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DOE OSTI2019

Calculating the Symmetry Number of Flexible Sphere Clusters

We present a theoretical and computational framework to compute the symmetry number of a flexible sphere cluster in R 3 , using a definition of symmetry that arises naturally when calculating the equilibrium probability of a cluster of spheres in the sticky-sphere limit. We define the sticky symmetry group of the cluster as the set of permutations and inversions of the spheres which preserve adjacency and can be realized by continuous deformations of the cluster that do not change the set of contacts or cause particles to overlap. The symmetry number is the size of the sticky symmetry group. We introduce a numerical algorithm to compute the sticky symmetry group and symmetry number, and show it works well on several test cases. Furthermore, we show that once the sticky symmetry group has been calculated for indistinguishable spheres, the symmetry group for partially distinguishable spheres (those with nonidentical interactions) can be efficiently obtained without repeating the laborious parts of the computations. Finally, we use our algorithm to calculate the partition functions of every possible connected cluster of six identical sticky spheres, generating data that may be used to design interactions between spheres so they self-assemble into a desired structure.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Equation-of-motion internally contracted multireference unitary coupled-cluster theory

The accurate computation of excited states remains a challenge in electronic structure theory, especially for systems with a ground state that requires a multireference treatment. In this work, we introduce a novel equation-of-motion (EOM) extension of the internally contracted multireference unitary coupled-cluster framework (ic-MRUCC), termed EOM-ic-MRUCC. EOM-ic-MRUCC follows the transform-then-diagonalize approach, in analogy to its non-unitary counterpart. By employing a projective approach to optimize the ground state, the method retains additive separability and proper scaling with system size. We show that excitation energies are size-intensive if the EOM operator satisfies the “killer” and the projective conditions. Furthermore, we propose to represent changes in the reference state upon electron excitation via projected many-body operators that span the active orbitals and show that the EOM equations formulated in this way are invariant with respect to active orbital rotations. We test the EOM-ic-MRUCC method truncated to single and double excitations by computing the potential energy curves for several excited states of a BeH2 model system, the HF molecule, and water undergoing symmetric dissociation. Across these systems, our method delivers accurate excitation energies and potential energy curves within 5 mE h (∼0.14 eV) from full configuration interaction. Here, we find that truncating the Baker–Campbell–Hausdorff series to fourfold commutators contributes negligible errors (on the order of 10 −5 E h or less), offering a practical route to highly accurate excited-state calculations with reduced computational overhead.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2015

Coarse-Grained Clustering Dynamics of Heterogeneously Coupled Neurons

The formation of oscillating phase clusters in a network of identical Hodgkin–Huxley neurons is studied, along with their dynamic behavior. The neurons are synaptically coupled in an all-to-all manner, yet the synaptic coupling characteristic time is heterogeneous across the connections. In a network of N neurons where this heterogeneity is characterized by a prescribed random variable, the oscillatory single-cluster state can transition—through (possibly perturbed) period-doubling and subsequent bifurcations—to a variety of multiple-cluster states. The clustering dynamic behavior is computationally studied both at the detailed and the coarse-grained levels, and a numerical approach that can enable studying the coarse-grained dynamics in a network of arbitrarily large size is suggested. Among a number of cluster states formed, double clusters, composed of nearly equal sub-network sizes are seen to be stable; interestingly, the heterogeneity parameter in each of the double-cluster components tends to be consistent with the random variable over the entire network: Given a double-cluster state, permuting the dynamical variables of the neurons can lead to a combinatorially large number of different, yet similar “fine” states that appear practically identical at the coarse-grained level. For weak heterogeneity we find that correlations rapidly develop, within each cluster, between the neuron’s “identity” (its own value of the heterogeneity parameter) and its dynamical state. For single- and double-cluster states we demonstrate an effective coarse-graining approach that uses the Polynomial Chaos expansion to succinctly describe the dynamics by these quickly established “identity-state” correlations. This coarse-graining approach is utilized, within the equation-free framework, to perform efficient computations of the neuron ensemble dynamics.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

FPDeep: Scalable Acceleration of CNN Training on Deeply-Pipelined FPGA Clusters

In this paper, we propose a framework called FPDeep, which uses a hybrid of model and layer paral- lelism to configure distributed reconfigurable clusters to train DNNs. This approach has numerous benefits. First, the design does not suffer from batch size growth. Second, novel workload and weight partitioning leads to balanced loads of both among nodes. And third, the entire system is fine-grained pipeline. This leads to high parallelism and utilization and also minimizes the time features need to be cached while waiting for back-propagation.

Wang, Tianqi↗

DOE OSTI2014

Parallel Optical Flow Processing of 4D Cardiac CT Data on Multicore Clusters, In: 2014 IEEE 17th International Conference on Computational Science and Engineering

Optical flow is the distribution of apparent velocities of movement of brightness patterns in a sequence of images. For large 3D image sequences, optical flow applications are time consuming and memory-bound. To cope with these problems, in this paper, we present parallel optical flow processing of 4D cardiac CT data on multicore cluster systems to significantly shorten the time for computing velocity fields of the heart in order to aid cardiologists in diagnosing heart disease such as myocardial infarction and cardiac dysrhythmia in time. First, we modify and extend two traditional 2D optical flow methods Horn-Schunck and Lucas-Kanade to three-dimensional cases to process the 4D cardiac CT data. Second, we extend Mat lab MPI to support parallel computing with Mat lab and Octave on these cluster systems. Then we develop the parallel Mat lab/Octave optical flow applications for the 4D cardiac CT data in detail. Our experimental results show that these parallel optical flow applications have good scalability with close to linear speedup, and are able to shorten the image processing time significantly from more than 5 hours on 4 cores to 1.5 minutes on 1024 cores.

Engineering↗

DOE OSTI2014

Evaluation of the Computing Systems for Yucca Mountain Repository TSPA-LA Model Operational Readiness

Sandia National Laboratories (SNL) was tasked to conduct an evaluation of the legacy computing systems of the now-closed Yucca Mountain Project (YMP) to maintain the operational readiness of the computing infrastructure (computer hardware and software) and knowledge capability for total system performance assessment (TSPA) type analysis, in the event that the License Application (LA) review by the U.S. Nuclear Regulatory Commission (NRC) is re-started and involves additional requests for information (RAIs). Six problem areas or components of the computing system were identified and subsequently resolved or improved to ensure the operational readiness of the TSPA-LA model capability on the server cluster. As part of this readiness review, the legacy TSPA computational cluster that was relocated from the SNL YMP Lead Lab Project Office in Las Vegas, Nevada to the SNL offices in Albuquerque, New Mexico was replaced with new hardware. Three floating licenses of Goldsim Version 9.60.300 were installed on the new cluster head node, and its distributed processing capability was mapped on the cluster processors. Other supporting software was tested and installed to support the TSPA- type analysis on the server cluster. TSPA-LA modeling cases were tested and verified for the model reproducibility on the current server cluster. All test runs were executed on multiple processors on the server cluster utilizing the Goldsim distributed processing capability, and all runs were completed successfully. The model reproducibility verification was evaluated by two approaches: numerical value comparison and graphical comparison, and the analysis demonstrated an excellent reproducibility of the TSPA-LA model runs on the server cluster. The current server cluster and supporting software systems are fully operational to support TSPA-LA type analysis.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

Toward the “platinum standard” of quantum chemistry on quantum computers: Perturbative quadruple corrections in unitary coupled cluster theory

We propose a non-iterative, post-hoc correction to the unitary coupled cluster theory with the single, double, and triple excitations (UCCSDT) Ansatz, which considers the leading-order effects of neglected quadruple excitations. We present two ways to derive this correction, henceforth referred to as [Q-6], which leads to an improvement in the correlation energy shown to be truncated to sixth-order in many-body perturbation theory. Furthermore, a comparison between the UCC-based [Q-6] correction proposed in this work and analogous, “platinum standard” quadruple corrections proposed in conventional coupled cluster theory recognizes that [Q-6] is distinct from prior corrections since it is constructed entirely from internally connected components. Although trotterized (t) and full operator variants of UCCSDT exhibit errors in scans of small molecule potential energy surfaces that routinely exceed 1.6 mH, we find that t/UCCSDT[Q-6] is, nevertheless, able to achieve chemical accuracy as measured by the mean unsigned error.

Correlation energy↗

DOE OSTI2020

Beyond Limber: efficient computation of angular power spectra for galaxy clustering and weak lensing

Angular two-point statistics of large-scale structure observables are important cosmological probes. To reach the high accuracy required by the statistical precision of future surveys, some of these statistics may need to be computed without the commonly employed Limber approximation; the exact computation however requires integration over Bessel functions, and a brute-force evaluation is slow to converge. Here, we present a new method based on our generalized FFTLog algorithm for the efficient computation of angular power spectra beyond the Limber approximation. The new method significantly simplifies the calculation and improves the numerical speed and stability. It is easily extended to handle integrals involving derivatives of Bessel functions, making it equally applicable to numerically more challenging cases such as contributions from redshift-space distortions and Doppler effects. We implement our method for galaxy clustering and galaxy-galaxy lensing power spectra. We find that using the Limber approximation for galaxy clustering in future analyses like LSST Year 1 and DES Year 6 may cause significant biases in cosmological parameters, indicating that going beyond the Limber approximation is necessary for these analyses.

weak gravitational lensing↗

DOE OSTI2020

Iron(III)–Oxo Cluster Chemistry with Dimethylarsinate Ligands: Structures, Magnetic Properties, and Computational Studies

A program has been initiated to develop Fe III /oxo cluster chemistry with the ‘pseudo-carboxylate’ ligand dimethylarsinate (Me 2 AsO 2 - ) for comparison with the well investigated Fe III /oxo/carboxylate cluster area. The synthesis and characterization of three polynuclear Fe III complexes are reported, [Fe 12 O 4 (O 2 C t Bu) 8 (O 2 AsMe 2 ) 17 (H 2 O) 3 ]Cl 3 (1), Na 2 [Fe 12 Na 2 O 4 (O 2 AsMe 2 ) 20 (NO 3 ) 6 (Me 2 AsO 2 H) 2 (H 2 O) 4 ](NO 3 ) 6 (2) and [Fe 3 (O 2 AsMe 2 ) 6 (Me 2 AsO 2 H) 2 (hqn) 2 ](NO 3 ) (3), where hqn is 8-hydroxyquinoline. The Fe 12 core of 1 is a type never previously encountered in Fe III carboxylate chemistry, consisting of two Fe 6 units each of which comprises two {Fe 3 (μ 3 -O 2- )} units bridged by three Me 2 AsO 2 - groups and linked into an Fe 12 loop structure by two anti-anti η 1 :η 1 :μ Me 2 AsO 2 - groups, a bridging mode extremely rare with carboxylates. 2 also consists of two Fe 6 units, differing in their ligation from those in 1, and this time linked together into a linear structure by a central {Na 2 (NO 3 ) 2 } bridging unit. 3 is a linear Fe 3 complex with no monoatomic bridges between Fe III ions, a very rare situation in Fe III chemistry with any ligands, and unprecedented in Fe carboxylate chemistry. The distinct differences observed in arsinate vs carboxylate ligation modes are rationalized largely based on the greater basicity of the former vs the latter. Variable-temperature dc and ac magnetic susceptibility data reveal all Fe 2 pairwise interactions to be antiferromagnetic. For 1 and 2, the different J ij couplings were estimated by use of a magnetostructural correlation for high nuclearity Fe III -oxo clusters and by density functional theory calculations using broken symmetry methods, allowing identification of their relative spin vector alignments and thus rationalization of their S = 0 ground states. The J ij values were then used as input values to give excellent fits of the experimental χM T vs T data. For 3, the fits of the experimental χM T vs T data to the Van Vleck equation or with PHI gave a very weak J 12 = -0.8(1) cm -1 (H = –2JŠ i ·Š j convention) between adjacent Fe III ions, and an S = 5/2 ground state. Furthermore, these initial Fe III arsinate complexes also provide structural parameters that help validate literature assignments of arsinate binding modes to iron oxide/hydroxide minerals as part of environmental concerns of using arsenic-containing herbicides in agriculture.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2006

PVM Enhancement for Beowulf Multiple-Processor Nodes

A recent version of the Parallel Virtual Machine (PVM) computer program has been enhanced to enable use of multiple processors in a single node of a Beowulf system (a cluster of personal computers that runs the Linux operating system). A previous version of PVM had been enhanced by addition of a software port, denoted BEOLIN, that enables the incorporation of a Beowulf system into a larger parallel processing system administered by PVM, as though the Beowulf system were a single computer in the larger system. BEOLIN spawns tasks on (that is, automatically assigns tasks to) individual nodes within the cluster. However, BEOLIN does not enable the use of multiple processors in a single node. The present enhancement adds support for a parameter in the PVM command line that enables the user to specify which Internet Protocol host address the code should use in communicating with other Beowulf nodes. This enhancement also provides for the case in which each node in a Beowulf system contains multiple processors. In this case, by making multiple references to a single node, the user can cause the software to spawn multiple tasks on the multiple processors in that node.

Springer, Paul↗

DOE OSTI2014

Region templates: Data representation and management for high-throughput image analysis

Compartment fires exhibit unique features associated with smoke accumulation and restricted air ventilation. The objective of the present study is to evaluate the ability of CFD-based fire models to simulate these features and in particular the effects of flame extinction that results from under-ventilated fire conditions. The study is performed using FireFOAM; FireFOAM is an advanced fire modeling software developed by FM Global and is based on a general-purpose open-source software called OpenFOAM. A new flame extinction model based on the concept of a critical value of the flame Damköhler number is incorporated into FireFOAM. The performance of the extinction model is evaluated via comparisons with a previously developed experimental database corresponding to a reduced-scale, heptane-fueled, compartment fire configuration. The numerical simulations also include a description of fuel evaporation driven by the computed gas-to-liquid heat feedback. Comparisons between experimental data and numerical results provide a suitable test bed to evaluate the ability of CFD-based fire models to describe the transition from over- to under-ventilated fire conditions, as well as the transition from extinction-free conditions to conditions in which the flame experiences partial or total quenching.

Energy & Fuels↗

DOE OSTI2015

Reproduction of the Yucca Mountain Project TSPA-LA Model Runs using TSPA Computing Systems

Sandia National Laboratories (SNL) conducted an evaluation of total system performance assessment (TSPA) related computing systems for the previously considered Yucca Mountain Project (YMP). This was done to maintain the operational readiness of the computing infrastructure (computer hardware and software) and knowledge capability for total system performance assessment (TSPA) type analysis, as directed by the National Nuclear Security Administration (NNSA), DOE 2010. This work is a continuation of the ongoing readiness evaluation reported in Lee and Hadgu (2014). The current work examined main components of the computing system identified in the previous work (Lee and Hadgu, 2014) to ensure the operational readiness of the TSPA-LA model capability on the server cluster. The TSPA computing hardware and storage system were replaced in late 2014 to maintain core capability and improve computation efficiency. One floating license of GoldSim Version 9.60.300 was installed on the upgraded cluster head node, and its distributed processing capability was mapped on the cluster processors. Other supporting software was tested and installed to support the TSPA-type analysis on the server cluster. All the TSPA-LA modeling cases were tested and verified for the model reproducibility on the upgraded 2014 server cluster (CL2014). All test runs were executed on multiple processors on the server cluster utilizing the GoldSim distributed processing capability, and all runs completed successfully. The model reproducibility verification was evaluated by two approaches: numerical value comparison and graphical comparison. The analysis demonstrated an excellent reproducibility of the TSPA-LA model runs on the upgraded server cluster. The 2014 server cluster and supporting software systems are fully operational to support TSPA- LA type analysis.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2015

Reproduction of the Yucca Mountain Project TSPA-LA Model Runs using TSPA Computing Systems

97 MATHEMATICS AND COMPUTING↗

NASA NTRS2013

Scheduling Operations for Massive Heterogeneous Clusters

High-performance computing (HPC) programming has become increasingly difficult with the advent of hybrid supercomputers consisting of multicore CPUs and accelerator boards such as the GPU. Manual tuning of software to achieve high performance on this type of machine has been performed by programmers. This is needlessly difficult and prone to being invalidated by new hardware, new software, or changes in the underlying code. A system was developed for task-based representation of programs, which when coupled with a scheduler and runtime system, allows for many benefits, including higher performance and utilization of computational resources, easier programming and porting, and adaptations of code during runtime. The system consists of a method of representing computer algorithms as a series of data-dependent tasks. The series forms a graph, which can be scheduled for execution on many nodes of a supercomputer efficiently by a computer algorithm. The schedule is executed by a dispatch component, which is tailored to understand all of the hardware types that may be available within the system. The scheduler is informed by a cluster mapping tool, which generates a topology of available resources and their strengths and communication costs. Software is decoupled from its hardware, which aids in porting to future architectures. A computer algorithm schedules all operations, which for systems of high complexity (i.e., most NASA codes), cannot be performed optimally by a human. The system aids in reducing repetitive code, such as communication code, and aids in the reduction of redundant code across projects. It adds new features to code automatically, such as recovering from a lost node or the ability to modify the code while running. In this project, the innovators at the time of this reporting intend to develop two distinct technologies that build upon each other and both of which serve as building blocks for more efficient HPC usage. First is the scheduling and dynamic execution framework, and the second is scalable linear algebra libraries that are built directly on the former.

Humphrey, John↗

DOE OSTI2022

Quantum annealing for jet clustering with thrust

Quantum computing holds the promise of substantially speeding up computationally expensive tasks, such as solving optimization problems over a large number of elements. In high-energy collider physics, quantum-assisted algorithms might accelerate the clustering of particles into jets. In this study, we benchmark quantum annealing strategies for jet clustering based on optimizing a quantity called “thrust” in electron-positron collision events. Here, we find that quantum annealing yields similar performance to exact classical approaches and classical heuristics, after tuning the annealing parameters. Without tuning, comparable performance can be obtained through a hybrid quantum/classical approach.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2020

SPIDERS: overview of the X-ray galaxy cluster follow-up and the final spectroscopic data release

ABSTRACT SPIDERS (The SPectroscopic IDentification of eROSITA Sources) is a large spectroscopic programme for X-ray selected galaxy clusters as part of the Sloan Digital Sky Survey-IV (SDSS-IV). We describe the final data set in the context of SDSS Data Release 16 (DR16): the survey overall characteristics, final targeting strategies, achieved completeness, and spectral quality, with special emphasis on its use as a galaxy cluster sample for cosmology applications. SPIDERS now consists of about 27 000 new optical spectra of galaxies selected within 4000 photometric red sequences, each associated with an X-ray source. The excellent spectrograph efficiency and a robust analysis pipeline yield a spectroscopic redshift measurement success rate exceeding 98 per cent, with a median velocity accuracy of 20 km s−1 (at z = 0.2). Using the catalogue of 2740 X-ray galaxy clusters confirmed with DR16 spectroscopy, we reveal the 3D map of the galaxy cluster distribution in the observable Universe up to z ∼ 0.6. We highlight the homogeneity of the member galaxy spectra among distinct regions of the galaxy cluster phase space. Aided by accurate spectroscopic redshifts and by a model of the sample selection effects, we compute the galaxy cluster X-ray luminosity function and we present its lack of evolution up to z = 0.6. Finally we discuss the prospects of forthcoming large multiplexed spectroscopic programmes dedicated to follow up the next generation of all-sky X-ray source catalogues.

Clerc, N.↗

DOE OSTI2017

BD-CATS-IO

Modern cosmology and plasma physics codes are now capable of simulating trillions of particles on petascale systems. Each timestep output from such simulations is on the order of 10s of TBs. Summarizing and visualizing raw particle data is challenging, and scientists often focus on density structures, whether in the real 3D space, or a high-dimensional phase space. In this work, code was developed for reading 10s of terabytes of data and for writing the resultant cluster IDs for each particle. This code will be part of a highly scalable version of the clustering algorithm DBSCAN, and apply it to the largest datasets produced by state-of-the-art codes. The overall function of BD-CATS (Big Data Clustering at Trillion Particles Scale) is to perform end-to-end analysis: loading the data, dynamic partitioning, computing kdtrees, performing clustering analysis, and storing the results. BD-CATS-IO provides the functionality of loading the data and storing the results.

Byna, Surendra↗

NASA NTRS2003

A Fast Implementation of the ISOCLUS Algorithm

Unsupervised clustering is a fundamental tool in numerous image processing and remote sensing applications. For example, unsupervised clustering is often used to obtain vegetation maps of an area of interest. This approach is useful when reliable training data are either scarce or expensive, and when relatively little a priori information about the data is available. Unsupervised clustering methods play a significant role in the pursuit of unsupervised classification. One of the most popular and widely used clustering schemes for remote sensing applications is the ISOCLUS algorithm, which is based on the ISODATA method. The algorithm is given a set of n data points (or samples) in d-dimensional space, an integer k indicating the initial number of clusters, and a number of additional parameters. The general goal is to compute a set of cluster centers in d-space. Although there is no specific optimization criterion, the algorithm is similar in spirit to the well known k-means clustering method in which the objective is to minimize the average squared distance of each point to its nearest center, called the average distortion. One significant feature of ISOCLUS over k-means is that clusters may be merged or split, and so the final number of clusters may be different from the number k supplied as part of the input. This algorithm will be described in later in this paper. The ISOCLUS algorithm can run very slowly, particularly on large data sets. Given its wide use in remote sensing, its efficient computation is an important goal. We have developed a fast implementation of the ISOCLUS algorithm. Our improvement is based on a recent acceleration to the k-means algorithm, the filtering algorithm, by Kanungo et al.. They showed that, by storing the data in a kd-tree, it was possible to significantly reduce the running time of k-means. We have adapted this method for the ISOCLUS algorithm. For technical reasons, which are explained later, it is necessary to make a minor modification to the ISOCLUS specification. We provide empirical evidence, on both synthetic and Landsat image data sets, that our algorithm's performance is essentially the same as that of ISOCLUS, but with significantly lower running times. We show that our algorithm runs from 3 to 30 times faster than a straightforward implementation of ISOCLUS. Our adaptation of the filtering algorithm involves the efficient computation of a number of cluster statistics that are needed for ISOCLUS, but not for k-means.

Memarsadeghi, Nargess↗