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Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla

Cultivation-independent surveys of microbial diversity have revealed many bacterial phyla that lack cultured representatives. These lineages, referred to as candidate phyla, have been detected across many environments. Here, we deeply sequenced microbial communities from acetate-stimulated aquifer sediment to recover the complete and essentially complete genomes of single representatives of the candidate phyla SR1, WWE3, TM7, and OD1. All four of these genomes are very small, 0.7 to 1.2 Mbp, and have large inventories of novel proteins. Additionally, all lack identifiable biosynthetic pathways for several key metabolites. The SR1 genome uses the UGA codon to encode glycine, and the same codon is very rare in the OD1 genome, suggesting that the OD1 organism could also transition to alternate coding. Interestingly, the relative abundance of the members of SR1 increased with the appearance of sulfide in groundwater, a pattern mirrored by a member of the phylum Tenericutes . All four genomes encode type IV pili, which may be involved in interorganism interaction. On the basis of these results and other recently published research, metabolic dependence on other organisms may be widely distributed across multiple bacterial candidate phyla. Few or no genomic sequences exist for members of the numerous bacterial phyla lacking cultivated representatives, making it difficult to assess their roles in the environment. This paper presents three complete and one essentially complete genomes of members of four candidate phyla, documents consistently small genome size, and predicts metabolic capabilities on the basis of gene content. These metagenomic analyses expand our view of a lifestyle apparently common across these candidate phyla.

59 BASIC BIOLOGICAL SCIENCES↗

Sparse triangular solves for ILU revisited: data layout crucial to better performance.; .

A key to good processor utilization for sparse matrix computations is storing the data in the format that is most conducive to fast access by the memory system. In particular, for sparse matrix triangular solves the traditional compressed sparse matrix format is poor, and minor adjustments to the data structure can increase the processor utilization dramatically. Such adjustments involve storing the L and U factors separately and storing the U rows 'backwards' so that they are accessed in a simple streaming fashion during the triangular solves. Changes to the PETSc libraries to use this modified storage format resulted in over twice the floating-point rate for some matrices. This improvement can be accounted for by a decrease in the cache misses and TLB (transaction lookaside buffer) misses in the modified code.

99 GENERAL AND MISCELLANEOUS↗

Application of adaptive hierarchical sparse grid collocation to the uncertainty quantification of nuclear reactor simulators

Recent efforts in the application of uncertainty quantification to nuclear systems have utilized methods based on generalized perturbation theory and stochastic sampling. While these methods have proven to be effective they both have major drawbacks that may impede further progress. A relatively new approach based on spectral elements for uncertainty quantification is applied in this paper to several problems in reactor simulation. Spectral methods based on collocation attempt to couple the approximation free nature of stochastic sampling methods with the determinism of generalized perturbation theory. The specific spectral method used in this paper employs both the Smolyak algorithm and adaptivity by using Newton-Cotes collocation points along with linear hat basis functions. Using this approach, a surrogate model for the outputs of a computer code is constructed hierarchically by adaptively refining the collocation grid until the interpolant is converged to a user-defined threshold. The method inherently fits into the framework of parallel computing and allows for the extraction of meaningful statistics and data that are not within reach of stochastic sampling and generalized perturbation theory. This paper aims to demonstrate the advantages of spectral methods-especially when compared to current methods used in reactor physics for uncertainty quantification-and to illustrate their full potential. (authors)

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

On a Simplified Approach to Achieve Parallel Performance and Portability Across CPU and GPU Architectures

This paper presents software advances to easily exploit computer architectures consisting of a multi-core CPU and CPU+GPU to accelerate diverse types of high-performance computing (HPC) applications using a single code implementation. The paper describes and demonstrates the performance of the open-source C++ matrix and array (MATAR) library that uniquely offers: (1) a straightforward syntax for programming productivity, (2) usable data structures for data-oriented programming (DOP) for performance, and (3) a simple interface to the open-source C++ Kokkos library for portability and memory management across CPUs and GPUs. The portability across architectures with a single code implementation is achieved by automatically switching between diverse fine-grained parallelism backends (e.g., CUDA, HIP, OpenMP, pthreads, etc.) at compile time. The MATAR library solves many longstanding challenges associated with easily writing software that can run in parallel on any computer architecture. This work benefits projects seeking to write new C++ codes while also addressing the challenges of quickly making existing Fortran codes performant and portable over modern computer architectures with minimal syntactical changes from Fortran to C++. We demonstrate the feasibility of readily writing new C++ codes and modernizing existing codes with MATAR to be performant, parallel, and portable across diverse computer architectures.

97 MATHEMATICS AND COMPUTING↗

Physics consistent machine learning framework for inverse modeling with applications to ICF capsule implosions

In high energy density physics (HEDP) and inertial confinement fusion (ICF), predictive modeling is complicated by uncertainty in parameters that characterize various aspects of the modeled system, such as those characterizing material properties, equation of state (EOS), opacities, and initial conditions. Typically, however, these parameters are not directly observable. What is observed instead is a time sequence of radiographic projections using X-rays. In this work, we define a set of sparse hydrodynamic features derived from the outgoing shock profile and outer material edge, which can be obtained from radiographic measurements, to directly infer such parameters. Our machine learning (ML)-based methodology involves a pipeline of two architectures, a radiograph-to-features network (R2FNet) and a features-to-parameters network (F2PNet), that are trained independently and later combined to approximate a posterior distribution for the parameters from radiographs. We show that the machine learning architectures are able to accurately infer initial conditions and EOS parameters, and that the estimated parameters can be used in a hydrodynamics code to obtain density fields, shocks, and material interfaces that satisfy thermodynamic and hydrodynamic consistency. Finally, we demonstrate that features resulting from an unknown EOS model can be successfully mapped onto parameters of a chosen analytical EOS model, implying that network predictions are learning physics, with a degree of invariance to the underlying choice of EOS model. To the best of our knowledge, our framework is the first demonstration of recovering both thermodynamic and hydrodynamic consistent density fields from noisy radiographs.

97 MATHEMATICS AND COMPUTING↗

SkyFACT: high-dimensional modeling of gamma-ray emission with adaptive templates and penalized likelihoods

We present SkyFACT (Sky Factorization with Adaptive Constrained Templates), a new approach for studying, modeling and decomposing diffuse gamma-ray emission. Like most previous analyses, the approach relies on predictions from cosmic-ray propagation codes like GALPROP and DRAGON. However, in contrast to previous approaches, we account for the fact that models are not perfect and allow for a very large number (∼> 10{sup 5}) of nuisance parameters to parameterize these imperfections. We combine methods of image reconstruction and adaptive spatio-spectral template regression in one coherent hybrid approach. To this end, we use penalized Poisson likelihood regression, with regularization functions that are motivated by the maximum entropy method. We introduce methods to efficiently handle the high dimensionality of the convex optimization problem as well as the associated semi-sparse covariance matrix, using the L-BFGS-B algorithm and Cholesky factorization. We test the method both on synthetic data as well as on gamma-ray emission from the inner Galaxy, |ℓ|<90{sup o} and | b |<20{sup o}, as observed by the Fermi Large Area Telescope. We finally define a simple reference model that removes most of the residual emission from the inner Galaxy, based on conventional diffuse emission components as well as components for the Fermi bubbles, the Fermi Galactic center excess, and extended sources along the Galactic disk. Variants of this reference model can serve as basis for future studies of diffuse emission in and outside the Galactic disk.

79 ASTRONOMY AND ASTROPHYSICS↗

Influence of Coronal Abundance Variations

The PI of this project was Jeff Scargle of NASA/Ames. Co-I's were Alma Connors of Eureka Scientific/Wellesley, and myself. Part of the work was subcontracted to Eureka Scientific via SAO, with Vinay Kashyap as PI. This project was originally assigned grant number NCC2-1206, and was later changed to NCC2-1350 for administrative reasons. The goal of the project was to obtain, derive, and develop statistical and data analysis tools that would be of use in the analyses of high-resolution, high-sensitivity data that are becoming available with new instruments. This is envisioned as a cross-disciplinary effort with a number of "collaborators" including some at SA0 (Aneta Siemiginowska, Peter Freeman) and at the Harvard Statistics department (David van Dyk, Rostislav Protassov, Xiao-li Meng, Epaminondas Sourlas, et al). We have developed a new tool to reliably measure the metallicities of thermal plasma. It is unfeasible to obtain high-resolution grating spectra for most stars, and one must make the best possible determination based on lower-resolution, CCD-type spectra. It has been noticed that most analyses of such spectra have resulted in measured metallicities that were significantly lower than when compared with analyses of high- resolution grating data where available (see, e.g., Brickhouse et al., 2000, ApJ 530,387). Such results have led to the proposal of the existence of so-called Metal Abundance Deficient, or "MAD" stars (e.g., Drake, J.J., 1996, Cool Stars 9, ASP Conf.Ser. 109, 203). We however find that much of these analyses may be systematically underestimating the metallicities, and using a newly developed method to correctly treat the low-counts regime at the high-energy tail of the stellar spectra (van Dyk et al. 2001, ApJ 548,224), have found that the metallicities of these stars are generally comparable to their photospheric values. The results were reported at the AAS (Sourlas, Yu, van Dyk, Kashyap, and Drake, 2000, BAAS 196, v32, #54.02), and at the conference on Statistical Challenges in Modem Astronomy (Sourlas, van Dyk, Kashyap, Drake, and Pease, 2003, SCMA 111, Eds. E.D.Feigelson, G.J.Babu, New York:Springer, p489-490). We also described the limitations of one of the most egregiously misused and misapplied statistical tests in astrophysical literature, the F-test for verifying model components (Protassov, van Dyk, Connors, Kashyap, and Siemiginowska, 2002, ApJ, 571,545). Indeed, a search through the ApJ archives turned up 170 papers in the 5 previous years that used the F-test explicitly in some form or the other, and with the vast majority of them not using it correctly! Indeed, looking at just 4 issues of the ApJ in 2001, we found 13 instances of its use, of which nine were demonstrably incorrect. Clearly, it is difficult to understate the importance of this issue. We also worked on speeding up Bayes Blocks and Sparse Bayes Blocks algorithms to make them more tractable for large searches. We also supported staistics students and postdocs in both explicit physics- model-based (spectra with tens of thousands of atomic lines) and "model-free" -- i.e. non-parametric or semi-parametric -- algorithms. Work on using more of the latter is just beginning; while using multi-scale methods for Poisson imaging has come to hition. In fact, "An Image Restoration Technique with Error Estimates", by D. Esch, A. Connors, M. Karovska, and D. van Dyk, was published by ApJ (Esch et a1.2004, ApJ, 610, 1213). The code has been delivered to M. Karovska for CXC; and is available for beta-testing upon request. The other large project we worked on was on the self-consistent modeling of logN-logs curves in the Poisson limit. logN-logs curves are a fundamental tool in the study of source populations, luminosity functions, and cosmological parameters. However, their determination is hampered by statistical effects such as the Eddington bias, incompleteness due to detection efficiency, faint source flux fluctuations, etc. We have develed a new and powerful method using the full Poisson machinery that allows us to model the logN-logs distribution of X-ray sources in a self-consistent manner. Because we properly account for all the above statistical effects, our modeling is valid over the full range of the data, and not just for strong sources, as is normally done. Using a Bayesian approach and modeling the fluxes with known functional forms such as simple or broken power-laws, and conditioning the expected photon counts on the fluxes, the background contamination, effective area, detector vignetting, and detection probability, we can delve deeply into the low counts regime and extend the usefulness of medium sensitivity surveys such as ChAMP by orders of magnitude. The built-in flexibility of the algorithm also allows a simultaneous analysis of multiple datasets. We have applied this analysis to a set a Chandra observations (Sourlas, Kashyap, Zezas, van Dyk, 2004, HEAD #8, #16.32)

Scargle, Jeffrey D.↗

NASA Tech Briefs, August 2005

Topics include: Hidden Identification on Parts: Magnetic Machine-Readable Matrix Symbols; System for Processing Coded OFDM Under Doppler and Fading; Multipurpose Hyperspectral Imaging System; Magnetic-Flux-Compensated Voltage Divider; High-Performance Satellite/Terrestrial-Network Gateway; Internet-Based System for Voice Communication With the ISS; Stripline/Microstrip Transition in Multilayer Circuit Board; Dual-Band Feed for a Microwave Reflector Antenna; Quadratic Programming for Allocating Control Effort; Range Process Simulation Tool; Simulator of Space Communication Networks; Computing Q-D Relationships for Storage of Rocket Fuels; Contour Error Map Algorithm; Portfolio Analysis Tool; Glass Frit Filters for Collecting Metal Oxide Nanoparticles; Anhydrous Proton-Conducting Membranes for Fuel Cells; Portable Electron-Beam Free-Form Fabrication System; Miniature Laboratory for Detecting Sparse Biomolecules; Multicompartment Liquid-Cooling/Warming Protective Garments; Laser Metrology for an Optical-Path-Length Modulator; PCM Passive Cooling System Containing Active Subsystems; Automated Electrostatics Environmental Chamber; Estimating Aeroheating of a 3D Body Using a 2D Flow Solver; Artificial Immune System for Recognizing Patterns; Computing the Thermodynamic State of a Cryogenic Fluid; Safety and Mission Assurance Performance Metric; Magnetic Control of Concentration Gradient in Microgravity; Avionics for a Small Robotic Inspection Spacecraft; and Simulation of Dynamics of a Flexible Miniature Airplane.

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NASA Tech Briefs, July 2012

Topics covered include: Instrument Suite for Vertical Characterization of the Ionosphere-Thermosphere System; Terahertz Radiation Heterodyne Detector Using Two-Dimensional Electron Gas in a GaN Heterostructure; Pattern Recognition Algorithm for High-Sensitivity Odorant Detection in Unknown Environments; Determining Performance Acceptability of Electrochemical Oxygen Sensors; Versatile Controller for Infrared Lamp and Heater Arrays; High-Speed Scanning Interferometer Using CMOS Image Sensor and FPGA Based on Multifrequency Phase-Tracking Detection; Ultra-Low-Power MEMS Selective Gas Sensors; Compact Receiver Front Ends for Submillimeter-Wave Applications; Dynamically Reconfigurable Systolic Array Accelerator; Blocking Losses With a Photon Counter; Motion-Capture-Enabled Software for Gestural Control of 3D Mod; Orbit Software Suite; CoNNeCT Baseband Processor Module Boot Code SoftWare (BCSW); Trajectory Software With Upper Atmosphere Model; ALSSAT Version 6.0; Employing a Grinding Technology to Assess the Microbial Density for Encapsulated Organisms; Demonstration of Minimally Machined Honeycomb Silicon Carbide Mirrors; Polyimide Aerogel Thin Films; Nanoengineered Thermal Materials Based on Carbon Nanotube Array Composites; Composite Laminate With Coefficient of Thermal Expansion Matching D263 Glass; Robust Tensioned Kevlar Suspension Design; Focal Plane Alignment Utilizing Optical CMM; Purifying, Separating, and Concentrating Cells From a Sample Low in Biomass; Virtual Ultrasound Guidance for Inexperienced Operators; Beat-to-Beat Blood Pressure Monitor; Non-Contact Conductivity Measurement for Automated Sample Processing Systems; An MSK Radar Waveform; Telescope Alignment From Sparsely Sampled Wavefront Measurements Over Pupil Subapertures; Method to Remove Particulate Matter from Dusty Gases at Low Pressures; Terahertz Quantum Cascade Laser With Efficient Coupling and Beam Profile; Measurement Via Optical Near-Nulling and Subaperture Stitching; 885-nm Pumped Ceramic Nd:YAG Master Oscillator Power Amplifier Laser System; Airborne Hyperspectral Imaging System; Heat Shield Employing Cured Thermal Protection Material Blocks Bonded in a Large-Cell Honeycomb Matrix; and Asymmetric Supercapacitor for Long-Duration Power Storage.

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O(N) Quantum Molecular Dynamics (QMD) Algorithms, Code Requirements, Release Notes, and Library Deployment

The Exascale Computing Project (ECP) Co-design Center for Particle Applications (CoPA) is addressing the challenges for particle applications to run on upcoming exascale computing architectures. This includes short- and long-range molecular dynamics (MD), particle-in-cell (PIC), and quantum molecular dynamics (QMD). This document addresses $\mathcal{O}(N)$ QMD. The goal of this CoPA team is to develop $\mathcal{O}(N)$ linear scaling methods for QMD optimized for new and next generation architectures. This will provide the capability to simulate larger systems and run for longer timeframes than is possible today. Focus is initially on the density matrix construction. This requires efficient matrix formats and linear algebra operations for distributed architectures. A significant reduction in the wallclock time for an MD timestep is necessary to achieve practical large scale QMD. Equally challenging is to develop scalable distributed implementations. This requires the exploration of efficient data formats (dense, sparse, etc.), data decomposition and distribution across compute nodes using block- and graph-based methods. Traditional programming models such as MPI/OpenMP, hybrid MPI/OpenMP/Accelerator, as well as asynchronous task-based models will be explored to achieve maximum parallelism. Parallelism at the level of a matrix operation, solver, and/or application needs to be explored to gain the most benefit on new and emerging architectures. This report serves as a “living document” of the additions and enhancements throughout the ECP CoPA project for $\mathcal{O}(N)$ QMD. The following sections address the applications we are working with, the quantum chemistry libraries (BML and PROGRESS), and our co-design exploration through the use of a proxy application.

36 MATERIALS SCIENCE↗

MO-FG-CAMPUS-IeP2-05: Feasibility Demonstration of High-Voltage Clinical CT and Impact On X-Ray Penetration Through Metal Objects

Purpose: To demonstrate the possibility and quantify the impact of operating a clinical CT scanner at exceptionally high x-ray tube voltage for better penetration through metal objects and facilitating metal artifact reduction. Methods: We categorize metal objects according to the data corruption severeness (level of distortion and complete photon starvation fraction). To demonstrate feasibility and investigate the impact of high voltage scanning we modified a commercial GE LightSpeed VCT scanner (generator and software) to enable CT scans with x-ray tube voltages as high as 175 kVp. A 20 cm diameter water phantom with two metal rods (10 mm stainless and 25 mm titanium) and a water phantom with realistic metal object (spine cage) were used to evaluate the data corruption and image artifacts in the absence of any algorithm correction. We also performed simulations to confirm our understanding of the transmitted photon levels through metal objects with different size and composition. Results: The reconstructed images at 175 kVp still have significant dark shading artifacts, as expected since no special scatter correction or beam hardening was performed but show substantially lower noise and photon starvation than at lower kVp due to better beam penetration. Analysis of the raw data shows that the photon starved data is reduced from over 4% at 140 kVp to below 0.2% at 175 kVp. The simulations indicate that for clinically relevant titanium and stainless objects a 175 kVp tube voltage effectively avoids photon starvation. Conclusion: The use of exceptionally high tube voltage on a clinical CT system is a practical and effective solution to avoid photon starvation caused by certain metal implants. Sparse and hybrid high-voltage protocols are being considered to maintain low patient dose. This opens the door to algorithmic physics-based corrections rather than treating the data as missing and relying on missing data algorithms. Some of the authors are employees of General Electric.

60 APPLIED LIFE SCIENCES↗

The FORCE: A portable parallel programming language supporting computational structural mechanics

This project supports the conversion of codes in Computational Structural Mechanics (CSM) to a parallel form which will efficiently exploit the computational power available from multiprocessors. The work is a part of a comprehensive, FORTRAN-based system to form a basis for a parallel version of the NICE/SPAR combination which will form the CSM Testbed. The software is macro-based and rests on the force methodology developed by the principal investigator in connection with an early scientific multiprocessor. Machine independence is an important characteristic of the system so that retargeting it to the Flex/32, or any other multiprocessor on which NICE/SPAR might be imnplemented, is well supported. The principal investigator has experience in producing parallel software for both full and sparse systems of linear equations using the force macros. Other researchers have used the Force in finite element programs. It has been possible to rapidly develop software which performs at maximum efficiency on a multiprocessor. The inherent machine independence of the system also means that the parallelization will not be limited to a specific multiprocessor.

Jordan, Harry F.↗

Parallel beamlet dose calculation via beamlet contexts in a distributed multi‐GPU framework

Purpose Dose calculation is one of the most computationally intensive, yet essential tasks in the treatment planning process. With the recent interest in automatic beam orientation and arc trajectory optimization techniques, there is a great need for more efficient model‐based dose calculation algorithms that can accommodate hundreds to thousands of beam candidates at once. Foundational work has shown the translation of dose calculation algorithms to graphical processing units ( GPU s), lending to remarkable gains in processing efficiency. But these methods provide parallelization of dose for only a single beamlet, serializing the calculation of multiple beamlets and under‐utilizing the potential of modern GPU s. In this paper, the authors propose a framework enabling parallel computation of many beamlet doses using a novel beamlet context transformation and further embed this approach in a scalable network of multi‐ GPU computational nodes. Methods The proposed context‐based transformation separates beamlet‐local density and TERMA into distinct beamlet contexts that independently provide sufficient data for beamlet dose calculation. Beamlet contexts are arranged in a composite context array with dosimetric isolation, and the context array is subjected to a GPU collapsed‐cone convolution superposition procedure, producing the set of beamlet‐specific dose distributions in a single pass. Dose from each context is converted to a sparse representation for efficient storage and retrieval during treatment plan optimization. The context radius is a new parameter permitting flexibility between the speed and fidelity of the dose calculation process. A distributed manager‐worker architecture is constructed around the context‐based GPU dose calculation approach supporting an arbitrary number of worker nodes and resident GPU s. Phantom experiments were executed to verify the accuracy of the context‐based approach compared to Monte Carlo and a reference CPU ‐ CCCS implementation for single beamlets and broad beams composed by addition of beamlets. Dose for representative 4 π beam sets was calculated in lung and prostate cases to compare its efficiency with that of an existing beamlet‐sequential GPU ‐ CCCS implementation. Code profiling was also performed to evaluate the scalability of the framework across many networked GPU s. Results The dosimetric accuracy of the context‐based method displays <1.35% and 2.35% average error from the existing serialized CPU ‐ CCCS algorithm and Monte Carlo simulation for beamlet‐specific PDD s in water and slab phantoms, respectively. The context‐based method demonstrates substantial speedup of up to two orders of magnitude over the beamlet‐sequential GPU ‐ CCCS method in the tested configurations. The context‐based framework demonstrates near linear scaling in the number of distributed compute nodes and GPU s employed, indicating that it is flexible enough to meet the performance requirements of most users by simply increasing the hardware utilization. Conclusions The context‐based approach demonstrates a new expectation of performance for beamlet‐based dose calculation methods. This approach has been successful in accelerating the dose calculation process for very large‐scale treatment planning problems ‐ such as automatic 4 π IMRT beam orientation and VMAT arc trajectory selection, with hundreds of thousands of beamlets ‐ in clinically feasible timeframes. The flexibility of this framework makes it as a strong candidate for use in a variety of other very large‐scale treatment planning tasks and clinical workflows.

Neph, Ryan↗

High-Performance Sparse Matrix-Matrix Products on Intel KNL and Multicore Architectures

Sparse matrix-matrix multiplication (SpGEMM) is a computational primitive that is vastly used in areas ranging from traditional numerical applications to recent big data analysis and machine learning. While many SpGEMM algorithms have been proposed, hardware specific optimizations for multi- and many-core processors are lacking and a detailed analysis of their performance under various use cases and matrices is not available. We firstly identify and mitigate multiple bottlenecks with memory management and thread scheduling on Intel Xeon Phi (Knights Landing or KNL). Specifically targeting multi- and many-core processors, we develop a hash-table-based algorithm and optimize a heap-based shared-memory SpGEMM algorithm. We investigate their performance together with other publicly available codes. Different from the literature, our evaluation also includes use cases that are representative of real graph algorithms, such as multi-source breadth-first search or triangle counting. Our hash-table and heap-based algorithms are showing significant speedups from libraries in the majority of the cases while different algorithms dominate the other scenarios with different matrix size, sparsity, compression factor and operation type. We wrap up in-depth evaluation results and make a recipe to give the best SpGEMM algorithm for target scenario. In conclusion, a critical finding is that hash-table-based SpGEMM gets a significant performance boost if the nonzeros are not required to be sorted within each row of the output matrix.

97 MATHEMATICS AND COMPUTING↗

Factorization in large-scale many-body calculations

One approach for solving interacting many-fermion systems is the configuration-interaction method, also sometimes called the interacting shell model, where one finds eigenvalues of the Hamiltonian in a many-body basis of Slater determinants (antisymmetrized products of single-particle wavefunctions). The resulting Hamiltonian matrix is typically very sparse, but for large systems the nonzero matrix elements can nonetheless require terabytes or more of storage. An alternate algorithm, applicable to a broad class of systems with symmetry, in our case rotational invariance, is to exactly factorize both the basis and the interaction using additive/multiplicative quantum numbers; such an algorithm recreates the many-body matrix elements on the fly and can reduce the storage requirements by an order of magnitude or more. Here, we discuss factorization in general and introduce a novel, generalized factorization method, essentially a ‘double-factorization’ which speeds up basis generation and set-up of required arrays. Although we emphasize techniques, we also place factorization in the context of a specific (unpublished) configuration-interaction code, BIGSTICK, which runs both on serial and parallel machines, and discuss the savings in memory due to factorization.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Ultrafast processing of pixel detector data with machine learning frameworks

Modern photon science performed at high repetition rate free-electron laser (FEL) facilities and beyond relies on 2D pixel detectors operating at increasing frequencies (towards 100 kHz at LCLS-II) and producing rapidly increasing amounts of data (towards TB/s). This data must be rapidly stored for offline analysis and summarized in real time for online feedback to the scientists. While at LCLS all raw data has been stored, at LCLS-II this would lead to a prohibitive cost; instead, enabling real time processing of pixel detector data (dark, gain, common mode, background, charge summing, subpixel position, photon counting, data summarization) allows reducing the size and cost of online processing, offline processing and storage by orders of magnitude while preserving full photon information. This could be achieved by taking advantage of the compressibility of sparse data typical for LCLS-II applications. Faced with a similar big data challenge a decade ago, computer vision stimulated revolutionary advances in machine learning hardware and software. We investigated if these developments are useful in the field of data processing for high speed pixel detectors and found that typical deep learning models and autoencoder architectures failed to yield useful noise reduction while preserving full photon information, presumably because of the very different statistics and feature sets in computer vision and radiation imaging. However, the raw performance of modern frameworks like Tensorflow inspired us to redesign in Tensorflow mathematically equivalent versions of the state-of-the-art, “classical” algorithms used at LCLS. The novel Tensorflow models resulted in elegant, compact and hardware agnostic code, gaining 1 to 2 orders of magnitude faster processing on an inexpensive consumer GPU, reducing by 3 orders of magnitude the projected cost of online analysis and compression without photon loss at LCLS-II. The novel Tensorflow models also enabled ongoing development of a pipelined hardware system expected to yield an additional 3 to 4 orders of magnitude speedup, necessary for meeting the data acquisition and storage requirements at LCLS-II, potentially enabling acquiring every single FEL pulse at full speed. Computer vision a decade ago was dominated by hand-crafted filters; their structure inspired the deep learning revolution resulting in modern deep convolutional networks; similarly, our novel Tensorflow filters provide inspiration for designing future deep learning models for ultrafast and efficient processing and classification of pixel detector images at FEL facilities.

47 OTHER INSTRUMENTATION↗

Bayesian differential programming for robust systems identification under uncertainty

This paper presents a machine learning framework for Bayesian systems identification from noisy, sparse and irregular observations of nonlinear dynamical systems. The proposed method takes advantage of recent developments in differentiable programming to propagate gradient information through ordinary differential equation solvers and perform Bayesian inference with respect to unknown model parameters using Hamiltonian Monte Carlo sampling. This allows an efficient inference of the posterior distributions over plausible models with quantified uncertainty, while the use of sparsity-promoting priors enables the discovery of interpretable and parsimonious representations for the underlying latent dynamics. A series of numerical studies is presented to demonstrate the effectiveness of the proposed methods, including nonlinear oscillators, predator–prey systems and examples from systems biology. Taken together, our findings put forth a flexible and robust workflow for data-driven model discovery under uncertainty. All codes and data accompanying this article are available at https://bit.ly/34FOJMj .

Science & Technology - Other Topics↗

A universal preconditioner for simulating condensed phase materials

We introduce a universal sparse preconditioner that accelerates geometry optimisation and saddle point search tasks that are common in the atomic scale simulation of materials. Our preconditioner is based on the neighbourhood structure and we demonstrate the gain in computational efficiency in a wide range of materials that include metals, insulators, and molecular solids. The simple structure of the preconditioner means that the gains can be realised in practice not only when using expensive electronic structure models but also for fast empirical potentials. Even for relatively small systems of a few hundred atoms, we observe speedups of a factor of two or more, and the gain grows with system size. An open source Python implementation within the Atomic Simulation Environment is available, offering interfaces to a wide range of atomistic codes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗