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"Derecho" is the most powerful supercomputer at the National Center for Atmospheric Research (NCAR), running at a peak speed of 19.87 petaflops and ranking as the 59th fastest supercomputer in the world. It supports a wide range of atmospheric science research, including climate modeling, weather forecasting, and space weather analysis. Derecho's heterogenous architecture, combining CPUs and GPUs, allows it to efficiently handle physics-based simulations and machine learning applications. The supercomputer is housed in the NCAR-Wyoming Supercomputing Center in Cheyenne, Wyoming, and requires continuous maintenance and monitoring to ensure optimal performance for researchers worldwide. [Extracted from the article]

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]

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]

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]

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]

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]

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]