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At least 613 records · Page 34

Applying the FAIR Principles to computational workflows

Recent trends within computational and data sciences show an increasing recognition and adoption of computational workflows as tools for productivity and reproducibility that also democratize access to platforms and processing know-how. As digital objects to be shared, discovered, and reused, computational workflows benefit from the FAIR principles, which stand for Findable, Accessible, Interoperable, and Reusable. The Workflows Community Initiative’s FAIR Workflows Working Group (WCI-FW), a global and open community of researchers and developers working with computational workflows across disciplines and domains, has systematically addressed the application of both FAIR data and software principles to computational workflows. We present recommendations with commentary that reflects our discussions and justifies our choices and adaptations. These are offered to workflow users and authors, workflow management system developers, and providers of workflow services as guidelines for adoption and fodder for discussion. The FAIR recommendations for workflows that we propose in this paper will maximize their value as research assets and facilitate their adoption by the wider community.

97 MATHEMATICS AND COMPUTING↗

A multilayer multi-configurational approach to efficiently simulate large-scale circuit-based quantum computers on classical machines

Here, a multilayer multi-configurational theory framework is adapted to simulate circuit-based quantum computers. Quantum addition of superpositions of an exponential number of summands is performed in polynomial time with high accuracy. We demonstrate numerically accurate calculations including up to one million qubits for entangling benchmarks. Simulation cost can be assessed by entropy-based entanglement measures. For the considered systems, we show that the entanglement only grows weakly with the system size. The present simulations demonstrate how quantum algorithms in low-entropy regimes can be used efficiently on classically simulated quantum computers.

97 MATHEMATICS AND COMPUTING↗

Integrating subsystem embedding subalgebras and coupled cluster Green’s function: a theoretical foundation for quantum embedding in excitation manifold

Here, in this study, we introduce a novel approach to coupled-cluster Green's function (CCGF) embedding by seamlessly integrating conventional CCGF theory with the state-of-the-art sub-system embedding sub-algebras coupled cluster (SES-CC) formalism. This integration focuses primarily on delineating the characteristics of the sub-system and the corresponding segments of the Green's function, defined explicitly by active orbitals. Crucially, our work involves the adaptation of the SES-CC paradigm, addressing the left eigenvalue problem through a distinct form of Hamiltonian similarity transformation. This advancement not only facilitates a comprehensive representation of the interaction between the embedded sub-system and its surrounding environment but also paves the way for the quantum mechanical description of multiple embedded domains, particularly by employing the emergent quantum flow algorithms. Our theoretical underpinnings further set the stage for a generalization to multiple embedded sub-systems. This expansion holds significant promise for the exploration and application of non-equilibrium quantum systems, enhancing the understanding of system–environment interactions. In doing so, the research underscores the potential of SES-CC embedding within the realm of quantum computations and multi-scale simulations, promising a good balance between accuracy and computational efficiency.

97 MATHEMATICS AND COMPUTING↗

Ensemble approximate control variate estimators: Applications to multi-fidelity importance sampling.

The recent growth in multifidelity uncertainty quantification has given rise to a large set of variance reduction techniques that leverage information from model ensembles to provide variance reduction for estimates of the statistics of a high-fidelity model. In this paper we provide two contributions: (1) we utilize an ensemble estimator to account for uncertainties in the optimal weights of approximate control variate (ACV) approaches and derive lower bounds on the number of samples required to guarantee variance reduction; and (2) we extend an existing multifidelity importance sampling (MFIS) scheme to leverage control variates. Our approach directly addresses a limitation of many multifidelity sampling strategies that require the usage of pilot samples to estimate covariances. As such we make significant progress towards both increasing the practicality of approximate control variates—for instance, by accounting for the effect of pilot samples—and using multifidelity approaches more effectively for estimating low-probability events. The numerical results indicate our hybrid MFIS-ACV estimator achieves up to 50% improvement in variance reduction over the existing state-of-the-art MFIS estimator, which had already shown an outstanding convergence rate compared to the Monte Carlo method, on several problems of computational mechanics.

97 MATHEMATICS AND COMPUTING↗

Program Verification for Extreme-Scale Applications (Final Scientific/Technical Report)

The project seeks to develop tools and techniques to help software developers verify the correctness and accuracy of their code. The target domain is scientific software of the kind widely used and developed in the Department of Energy research community, with a particular focus on "extreme scale" programs - those that are expected to involve possibly millions of parallel threads of execution. The report covers the University of Delaware contribution to the collaborative project. The project had a number of successful outcomes, especially regarding the development and extension of the CIVL software verification framework. CIVL is a verification tool for C or Fortran programs that use MPI, OpenMP, CUDA, and/or Pthreads for parallelization. CIVL went through vast improvements and extensions, and was successfully applied to a number of challenging codes. It found a subtle bug in the Devito PDE framework. It was able to verify the functional correctness of a conjugate gradient solver using a novel probabilistic technique with vanishingly small chance of error. CIVL was used very successfully in verification competitions, and the CIVL solutions to the competition challenges were presented and published. CIVL was also used successfully by other researchers on a computational chemistry kernel.

97 MATHEMATICS AND COMPUTING↗

Understanding Interactive and Reproducible Computing With Jupyter Tools at Facilities

Increasingly Jupyter tools are being adopted and incorporated into High Performance Computing (HPC) and scientific user facilities. Adopting Jupyter tools enables more interactive and reproducible computational work at facilities across data life cycles. As the volume, variety, and scope of data grow, scientists need to be able to analyze and share results in user friendly ways. Human-centered research highlights design challenges around computational notebooks, and our qualitative user study shifts focus to better characterize how Jupyter tools are being used in HPC and science user facilities today. We conducted twenty-nine interviews, and obtained 103 survey responses from NERSC Jupyter users, to better understand the increasing role of interactive computing tools in DOE sponsored scientific work. We examine a range of issues that emerge using and supporting Jupyter in HPC ecosystems, including: how Jupyter is being used by scientists in HPC and user facility ecosystems; how facilities are purposefully supporting Jupyter in their ecosystems; feedback NERSC users have about the facility’s deployment, and, discuss features NERSC indicated would be helpful. We offer a variety of takeaways for staff supporting Jupyter at facilities, Project Jupyter and related open source communities, and funding agencies supporting interactive computing work.

97 MATHEMATICS AND COMPUTING↗

Efficient Application of the Factorized form of the Unitary Coupled-Cluster Ansatz for the Variational Quantum Eigensolver Algorithm by Using Linear Combination of Unitaries

The variational quantum eigensolver is one of the most promising algorithms for near-term quantum computers. It has the potential to solve quantum chemistry problems involving strongly correlated electrons with relatively low-depth circuits, which are otherwise difficult to solve on classical computers. The variational eigenstate is constructed from a number of factorized unitary coupled-cluster terms applied onto an initial (single-reference) state. Current algorithms for applying one of these operators to a quantum state require a number of operations that scale exponentially with the rank of the operator. We exploit a hidden SU(2) symmetry to allow us to employ the linear combination of unitaries approach, Our Prepare subroutine uses n+2 ancilla qubits for a rank-n operator. Our Select (U) scheme uses O(n) Cnot gates. This results in a full algorithm that scales like the cube of the rank of the operator n 3 , a significant reduction in complexity for rank five or higher operators. This approach, when combined with other algorithms for lower-rank operators (when compared to the standard implementation), will make the factorized form of the unitary coupled-cluster approach much more efficient to implement on all types of quantum computers.

97 MATHEMATICS AND COMPUTING↗

Riemannian Optimization Applied to AC Optimal Power Flow: Preprint

The nonlinear, nonconvex AC optimal power flow problem is of growing importance as the nature of the power grid evolves. This problem can be difficult to solve for interior point methods. However, the advent of optimization algorithms over smooth Riemannian manifolds presents an alternative approach. The nonlinear, nonconvex constraints in the AC power flow problem form an embedded submanifold of Euclidean space. In this paper, the authors explore the performance of Riemannian optimization algorithms for the ACOPF problem where the optimization is performed directly on the AC power flow manifold. They demonstrate that these are viable computational alternatives to interior point methods. This is done by using Julia and the packages PowerModels.jl and Manopt.jl.

manifold optimization↗

Machine learning unifies flexibility and efficiency of spinodal structure generation for stochastic biomaterial design

Abstract Porous biomaterials design for bone repair is still largely limited to regular structures (e.g. rod-based lattices), due to their easy parameterization and high controllability. The capability of designing stochastic structure can redefine the boundary of our explorable structure–property space for synthesizing next-generation biomaterials. We hereby propose a convolutional neural network (CNN) approach for efficient generation and design of spinodal structure—an intriguing structure with stochastic yet interconnected, smooth, and constant pore channel conducive to bio-transport. Our CNN-based approach simultaneously possesses the tremendous flexibility of physics-based model in generating various spinodal structures (e.g. periodic, anisotropic, gradient, and arbitrarily large ones) and comparable computational efficiency to mathematical approximation model. We thus successfully design spinodal bone structures with target anisotropic elasticity via high-throughput screening, and directly generate large spinodal orthopedic implants with desired gradient porosity. This work significantly advances stochastic biomaterials development by offering an optimal solution to spinodal structure generation and design.

59 BASIC BIOLOGICAL SCIENCES↗

Spherical Parameter Estimation and MPDV Applications

A new algebraic least square approach is presented for estimating effective zero center for verification of MPDV(Multichannel Photon Doppler Velocimetry) probe designs. Unlike previous algebraic least square methods for spherical parameter estimation, the new method can be shown to be concise in mathematic formulations, easy of computations, invariant under rigid -body transformations, no need for numerical approximations, and precise in dealing with precise data.

97 MATHEMATICS AND COMPUTING↗

Effect of Surface Roughness on Dynamic Stall in Pitching Motion

Dynamic stall plays a critical role in determining the performance and stability of a wide range of fluid-dynamics systems in various engineering applications. This unsteady aerodynamic phenomenon is particularly significant for maneuvering aircraft wings, jet aircraft subjected to gust encounters, helicopter rotor blades, and wind turbine blades [1–3]. The prediction of the dynamic stall vortex (DSV) is challenging due to factors such as unsteady aerodynamics, three-dimensional (3-D) effects, turbulence and flow separation, incoming gust, and surface impact effects [4–6]. Hence, advanced computational techniques and modeling approaches in computational fluid dynamics (CFD) would be required to enhance the accuracy and reliability of DSV predictions in dynamic stall scenarios. In the past, Batther and Lee [7] employed delayed detached eddy simulations (DDES) to understand the flow physics associated with the onset of dynamic stall. Their approach demonstrated that DDES achieves results comparable to those obtained from large-eddy simulations at a reduced computational cost. In another study, Khalifa et al. [8] examined the 3-D aspects of dynamic stall on a NACA 0012 airfoil using DES solvers. In conclusion, the findings underlined the superiority of 3-D simulations over two-dimensional approaches, particularly in predicting the lift coefficient values and capturing dynamic stall stages more precisely.

97 MATHEMATICS AND COMPUTING↗

Provable Repair of Vision Transformers

Vision Transformers have emerged as state-of-the-art image recognition tools, but may still exhibit incorrect behavior. Incorrect image recognition can have disastrous consequences in safety-critical real-world applications such as self-driving automobiles. In this paper, we present Provable Repair of Vision Transformers (PRoViT), a provable repair approach that guarantees the correct classification of images in a repair set for a given Vision Transformer without modifying its architecture. PRoViT avoids negatively affecting correctly classified images (drawdown) by minimizing the changes made to the Vision Transformer’s parameters and original output. Here, we observe that for Vision Transformers, unlike for other architectures such as ResNet or VGG, editing just the parameters in the last layer achieves correctness guarantees and very low drawdown. We introduce a novel method for editing these last-layer parameters that enables PRoViT to efficiently repair state-of-the-art Vision Transformers for thousands of images, far exceeding the capabilities of prior provable repair approaches.

97 MATHEMATICS AND COMPUTING↗

Increasing the hardness of posiform planting using random QUBOs for programmable quantum annealer benchmarking

Posiform planting is a method for constructing QUBO instances with a unique planted solution that can be tailored to arbitrary connectivity graphs. In this study we investigate making posiform planted QUBOs computationally harder by fusing many smaller random Ising models, whose global minimum is computed classically, with posiform planted QUBOs. The unique ground state of the resulting QUBO is the concatenation of (exactly one of) the ground states of each smaller problem. Our method generates QUBO instances that have a unique solution, are native to the hardware graph, and have tunable computational hardness. We use our QUBOs to benchmark three D-Wave quantum annealing processors (with 563–5627 qubits), and compare them against simulated annealing and Gurobi. Surprisingly, we find that the D-Wave ground state sampling success rate is not dependent on the glued random QUBO size, and that some QUBO classes are solved at high success rates at short annealing times on the Zephyr processors.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

ENDFtk: A robust tool for reading and writing ENDF-formatted nuclear data

ENDFtk is a recently developed C++ and Python interface to interact with ENDF-6 formatted nuclear data files. It provides a robust and complete interface, allowing the reading and writing of all formats currently part of the ENDF-6 formats manual, as well as some non-ENDF formats used by the NJOY processing code. It provides an interface that mimics the names in the ENDF-6 formats manual as well as an equivalent interface using human-readable attribute names. It is robust and powerful enogh for nuclear data experts to develop complex applications, while also simple enough to be used non-experts to retrieve and manipulate evaluated nuclear data. ENDFtk offers the ability to easily interrogate and manipulate data either in large-scale code projects or in simple Python scripts. Here, in this paper, a brief overview of the interface is given, as well as more substantial examples demonstrating plotting simple data, interacting with more complex data, and writing new data to files. ENDFtk is open source and available for download via GitHub (https://github.com/njoy/ENDFtk).

97 MATHEMATICS AND COMPUTING↗

Fluidization of Group A Glass Particles: Experiments and Preliminary Validation

This work is aimed at providing reliable high-quality data from fluidization experiments. Geldart Group A glass beads are used as bed material. The fluidizing medium is air at atmospheric pressure which enters the system at 40% relative humidity. The air inlet velocity is varied over a broad range from 2 U mf to 26 U mf , where the minimum fluidization velocity, U mf , is 0.608 cm/s. There is not a significant change in the mean values of differential pressure; however, there are noticeable trends in their standard deviation values. Preliminary validation studies are performed using the open-source software Multiphase Flow with Interphase eXchanges (MFiX) developed by the National Energy Technology Laboratory (NETL). The results from Eulerian-Eulerian (MFiX-TFM, two-fluid model) and Eulerian-Lagrangian (MFiX-PIC, particle-in-cell) formulations are compared. The work presented in this report highlights the applicability of MFiX-PIC for large-scale applications, and reveals that PIC simulation offers a suitable alternative to TFM simulation when effects due to multiple components or polydispersity are significant. PIC modeling provides a readily extendible framework for such systems. However, PIC models do rely on an empirical closure for inter-particle stress. Some solution discrepancies were evident in MFiX-PIC predictions which require further analysis. As such, the study underlines the need for a systematic approach to quantify the sources of numerical uncertainty within the PIC model. However, even with known empiricism, MFiX-PIC has demonstrated considerable potential in analyzing gas-solid systems. The results obtained are encouraging and warrant further investigation to improve the predictive capability of MFiX-PIC.

36 MATERIALS SCIENCE↗