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At least 559 records · Page 31
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Evaluating the Use of Foundational Chemical Language Models in Multimodal Graph Fusion

Rapid and accurate prediction of the physicochemical properties of molecules given their structures remains a key challenge in cheminformatics. Machine learning approaches offer high-throughput options, but the optimality of inductive biases and data representations are up for debate. For example, BERT-based masked language models (MLMs) can be trained in a self-supervised way on hundreds of millions to billions of readily available SMILES strings. Another option is graph neural networks (GNNs), which can operate directly on molecular structures. Yet, generating accurate molecular geometry is computationally expensive, leading to a relative scarcity in data compared to SMILES strings. It is attractive to combine these two paradigms by pre-training an LM on a large corpus of SMILES strings and embedding these representation into a geometric graph neural network. Despite the promise of such an approach, and contrary to previous studies, we find mixed results with the combination of the LMs and GNNs on several molecule datasets. In particular, we found evidence for improvement on the FreeSolv and QM7 benchmarks, but degraded performance on the ESOL, LIPO and QM9 datasets compared to a GNN baseline.

Francel, Collin [University of Alabama]↗
NASA NTRS2000

Testing New Programming Paradigms with NAS Parallel Benchmarks

Over the past decade, high performance computing has evolved rapidly, not only in hardware architectures but also with increasing complexity of real applications. Technologies have been developing to aim at scaling up to thousands of processors on both distributed and shared memory systems. Development of parallel programs on these computers is always a challenging task. Today, writing parallel programs with message passing (e.g. MPI) is the most popular way of achieving scalability and high performance. However, writing message passing programs is difficult and error prone. Recent years new effort has been made in defining new parallel programming paradigms. The best examples are: HPF (based on data parallelism) and OpenMP (based on shared memory parallelism). Both provide simple and clear extensions to sequential programs, thus greatly simplify the tedious tasks encountered in writing message passing programs. HPF is independent of memory hierarchy, however, due to the immaturity of compiler technology its performance is still questionable. Although use of parallel compiler directives is not new, OpenMP offers a portable solution in the shared-memory domain. Another important development involves the tremendous progress in the internet and its associated technology. Although still in its infancy, Java promisses portability in a heterogeneous environment and offers possibility to "compile once and run anywhere." In light of testing these new technologies, we implemented new parallel versions of the NAS Parallel Benchmarks (NPBs) with HPF and OpenMP directives, and extended the work with Java and Java-threads. The purpose of this study is to examine the effectiveness of alternative programming paradigms. NPBs consist of five kernels and three simulated applications that mimic the computation and data movement of large scale computational fluid dynamics (CFD) applications. We started with the serial version included in NPB2.3. Optimization of memory and cache usage was applied to several benchmarks, noticeably BT and SP, resulting in better sequential performance. In order to overcome the lack of an HPF performance model and guide the development of the HPF codes, we employed an empirical performance model for several primitives found in the benchmarks. We encountered a few limitations of HPF, such as lack of supporting the "REDISTRIBUTION" directive and no easy way to handle irregular computation. The parallelization with OpenMP directives was done at the outer-most loop level to achieve the largest granularity. The performance of six HPF and OpenMP benchmarks is compared with their MPI counterparts for the Class-A problem size in the figure in next page. These results were obtained on an SGI Origin2000 (195MHz) with MIPSpro-f77 compiler 7.2.1 for OpenMP and MPI codes and PGI pghpf-2.4.3 compiler with MPI interface for HPF programs.

Jin, H.↗
DOE OSTI2022

IER-501 CED-3b: Experiment Execution Summary for the Pulsed-Neutron Die-Away Experimental Testbed for Thermal Scattering Law Benchmarks (PNDA)

This report summarizes the experiments performed for IER-501, a testbed for pulsed-neutron die-away (PNDA) experiments at Lawrence Livermore National Laboratory (LLNL). The PNDA experiments were conducted in two separate two-day campaigns: one campaign for high-density polyethylene and another for Lucite. All experiments were performed at LLNL. They will become high-quality benchmarks that serve to optimize and validate thermal neutron scattering laws (TSLs), which are high-priority nuclear data for the Department of Energy’s Nuclear Criticality Safety Program (NCSP). The report presents the PNDA design and its equipment, and it documents the experimental die-away curves. It presents the characterization measurements that have been performed to-date. Importantly, mass spectrometry measurements to determine sample impurities were not yet completed. These will be included in the final benchmark. The report gives the fitted decay constants for the die-away curves of each target sample. It also provides the data for the die-away curves in the appendices. The HDPE experiments examined twelve targets of varying size. The Lucite measurements included ten targets of varying size.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

MP-ALOE: an r2SCAN dataset for universal machine learning interatomic potentials

We present MP-ALOE, a dataset of nearly 1 million DFT calculations using the accurate r2SCAN meta-generalized gradient approximation. Covering 89 elements, MP-ALOE was created using active learning and primarily consists of off-equilibrium structures. We benchmark a machine learning interatomic potential trained on MP-ALOE, and evaluate its performance on a series of benchmarks, including predicting the thermochemical properties of equilibrium structures; predicting forces of far-from-equilibrium structures; maintaining physical soundness under static extreme deformations; and molecular dynamic stability under extreme temperatures and pressures. MP-ALOE shows strong performance on all of these benchmarks and is made public for the broader community to utilize.

Kuner, Matthew C↗
DOE OSTI2023

An extensive assessment of the performance of pairwise and many-body interaction potentials in reproducing ab initio benchmark binding energies for water clusters n = 2–25

We assess the performance of 7 pairwise additive (TIP3P, TIP4P, TIP4P-ice, TIP5P, OPC, SPC, SPC/E) and 8 families of many-body potentials (q-AQUA, HIPPO, AMOEBA, EFP, TTM, WHBB, MB-pol, MB-UCB) in reproducing high-level ab initio benchmark values, CCSD(T) or MP2 at the complete basis set (CBS) limit for the binding energy and the many-body expansion (MBE) of water clusters n = 2–11, 16–17, 20, 25. By including a large range of cluster sizes having dissimilar hydrogen bonding networks, we obtain an understanding of how these potentials perform for different hydrogen bonding arrangements that are mostly outside of their parameterization range. While it is appropriate to compare the results of ab initio based many-body potentials directly to the electronic binding energies (D e 's), the pairwise additive ones are compared to the enthalpies at T = 298 K, ΔH(298 K), as the latter class of force fields are parametrized to reproduce enthalpies (implicitly accounting for zero-point energy corrections) rather than binding energies. We find that all pairwise additive potentials considered overestimate the reference ΔH values for the n = 2–25 clusters by >13%. For the water dimer (n = 2) in particular, the errors are in the range 83–119% for the pairwise additive potentials studied since these are based on an effective rather than the true 2-body interaction specifically designed as a means of partially accounting for the missing many-body terms. This stronger 2-body interaction is achieved by an enhanced monomer dipole moment that mimics its increase from the gas phase monomer to the condensed phase value. Indeed, for cluster sizes n ≥ 4 the percent deviations become slightly smaller (albeit all exceeding 13%). In contrast, we find that the many-body potentials perform more accurately in reproducing the electronic binding energies (D e 's) throughout the entire cluster range (n = 2–25), all reproducing the ab initio benchmark binding energies within ±7% of the respective CBS values. We further assess the ability of a subset of the many-body potentials (MB-UCB, q-AQUA, MB-pol, and TTM2.1-F) to also reproduce the magnitude of the ab initio many-body energy terms for water cluster sizes n = 7, 10, 16 and 17. The potentials show an overall good agreement with the available benchmark values. However, we identify characteristic differences upon comparing the many-body terms at both the ab initio-optimized geometries and the respective potential-optimized geometries to the reference ab initio values. Additionally, by applying this analysis to a wide range of cluster sizes, trends in the MBE of the potentials with increasing cluster size can be identified. Finally, in an attempt to draw a parallel between the pairwise additive and many-body potentials, we report the analysis of the individual molecular dipole moments for water clusters with 1 to ~4 solvation shells with the TTM2.1-F potential. We find that the internally solvated water molecules have in general a larger molecular dipole moment ranging from 2.6–3.0 D. This justifies the use of an enhanced, with respect to the gas-phase value, molecular dipole moment for the pairwise additive potentials, which is intended to fold in the many body terms into an effective (enhanced) pairwise interaction through the choice of the charges. These results have important implications for the development of future generations of efficient, transferable, and highly accurate classical interaction potentials in both the pairwise additive and many-body categories.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2003

Performance Characteristics of the Multi-Zone NAS Parallel Benchmarks

We describe a new suite of computational benchmarks that models applications featuring multiple levels of parallelism. Such parallelism is often available in realistic flow computations on systems of grids, but had not previously been captured in bench-marks. The new suite, named NPB Multi-Zone, is extended from the NAS Parallel Benchmarks suite, and involves solving the application benchmarks LU, BT and SP on collections of loosely coupled discretization meshes. The solutions on the meshes are updated independently, but after each time step they exchange boundary value information. This strategy provides relatively easily exploitable coarse-grain parallelism between meshes. Three reference implementations are available: one serial, one hybrid using the Message Passing Interface (MPI) and OpenMP, and another hybrid using a shared memory multi-level programming model (SMP+OpenMP). We examine the effectiveness of hybrid parallelization paradigms in these implementations on three different parallel computers. We also use an empirical formula to investigate the performance characteristics of the multi-zone benchmarks.

Jin, Haoqiang↗
NASA NTRS1983

VTOL shipboard letdown guidance system analysis

Alternative letdown guidance strategies are examined for landing of a VTOL aircraft onboard a small aviation ship under adverse environmental conditions. Off line computer simulation of shipboard landing task is utilized for assessing the relative merits of the proposed guidance schemes. The touchdown performance of a nominal constant rate of descent (CROD) letdown strategy serves as a benchmark for ranking the performance of the alternative letdown schemes. Analysis of ship motion time histories indicates the existence of an alternating sequence of quiescent and rough motions called lulls and swells. A real time algorithms lull/swell classification based upon ship motion pattern features is developed. The classification algorithm is used to command a go/no go signal to indicate the initiation and termination of an acceptable landing window. Simulation results show that such a go/no go pattern based letdown guidance strategy improves touchdown performance.

Phatak, A. V.↗
NASA NTRS1994

High Performance Programming Using Explicit Shared Memory Model on Cray T3D1

The Cray T3D system is the first-phase system in Cray Research, Inc.'s (CRI) three-phase massively parallel processing (MPP) program. This system features a heterogeneous architecture that closely couples DEC's Alpha microprocessors and CRI's parallel-vector technology, i.e., the Cray Y-MP and Cray C90. An overview of the Cray T3D hardware and available programming models is presented. Under Cray Research adaptive Fortran (CRAFT) model four programming methods (data parallel, work sharing, message-passing using PVM, and explicit shared memory model) are available to the users. However, at this time data parallel and work sharing programming models are not available to the user community. The differences between standard PVM and CRI's PVM are highlighted with performance measurements such as latencies and communication bandwidths. We have found that the performance of neither standard PVM nor CRI s PVM exploits the hardware capabilities of the T3D. The reasons for the bad performance of PVM as a native message-passing library are presented. This is illustrated by the performance of NAS Parallel Benchmarks (NPB) programmed in explicit shared memory model on Cray T3D. In general, the performance of standard PVM is about 4 to 5 times less than obtained by using explicit shared memory model. This degradation in performance is also seen on CM-5 where the performance of applications using native message-passing library CMMD on CM-5 is also about 4 to 5 times less than using data parallel methods. The issues involved (such as barriers, synchronization, invalidating data cache, aligning data cache etc.) while programming in explicit shared memory model are discussed. Comparative performance of NPB using explicit shared memory programming model on the Cray T3D and other highly parallel systems such as the TMC CM-5, Intel Paragon, Cray C90, IBM-SP1, etc. is presented.

Simon, Horst D.↗
NASA NTRS2000

Performance Monitoring of Distributed Data Processing Systems

Test and checkout systems are essential components in ensuring safety and reliability of aircraft and related systems for space missions. A variety of systems, developed over several years, are in use at the NASA/KSC. Many of these systems are configured as distributed data processing systems with the functionality spread over several multiprocessor nodes interconnected through networks. To be cost-effective, a system should take the least amount of resource and perform a given testing task in the least amount of time. There are two aspects of performance evaluation: monitoring and benchmarking. While monitoring is valuable to system administrators in operating and maintaining, benchmarking is important in designing and upgrading computer-based systems. These two aspects of performance evaluation are the foci of this project. This paper first discusses various issues related to software, hardware, and hybrid performance monitoring as applicable to distributed systems, and specifically to the TCMS (Test Control and Monitoring System). Next, a comparison of several probing instructions are made to show that the hybrid monitoring technique developed by the NIST (National Institutes for Standards and Technology) is the least intrusive and takes only one-fourth of the time taken by software monitoring probes. In the rest of the paper, issues related to benchmarking a distributed system have been discussed and finally a prescription for developing a micro-benchmark for the TCMS has been provided.

Ojha, Anand K.↗
DOE OSTI2020

Evaluating three evapotranspiration estimates from model of different complexity over China using the ILAMB benchmarking system

The land surface models range in complexity of terrestrial evapotranspiration, yet it is unknown how model complexity translates to accuracy of modeled evapotranspiration estimates. Here, we use the International Land Model Benchmarking system to assess ET estimates from three models of varying complexity driven by the same forcing datasets: an earth system model, a terrestrial biosphere model, and a stand-alone ET model. The performance assessment includes both temporal and spatial evaluation, and different plant functional types across China. Our results indicate that the most complex model, an earth system model, performed best against the benchmarking datasets and metrics. Terrestrial biosphere model performed best in simulating inter-annual variability of ET, while earth system model performed best in simulating the seasonal cycle. The more complex models (earth system model and terrestrial biosphere model) perform better in forest, shrub and crop ecosystems, while the simpler model (stand-alone ET model) perform better in grass ecosystems. Our study demonstrates the impact of model complexity on ET estimates and highlights directions for future ET model improvements.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Thermal Neutron Scattering Law Benchmark and Validation at NCSU [Slides]

The presentation discusses how the NCSU graphite SDT ORELA experiment is under development as a benchmark. It discusses the testing of various ENDF/B-VII.1 and ENDF/B-VIII.0 graphite libraries that have been performed using the PROTEUS benchmark. The presentation demonstrates that the NSCU Polyethylene ENDF/B-VIII.0 TSL improves agreement with total cross section measurements. The presentation concludes by stating that the NCSU single crystal sapphire TSL library is based on realistic data.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
NASA NTRS1983

Ship motion pattern directed VTOL letdown guidance

This paper examines ship motion pattern directed letdown guidance strategies for landing a VTOL aircraft onboard a small aviation ship under adverse environmental conditions. Off-line computer simulation of the shipboard landing task is utilized for assessing the relative merits of the proposed guidance schemes. A sum of seventy sinusoids representation is used to model the ship motion time histories. The touchdown performance of a nonimal constant-rate-of-descent (CROD) letdown strategy serves as a benchmark for ranking the performance of the alternative letdown schemes.

Phatak, A. V.↗
DOE OSTI2025

Nuclear Data Adjustment for Nonlinear Applications in the OECD/NEA WPNCS SG14 Benchmark -- A Bayesian Inverse UQ-based Approach for Data Assimilation

The Organization for Economic Cooperation and Development (OECD) Working Party on Nuclear Criticality Safety (WPNCS) proposed a benchmark exercise to assess the performance of current nuclear data adjustment techniques applied to nonlinear applications and experiments with low correlation to applications. This work introduces Bayesian Inverse Uncertainty Quantification (IUQ) as a method for nuclear data adjustments in this benchmark, and compares IUQ to the more traditional methods of Generalized Linear Least Squares (GLLS) and Monte Carlo Bayes (MOCABA). Posterior predictions from IUQ showed agreement with GLLS and MOCABA for linear applications. When comparing GLLS, MOCABA, and IUQ posterior predictions to computed model responses using adjusted parameters, we observe that GLLS predictions fail to replicate computed response distributions for nonlinear applications, while MOCABA shows near agreement, and IUQ uses computed model responses directly. We also discuss observations on why experiments with low correlation to applications can be informative to nuclear data adjustments and identify some properties useful in selecting experiments for inclusion in nuclear data adjustment. Performance in this benchmark indicates potential for Bayesian IUQ in nuclear data adjustments.

FOS: Computer and information sciences↗
DOE OSTI2021

An Integrated High-performance Computing and Digital Real-time Simulation Testbed to Benchmark Closed-loop Load Shedding Algorithms in Power Systems

An integrated testbed using digital real-time simulator (DRTS) and a high-performance computing (HPC) cluster is presented here to compare speed and performance of computational schemes to mitigate time-critical issues in electric power systems. The first approach in this testbed validation is taken by running a set of closed-loop load shedding algorithms to compare and contrast two paradigms of arresting cascading failure propagation. Two algorithms involve solving DC and AC power flow model-based optimization problems to compute load shedding at different buses, while a model-based stochastic search using parallel computing provides a viable alternative. The algorithms are implemented in the DRTS-HPC testbed for the IEEE 14-bus benchmark transmission system. As a proof of the concept, simulation results are presented for implementation of closed-loop load-shedding algorithms for cascading failures in the DRTS-HPC testbed

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2020

Comparative study of Minnesota functionals performance on ferroelectric BaTiO 3 and PbTiO 3

Density functional theory based simulations are the leading tool for the computational investigation of ferroelectrics and the parametrization of their classical potentials. However, the predictions often depend strongly on the exchange correlation functional. The most popular choices, LDA and GGA, tend to underestimate or overestimate some structural, electric, and energy properties. These impede development of highly accurate classical potentials that extend the reach of first-principles simulations to finite temperatures and realistic sizes. In this work, we investigate the performance of recently developed Minnesota exchange correlation functionals on prototypical ferroelectrics BaTiO 3 , and PbTiO 3 , in comparison with some popular ones. We find that there exists strong correlation between predictions for some properties (tetragonality, phase energy difference, and polarization) by different functionals. Along the correlation line, we find a range of functionals (including some from the Minnesota suite) whose predictions fall in between those of LDA and GGA and, therefore, offer an improvement. A way to relatively rank functional performance with respect to chosen benchmarks is proposed and applied to identify the top performers for BaTiO 3 and PbTiO 3 . Here, the performance is found to be material dependent. Therefore, we propose that the performance assessment carried out in this work is employed to "screen" functionals prior to their use on ferroelectrics. Quick and computationally inexpensive, it is likely to lead to improved descriptions, especially for classical potential parametrization. The Minnesota functional suite is found to be suitable for this task.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Nuclear Data Adjustment for Nonlinear Applications in the OECD/NEA WPNCS SG14 Benchmark—A Bayesian Inverse UQ-Based Approach for Data Assimilation

The Organisation for Economic Co-operation and Development Working Party on Nuclear Criticality Safety has proposed a benchmark exercise to assess the performance of current nuclear data adjustment techniques applied to nonlinear applications and experiments with low correlation to applications. This work introduces Bayesian inverse uncertainty quantification (IUQ) employing scientific machine learning surrogate models as a method for nuclear data adjustments in this benchmark, and compares IUQ to the more traditional methods of generalized linear least squares (GLLS) and Monte Carlo Bayes (MOCABA). Posterior predictions from IUQ showed agreement with GLLS and MOCABA for linear applications. Here, when comparing GLLS, MOCABA, and IUQ posterior predictions to computed model responses using adjusted parameters, we observe that the GLLS predictions failed to replicate the computed response distributions for nonlinear applications, while MOCABA showed near agreement, and IUQ used the computed model responses directly. We also discuss observations on why experiments with low correlation to applications can be informative to nuclear data adjustments and identify some properties useful in selecting experiments for inclusion in nuclear data adjustment. Performance in this benchmark indicates potential for Bayesian IUQ in nuclear data adjustments.

Bayesian calibration↗