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At least 559 records · Page 31

Contributions to MoDELib SOFTWARE

The purpose of the current request is to enable LANL employees to contribute computer source code to the existing public repository of the MoDELib software package. This software implements discrete dislocation dynamics (DDD) and finite element (FEM) methods and is currently a vital component of an ongoing DR project at LANL, in collaboration with its original author and maintainer Giacomo Po. Contributions from LANL employees would aim to enhance the reliability, accuracy, and performance of MoDELib simulations using LANL's high performance computing platforms through bug fixes, algorithmic refinements, and parallelization.

Julian, Nicholas↗

Differentiable Multiphysics Codes: A Breakthrough Technology for Simulation and Computing

This document summarizes the findings of a strategic planning exercise commissioned by the Weapons Simulation and Computing, Computational Physics (WSC/CP) program at the Lawrence Livermore National Laboratory (LLNL) in FY24. During the year, the committee met with multiple stakeholder communities to gather input, opinions, suggestions and concerns which have been incorporated throughout this document. The key findings from this exercise are summarized: • The development of multiphysics modelling and simulation (mod/sim) codes and software technologies, their deployment on exascale compute platforms, and their broad adoption across the NNSA is a major success of the Advanced Simulation and Computing (ASC) program and the Exascale Computing Project (ECP). Sustained investment in these core technologies is essential. • Today’s state of the art involves running ensembles of O(100K) simulations to perform uncertainty quantification (UQ) and design studies using multiple statistical methods such as Bayesian optimization to understand sensitivities of our models and explore parameterized design spaces. Even with exascale computing, we are practically limited to O(10) parameters in these studies since the number of simulations required to sample the space scales exponentially with the number of design parameters. • The data from these simulation ensembles is increasingly being used to train machine learned (ML) surrogates (or reduced order models, ROMs) which can then be used for optimization or real time design exploration. However, the trained surrogates are still limited in the number of parameters they can represent due to the sampling limitations previously noted. • Augmenting our suite of integrated multiphysics simulation codes, both current and emerging, with the ability to compute gradients (solution derivatives) of arbitrary simulation outputs with respect to (some or all) simulation inputs would be a breakthrough technology, opening the door to a new era of efficient and automated inverse design based on verified and validated mod/sim capabilities. • This capability, which we refer to as differentiable multiphysics codes (DMCs), would revolutionize both UQ and optimization studies by breaking the curse of dimensionality that presently limits our “gradient-free” ensemble based computing approach. A similar breakthrough occurred in the AI/ML community once the ability to compute gradients of arbitrary loss functions using back-propagation became commonplace. Gradient information from the multiphysics codes can also be used to dramatically improve the efficiency and scale of training of ML/ROM surrogates for rapid assessments. • Achieving this in our suite of codes will be a grand challenge, similar to the amount of effort that was required to transition from CPU to GPU computing. It will require buy-in from the entire WSC/CP program and beyond, including all integrated codes, physics and engineering models, third-party library dependencies and performance portability abstractions. It will also require investment in research and development of numerical methods for computing adjoints of coupled physics across multiple adaptively refined moving meshes and of stochastic (Monte Carlo) and mesh free (SPH) methods. • New software and numerical techniques, largely pioneered by the AI/ML community, make this feasible. Chief among these is automatic differentiation (AD), the ability to employ AD at point-wise locations in a physics calculation (instead of traditional black-box approaches) and the ability to perform “back-propagation in time” (or reverse mode AD) for non-linear partial differential equations (PDEs). Fundamentally, the conclusion of this strategic planning exercise is that the time is right to undertake a large scale effort in WSC, centered on the existing integrated codes, to continue the natural evolution of mod/sim in the age of AI/ML. Instead of attempting to replace mod/sim with purely data driven AI/ML models, we believe the key to success is to integrate AI/ML by building on top of the decades of hard-won knowledge and the verified/validated multiphysics modelling capability that is the hallmark of the ASC program.

97 MATHEMATICS AND COMPUTING↗

Theoretical Multinary Perovskite Oxides Dataset

Perovskite oxides (ternary chemical formula ABO3) are a diverse class of materials with applications including heterogeneous catalysis, solid-oxide fuel cells, thermochemical conversion, and oxygen transport membranes. However, their multicomponent chemical space is underexplored due to the immense number of possible compositions. To expand the number of computed compounds we report a dataset of 66,516 theoretical multinary oxides, 59,708 of which are perovskites. First, the AA'BB'O6 compositions were generated in the a-b+a- Glazer tilting mode using the computationally-inexpensive Structure Prediction and Diagnostic Software (SPuDS) program. Next, we optimized these structures with DFT using parameters compatible with the Materials Project (MP) database. Our dataset contains these optimized structures and their formation (ΔHf) and decomposition enthalpies (ΔHd) computed relative to MP tabulated elemental references and competing phases, respectively. This dataset can be mined, used to train machine learning models, and rapidly and systematically expanded by optimizing more SPuDS-generated AA'BB'O6 perovskite structures using MP-compatible DFT calculations

Bare, Zachary↗

An Extension of the Athena++ Code Framework for Radiation-magnetohydrodynamics in General Relativity Using a Finite-solid-angle Discretization

We extend the general-relativistic magnetohydrodynamics (GRMHD) capabilities of Athena++ to incorporate radiation. The intensity field in each finite-volume cell is discretized in angle, with explicit transport in both space and angle properly accounting for the effects of gravity on null geodesics, and with matter and radiation coupled in a locally implicit fashion. Here we describe the numerical procedure in detail, verifying its correctness with a suite of tests. Motivated in particular by black hole accretion in the high-accretion-rate, thin-disk regime, we demonstrate the application of the method to this problem. With excellent scaling on flagship computing clusters, the port of the algorithm to the GPU-enabled AthenaK code now allows the simulation of many previously intractable radiation-GRMHD systems.

79 ASTRONOMY AND ASTROPHYSICS↗

Systematic Crosstalk Mitigation for Superconducting Qubits via Frequency-Aware Compilation

One of the key challenges in current Noisy Intermediate-Scale Quantum (NISQ) computers is to control a quantum system with high-fidelity quantum gates. There are many reasons a quantum gate can go wrong - for superconducting transmon qubits in particular, one major source of gate error is the unwanted crosstalk between neighboring qubits due to a phenomenon called frequency crowding. We motivate a systematic approach for understanding and mitigating the crosstalk noise when executing near-term quantum programs on superconducting NISQ computers. Here, we present a general software solution to alleviate frequency crowding by systematically tuning qubit frequencies according to input programs, trading parallelism for higher gate fidelity when necessary. The net result is that our work dramatically improves the crosstalk resilience of tunable-qubit, fixed-coupler hardware, matching or surpassing other more complex architectural designs such as tunable-coupler systems. On NISQ benchmarks, we improve worst-case program success rate by 13.3x on average, compared to existing traditional serialization strategies.

Computer architecture↗

Portable Software Environment for Ultrahigh-Resolution ELM Development on GPUs

This paper presents our endeavors in developing the large-scale, ultra-high-resolution E3SM Land Model (uELM), specifically designed for exascale computers furnished with accelerators such as Nvidia GPUs. The uELM is a sophisticated code that substantially relies on High-Performance Computing (HPC) environments, necessitating particular machine and software configurations. To facilitate community-based uELM developments employing GPUs, we have created a portable, standalone software environment preconfigured with uELM input datasets, simulation cases, and source code. This environment, utilizing Docker, encompasses all essential code, libraries, and system software for uELM development on GPUs. It also features a functional unit test framework and an offline model testbed for comprehensive numerical experiments. From a technical perspective, the paper discusses GPU-ready container generations, uELM code management, and input data distribution across computational platforms. Lastly, the paper demonstrates the use of environment for functional unit testing, end-to-end simulation on CPUs and GPUs, and collaborative code development.

E3SM Land Model↗

Towards Ultra-high-resolution E3SM Land Modeling on Exascale Computers

Here we present an ultra-high-resolution E3SM land model (uELM) for high-fidelity land simulations targeting new Exascale computers. After considering modeling infrastructure compatibility and ELM software features, we designed a parallel model for the uELM development targeting hybrid architectures of new US Exascale computers. We also described a function unit test framework to expedite the piece-wise code porting (with compiler directives), verification, and global variable management. Furthermore, in this study, we report an early uELM model development using OpenACC within a function unit test framework on a pre-Exascale computer, demonstrate the performance of a uLEM submodel with a 3.0-time speedup, and summarize the code porting experience regarding global variable handling, deepcopy, memory reduction, and parallel loop reconstruction.

97 MATHEMATICS AND COMPUTING↗

Dataset of theoretical multinary perovskite oxides

Perovskite oxides (ternary chemical formula ABO 3 ) are a diverse class of materials with applications including heterogeneous catalysis, solid-oxide fuel cells, thermochemical conversion, and oxygen transport membranes. However, their multicomponent (chemical formula $A_xA^{'}_{1-x}B_yB^{'}_{1-y}O_3$) chemical space is underexplored due to the immense number of possible compositions. To expand the number of computed $A_xA^{'}_{1-x}B_yB^{'}_{1-y}O_3$ compounds we report a dataset of 66,516 theoretical multinary oxides, 59,708 of which are perovskites. First, 69,407 $A_{0.5}A^{'}_{0.5}B_{0.5}B^{'}_{0.5}O_3$ compositions were generated in the a - b + a - Glazer tilting mode using the computationally-inexpensive Structure Prediction and Diagnostic Software (SPuDS) program. Next, we optimized these structures with density functional theory (DFT) using parameters compatible with the Materials Project (MP) database. Our dataset contains these optimized structures and their formation (ΔH f ) and decomposition enthalpies (ΔH d ) computed relative to MP tabulated elemental references and competing phases, respectively. This dataset can be mined, used to train machine learning models, and rapidly and systematically expanded by optimizing more SPuDS-generated $A_{0.5}A^{'}_{0.5}B_{0.5}B^{'}_{0.5}O_3$ perovskite structures using MP-compatible DFT calculations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The Elastic Analysis Facility's (EAF's) Contribution to the Future of Analysis at Multi-Experiment Institutions and Future Colliders

The Elastic Analysis Facility (EAF) hosted at Fermi National Accelerator Laboratory (Fermilab) is a platform being developed with the goal of providing a fast and efficient facility for physics analysis. As high-energy physics moves towards collecting larger datasets, such as those from the High-Luminosity LHC, the EAF strives to provide a powerful and adaptable framework for future colliders and multi-experiment institutions. Currently, the EAF supports several experiments including CMS, NOvA, and DUNE as well as serving accelerator physicists and beam line operations through integrated software and secure connections to Fermilab's computing resources. In addition, the EAF was designed with a user-friendly interface, intended to be more intuitive for emerging generations of physicists, that is still accessible for established styles of analysis. The EAF can also achieve better analysis efficiency due to the modernization of software and tools that can better utilize Fermilab's computing power. Furthermore, its design incorporates industry standards whenever possible, enhancing its sustainability and making it a possible template for other national or international laboratories and research facilities. Overall, the EAF is a forward-looking solution that will meet the evolving needs of particle physics, ensuring readiness for future colliders and multi-experiment research institutions.

Chavez, Elise [Wisconsin U., Madison]↗

Python Group Additivity (pGrAdd) software for estimating species thermochemical properties

ncreasingly complex chemistry models require thermochemical data for many species often estimated from costly first-principles DFT computations. Here we introduce the Python Group Additivity software (pGrAdd) that implements comprehensive group additivity in a simple, modular, lightweight Python package that is extensible and easy to implement. It includes 6 group additivity databases for gas species and Pt(111) adsorbates allowing users to immediately compute thermochemical properties for a wide range of molecules and build new databases.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DL_POLY Quantum 2.0: A modular general-purpose software for advanced path integral simulations

DL_POLY Quantum 2.0, a vastly expanded software based on DL_POLY Classic 1.10, is a highly parallelized computational suite written in FORTRAN77 with a modular structure for incorporating nuclear quantum effects into large-scale/long-time molecular dynamics simulations. This is achieved by presenting users with a wide selection of state-of-the-art dynamics methods that utilize the isomorphism between a classical ring polymer and Feynman’s path integral formalism of quantum mechanics. Here, the flexible and user-friendly input/output handling system allows the control of methodology, integration schemes, and thermostatting. DL_POLY Quantum is equipped with a module specifically assigned for calculating correlation functions and printing out the values for sought-after quantities, such as dipole moments and center-of-mass velocities, with packaged tools for calculating infrared absorption spectra and diffusion coefficients.

36 MATERIALS SCIENCE↗

Automated reaction kinetics and network exploration (Arkane): A statistical mechanics, thermodynamics, transition state theory, and master equation software

The open-source statistical mechanics software described here, Arkane–Automated Reaction Kinetics and Network Exploration–facilitates computations of thermodynamic properties of chemical species, high-pressure limit reaction rate coefficients, and pressure-dependent rate coefficient over multi-well molecular potential energy surfaces (PES) including the effects of collisional energy transfer on phenomenological kinetics. Arkane can use estimates to fill in information for molecules or reactions where quantum chemistry information is missing. The software solves the internal energy master equation for complex unimolecular reaction systems. Inputs to the software include converged electronic structure computations performed by the user using a variety of supported software packages (Gaussian, Molpro, Orca, TeraChem, Q-Chem, Psi4). The software outputs high-pressure limit rate coefficients and pressure-dependent phenomenological rate coefficients, as well as computed thermodynamic properties (enthalpy, entropy, and constant pressure heat capacity) with added energy corrections. Some of the key features of Arkane include treatment of 1D, 2D or ND hindered internal rotation modes, treatment of free internal rotation modes, quantum tunneling effect consideration, transition state theory (TST) and Rice-Ramsperger-Kassel-Marcus (RRKM) rate coefficient computations, master equation solution with four implemented methods, inverse-Laplace transform of high-pressure limit rate coefficients into the energy domain, energy corrections based on bond-additivity or isodesmic reactions, automated and efficient PES exploration, and PES sensitivity analysis. The present work describes the design of Arkane, how it should be used, and refers to the theory that it employs. Arkane is distributed via the RMG-Py software suite (https://github.com/ReactionMechanismGenerator/RMG-Py).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Emulation Framework for Distributed Large-Scale Systems Integration

Recent trends in systems engineering include integration of very large-scale systems, which entails significant challenges when they are geographically dispersed. In these scenarios, intelligent integration of distributed large-scale systems requires significant coordination among hardware elements as well as all software components. The approach of integrated systems (both computing platform and experimental equipment) for end-to-end orchestration is called federation. Virtual frameworks can aid in the testing, assessment, and implementation of a functional system of interconnected resources. We present an emulation framework that replicates the software environments of multi-site federations of computing systems and instruments. Our emulation framework allows systems engineers to reduce developmentcost and avoid disruptions to production infrastructure. Our framework was effectively used to develop and test software modules for various tasks including container orchestration and instrument access. For performance assessment, however, the emulated framework is severely limited in providing accurate network and IO measurements at 10 Gbps and higher data rates. The data transfer performance profiles estimated using these emulated measurements are usually inaccurate for high bandwidth and high latency connections, since emulation does not accurately reflect the critical network transport dynamics.We utilize measurements from a physical testbed with hardware network emulators to obtain data transfer profiles that closely match the expected profiles for the emulated federations. We show the effectiveness of our approach by an illustrative example of integrated (federated) multi-site ultra large-scale systems that are connected via high speed wide area networks.

Imam, Neena↗

Development of a Method for Shape Optimization for a Gas Turbine Fuel Injector Design Using Metal-Additive Manufacturing

Adjoint shape optimization has enabled physics-based optimal designs for aerodynamic surfaces. Additive manufacturing (AM) makes it possible to manufacture complex shapes. However, there has been a gap between optimal and manufacturable surfaces due to the inherent limitations of commercial computational fluid dynamics (CFD) codes to implement geometric constraints during adjoint computation. In such cases, the design sensitivities are exported and used to perform constrained shape modifications using parametric information stored in computer aided design (CAD) files to satisfy manufacturability constraints. However, modifying the design using adjoint methods in CFD solvers and performing constrained shape modification in CAD can lead to inconsistencies due to different shape parameterization schemes. This paper describes a method to enable the simultaneous optimization of the fluid domain and impose AM manufacturability constraints, resolving one of the key issues of geometry definition for isogeometric analysis. Similar to a grid convergence study, the proposed method verifies the consistencies between shape parameterization techniques present within commercial CAD and CFD software during mesh movement as a part of the adjoint shape optimization routine. By identifying the appropriate parameters essential to a shape optimization study, the error metric between the different parameterization techniques converges to demonstrate sufficient consistencies for justifiable exchange of data between CAD and CFD. For the identified shape optimization parameters, the error metric to measure the deviation between the two parameterization schemes lies within the AM laser-powder bed fusion (L-PBF) process tolerance. Additionally, comparison for subsequent objective function calculations between iterations of the optimization loop showed acceptable differences within 1% variation between the modified geometries obtained using the two parameterization schemes. This method provides justification for the use of multiphysics guided adjoint design sensitivities computed in CFD software to perform shape modifications in CAD to incorporate AM manufacturability constraints during the shape optimization loop such that optimal designs are also additively manufacturable.

33 ADVANCED PROPULSION SYSTEMS↗

Cooperative Education

Los Alamos National Laboratory (LANL) is a multidisciplinary national laboratory that conducts research and development in national security, engineering, materials science, computational modeling, and advanced manufacturing. The laboratory develops innovative technologies to address complex scientific and engineering challenges. This project focuses on the development and evaluation of high-performance absorbing structures through computational design, simulation, and engineering analysis. Absorbing structures are used in applications where damage mitigation, structural protection, and material efficiency are critical performance requirements. The increasing demand for lightweight, high-strength, and highly efficient structural systems has created a need for improved design methodologies capable of maximizing absorption while minimizing weight and material usage. The project utilizes advanced engineering software, including 3D CAD software and FEA, to generate and optimize structural concepts. Computational simulations are performed to evaluate structural behavior under loading conditions, while mathematical analyses are conducted using Python-based tools as well as established analytical equations from material and structural mechanics. The project benefits LANL by supporting the development of advanced design methodologies and improving the understanding of material and structural performance. During the internship term, a significant portion of the design development, simulation, and data analysis activities will be completed. Success of the project depends on collaboration among engineering mentors and technical staff members. Work will be conducted at Los Alamos National Laboratory using laboratory computing resources and engineering software.

42 ENGINEERING↗

On the Marriage of Asynchronous Many Task Runtimes and Big Data: A Glance

The rise of the accelerator-based architectures and reconfigurable computing have showcased the weakness of software stack toolchains that still maintain a static view of the hardware instead of relying on a symbiotic relationship between static (e.g., compilers) and dynamic tools (e.g., runtimes). In the past decades, this need has given rise to adaptive runtimes with increasingly finer computational tasks. These finer tasks help to take advantage of the hardware by switching out when a long latency operation is encountered (because of the deeper memory hierarchies and new memory technologies that might target streaming instead of random access), thus trading off idle time for unrelated work. Examples of these finer task runtimes are Asynchronous Many Task (AMT) runtimes, in which highly efficient computational graphs run on a variety of hardware. Due to its inherent latency tolerant characteristics, Latency-sensitive applications, such as Graph Analytics and Big Data can effectively use these runtimes. This paper aims to present an example of how the careful design of an AMT can exploit the hardware substrate when faced with high latency applications such as the ones given in the Big Data domain. Moreover, with its introspection and adaptive capabilities, we aim to show the power of these runtimes when facing the changing requirements of the application workloads. We use the Performance Open Community Runtime (P-OCR) as our vehicle to demonstrate the concepts presented here.

adaptive runtime, big data analysis↗

A Framework for Error-Bounded Approximate Computing, with an Application to Dot Products

Approximate computing techniques, which trade off the computation accuracy of an algorithm for better performance and energy efficiency, have been successful in reducing computation and power costs in several domains. However, error sensitive applications in high-performance computing are unable to benefit from existing approximate computing strategies that are not developed with guaranteed error bounds. While approximate computing techniques can be developed for individual high-performance computing applications by domain specialists, this often requires additional theoretical analysis and potentially extensive software modification. Hence, the development of low-level error-bounded approximate computing strategies that can be introduced into any high-performance computing application without requiring additional analysis or significant software alterations is desirable. In this paper, we provide a contribution in this direction by proposing a general framework for designing error-bounded approximate computing strategies and apply it to the dot product kernel to develop \bf qdot---an error-bounded approximate dot product kernel. Following the introduction of qdot, here we perform a theoretical analysis that yields a deterministic bound on the relative approximation error introduced by qdot. Empirical tests are performed to illustrate the tightness of the derived error bound and to demonstrate the effectiveness of qdot on a synthetic dataset, as well as two scientific benchmarks---the conjugate gradient (CG) and power methods. In some instances, using qdot for the dot products in CG can result in many components being quantized to half precision without increasing the iteration count required for convergence to the same solution as CG using a double precision dot product.

97 MATHEMATICS AND COMPUTING↗

Final Report

This final progress report describes the development of the CANDO Software package at ThirdLaw Technologies LLC (TLT) towards a software platform that will be used by its subsidiary company ThirdLaw Molecular LLC (TLM) for the development of therapeutic Spiroligomer™ molecules. ThirdLaw Molecular LLC is 95% owned by ThirdLaw Technologies LLC. TLM is developing a new therapeutics platform based on Spiroligomer™ molecules and is currently funded by the Department of Defense, Defense Threat Reduction Agency (DOD/DTRA W15QKN209C004). Spiroligomer™ molecules are complex, highly-preorganized macromolecules with programmable three-dimensional shapes. Spiroligomer™ molecules are currently synthesized by TLM in the form of large (>880,000 member) DNA-encoded libraries and screened against dangerous bacteria and viruses as part of the DOD/DTRA project. The CANDO software package is being developed to enable the computational design of Spiroligomer™ molecules for the development of therapeutic and diagnostic molecules. Towards this end, over the period of the grant we implemented software algorithms and a user interface within CANDO to enable the computational design of Spiroligomer™ molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗