and Problem Solving at PDPTA'23, the 29th International Conference on Parallel and Distributed Processing Techniques and Applications. Covering fundamental research in matrix operations and heuristic searches to real-world applications in computer vision and drug discovery, the issue underscores the crucial role of supercomputing and parallel and distributed computing infrastructure in research. Featuring nine key studies, this issue pushes forward computational technologies in mathematical modeling, refines techniques for analyzing images and time-series data, and introduces new methods in pharmaceutical and materials science, making significant contributions to these areas. [ABSTRACT FROM AUTHOR]

In the past few years, Transformer-based large language models (LLM) have become the dominant technology in a series of applications. To scale up the sequence length of the Transformer, FlashAttention is proposed to compute exact attention with reduced memory requirements and faster execution. However, implementing the FlashAttention algorithm on the new generation Sunway Supercomputer faces many constraints such as the unique heterogeneous architecture and the limited memory bandwidth. This work proposes SWattention, a highly efficient method for computing the exact attention on the SW26010pro processor. To fully utilize the 6 core groups (CG) and 64 cores per CG on the processor, we design a two-level parallel task partition strategy. Asynchronous memory access is employed to ensure that memory access overlaps with computation. Additionally, a tiling strategy is introduced to determine optimal SRAM block sizes. Compared with the standard attention, SWattention achieves around 2.0x speedup for FP32 training and 2.5x speedup for mixed-precision training. The sequence lengths range from 1k to 8k and scale up to 16k without being out of memory. As for the end-to-end performance, SWattention achieves up to 1.26x speedup for training GPT-style models, which demonstrates that SWattention enables longer sequence length for LLM training. [ABSTRACT FROM AUTHOR]

The article discusses the author's experience at the IUPAB2024 CHARMM-GUI/GENESIS Workshop, focusing on molecular dynamics simulations. The workshop covered topics such as enzyme mechanisms, membrane biology, and cellular component modeling. Hands-on training sessions with GENESIS and CHARMM-GUI software were highlighted, emphasizing the practical application of theoretical knowledge. The advanced techniques learned, such as generalized ensemble simulations and enhanced sampling methods, are seen as valuable tools for conducting sophisticated biomolecular simulations. The article also suggests improvements for future workshops to enhance participant learning and engagement. [Extracted from the article]

Sorting is one of the basic algorithms in computer science, and has been extensively used in a variety of applications. In the big data era, as the volumes of data increase rapidly, parallel sorting has attracted much attention. Existing parallel sorting algorithms suffered from excessive communication overhead and load imbalance, making it difficult to scale massively. To solve above problems, a scalable parallel algorithm sorting by regular sampling (ScaPSRS) was proposed, which sampled the p-1 pivot elements to divide the entire data set into p disjoint subsets by all parallel processes, rather than by only one given process as PSRS did. Furthermore, ScaPSRS adopted a novel iterative update strategy of selecting pivots to guarantee that the workloads and data were evenly scheduled among the parallel processes, thus ensuring superior overall performance. A variety of experiments conducted on the Tianhe-Ⅱ supercomputer demonstrated that ScaPSRS succeeded in scaling to 32 000 cores and outperformed state-of-the-art works significantly. [ABSTRACT FROM AUTHOR]

Feynman integral reduction by means of integration-by-parts identities is a major power gadget in a theorist toolbox indispensable for calculation of multiloop quantum effects relevant for particle phenomenology and formal theory alike. An algorithmic approach consists of solving a large sparse non-square system of homogeneous linear equations with polynomial coefficients. While an analytical way of doing this is legitimate and was pursued for decades, it undoubtedly has its limitations when applied in complicated circumstances. Thus, a complementary framework based on modular arithmetic becomes critical on the way to conquer the current "what is possible" frontier. This calls for use of supercomputers to address the reduction problem. In order to properly utilize these computational resources, one has to efficiently optimize the technique for this purpose. Presently, we discuss and implement various methods which allow us to significantly improve performance of Feynman integral reduction within the FIRE environment. [ABSTRACT FROM AUTHOR]

Understanding the function of eukaryotic genomes, including the human genome, is undoubtedly one of the major scientific challenges of the 21st century. The cornerstone of eukaryotic genome organization is nucleosomes—elementary building blocks of chromatin about 10 nm in size that wrap DNA around an octamer of histone proteins. Nucleosomes are integral players in all genomic processes, including transcription, DNA replication and repair. They mediate genome regulation at the epigenetic level, bridging the discrete nature of the genetic information encoded in DNA with the analog physical nature of the intermolecular interactions required to access that information. Due to their relatively large size and dynamic nature, nucleosomes are difficult objects for experimental characterization. Molecular dynamics (MD) simulations have emerged over the years as a useful tool to complement experimental studies. Particularly in recent years, advances in computing power, refinement of MD force fields and codes have opened up new frontiers in terms of simulation timescales and quality for nucleosomes and related systems. It has become possible to elucidate in atomistic detail their functional dynamics modes such as DNA unwrapping and sliding, to characterize the effects of epigenetic modifications, DNA and protein sequence variation on nucleosome structure and stability, to describe the mechanisms governing nucleosome interactions with chromatin‐associated proteins and the formation of supranucleosome structures. In this review, we systematically analyzed all‐atom MD simulation studies of nucleosomes and related structures published since 2018 and discussed their relevance in the context of older studies, experimental data, and related coarse‐grained and multiscale studies. This article is categorized under:Software > Molecular ModelingMolecular and Statistical Mechanics > Molecular Dynamics and Monte‐Carlo MethodsStructure and Mechanism > Computational Biochemistry and Biophysics [ABSTRACT FROM AUTHOR]

Summary: Supercomputers are advanced computing systems interconnected through high‐speed communication networks, consisting of independent computational nodes. During the unfolding of the big data era, the potent computational capabilities of these supercomputers play a pivotal role in scientific computing. Despite executing numerous advanced computational science and engineering tasks on supercomputers, many submitted jobs fail due to various factors, resulting in user inefficiencies. These failures not only consume system resources but also reduce the overall efficiency of the system. Previous research often couples job performance features with a single machine learning method for predicting job failure. However, a primary hurdle emerges from the high cost of gathering these features, complicating their real‐world applicability. To address this challenge, our study establishes correlations among job applications through extensive job log analysis. Leveraging correlations, we propose a predictive framework based on job application sequence correlation (called FP‐JSC). This innovative framework employs multiple machine learning models to offer holistic predictions, selecting the most suitable model based on its learning effectiveness. Moreover, the framework optimizes feature collection expenses without adversely affecting job execution. We determine job applications using both job paths and job names, with the former emerging as a novel feature derived from supplementary monitoring data. Empirical results underscore FP‐JSC's effectiveness, accurately identifying over 89% of jobs with 95% specificity and 89% sensitivity—outperforming single prediction methods employed in related works. [ABSTRACT FROM AUTHOR]

We explore the domain-specific Python library GT4Py (GridTools for Python) for implementing a representative physical parametrization scheme and the related tangent-linear and adjoint algorithms from the Integrated Forecasting System (IFS) of ECMWF. GT4Py encodes stencil operators in an abstract and hardware-agnostic fashion, thus enabling more concise, readable and maintainable scientific applications. The library achieves high performance by translating the application into targeted low-level coding implementations. Here, the main goal is to study the correctness and performance-portability of the Python rewrites with GT4Py against the reference Fortran code and a number of automatically and manually ported variants created by ECMWF. The present work is part of a larger cross-institutional effort to port weather and climate models to Python with GT4Py. The focus of the current work is the IFS prognostic cloud microphysics scheme, a core physical parametrization represented by a comprehensive code that takes a significant share of the total forecast model execution time. In order to verify GT4Py for Numerical Weather Prediction (NWP) systems, we put additional emphasis on the implementation and validation of the tangent-linear and adjoint model versions which are employed in data assimilation. We benchmark all prototype codes on three European supercomputers characterized by diverse GPU and CPU hardware, node designs, software stacks and compiler suites. Once the application is ported to Python with GT4Py, we find excellent portability, competitive performance, and robust execution in all tested scenarios including with reduced precision. [ABSTRACT FROM AUTHOR]

This paper reports experimental investigations on cold plates made from Low-Temperature Co-fired Ceramic (LTCC) technology for liquid cooling of supercomputer microprocessors. LTCC, a ceramic substrate-based technology with lightweight and ease of fabrication for miniaturization of cooling devices, can be a potential alternative to the existing copper cold plates for future three-dimensional stacked chip architectures. LTCC cold plates were fabricated using ceramic substrates whose thermal conductivity was enhanced using thermal vias. They were embedded with microchannels for liquid with different flow configurations. Their thermal performance is compared against copper cold plates. Deionized (DI) water is used as a coolant. Pressure drop and thermal resistance across different cold plates are measured as per water-cooled data center standards (W3 and W4 class). Obtained experimental results show that the tested LTCC cold plates can be used to cool supercomputer processors. It is concluded that LTCC cold plates can be a potential alternative for existing copper cold plates. [ABSTRACT FROM AUTHOR]

Multidimensional torus networking topology has become widespread recently in the domain of high-performance computers, clusters, and grids, as well as in the domain of networks on chip. Torus represents an ideal communication structure with the shortest distance and multitude of alternative shortest paths between a pair of nodes. We study simple and powerful local packet forwarding (switching) rules that provide packet delivery with quasi-optimal load balancing and do not use tables of addresses (routes). Implementation of these rules in the form of micro-program code within switching nodes increases considerably network performance, security, and QoS. We use infinite Petri nets and reenterable models in the form of colored Petri nets for prototyping the multi-dimensional torus interconnect simulator to study and compare the packet forwarding rules. Then, an ad-hoc simulator of torus interconnect ts is implemented in the C language to provide high performance and the possibility of simulation over prolonged intervals of time. The simulation results acknowledge the advantages of local packet forwarding rules. [ABSTRACT FROM AUTHOR]

Risk assessment studies of local asteroid hazards traditionally simulate the physics of meteors with engineering models tailored to analyze tens-of-millions of scenarios. However, these simplified approaches still need to solve time-dependent ODEs to model the entry process and the resulting ground damage. With a computational cost of O(0.01 CPU.s) per scenario, simulating these large numbers of potential entry conditions can take several days on local computers. To improve computational efficiency, we propose in this paper an orthogonal approach based on machine learning models to predict the size of damaged areas given a list of entry parameters. We train 5 machine learning methods and compare the predictions to the outputs of NASA's state-of-the-art Probabilistic Asteroid Impact Risk (PAIR) model. PAIR's remarkable capability to handle a broad spectrum of entry conditions and a high volume of scenarios establishes it as our reference model, with PAIR estimates assumed ground truth and used to train, test, and validate the machine learning models. The ML models, initially trained with PAIR's primitive input variables, are then further enhanced with engineered features to improve the performance of interpretable models. We find that complex models like neural networks are well-suited to estimate blast hazards, while simpler, interpretable linear models can accurately assess thermal damage. For both types of hazards, the radii of damaged areas can be predicted with less than 10% average relative errors for radii greater than 100 km. The CPU time is decreased by a factor O(1 0 3 ) compared to the PAIR model, enabling the simulation of millions of scenarios within minutes on a local computer. Beyond serving as surrogate models, we incorporate the machine learning models into a comprehensive Shapley sensitivity analysis, yielding a ranking of entry parameters based on their contributions to ground damages. These results offer valuable insights for prioritizing observation missions. • Machine learning models enable accurate and rapid simulations of asteroid hazards. • Data-driven methods can assess the radius of damaged areas with 10% average errors. • Models provide insights on the relative importance of entry parameters. • Risk studies can be performed on local machines instead of supercomputers. [ABSTRACT FROM AUTHOR]

For the first time in history, we are seeing a branching point in computing paradigms with the emergence of quantum processing units (QPUs). Extracting the full potential of computation and realizing quantum algorithms with a super-polynomial speedup will most likely require major advances in quantum error correction technology. Meanwhile, achieving a computational advantage in the near term may be possible by combining multiple QPUs through circuit knitting techniques, improving the quality of solutions through error suppression and mitigation, and focusing on heuristic versions of quantum algorithms with asymptotic speedups. For this to happen, the performance of quantum computing hardware needs to improve and software needs to seamlessly integrate quantum and classical processors together to form a new architecture that we are calling quantum-centric supercomputing. In the long term, we see hardware that exploits qubit connectivity in higher than 2D topologies to realize more efficient quantum error correcting codes, modular architectures for scaling QPUs and parallelizing workloads, and software that evolves to make the intricacies of the technology invisible to the users and realize the goal of ubiquitous, frictionless quantum computing. [ABSTRACT FROM AUTHOR]

Mesocrystals introduce high‐level orders, such as chirality, topology, and hierarchy to the crystallography, and thus bring collective and emergent properties beyond traditional crystals. Orthogonally modulating the multiple degrees of light is highly pursued to fully explore the intrinsic multidimensional and large‐scale parallel processing capability of photon informatics. Unfortunately, it is unachievable with traditional light–matter interaction systems. Here, the multi‐degree light modulation is realized based on the hierarchical architecture of a soft mesocrystal. High‐quality monodomains of both blue phase I and blue phase II are formed via regulating the assembly of liquid crystals by photoalignment anchoring and electricity. The mapping relationship between optical freedoms (the spin, wavelength, and geometric phase of light) and hierarchical structures (the chirality of helix, lattice constant, and the azimuthal orientation of cubic lattices) is established. Omnidirectional spatial phase modulation with spin and full color selectivity is demonstrated. Based on the multi‐degree light modulation, 3D and wavelength‐selective orbital angular momentum generation as well as multichannel color holographic display are presented. This work extends the fundamental understanding of blue phase mesocrystals and provides a promising strategy for large‐scale parallel and multi‐degree light modulation that may be utilized in vital fields, such as supercomputing, optical communications, and virtual/augmented realities. [ABSTRACT FROM AUTHOR]

The imbalanced I/O load on large parallel file systems affects the parallel I/O performance of high-performance computing (HPC) applications. One of the main reasons for I/O imbalances is the lack of a global view of system-wide resource consumption. While approaches to address the problem already exist, the diversity of HPC workloads combined with different file striping patterns prevents widespread adoption of these approaches. In addition, load-balancing techniques should be transparent to client applications. To address these issues, we propose Tarazu, an end-to-end control plane where clients transparently and adaptively write to a set of selected I/O servers to achieve balanced data placement. Our control plane leverages real-time load statistics for global data placement on distributed storage servers, while our design model employs trace-based optimization techniques to minimize latency for I/O load requests between clients and servers and to handle multiple striping patterns in files. We evaluate our proposed system on an experimental cluster for two common use cases: the synthetic I/O benchmark IOR and the scientific application I/O kernel HACC-I/O. We also use a discrete-time simulator with real HPC application traces from emerging workloads running on the Summit supercomputer to validate the effectiveness and scalability of Tarazu in large-scale storage environments. The results show improvements in load balancing and read performance of up to 33% and 43%, respectively, compared to the state-of-the-art. [ABSTRACT FROM AUTHOR]

This paper analyzes the factors influencing the selection of supercomputing resources. Using the results of a survey targeting supercomputing resources in the public sector, a resource selection model was presented through logistic regression and principal component analysis methods. As a result of the analysis, it was confirmed that affiliation, purpose of use, size of research funding, possession of a supercomputer, and whether specialized services are needed have a significant impact on resource selection. In the future, we expect that the results of this study will be used in various ways to manage demand for supercomputing resources. [ABSTRACT FROM AUTHOR]

Copyright of Elektronik Industrie is the property of Hüthig GmbH and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Optical interconnects are being discussed as a replacement for conventional electrical interconnects and are expected to be applied for future generations of high-performance supercomputers and data centers. Benes networks have attracted much attention because they require only 2 × 2 optical switches, which reduce the cost of rearrangeable nonblocking. However, optical power imbalances can significantly challenge receiver sensitivity. In this work, insertion loss (IL) fairness has been proposed and applied to the field of switches to achieve a relative balance of optical path data transmission in Benes networks. Fairness can be achieved when the port count is small (4 × 4) if the IL between ports is balanced. When the number of ports is moderate (8 × 8), we must use a suitable algorithm or determine the appropriate operating wavelength to minimize the power imbalance. An efficient two-step algorithm (ETS) has particular advantages in solving the path fairness problem and mitigating the power imbalance. As the number of ports increases, the switch states and topology jointly deteriorate the power imbalance. Finally, the ETS algorithm narrows the dynamic range requirement to 13.66 dB, with a 2 dB improvement. It achieves an extinction ratio of 24 dB and a bandwidth of 375 GHz, which outperforms the conventional 32 × 32 Benes network, respectively. [ABSTRACT FROM AUTHOR]

Summary: The development of computational fluid dynamics (CFD) highly depends on high‐performance computers. Computer hardware has evolved rapidly, yet scalable CFD parallel software remains scarce. In this article, we design a highly scalable CFD parallel paradigm for both homogeneous and heterogeneous supercomputers. The paradigm achieves the separation of communication and computation and automatically adapts to various solvers and hardware environments, thus reducing programming difficulties and increasing automatic parallelization. Meanwhile, the number of communications is greatly reduced and the scalability of the program is improved through implementing centralized communication and two‐level partitioning techniques. Complex flow problems for real aircraft were then computed on different hardware platforms with a grid size of ten billion. The homogeneous computer hardware includes Intel Xeon Gold 6258R and Phytium 2000+ processors, and the heterogeneous computer platforms include NVIDIA Tesla V100 and SW26010 processors. High parallel efficiency was obtained on all computer platforms, verifying that the paradigm has good automatic parallelization, scalability, and stability. The paradigm in this article has an important reference value for CFD massively parallel computing and can promote the development and application of CFD technology. [ABSTRACT FROM AUTHOR]

Gravitational N -body simulations calculate numerous interactions between particles. The tree algorithm reduces these calculations by constructing a hierarchical oct-tree structure and approximating gravitational forces on particles. Over the last three decades, the tree algorithm has been extensively used in large-scale simulations, and its parallelization in distributed memory environments has been well studied. However, recent supercomputers are equipped with many CPU cores per node, and optimizations of the tree construction in shared memory environments are becoming crucial. We propose a novel tree construction method in contrast to the conventional top-down approach. It first creates all leaf cells without traversing the tree and then constructs the remaining cells by a bottom-up approach. We evaluated the performance of our novel method on the supercomputer Fugaku and an Intel machine. On a single thread, our method accelerates one of the most time-consuming processes of the conventional tree construction method by a factor of above 3.0 on Fugaku and 2.2 on the Intel machine. Furthermore, as the number of threads increases, our parallel tree construction time reduces considerably. Compared to the conventional sequential tree construction method, we achieve a speed up of over 45 on 48 threads of Fugaku and more than 56 on 112 threads of the Intel machine. In stark contrast to the conventional method, the tree construction with our method no longer constitutes a bottleneck in the tree algorithm, even when using many threads. [ABSTRACT FROM AUTHOR]

The growing demand for semiconductor devices simulation poses a big challenge for large-scale electronic structure calculations. Among various methods, the linearly scaling three-dimensional fragment (LS3DF) method exhibits excellent scalability in large-scale simulations. Based on algorithmic and system-level optimizations, we propose a highly scalable and highly efficient implementation of LS3DF on a domestic heterogeneous supercomputer equipped with accelerators. In terms of algorithmic optimizations, the original all-band conjugate gradient algorithm is refined to achieve faster convergence, and mixed precision computing is adopted to increase overall efficiency. In terms of system-level optimizations, the original two-layer parallel structure is replaced by a coarse-grained parallel method. Optimization strategies such as multi-stream, kernel fusion, and redundant computation removal are proposed to increase further utilization of the computational power provided by the heterogeneous machines. As a result, our optimized LS3DF can scale to a 10-million silicon atoms system, attaining a peak performance of 34.8 PFLOPS (21.2% of the peak). All the improvements can be adapted to the next-generation supercomputers for larger simulations. [ABSTRACT FROM AUTHOR]

Summary: Given the complexity of current supercomputers and applications, being able to trace application executions to understand their behavior is not a luxury. As constraints, tracing systems have to be as little intrusive as possible in the application code and performances, and be precise enough in the collected data. In this article, we present how works the tracing system used by the task‐based runtime system StarPU. We study the different sources of performance overhead coming from the tracing system and how to reduce these overheads. Then, we evaluate the accuracy of distributed traces with different clock synchronization techniques. Finally, we summarize our experiments and conclusions with the lessons we learned to efficiently trace applications, and the list of characteristics each tracing system should feature to be competitive. The reported experiments and implementation details comprise a feedback of integrating into a task‐based runtime system state‐of‐the‐art techniques to efficiently and precisely trace application executions. We highlight the points every application developer or end‐user should be aware of to seamlessly integrate a tracing system or just trace application executions. [ABSTRACT FROM AUTHOR]

Nowadays, we are in a world of large amounts of heterogeneous devices with varying computational resources, ranging from small devices to large supercomputers, located on the cloud, edge or other abstraction layers in between. At the same time, software tasks need to be performed. They have specific computational or other types of requirements and must also be executed at a particular physical location. Moreover, both services and devices may change dynamically. In this context, methods are needed to effectively schedule efficient allocations of services to computational resources. In this article, we present a framework to address this problem. Our proposal first uses knowledge graphs for describing software requirements and the availability of resources for services and computing nodes, respectively. To this end, we proposed an ontology that extends our previous work. Then, we proposed a hierarchical filtering approach to decide the best allocation of services to computational nodes. We carried out simulations to evaluate four different clustering strategies. The results showed different performances in terms of the number of allocated services and node overload. [ABSTRACT FROM AUTHOR]

Background: Single-nucleotide polymorphisms (SNPs) are the most widely used form of molecular genetic variation studies. As reference genomes and resequencing data sets expand exponentially, tools must be in place to call SNPs at a similar pace. The genome analysis toolkit (GATK) is one of the most widely used SNP calling software tools publicly available, but unfortunately, high-performance computing versions of this tool have yet to become widely available and affordable. Results: Here we report an open-source high-performance computing genome variant calling workflow (HPC-GVCW) for GATK that can run on multiple computing platforms from supercomputers to desktop machines. We benchmarked HPC-GVCW on multiple crop species for performance and accuracy with comparable results with previously published reports (using GATK alone). Finally, we used HPC-GVCW in production mode to call SNPs on a "subpopulation aware" 16-genome rice reference panel with ~ 3000 resequenced rice accessions. The entire process took ~ 16 weeks and resulted in the identification of an average of 27.3 M SNPs/genome and the discovery of ~ 2.3 million novel SNPs that were not present in the flagship reference genome for rice (i.e., IRGSP RefSeq). Conclusions: This study developed an open-source pipeline (HPC-GVCW) to run GATK on HPC platforms, which significantly improved the speed at which SNPs can be called. The workflow is widely applicable as demonstrated successfully for four major crop species with genomes ranging in size from 400 Mb to 2.4 Gb. Using HPC-GVCW in production mode to call SNPs on a 25 multi-crop-reference genome data set produced over 1.1 billion SNPs that were publicly released for functional and breeding studies. For rice, many novel SNPs were identified and were found to reside within genes and open chromatin regions that are predicted to have functional consequences. Combined, our results demonstrate the usefulness of combining a high-performance SNP calling architecture solution with a subpopulation-aware reference genome panel for rapid SNP discovery and public deployment. [ABSTRACT FROM AUTHOR]

Owing to the enormous advancement in miniature hardware, modern smart mobile devices (SMDs) have become computationally powerful. Mobile crowd computing (MCC) is the computing paradigm that uses public-owned SMDs to garner affordable high-performance computing (HPC). Though several empirical works have established the feasibility of mobile-based computing for various applications, there is a lack of comprehensive coverage of MCC. This paper aims to explore the fundamentals and other nitty–gritty of the idea of MCC in a comprehensive manner. Starting with an explicit definition of MCC, the enabling backdrops and the detailed architectural layouts of different models of MCC are presented, along with categorising different types of MCC based on infrastructure and application demands. MCC is compared extensively with other HPC systems (e.g. desktop grid, cloud, clusters and supercomputers) and similar mobile computing systems (e.g. mobile grid, mobile cloud, ad hoc mobile cloud, and mobile crowdsourcing). MCC being a complex system, various design requirements and considerations are extensively analysed. The potential benefits of MCC are meticulously mentioned, with special discussions on the ubiquity and sustainability of MCC. The issues and challenges of MCC are critically presented in light of further research scopes. Several real-world applications of MCC are identified and propositioned. Finally, to carry forward the accomplishment of the MCC vision, the future prospects are briefly elucidated. [ABSTRACT FROM AUTHOR]