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At least 1,603 records · Page 89

Programming Abstractions for Managing Workflows on Tiered Storage Systems

Scientific workflows in High Performance Computing (HPC) environments are processing large amounts of data. The storage hierarchy on HPC systems is getting deeper, driven by new technologies (NVRAMs, SSDs, etc.) There is a need for new programming abstractions that allow users to seamlessly manage data at the workflow level on multi-tiered storage systems, and provide optimal workflow performance and use of storage resources. In previous work, we introduced a software architecture Managing Data on Tiered Storage for Scientific Workflows (MaDaTS) that used a Virtual Data Space (VDS) abstraction to hide the complexities of the underlying storage system while allowing users to control data management strategies. In this article, we detail the data-centric programming abstractions that allow users to manage a workflow around its data on the storage layer. The programming abstractions simplify data management for scientific workflows on multi-tiered storage systems, without affecting workflow performance or storage capacity. We measure the overheads and effectiveness introduced by the programming abstractions of MaDaTS. Our results show that these abstractions can optimally use the storage capacity in lesser capacity storage tiers, and simplify data management without adding any performance overheads.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

NMACFoam (Numerical-model for Membrane-spacer Assemblies and Configurations in OpenFOAM) [SWR-23-57]

NMACFoam is a computational fluid dynamics tool for simulating flow and solids transport in membrane-spacer channels pertaining to reverse osmosis or nanofiltration applications. It is developed on the OpenFOAM framework and allows for simulating spacers with complex geometries. It includes porous wall boundary conditions for membranes and can accurately capture concentration polarization effects. One can perform large calculations at module-scale domain sizes using high performance computing resources with NMACFoam, which scales to 1000s of processors for problems with 1-10 million cells.

Sitaraman, Hariswaran↗

guppy i : a code for reducing the storage requirements of cosmological simulations

ABSTRACT As cosmological simulations have grown in size, the permanent storage requirements of their particle data have also grown. Even modest simulations present a major logistical challenge for the groups which run these boxes and researchers without access to high performance computing facilities often need to restrict their analysis to lower quality data. In this paper, we present guppy, a compression algorithm and code base tailored to reduce the sizes of dark matter-only cosmological simulations by approximately an order of magnitude. guppy is a ‘lossy’ algorithm, meaning that it injects a small amount of controlled and uncorrelated noise into particle properties. We perform extensive tests on the impact that this noise has on the internal structure of dark matter haloes, and identify conservative accuracy limits which ensure that compression has no practical impact on single-snapshot halo properties, profiles, and abundances. We also release functional prototype libraries in C, Python, and Go for reading and creating guppy data.

79 ASTRONOMY AND ASTROPHYSICS↗

Development of dispensing hardware for safe fueling of heavy duty vehicles

The development of safe dispensing equipment for the fueling of heavy duty (HD) vehicles is critical to the expansion of this newly and quickly expanding market. This paper discusses the development of a HD dispenser and nozzles assembly (nozzle, hose, breakaway) for these new, larger vehicles where flow rates are more than double compared to light duty (LD) vehicles. This equipment must operate at nominal pressures of 700 bar, -40o C gas temperature, and average flow rate of 5-10 kg/min at a high throughput commercial hydrogen fueling station without leaking hydrogen. The project surveyed HD vehicle manufacturers, station developers, and component suppliers to determine the basic specifications of the dispensing equipment and nozzle assembly. The team also examined existing codes and standards to determine necessary changes to accommodate HD components. From this information, the team developed a set of specifications which will be used to design the dispensing equipment. In order to meet these goals, the team performed computational fluid dynamic, pressure modelling, and temperature analysis in order to determine the necessary parameters to meet existing safety standards modified for HD fueling. The team also considered user, operational, and maintenance requirements, such as freeze lock which has been an issue which prevents the removal of the nozzle from LD vehicles. The team also performed a failure mode and effects analysis (FMEA) to identify the possible failures in the design. The dispenser and nozzle assembly will be tested separately, and then installed on an innovative, HD fueling station which will use a HD vehicle simulator to test the entire system.

08 HYDROGEN↗

TTDFT: A GPU accelerated Tucker tensor DFT code for large-scale Kohn-Sham DFT calculations

We present the Tucker tensor DFT (TTDFT) code which uses a tensor-structured algorithm with graphic processing unit (GPU) acceleration for conducting ground-state DFT calculations on large-scale systems. The Tucker tensor DFT algorithm uses a localized Tucker tensor basis computed from an additive separable approximation to the Kohn-Sham Hamiltonian. The discrete Kohn-Sham problem is solved using Chebyshev filtered subspace iteration method that relies on matrix-matrix multiplications of a sparse symmetric Hamiltonian matrix and a dense wavefunction matrix, expressed in the localized Tucker tensor basis. These matrix-matrix multiplication operations, which constitute the most computationally intensive step of the solution procedure, are GPU accelerated providing ~8-fold GPU-CPU speedup for these operations on the largest systems studied. In conclusion, the computational performance of the TTDFT code is presented using benchmark studies on aluminum nano-particles and silicon quantum dots with system sizes ranging up to ~7,000 atoms.

97 MATHEMATICS AND COMPUTING↗

Low-synch Gram–Schmidt with delayed reorthogonalization for Krylov solvers

The parallel strong-scaling of iterative methods is often determined by the number of global reductions at each iteration. Low-synch Gram-Schmidt algorithms are applied here to the Arnoldi algorithm to reduce the number of global reductions and therefore to improve the parallel strong-scaling of iterative solvers for nonsymmetric matrices such as the GMRES and the Krylov-Schur iterative methods. In the Arnoldi context, the factorization is "left-looking" and processes one column at a time. Among the methods for generating an orthogonal basis for the Arnoldi algorithm, the classical Gram-Schmidt algorithm, with reorthogonalization (CGS2) requires three global reductions per iteration. A new variant of CGS2 that requires only one reduction per iteration is presented and applied to the Arnoldi algorithm. Delayed CGS2 (DCGS2) employs the minimum number of global reductions per iteration (one) for a one-column at-a-time algorithm. The main idea behind the new algorithm is to group global reductions by rearranging the order of operations. DCGS2 must be carefully integrated into an Arnoldi expansion or a GMRES solver. Numerical stability experiments assess robustness for Krylov-Schur eigenvalue computations. Performance experiments on the ORNL Summit supercomputer then establish the superiority of DCGS2 over CGS2.

97 MATHEMATICS AND COMPUTING↗

Performance of modern color decompositions for standard candle LHC tree amplitudes

In the last decade, developments of matrix element and phase space generators have focused on providing good efficiency and maximal flexibility and automation for a wide range of physical processes. However, as recent studies have shown, they are a major bottleneck in the established Monte Carlo event generator toolchains. With the advent of the HL-LHC and ever rising precision requirements, future developments will need to focus on computational performance, especially at intermediate to large jet multiplicities. We present the novel BlockGen family of fast matrix element algorithms that are amenable for GPU acceleration, making use of modern, minimal color decompositions. Moreover, we discuss the performance achieved for standard candle processes such as V +jets and tt̄+jets production.

Bothmann, E. [Gottingen U.]↗

Performance of a supercharged direct-injection stratified-charge rotary combustion engine

A zero-dimensional thermodynamic performance computer model for direct-injection stratified-charge rotary combustion engines was modified and run for a single rotor supercharged engine. Operating conditions for the computer runs were a single boost pressure and a matrix of speeds, loads and engine materials. A representative engine map is presented showing the predicted range of efficient operation. After discussion of the engine map, a number of engine features are analyzed individually. These features are: heat transfer and the influence insulating materials have on engine performance and exhaust energy; intake manifold pressure oscillations and interactions with the combustion chamber; and performance losses and seal friction. Finally, code running times and convergence data are presented.

Bartrand, Timothy A.↗

Experimental and modeling study of the autoignition behavior of a standard oxygenated gasoline fuel

Gasoline surrogate models can be conveniently used to simulate the combustion behavior of fuels in internal combustion engines. Because of limitations in the number of robust models available and the high computational cost of running them, simple surrogates with only 2 or 3 components (namely n-heptane, iso-octane and toluene) have been long preferred to simulate the ignition behavior of gasoline in engine calculations. More recently, thanks to the development of new, well-validated kinetic models and the access to cheap high-performance computing, the scientific and engineering community is utilizing the higher fidelity provided by more complex mixture models. The added detail in composition can in fact better reproduce variation in the fuel reactivity with pressure (an important feature for downsized, boosted conditions) and blending behavior of real fuels. In this study, the ignition behavior of a research grade full blend oxygenated fuel matching the typical specification of US standard grade gasoline has been investigated by means of rapid compression experiments and detailed kinetic calculations. A multicomponent fuel surrogate model has been developed using compositional information and a surrogate optimization tool. Based on the experimental and computational results presented in this study, general considerations about guidelines in the formulation of gasoline fuel surrogates are provided.

autoignition↗

Open Source Platform for Live Processing of High Data Rate Electron Microscopy (SBIR Phase I Award Topic 15, Subtopic B, Final Scientific / Technical Report)

4D scanning transmission electron microscopy (STEM) is experiencing a revolution both in terms of data size, and data veracity, as are many other areas of experimental data acquisition. This presents enormous opportunities to make new scientific discoveries, but is also hamstrung by aging software that is no longer fit for purpose. Experimental data acquisition platforms must make the same investments in software infrastructure that the simulation community made decades ago to take advantage of high-performance computing (HPC) if they hope to realize the full potential of the latest advances made in detector technology. This requires rethinking the design and deployment of hardware, moving away from small, fixed commodity computing capabilities with closed interfaces to open, modular, scalable systems designed for parallelism and throughput. The technical approach will leverage best-in-class open source technologies, and develop new approaches strategically to build an open source platform for experimental data acquisition targeting high data rate electron microscopy. The project will develop a software platform that uses the power and performance of modern HPC resources to ingest the large volume of data produced by electron microscopes using direct electron detectors. A set of configurable pipelines will be used to enable the processing to be tailored to the problem being investigated with builtin visualization of data at interactive rates. This project will leverage investments made by the DOE and other agencies to provide a powerful software platform for the experimental data community working with most powerful electron microscopes, such as 4D STEM detectors. It will create a platform that serves as a reference for the community. Permissive open source licensing will make the platform available to all, with a simple deployment strategy offering the ability to keep data close to where it is generated. This advanced software platform will require customization for each deployment, creating opportunities for software services that are typically offered to extend open source software platforms.

97 MATHEMATICS AND COMPUTING↗

Machine learning enabled discovery of superhard and ultrahard carbon polymorphs

The demand for multifunctional materials has motivated the move from near-equilibrium materials to metastable i.e. out-of-equilibrium phases that can meet several desired target properties. The search for such metastable phases with exotic properties is non-trivial and often serendipitous. Inverse design approaches based on evolutionary search have been powerful tools, but such traditional searches have focused on identifying primarily stable and metastable materials with the lowest enthalpy. The inverse design of materials, with a focus on a desired property such as, for example, hardness is a challenging task because of the expensive computational cost involved in sampling multiple structures. The recent advances in machine learning have brought new powerful AI techniques to the forefront which can potentially revolutionize the inverse design and discovery of materials, especially metastable phases capable of meeting multifunctionality. Here, in this work, we develop and apply an automated reinforcement learning workflow for inverse design that integrates first principles physics and atomistic simulations with machine learning (ML), and high-performance computing to allow rapid exploration of the superhard and ultrahard metastable phases of Carbon. We demonstrate an automatic machine learning based inverse design workflow to map new undiscovered metastable states ranging from near equilibrium to those far-from-equilibrium that satisfy multiple property objectives, specifically bulk moduli, shear moduli and hardness. We create a comprehensive library of carbon stable and metastable phases with varying hardness and subsequently shortlist 10 top performing candidate carbon structures, including two newly reported phases, based on their hardness and characterize their temperature dependent mechanical properties. A neural network model is built using featurization of allotropes of carbon to predict the quasi-harmonic Gibbs free energies. The Gibbs free energies of the top performing phases are analyzed to get an estimate of the experimental synthesizability of these superhard and ultrahard carbon phases. In general, we show using machine learning based inverse design approaches how hitherto inaccessible metastable states can be identified and potentially synthesized to meet the demand for multifunctional materials.

Balasubramanian, Karthik [Univ. of Illinois, Chica↗

Correction to Reconciling Work Functions and Adsorption Enthalpies for Implicit Solvent Models: A Pt (111)/Water Interface Case Study

This errata is to correct the acknowledgment in the original published article. G.B. (partial support), V.-A.G., M.-T.N., and R.R. were supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division. Computer resources were provided by Research Computing at Pacific Northwest National Laboratory and the National Energy Research Scientific Computing Center (NERSC), a U.S. Department of Energy Office of Science User Facility operated under Contract No. DE-AC02-05CH11231. PNNL is operated by Battelle for the U.S. Department of Energy under Contract DE-AC05-76RL01830. G.B. acknowledges the EPSRC for partial support in PhD funding. The authors acknowledge the use of the IRIDIS High Performance Computing Facility (IRIDIS 5) and associated support services at the University of Southampton in the completion of this work. We are grateful to the UK Materials and Molecular Modeling Hub (Thomas HPC) for computational resources, which is partially funded by EPSRC (EP/P020194/1).

continuum solvation, metal/water interfaces, ab in↗

Real-space solution to the electronic structure problem for nearly a million electrons

We report a Kohn–Sham density functional theory calculation of a system with more than 200 000 atoms and 800 000 electrons using a real-space high-order finite-difference method to investigate the electronic structure of large spherical silicon nanoclusters. Our system of choice was a 20 nm large spherical nanocluster with 202 617 silicon atoms and 13 836 hydrogen atoms used to passivate the dangling surface bonds. To speed up the convergence of the eigenspace, we utilized Chebyshev-filtered subspace iteration, and for sparse matrix–vector multiplications, we used blockwise Hilbert space-filling curves, implemented in the PARSEC code. For this calculation, we also replaced our orthonormalization + Rayleigh–Ritz step with a generalized eigenvalue problem step. We utilized all of the 8192 nodes (458 752 processors) on the Frontera machine at the Texas Advanced Computing Center. We achieved two Chebyshev-filtered subspace iterations, yielding a good approximation of the electronic density of states. Our work pushes the limits on the capabilities of the current electronic structure solvers to nearly 106 electrons and demonstrates the potential of the real-space approach to efficiently parallelize large calculations on modern high-performance computing platforms.

Chemistry↗

Modeling of particle transport, neutrals and radiation in magnetically-confined plasmas with Aurora

In this work, we present Aurora, an open-source package for particle transport, neutrals and radiation modeling in magnetic confinement fusion plasmas. Aurora's modern multi-language interface enables simulations of 1.5D impurity transport within high-performance computing frameworks, particularly for the inference of particle transport coefficients. A user-friendly Python library allows simple interaction with atomic rates from the Atomic Data and Atomic Structure database as well as other sources. This enables a range of radiation predictions, both for power balance and spectroscopic analysis. We discuss here the superstaging approximation for complex ions, as a way to group charge states and reduce computational cost, demonstrating its wide applicability within the Aurora forward model and beyond. Aurora also facilitates neutral particle analysis, both from experimental spectroscopic data and other simulation codes. Leveraging Aurora's capabilities to interface SOLPS-ITER results, we demonstrate that charge exchange is unlikely to affect the total radiated power from the ITER core during high performance operation. Finally, we describe the ImpRad module in the one modeling framework for integrated task framework, developed to enable experimental analysis and transport inferences on multiple devices using Aurora.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

TEAM Project Review, Year 2

This report summarizes our research activities within the TEAM project between December 2020 and December 2021, funded by the ASCR Advanced Research in Quantum Computing program. During the reporting period the LLNL-MSU team has made progress on several fronts. An overarching goal of the team is to provide a comprehensive suite of software tools that can be used for the Characterize-Optimize-Compute loop needed to implement and execute algorithms on quantum devices. We are concurrently developing lightweight solvers that can be used on desktop computers to find optimal control pulses and to characterize small quantum systems (consisting of a few transmons and cavities). However, desktop computers are insufficient for simulating and characterizing larger quantum systems. We have therefore also developed parallel, distributed memory, simulators and optimization solvers, both for open and closed quantum systems. These parallel solvers have, for example, been used to study quantum optimal control for pure-state preparation, utilizing 1000’s of cores on a modern high-performance computing (HPC) platform.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Viskores: Integrating Parallel Scientific Visualization Research into Applications

Viskores is a scientific visualization library that is the primary deployment of such algorithms to the parallel accelerated processors of modern DOE supercomputers. In this paper, we review the capabilities provided by Viskores and how these capabilities are leveraged by other software in the high-performance computing ecosystem. We discuss the Viskores data representation and pay particular attention to array management. Through this array management we describe how data is adapted between Viskores and other software along with strategies for converting dynamic, polymorphic objects to static representations better suited to GPU processing. We conclude with several examples of Viskores integrating with high-performance software that is used in production today.

Moreland, Ken [ORNL] (ORCID:0000000270513288)↗

Neutron Characterization for Additive Manufacturing

Oak Ridge National Laboratory (ORNL) is leveraging decades of experience in neutron characterization of advanced materials together with resources such as the Spallation Neutron Source (SNS) and the High Flux Isotope Reactor (HFIR) shown in Fig. 1 to solve challenging problems in additive manufacturing (AM). Additive manufacturing, or three-dimensional (3-D) printing, is a rapidly maturing technology wherein components are built by selectively adding feedstock material at locations specified by a computer model. The majority of these technologies use thermally driven phase change mechanisms to convert the feedstock into functioning material. As the molten material cools and solidifies, the component is subjected to significant thermal gradients, generating significant internal stresses throughout the part (Fig. 2). As layers are added, inherent residual stresses cause warping and distortions that lead to geometrical differences between the final part and the original computer generated design. This effect also limits geometries that can be fabricated using AM, such as thin-walled, high-aspect- ratio, and overhanging structures. Distortion may be minimized by intelligent toolpath planning or strategic placement of support structures, but these approaches are not well understood and often "Edisonian" in nature. Residual stresses can also impact component performance during operation. For example, in a thermally cycled environment such as a high-pressure turbine engine, residual stresses can cause components to distort unpredictably. Different thermal treatments on as-fabricated AM components have been used to minimize residual stress, but components still retain a nonhomogeneous stress state and/or demonstrate a relaxation-derived geometric distortion. Industry, federal laboratory, and university collaboration is needed to address these challenges and enable the U.S. to compete in the global market. Work is currently being conducted on AM technologies at the ORNL Manufacturing Demonstration Facility (MDF) sponsored by the DOE's Advanced Manufacturing Office. The MDF is focusing on R&D of both metal and polymer AM pertaining to in-situ process monitoring and closed-loop controls; implementation of advanced materials in AM technologies; and demonstration, characterization, and optimization of next-generation technologies. ORNL is working directly with industry partners to leverage world-leading facilities in fields such as high performance computing, advanced materials characterization, and neutron sciences to solve fundamental challenges in advanced manufacturing. Specifically, MDF is leveraging two of the world's most advanced neutron facilities, the HFIR and SNS, to characterize additive manufactured components.

Watkins, Thomas↗

BULKI-Store v0.3.2

BULKI-Store is a distributed object storage system optimized for high-performance computing environments. Built with a Rust core and Python bindings, it efficiently manages scientific and machine learning datasets across HPC clusters. The system employs a client-server architecture with MPI integration, enabling seamless scaling on supercomputers like Perlmutter. BULKI-Store's object-oriented approach provides intuitive data organization with rich metadata support, contrasting with traditional file-based solutions. Key optimizations include selective checkpoint loading, unified checkpoint files, and object chunking for large data transfers. For machine learning workloads, BULKI-Store offers advantages through fine-grained access patterns, dynamic data sharing between training instances, and reduced memory pressure. Memory management features include strategic Python GC calls, minimized data copies, and batch processing capabilities. The system leverages Rayon's thread pool for asynchronous data prefetching and supports multiple CPU architectures (ARM64, x86, AMD, RISC-V). By combining performance optimizations with developer-friendly APIs, BULKI-Store addresses the complex data management challenges of modern HPC applications while maintaining compatibility across heterogeneous computing environments.

Zhang, Wei [Lawrence Berkeley National Laboratory ↗