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At least 757 records · Page 42

Parallel accelerated vector similarity calculations for genomics applications

The surge in availability of genomic data holds promise for enabling determination of genetic causes of observed individual traits, with applications to problems such as discovery of the genetic roots of phenotypes, be they molecular phenotypes such as gene expression or metabolite concentrations, or complex phenotypes such as diseases. However, the growing sizes of these datasets and the quadratic, cubic or higher scaling characteristics of the relevant algorithms pose a serious computational challenge necessitating use of leadership scale computing. In this study we describe a new approach to performing vector similarity metrics calculations, suitable for parallel systems equipped with graphics processing units (GPUs) or Intel Xeon Phi processors. Our primary focus is the Proportional Similarity metric applied to Genome Wide Association Studies (GWAS) and Phenome Wide Association Studies (PheWAS). We describe the implementation of the algorithms on accelerated processors, methods used for eliminating redundant calculations due to symmetries, and techniques for efficient mapping of the calculations to many-node parallel systems. Finally, results are presented demonstrating high per-node performance and parallel scalability with rates of more than five quadrillion (5 × 10 15 ) elementwise comparisons achieved per second on the ORNL Titan system. In a companion paper we describe corresponding techniques applied to calculations of the Custom Correlation Coefficient for comparative genomics applications.

59 BASIC BIOLOGICAL SCIENCES↗

A high accuracy/resolution spectral element/Fourier–Galerkin method for the simulation of shoaling non-linear internal waves and turbulence in long domains with variable bathymetry

A high-order hybrid continuous-Galerkin numerical method, designed for the simulation of non-linear, non -hydrostatic internal waves and turbulence in long computational domains with complex bathymetry, is presented. The spatial discretization in the non-periodic wave-propagating directions, utilizes the nodal spectral element method. Such a high-order element-based discretization allows the highly accurate representation of complex domain geometry along with the flexibility of concentrating resolution in areas of interest. Under the assumption of the normal-to-isobath propagation of non-linear internal waves, a third periodic direction is incorporated via a Fourier-Galerkin discretization. The distinct non-hydrostatic nature of non-linear internal waves and, any instabilities and turbulence therein, necessitates the numerically challenging solution of the pressure Poisson problem. A defining feature of this work is the application of a domain decomposition approach, combined with block-Jacobi/deflation-based preconditioning to the pressure Poisson problem. Such a combined approach is particularly suitable for the long high aspect-ratio complex domains of interest and enables the efficient high-accuracy reproduction of the non-hydrostatic dynamics of non-linear internal waves. Implementation details are also described in the context of the stability of the solver and its parallelization strategy. A series of benchmarks of increasing complexity demonstrate the robustness of the flow solver. The benchmarks culminate with the three-dimensional simulation of a convectively breaking mode-one non-linear internal wave over a realistic South-China-Sea bathymetric transect and background current/stratification profiles.

Deflation↗

An in situ shearing x-ray measurement system for exploring structures and dynamics at the solid–liquid interface

Revealing interfacial structure and dynamics has been one of the essential thematic topics in material science and condensed matter physics. Synchrotron-based x-ray scattering techniques can deliver unique and insightful probing of interfacial structures and dynamics, in particular, in reflection geometries with higher surface and interfacial sensitivity than transmission geometries. We demonstrate the design and implementation of an in situ shearing x-ray measurement system, equipped with both inline parallel-plate and cone-and-plate shearing setups and operated at the advanced photon source at Argonne National Laboratory, to investigate the structures and dynamics of end-tethered polymers at the solid-liquid interface. With a precise lifting motor, a micrometer-scale gap can be produced by aligning two surfaces of a rotating upper shaft and a lower sample substrate. A torsional shear flow forms in the gap and applies tangential shear forces on the sample surface. The technical combination with nanoscale rheology and the utilization of in situ x-ray scattering allow us to gain fundamental insights into the complex dynamics in soft interfaces under shearing. In this work, we demonstrate the technical scope and experimental capability of the in situ shearing x-ray system through the measurements of charged polymers at both flat and curved interfaces upon shearing. Furthermore, through the in situ shearing x-ray scattering experiments integrated with theoretical simulations, we aim to develop a detailed understanding of the short-range molecular structure and mesoscale ionic aggregate morphology, as well as ion transport and dynamics in soft interfaces, thereby providing fundamental insight into a long-standing challenge in ionic polymer brushes with a significant technological impact.

36 MATERIALS SCIENCE↗

A signature of anisotropic cosmic-ray transport in the gamma-ray sky

A crucial process in Galactic cosmic-ray (CR) transport is the spatial diffusion due to the interaction with the interstellar turbulent magnetic field. Usually, CR diffusion is assumed to be uniform and isotropic all across the Galaxy. However, this picture is clearly inaccurate: several data-driven and theoretical arguments, as well as dedicated numerical simulations, show that diffusion exhibits highly anisotropic properties with respect to the direction of a background (ordered) magnetic field (i.e., parallel or perpendicular to it). In this paper we focus on a recently discovered anomaly in the hadronic CR spectrum inferred by the Fermi-LAT gamma-ray data at different positions in the Galaxy, i.e. the progressive hardening of the proton slope at low Galactocentric radii. We propose the idea that this feature can be interpreted as a signature of anisotropic diffusion in the complex Galactic magnetic field: in particular, the harder slope in the inner Galaxy is due, in our scenario, to the parallel diffusive escape along the poloidal component of the large-scale, regular, magnetic field. We implement this idea in a numerical framework, based on the DRAGON code, and perform detailed numerical tests on the accuracy of our setup. We discuss how the effect proposed depends on the relevant free parameters involved. Based on low-energy extrapolation of the few focused numerical simulations aimed at determining the scalings of the anisotropic diffusion coefficients, we finally present a set of plausible models that reproduce the behavior of the CR proton slopes inferred by gamma-ray data.

79 ASTRONOMY AND ASTROPHYSICS↗

Parallel k-means++ for Multiple Shared-Memory Architectures

In recent years k-means++ has become a popular initialization technique for improved k-means clustering. To date, most of the work done to improve its performance has involved parallelizing algorithms that are only approximations of k-means++. In this paper we present a parallelization of the exact k-means++ algorithm, with a proof of its correctness. We develop implementations for three distinct shared-memory architectures: multicore CPU, high performance GPU, and the massively multithreaded Cray XMT platform. We demonstrate the scalability of the algorithm on each platform. In addition we present a visual approach for showing which platform performed k-means++ the fastest for varying data sizes.

data clustering↗

Iterated Gauss-Seidel GMRES

The GMRES algorithm of Saad and Schultz [SIAM J. Sci. Stat. Comput., 7 (1986), pp. 856-869] is an iterative method for approximately solving linear systems Ax = b, with initial guess x0 and residual r0 = b Ax0. The algorithm employs the Arnoldi process to generate the Krylov basis vectors (the columns of Vk ). It is well known that this process can be viewed as a QR factorization of the matrix Bk = [r0, AVk] at each iteration. Despite an O (..epsilon..)..kappa.. (Bk ) loss of orthogonality, for unit roundoff ..epsilon..and condition number ..kappa.. , the modified Gram-Schmidt formulation was shown to be backward stable in the seminal paper by Paige et al. [SIAM J. Matrix Anal.Appl., 28 (2006), pp. 264-284]. We present an iterated Gauss-Seidel formulation of the GMRES algorithm (IGS-GMRES) based on the ideas of Ruhe [Linear Algebra Appl., 52 (1983), pp. 591-601] and Swirydowicz et al. [Numer. Linear Algebra Appl., 28 (2020), pp. 1-20]. IGS-GMRES maintains orthogonality to the level O (..epsilon..)..kappa.. (Bk ) or O (..epsilon..), depending on the choice of one or two iterations; for two Gauss-Seidel iterations, the computed Krylov basis vectors remain orthogonal to working accuracy and the smallest singular value of Vk remains close to one. The resulting GMRES method is thus backward stable. We show that IGS-GMRES can be implemented with only a single synchronization point per iteration, making it relevant to large-scale parallel computing environments. We also demonstrate that, unlike MGS-GMRES, in IGS-GMRES the relative Arnoldi residual corresponding to the computed approximate solution no longer stagnates above machine precision even for highly nonnormal systems.

Arnoldi-QR↗

Dynamic Modeling, Trajectory Optimization, and Linear Control of Cable-Driven Parallel Robots for Automated Panelized Building Retrofits

The construction industry faces a growing need for automation to reduce costs, improve accuracy and productivity, and address labor shortages. One area that stands to benefit significantly from automation is panelized prefabricated building envelope retrofits, which can improve a building’s energy efficiency in heating and cooling interior spaces. In this paper, we propose using cable-driven parallel robots (CDPRs), which can effectively lift and handle large objects, to install these panels. However, implementing CDPRs presents significant challenges because of their nonlinear dynamics, complex trajectory planning, and precise control requirements. To tackle these challenges, this work focuses on a new application of established control and trajectory optimization theories in a CDPR simulation of a building envelope retrofit under real-world conditions. We first model the dynamics of CDPRs, highlighting the critical role of damping in system behavior. Building on this dynamic model, we formulate a trajectory optimization problem to generate feasible and efficient motion plans for the robot under operational and environmental constraints. Given the high precision required in the construction industry, accurately tracking the optimized trajectory is essential. However, challenges such as partial observability and external vibrations complicate this task. To address these issues, a Linear Quadratic Gaussian control framework is applied, enabling the robot to track the optimized trajectories with precision. Simulation results show that the proposed controller enables precise end effector positioning with errors under 4 mm, even in the presence of external wind disturbances. Through comprehensive simulations, our approach allows for an in-depth exploration of the system’s nonlinear dynamics, trajectory optimization, and control strategies under controlled yet highly realistic conditions. The results demonstrate the feasibility of CDPRs for automating panel installation and provide insights into their practical deployment.

CDPR↗

Case Study: BESS Capacity Building for Malawi

To strengthen Malawi's national electricity grid and to enhance reliability, the government of Malawi and the Electricity Supply Corporation of Malawi are partnering with the Global Alliance for People and Planet to develop a 20-megawatt/30-megawatt-hour battery energy storage system at Kanengo, Malawi, expected to come online in 2026. In parallel, the Global Energy Alliance for People and Planet and the National Laboratory of the Rockies implemented a comprehensive technical capacity-building program to equip the Electricity Supply Corporation of Malawi, the Malawi Energy Regulatory Authority, and the Malawi University of Business and Applied Sciences with the expertise needed to plan, regulate, and operate advanced storage systems.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

High-Performance I/O: HDF5 for Lattice QCD

Practitioners of lattice QCD/QFT have been some of the primary pioneer users of the state-of-the-art high-performance-computing systems, and contribute towards the stress tests of such new machines as soon as they become available. As with all aspects of high-performance-computing, I/O is becoming an increasingly specialized component of these systems. In order to take advantage of the latest available high-performance I/O infrastructure, to ensure reliability and backwards compatibility of data files, and to help unify the data structures used in lattice codes, we have incorporated parallel HDF5 I/O into the SciDAC supported USQCD software stack. Here we present the design and implementation of this I/O framework. Our HDF5 implementation outperforms optimized QIO at the 10-20% level and leaves room for further improvement by utilizing appropriate dataset chunking.

97 MATHEMATICS AND COMPUTING↗

An Integrated Electrochemical Approach to the Precision Synthesis of Sustainable Catalyst Materials

There is a pressing need to replace critical materials such as platinum group elements (PGE) in applications related to energy. This work responds to the need for fundamental principles of materials design to replace these metals by addressing a gap in the understanding of how to precisely control the surface structure of nanoscale materials. Electrochemical nanomaterials synthesis, such as techniques developed in the PI’s research group, expands the toolbox of available synthetic handles to include both electrochemical and chemical parameters, providing access to control over synthetic conditions in ways that are not possible in purely chemical nanoparticle growth. However, electrochemical materials synthesis (electrodeposition) is inherently serial, limiting throughput and preventing widespread implementation. Initial efforts in the short period of this award resulted in an innovative, high throughput, parallel approach to synthetic discovery for the electrodeposition of shaped metal nanoparticles that overcomes this limitation. Looking ahead, this work establishes an important capability that will enable researchers to push boundaries in the shape control of nanoparticles composed of non-PGE such as copper, iron, nickel, or cobalt.

36 MATERIALS SCIENCE↗

Reaction System Design for NO 2 Oxidation of Used Nuclear Fuel for the FY17 Hot Test

A dry pretreatment process based on the oxidation of used nuclear fuel to convert it to a fine powder is being studied for the removal and capture of tritium and iodine before subsequent processing. The process converts oxide fuel into a fine powder at low temperature using NO 2 /O 2 mixtures. The form of the powder product can be selected to be U 3 O 8 , UO 3 , or a nitrate by adjusting the processing conditions. All the fundamental tenets of the process have been successfully demonstrated as a proof of principle, and many aspects have been corroborated multiple times at laboratory scale. The present thrust is to develop the process to a technology-readiness level sufficient to evaluate and estimate the cost of an engineering-scale implementation. A previous roadmap analysis of the implementation determined that the most desirable approach would be based on kilogram-scale experiments using real fuel in parallel with multi-kg testing of prototype systems using surrogate material. Following the planned approach, kilogram-scale experiments will be conducted in FY 2017. This report describes the primary reaction system designs and the equipment that has been fabricated. Details related to instrumentation, data acquisition, and controls have been previously reported.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Scalable domain decomposition solvers for stochastic PDEs in high performance computing

Stochastic spectral finite element models of practical engineering systems may involve solutions of linear systems or linearized systems for non-linear problems with billions of unknowns. For stochastic modeling, it is therefore essential to design robust, parallel and scalable algorithms that can efficiently utilize high-performance computing to tackle such large-scale systems. Domain decomposition based iterative solvers can handle such systems. And though these algorithms exhibit excellent scalabilities, significant algorithmic and implementational challenges exist to extend them to solve extreme-scale stochastic systems using emerging computing platforms. Intrusive polynomial chaos expansion based domain decomposition algorithms are extended here to concurrently handle high resolution in both spatial and stochastic domains using an in-house implementation. Sparse iterative solvers with efficient preconditioners are employed to solve the resulting global and subdomain level local systems through multi-level iterative solvers. We also use parallel sparse matrix–vector operations to reduce the floating-point operations and memory requirements. Numerical and parallel scalabilities of these algorithms are presented for the diffusion equation having spatially varying diffusion coefficient modeled by a non-Gaussian stochastic process. Scalability of the solvers with respect to the number of random variables is also investigated.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Adaptive, Active Learning, and Multifidelity Monte Carlo Methods in the MOOSE Stochastic Tools Module

MOOSE is an open-source computational platform for constructing multi-physics models and executing them in a massively parallel fashion. It has a stochastic tools module (STM) for forward/inverse uncertainty quantification (UQ) and surrogate modeling. This presentation details some recent developments to the STM with respect to the implementation of adaptive, active learning, and multifidelity Monte Carlo methods for forward UQ of computational models. Specifically, the adaptive Monte Carlo methods include Markov Chain Monte Carlo (MCMC)-driven algorithms like adaptive importance sampling and parallelized subset simulation for statistical QoI estimation, rare events analysis, and stochastic gradient-free optimization. The active learning methods include Gaussian Process (GP) surrogates and their training via Adam optimization, design of acquisition functions, and integration with samplers like Monte Carlo, adaptive importance, and parallelized subset simulation. These active learning methods are also designed to work in a batch mode, wherein, the required calls to the full computational model are executed in parallel whenever a user-specified batch size is met. The multifidelity methods in STM are broadly divided into two categories: hierarchical, where a defined hierarchy exists among the low-fidelity models, and peer, where all the low-fidelity models are treated equally. A GP surrogate is used to learn the differences between the low- and high-fidelity models in both multifidelity categories, and acquisition functions from the active learning classes are used to decide whether to rely on a low-fidelity model or call the expensive high-fidelity model. Alongside the software description and usage, applications are also presented to nuclear engineering computational models including a TRISO nuclear fuel particle, a reactor pressure vessel, and a heat-pipe microreactor.

97 MATHEMATICS AND COMPUTING↗

Vision and Development of a Design, Implementation, and Verification Automation (DIVA) Software Platform for DNA Construction

Abstract DNA construction, while a prerequisite to many biological endeavors, is often a time-consuming distraction from an individual’s primary research objectives. We envisioned that with the right software infrastructure and cultural mindset, a single person could execute in parallel the batched DNA construction tasks of an entire research institute, at scales realizing efficiency gains through process and laboratory automation. In pursuit of this vision, we developed the Design, Implementation, and Verification Automation (DIVA) software platform. DIVA’s web interface enables researchers to design DNA constructs (using visual biological computer-aided design tools and biological parts repositories), submit designs for construction to dedicated staff, and track DNA construction as it progresses. DIVA supports the dedicated staff through the DNA construction process and records both successful and unsuccessful attempts toward improving the overall process. The platform is publicly available at public-diva.jbei.org and its open-source code through github.com/JBEI/DIVA.

Plahar, Hector [DOE Agile BioFoundry , , ,; DOE Jo↗

Generalizing mkFit and its Application to HL-LHC

mkFit is an implementation of the Kalman filter-based track reconstruction algorithm that exploits both thread- and data-level parallelism. In the past few years the project transitioned from the R&D phase to deployment in the Run-3 offline workflow of the CMS experiment. The CMS tracking performs a series of iterations, targeting reconstruction of tracks of increasing difficulty after removing hits associated to tracks found in previous iterations. mkFit has been adopted for several of the tracking iterations, which contribute to the majority of reconstructed tracks. When tested in the standard conditions for production jobs, speedups in track pattern recognition are on average of the order of 3.5x for the iterations where it is used (3-7x depending on the iteration). Multiple factors contribute to the observed speedups, including vectorization and a lightweight geometry description, as well as improved memory management and single precision. Efficient vectorization is achieved with both the icc and the gcc (default in CMSSW) compilers and relies on a dedicated library for small matrix operations, Matriplex, which has recently been released in a public repository. While the mkFit geometry description already featured levels of abstraction from the actual Phase-1 CMS tracker, several components of the implementations were still tied to that specific geometry. We have further generalized the geometry description and the configuration of the run-time parameters, in order to enable support for the Phase-2 upgraded tracker geometry for the HL-LHC and potentially other detector configurations. The implementation strategy and high-level code changes required for the HL-LHC geometry are presented. Speedups in track building from mkFit imply that track fitting becomes a comparably time consuming step of the tracking chain.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Spatiotemporal parallelization of an analytical heat conduction model for additive manufacturing via a hybrid OpenMP + MPI approach

The ability to do thermal simulations for entire additive manufacturing builds is a key computational problem facing the additive manufacturing community; however, complex numerical models considering multiple physical phenomena currently do not have the capacity for simulations at this scale. To this end, conduction only analytic models offer a viable approach due to the massive drop in computational expense. In this work, we extend an existing implementation which uses a governing equation which can be evaluated at any point in space and time. This implementation already utilizes OpenMP with a spatial decompositions scheme stemming from a melt pool tracking algorithm. Furthermore, we then combine this with a parallel in time (PinT) approach to make the problem highly parallelizable. The new scheme, which uses MPI for internode communication and OpenMP for intranode communication, is shown to scale very well across multiple computational nodes. This approach results in the ability to simulate the 3D solidification conditions for entire layers of additively manufactured parts in minutes making part scale thermal simulations more practical.

36 MATERIALS SCIENCE↗

A weighted state redistribution algorithm for embedded boundary grids

State redistribution is an algorithm that stabilizes cut cells for embedded boundary grid methods. This work extends the earlier algorithm in several important ways. First, state redistribution is extended to three spatial dimensions. Second, we discuss several algorithmic changes and improvements motivated by the more complicated cut cell geometries that can occur in higher dimensions. In particular, we introduce a weighted version with less dissipation in an easily generalizable framework. Third, we demonstrate that state redistribution can also stabilize a solution update that includes both advective and diffusive contributions. Notably, the stabilization algorithm is shown to be effective for incompressible as well as compressible reacting flows. Finally, we discuss the implementation of the algorithm for several exascale-ready simulation codes based on AMReX, demonstrating ease of use in combination with domain decomposition, hybrid parallelism and complex physics.

97 MATHEMATICS AND COMPUTING↗

Investigation of Portable Event-Based Monte Carlo Transport Using the NVIDIA Thrust Library

Power consumption considerations are driving future high performance computing platforms toward many-core computing architectures. Los Alamos National Laboratory's Trinity machine, available in 2016, will use both Intel Xeon Haswell processors and Intel Xeon Phi Knights Landing many integrated core (MIC) architecture coprocessors. Lawrence Livermore National Laboratory's Sierra machine, available in 2018, will use an IBM PowerPC architecture along with Nvidia graphics processing unit (GPU) architecture accelerators. These different advanced architectures make the computing landscape in upcoming years complex. Traditional approaches to Monte Carlo transport do not work efficiently on these new computing platforms. MIC architectures require vectorization to operate efficiently, and vectorization is difficult to achieve in Monte Carlo transport. GPU architectures require additional code to explicitly use the hardware, requiring significant code changes or hardware specific branches in the source code. A significant challenge for Monte Carlo transport projects is to simultaneously support within a single source code base efficient simulations for both the current generation of architectures and the different advanced computing architectures. In order to address these challenges, two important changes are typically required: a new algorithmic approach for solving Monte Carlo transport, and explicit use of hardware specific software. In this paper, we describe initial research investigations of an event-based Monte Carlo transport algorithm implemented using the Nvidia Thrust library on a GPU for a Monte Carlo test code. The event-based algorithm targets many-core architectures by increasing SIMD (single instruction multiple data) parallelism, while Thrust potentially provides portable performance by allowing one source code base to compile code targeted for both CPUs and GPUs. We described preliminary investigations of portable event-based Monte Carlo algorithms implemented using the Nvidia Thrust library in a research Monte Carlo test code. We found that an explicit CUDA implementation of an event-based Monte Carlo algorithm performed significantly more efficiently than a Thrust implementation on GPU platforms, most likely as a result of additional flexibility in access to different memory spaces on the GPU. Additionally, we showed that on GPU platforms and at large enough problem sizes the event-based implementations perform more efficiently than the serial history-based implementation running on the host CPU. While investigating this problem, we also discovered that the performance of the event-based algorithm is affected by what tallies are being used. A zonal scalar flux tally requires atomic operations that significantly impacted the performance of the code, in some cases producing slowdowns instead of speedups. We decided to remove the tally in order to focus on the effectiveness of the event-based algorithm. Future work will be required to research more effective ways of handling such tallies. Additionally, we would like to consider new ways for optimizing both the Thrust and CUDA versions, in order to see how much performance we have yet to achieve. The potential trade-off between portability and performance was demonstrated in this investigation. Thrust provides both CPU and GPU versions of the code in one code base, but it does so at a cost. We discovered approximately a factor of 2-5 performance difference between Thrust and CUDA on each GPU platform we tested. Thrust provides a tool to access the GPUs with less effort and specialization, but it does so by giving up fine grained control where extra performance can be found for this application. Future work will be required to determine whether this performance differential between Thrust and CUDA can be reduced for event-based Monte Carlo transport. (authors)

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗