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All sources NASA NTRS DOE OSTI

DOE OSTI2022

Profiling the BLAST bioinformatics application for load balancing on high-performance computing clusters

Abstract Background The Basic Local Alignment Search Tool (BLAST) is a suite of commonly used algorithms for identifying matches between biological sequences. The user supplies a database file and query file of sequences for BLAST to find identical sequences between the two. The typical millions of database and query sequences make BLAST computationally challenging but also well suited for parallelization on high-performance computing clusters. The efficacy of parallelization depends on the data partitioning, where the optimal data partitioning relies on an accurate performance model. In previous studies, a BLAST job was sped up by 27 times by partitioning the database and query among thousands of processor nodes. However, the optimality of the partitioning method was not studied. Unlike BLAST performance models proposed in the literature that usually have problem size and hardware configuration as the only variables, the execution time of a BLAST job is a function of database size, query size, and hardware capability. In this work, the nucleotide BLAST application BLASTN was profiled using three methods: shell-level profiling with the Unix “time” command, code-level profiling with the built-in “profiler” module, and system-level profiling with the Unix “gprof” program. The runtimes were measured for six node types, using six different database files and 15 query files, on a heterogeneous HPC cluster with 500+ nodes. The empirical measurement data were fitted with quadratic functions to develop performance models that were used to guide the data parallelization for BLASTN jobs. Results Profiling results showed that BLASTN contains more than 34,500 different functions, but a single function, RunMTBySplitDB, takes 99.12% of the total runtime. Among its 53 child functions, five core functions were identified to make up 92.12% of the overall BLASTN runtime. Based on the performance models, static load balancing algorithms can be applied to the BLASTN input data to minimize the runtime of the longest job on an HPC cluster. Four test cases being run on homogeneous and heterogeneous clusters were tested. Experiment results showed that the runtime can be reduced by 81% on a homogeneous cluster and by 20% on a heterogeneous cluster by re-distributing the workload. Discussion Optimal data partitioning can improve BLASTN’s overall runtime 5.4-fold in comparison with dividing the database and query into the same number of fragments. The proposed methodology can be used in the other applications in the BLAST+ suite or any other application as long as source code is available.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

RingX: Scalable Parallel Attention for Long-Context Learning on HPC

The attention mechanism has become foundational for remarkable AI breakthroughs since the introduction of the Transformer, driving the demand for increasingly longer context to power frontier models such as large-scale reasoning language models and high-resolution image/video generators. However, its quadratic computational and memory complexities present substantial challenges. Current state-of-the-art parallel attention methods, such as ring attention, are widely adopted for long-context training but utilize a point-to-point communication strategy that fails to fully exploit the capabilities of modern HPC network architectures. In this work, we propose ringX, a scalable family of parallel attention methods optimized explicitly for HPC systems. By enhancing workload partitioning, refining communication patterns, and improving load balancing, ringX achieves up to 3.4 × speedup compared to conventional ring attention on the Frontier supercomputer. Optimized for both bi-directional and causal attention mechanisms, ringX demonstrates its effectiveness through training benchmarks of a Vision Transformer (ViT) on a climate dataset and a Generative Pre-Trained Transformer (GPT) model, Llama3 8B. Our method attains an end-to-end training speedup of approximately 1.5 × in both scenarios. To our knowledge, the achieved 38% model FLOPs utilization (MFU) for training Llama3 8B with a 1M-token sequence length on 4,096 GPUs represents one of the highest training efficiencies reported for long-context learning on HPC systems. Our code implementation is available at https://github.com/jqyin/ringX-attention.

Yin, Junqi [ORNL] (ORCID:0000000338435520)↗

NASA NTRS1980

Control systems design for large flexible space structures

Several approaches for the design of reduced-order linear-quadratic-Gaussian type controllers for large space structures were proposed and evaluated using a continuous model of a long free-free beam. Sufficient conditions were derived for the asymptotic stability with this type of controller. A finite-element model of a free-free-free-free square plate was obtained for use in control systems studies. A method was developed for optimal damping enhancement in large space structures.

Joshi, S. M.↗

DOE OSTI2018

Mean-Variance Optimization-Based Energy Storage Scheduling Considering Day-Ahead and Real-Time LMP Uncertainties

In this letter, a new mean-variance optimization-based energy storage scheduling method is proposed with the consideration of both day-ahead (DA) and real-time (RT) energy markets price uncertainties. It considers the locational marginal price (LMP) forecast uncertainties in the DA and RT markets. The energy storage arbitrage risk associated with the LMP forecast uncertainty is explicitly modeled through the variance component in the objective function. The quadratic term of this variance is transformed into a second-order cone constraint using the charging and discharging power complementarity of the energy storage system. Finally, the proposed model is formulated as a mixed-integer conic programming problem. Numerical case studies demonstrate the effectiveness of the proposed model for energy storage scheduling considering price uncertainty.

25 ENERGY STORAGE↗

NASA NTRSDate not supplied

Improving Kinetic Consistency Across Elastic Model Transitions With Quadratic Inequality Constrained Weighted Least Squares (WLSQI)

Flexible body modeling presents a large challenge in the development of simulations to aid in design of flight control systems for launch and landing vehicles. Typically, the flexible body model is not a single continuous model but are rather discrete sets of Linear Time Invariant (LTI) Finite Element Models (FEM) incremented by propellant levels. This introduces the problem of smoothly transitioning modal and physical states of the vehicle when switching from one FEM to the next. This paper introduces a new approach to optimally transition flexible body states with weighted least squares, building off previous methods.

Convex Optimization↗

NASA NTRSDate not supplied

Improving Kinetic Consistency Across Elastic Model Transitions With Quadratic Inequality Constrained Weighted Least Squares (WLSQI)

GN&C↗

NASA NTRS1972

On stochastic control system design methods for weakly coupled large scale linear systems.

This paper considers the problem of decentralized control of two weakly coupled linear stochastic systems, using quadratic performance indices. The basic idea is to have each controller control independently his own system, based upon noisy measurements of his own output. To compensate for the effects of weak coupling upon the resultant performance, fake white plant noise is introduced to each system. The appropriate intensity of the fake plant noise is obtained through the solution of an off-line deterministic matrix optimal control problem. The effects of this design method upon the overall coupled system performance are analyzed as a function of the degree of intersystem coupling.

Kwong, R.↗

NASA NTRS2019

Scenario Complexity for Unmanned Aircraft System Traffic

This work introduces an approach to estimate the complexity of a low-altitude air traffic scenario involving multiple UASs using mathematical programming. Given a set of multi-point UAS flight trajectories, vehicle dynamics, and a conflict resolution algorithm, an abstract model is developed such that it can be solved quickly using a mathematical programming optimization software without running high-fidelity simulations that can be computationally expensive and may not suit real-time applications. In the abstract model, each vehicle is represented by a time-varied vector associated with position, speed, and heading information. The total extra distance that aircraft need to divert from their original routes to avoid collisions is computed and used to setup a quadratic programming formula. The metrics including the number of conflicts and extra distances travelled by all vehicles are then utilized to estimate the complexity of a given UAS flight scenario. Results and verification against high-fidelity simulations will be provided in the final draft.

UTM↗

DOE OSTI2021

Application of real‐time nonlinear model predictive control for wave energy conversion

Abstract This article presents an approach to implement a Nonlinear Model Predictive Controller (NMPC) in real‐time with a non‐standard cost index. The proposed technique's applications are presented to maximize the energy produced by a Wave Energy Converter (WEC) when the cost index is a non‐quadratic piecewise discontinuous functional of some design variables. The presented framework is based on pseudo‐quadratisation and weight scheduling, which is implemented using the ACADO toolkit for MATLAB/Simulink. The proposed strategy features code generation and deployment on the real‐time target machines for industrial applications. The simulations and experiments confirm the success of the proposed approach in achieving the feasible operation of the NMPC and an optimal power capture by the wave energy converters.

16 TIDAL AND WAVE POWER↗

DOE OSTI2021

Absorptive Weak Plume Detection on Gaussian and Non-Gaussian Background Clutter

For additive signals on Gaussian clutter, the optimal detector is a linear matched filter that is adapted to the known signal and the covariance of the background. This adaptive matched filter is widely used for gas-phase plume detection, even though the effect of the plume on the background is not strictly additive. Here, a derivation of the matched filter for a strictly absorptive plume produces, in the weak plume limit, a quadratic filter. This quadratic matched filter is extended in two ways: an elliptically-contoured multivariate t distribution is used to generalize the Gaussian background clutter, and a generalized likelihood ratio test detector is derived to extend applicability to stronger plumes. In addition to detectors whose purpose is to identify presence versus absence of a plume, expressions are also derived for estimating plume strength. The performance of these various detectors is evaluated by implanting simulated plume into background images that are either real hyperspectral images or simulated images based on different (Gaussian, multivariate t, and lognormal) clutter distributions.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2016

A Three-Phase Microgrid Restoration Model Considering Unbalanced Operation of Distributed Generation

Recent severe outages highlight the urgency of improving grid resiliency in the U.S. Microgrid formation schemes are proposed to restore critical loads after outages occur. Most distribution networks have unbalanced configurations that are not represented in sufficient detail by single-phase models. This study provides a microgrid formation plan that adopts a three-phase network model to represent unbalanced distribution networks. The problem formulation has a quadratic objective function with mixed-integer linear constraints. The three-phase network model enables us to examine the three-phase power outputs of distributed generators (DGs), preventing unbalanced operation that might trip DGs. Because the DG unbalanced operation constraint is non-convex, an iterative process is presented that checks whether the unbalanced operation limits for DGs are satisfied after each iteration of optimization. We also develop a relatively conservative linear approximation on the unbalanced operation constraint to handle larger networks. Compared with the iterative solution process, the conservative linear approximation is able to accelerate the solution process at the cost of sacrificing optimality to a limited extent. Simulation in the IEEE 34 node and IEEE 123 test feeders indicate that the proposed method yields more practical microgrid formations results. In addition, this paper explores the coordinated operation of DGs and energy storage (ES) installations. The unbalanced three-phase outputs of ESs combined with the relatively balanced outputs of DGs could supply unbalanced loads. In conclusion, the case study also validates the DG-ES coordination.

24 POWER TRANSMISSION AND DISTRIBUTION↗

NASA NTRS1980

Active flutter suppression using Linear Quadratic Gaussian theory

This paper describes the application of Linear Quadratic Gaussian (LQG) methodology to the design of active control systems for suppression of aerodynamic flutter. A full-size wind tunnel model of a supercritical wing with associated sensors and actuators comprises the system to be controlled. Results of a synthesis methodology that provide small values of rms response, insensitivity to flight condition, and robust stability are presented. Results of control surface and sensor position optimization are also presented. Both frequency response matching and residualization are used to obtain practical flutter controllers.

Mahesh, J. K.↗

DOE OSTI2014

Optimization of the pyrolysis process of empty fruit bunch (EFB) in a fixed-bed reactor through a central composite design (CCD)

The production of crude palm oil from the processing of palm fresh fruit bunches in the palm oil mills in Malaysia hs resulted in a huge quantity of empty fruit bunch (EFB) accumulated. The EFB was used as a feedstock in the pyrolysis process using a fixed-bed reactor in the present study. The optimization of process parameters such as pyrolysis temperature (factor A), biomass particle size (factor B) and holding time (factor C) were investigated through Central Composite Design (CCD) using Stat-Ease Design Expert software version 7 with bio-oil yield considered as the response. Twenty experimental runs were conducted. The results were completely analyzed by Analysis of Variance (ANOVA). The model was statistically significant. All factors studied were significant with p-values < 0.05. The pyrolysis temperature (factor A) was considered as the most significant parameter because its F-value of 116.29 was the highest. The value of R{sup 2} was 0.9564 which indicated that the selected factors and its levels showed high correlation to the production of bio-oil from EFB pyrolysis process. A quadratic model equation was developed and employed to predict the highest theoretical bio-oil yield. The maximum bio-oil yield of 46.2 % was achieved at pyrolysis temperature of 442.15 °C using the EFB particle size of 866 μm which corresponded to the EFB particle size in the range of 710–1000 μm and holding time of 483 seconds.

42 ENGINEERING↗

DOE OSTI2013

Dose-shaping using targeted sparse optimization

Purpose: Dose volume histograms (DVHs) are common tools in radiation therapy treatment planning to characterize plan quality. As statistical metrics, DVHs provide a compact summary of the underlying plan at the cost of losing spatial information: the same or similar dose-volume histograms can arise from substantially different spatial dose maps. This is exactly the reason why physicians and physicists scrutinize dose maps even after they satisfy all DVH endpoints numerically. However, up to this point, little has been done to control spatial phenomena, such as the spatial distribution of hot spots, which has significant clinical implications. To this end, the authors propose a novel objective function that enables a more direct tradeoff between target coverage, organ-sparing, and planning target volume (PTV) homogeneity, and presents our findings from four prostate cases, a pancreas case, and a head-and-neck case to illustrate the advantages and general applicability of our method.Methods: In designing the energy minimization objective (E{sub tot}{sup sparse}), the authors utilized the following robust cost functions: (1) an asymmetric linear well function to allow differential penalties for underdose, relaxation of prescription dose, and overdose in the PTV; (2) a two-piece linear function to heavily penalize high dose and mildly penalize low and intermediate dose in organs-at risk (OARs); and (3) a total variation energy, i.e., the L{sub 1} norm applied to the first-order approximation of the dose gradient in the PTV. By minimizing a weighted sum of these robust costs, general conformity to dose prescription and dose-gradient prescription is achieved while encouraging prescription violations to follow a Laplace distribution. In contrast, conventional quadratic objectives are associated with a Gaussian distribution of violations, which is less forgiving to large violations of prescription than the Laplace distribution. As a result, the proposed objective E{sub tot}{sup sparse} improves tradeoff between planning goals by 'sacrificing' voxels that have already been violated to improve PTV coverage, PTV homogeneity, and/or OAR-sparing. In doing so, overall plan quality is increased since these large violations only arise if a net reduction in E{sub tot}{sup sparse} occurs as a result. For example, large violations to dose prescription in the PTV in E{sub tot}{sup sparse}-optimized plans will naturally localize to voxels in and around PTV-OAR overlaps where OAR-sparing may be increased without compromising target coverage. The authors compared the results of our method and the corresponding clinical plans using analyses of DVH plots, dose maps, and two quantitative metrics that quantify PTV homogeneity and overdose. These metrics do not penalize underdose since E{sub tot}{sup sparse}-optimized plans were planned such that their target coverage was similar or better than that of the clinical plans. Finally, plan deliverability was assessed with the 2D modulation index.Results: The proposed method was implemented using IBM's CPLEX optimization package (ILOG CPLEX, Sunnyvale, CA) and required 1-4 min to solve with a 12-core Intel i7 processor. In the testing procedure, the authors optimized for several points on the Pareto surface of four 7-field 6MV prostate cases that were optimized for different levels of PTV homogeneity and OAR-sparing. The generated results were compared against each other and the clinical plan by analyzing their DVH plots and dose maps. After developing intuition by planning the four prostate cases, which had relatively few tradeoffs, the authors applied our method to a 7-field 6 MV pancreas case and a 9-field 6MV head-and-neck case to test the potential impact of our method on more challenging cases. The authors found that our formulation: (1) provided excellent flexibility for balancing OAR-sparing with PTV homogeneity; and (2) permitted the dose planner more control over the evolution of the PTV's spatial dose distribution than conventional objective functions. In particular, E{sub tot}{sup sparse}-optimized plans for the pancreas case and head-and-neck case exhibited substantially improved sparing of the spinal cord and parotid glands, respectively, while maintaining or improving sparing for other OARs and markedly improving PTV homogeneity. Plan deliverability for E{sub tot}{sup sparse}-optimized plans was shown to be better than their associated clinical plans, according to the two-dimensional modulation index.Conclusions: These results suggest that our formulation may be used to improve dose-shaping and OAR-sparing for complicated disease sites, such as the pancreas or head and neck. Furthermore, our objective function and constraints are linear and constitute a linear program, which converges to the global minimum quickly, and can be easily implemented in treatment planning software. Thus, the authors expect fast translation of our method to the clinic where it may have a positive impact on plan quality for challenging disease sites.

61 RADIATION PROTECTION AND DOSIMETRY↗

DOE OSTI2015

The compressed state Kalman filter for nonlinear state estimation: Application to large-scale reservoir monitoring

Reservoir monitoring aims to provide snapshots of reservoir conditions and their uncertainties to assist operation management and risk analysis. These snapshots may contain millions of state variables, e.g., pressures and saturations, which can be estimated by assimilating data in real time using the Kalman filter (KF). However, the KF has a computational cost that scales quadratically with the number of unknowns, m, due to the cost of computing and storing the covariance and Jacobian matrices, along with their prod-ucts. The compressed state Kalman filter (CSKF) adapts the KF for solving large-scale monitoring problems. The CSKF uses N preselected orthogonal bases to compute an accurate rank-N approximation of the covari-ance that is close to the optimal spectral approximation given by SVD. The CSKF has a computational cost that scales linearly in m and uses an efficient matrix-free approach that propagates uncertainties using N + 1 forward model evaluations, where N << m. Here in this paper we present a generalized CSKF algorithm for nonlin-ear state estimation problems such as CO 2 monitoring. For simultaneous estimation of multiple types of state variables, the algorithm allows selecting bases that represent the variability of each state type. Through synthetic numerical experiments of CO 2 monitoring, we show that the CSKF can reproduce the Kal-man gain accurately even for large compression ratios (m/N). For a given computational cost, the CSKF uses a robust and flexible compression scheme that gives more reliable uncertainty estimates than the ensemble Kalman filter, which may display loss of ensemble variability leading to suboptimal uncertainty estimates.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1994

Discretized energy minimization in a wave guide with point sources

An anti-noise problem on a finite time interval is solved by minimization of a quadratic functional on the Hilbert space of square integrable controls. To this end, the one-dimensional wave equation with point sources and pointwise reflecting boundary conditions is decomposed into a system for the two propagating components of waves. Wellposedness of this system is proved for a class of data that includes piecewise linear initial conditions and piecewise constant forcing functions. It is shown that for such data the optimal piecewise constant control is the solution of a sparse linear system. Methods for its computational treatment are presented as well as examples of their applicability. The convergence of discrete approximations to the general optimization problem is demonstrated by finite element methods.

Propst, G.↗

NASA NTRS2010

Methods of Optimizing X-Ray Optical Prescriptions for Wide-Field Applications

We are working on the development of a method for optimizing wide-field x-ray telescope mirror prescriptions, including polynomial coefficients, mirror shell relative displacements, and (assuming 4 focal plane detectors) detector placement and tilt that does not require a search through the multi-dimensional parameter space. Under the assumption that the parameters are small enough that second order expansions are valid, we show that the performance at the detector surface can be expressed as a quadratic function of the parameters with numerical coefficients derived from a ray trace through the underlying Wolter I optic. The best values for the parameters are found by solving the linear system of equations creating by setting derivatives of this function with respect to each parameter to zero. We describe the present status of this development effort.

Elsner, R. F.↗

DOE OSTI2024

Quantum Bipolaron Superconductivity from Quadratic Electron-Phonon Coupling

When the electron-phonon coupling is quadratic in the phonon coordinates, electrons can pair to form bipolarons due to phonon zero-point fluctuations, a purely quantum effect. Here we study superconductivity originating from this pairing mechanism in a minimal model and reveal that, in the strong coupling regime, the critical temperature (T c ) is only mildly suppressed by the coupling strength, in stark contrast to the exponential suppression in linearly coupled systems, thus implying higher optimal T c values. We demonstrate that large coupling constants of this flavor are achieved in known materials such as perovskites, and discuss strategies to realize such superconductivity using superlattices.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗