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At least 487 records · Page 27

High-Performance Deep Learning Toolbox for Genome-Scale Prediction of Protein Structure and Function

Computational biology is one of many scientific disciplines ripe for innovation and acceleration with the advent of high-performance computing (HPC). In recent years, the field of machine learning has also seen significant benefits from adopting HPC practices. In this work, we present a novel HPC pipeline that incorporates various machine-learning approaches for structure-based functional annotation of proteins on the scale of whole genomes. Our pipeline makes extensive use of deep learning and provides computational insights into best practices for training advanced deep-learning models for high-throughput data such as proteomics data. We showcase methodologies our pipeline currently supports and detail future tasks for our pipeline to envelop, including large-scale sequence comparison using SAdLSA and prediction of protein tertiary structures using AlphaFold2.

Gao, Mu↗

GPU-Accelerated Machine Learning Inference as a Service for Computing in Neutrino Experiments

Machine learning algorithms are becoming increasingly prevalent and performant in the reconstruction of events in accelerator-based neutrino experiments. These sophisticated algorithms can be computationally expensive. At the same time, the data volumes of such experiments are rapidly increasing. The demand to process billions of neutrino events with many machine learning algorithm inferences creates a computing challenge. We explore a computing model in which heterogeneous computing with GPU coprocessors is made available as a web service. The coprocessors can be efficiently and elastically deployed to provide the right amount of computing for a given processing task. With our approach, Services for Optimized Network Inference on Coprocessors (SONIC), we integrate GPU acceleration specifically for the ProtoDUNE-SP reconstruction chain without disrupting the native computing workflow. With our integrated framework, we accelerate the most time-consuming task, track and particle shower hit identification, by a factor of 17. This results in a factor of 2.7 reduction in the total processing time when compared with CPU-only production. For this particular task, only 1 GPU is required for every 68 CPU threads, providing a cost-effective solution.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Online multi-objective particle accelerator optimization of the AWAKE electron beam line for simultaneous emittance and orbit control

Multi-objective optimization is important for particle accelerators where various competing objectives must be satisfied routinely such as, for example, transverse emittance vs bunch length. We develop and demonstrate an online multi-time scale multi-objective optimization algorithm that performs real time feedback on particle accelerators. We demonstrate the ability to simultaneously minimize the emittance and maintain a reference trajectory of a beam in the electron beamline in CERN’s Advanced Proton Driven Plasma Wakefield Acceleration Experiment.

43 PARTICLE ACCELERATORS↗

Mixed-Precision S/DGEMM Using the TF32 and TF64 Frameworks on Low-Precision AI Tensor Cores

Using NVIDIA graphics processing units (GPUs) equipped with Tensor Cores has enabled the significant acceleration of general matrix multiplication (GEMM) for applications in machine learning (ML) and artificial intelligence (AI) and in high-performance computing (HPC) generally. The use of such power-efficient, specialized accelerators can provide a performance increase between 8 × and 20 ×, albeit with a loss in precision. However, a high level of precision is required in many large scientific and HPC applications, and computing in single or double precision is still necessary for many of these applications to maintain accuracy. Fortunately, mixed-precision methods can be employed to maintain a higher level of numerical precision while also taking advantage of the performance increases from computing with lower-precision AI cores. With this in mind, we extend the state of the art by using NVIDIA’s new TF32 framework. This new framework not only burdens some constraints of the previous frameworks, such as costly 32 16-bit castings but also provides an equivalent precision and performance by using a much simpler approach. We also propose a new framework called TF64 that attempts double-precision arithmetic with low-precision Tensor Cores. Although this framework does not exist yet, we validated the correctness of this idea and achieved an equivalent of 64-bit precision on 32-bit hardware.

Valero Lara, Pedro↗

PACT Data Management Plan (V.1.0)

The Perovskite PV Accelerator for Commercial Technology (PACT) is an independent validation center for the evaluation of perovskite PV technologies and their bankability. The center is led by Sandia National Laboratories and the National Renewable Energy Laboratory (NREL) and includes as part of its team Los Alamos National Laboratory (LANL), CFV Labs, Black and Veatch (B&V), and the Electric Power Research Institute (EPRI). The goals of the center are to: Develop and improve indoor and outdoor performance characterization methods, Develop and validate accelerated qualification testing for early failures (5-10 years), Research degradation and failure modes, Validate outdoor performance, and Provide bankability services to US perovskite PV (PSC) industry. The importance of data and data management to the success and outcomes of the PACT center is paramount. This report describes how data will be managed and protected by PACT and identifies important data management principles that will guide our approach.

14 SOLAR ENERGY↗

A GPU‐Accelerated Generative Adversarial Model for Causal Inference

We develop a GPU-accelerated machine learning generative adversarial model designed to facilitate causal inferences from observational data. Our model's theoretical framework is conceptualized in a manner that is amenable to being operable and scalable for high-performance computing platforms. We leverage GPU acceleration to develop a parallel evolutionary algorithm to achieve large-scale parallel computation of the model within a now widely accessible computing platform. This capability both enhances computational speedup and efficiency and also extends the use of the model to a broader range of substantive research domains while maintaining the underlying theoretical properties of the model.

GPU↗

Experimental Safe Extremum Seeking for Accelerators

Here, we demonstrate the recent designs of safe extremum seeking (Safe ES) on the 1-km-long charged particle accelerator at the Los Alamos Neutron Science Center (LANSCE). Safe ES is a modification of extremum seeking (ES) which, in addition to minimizing an analytically unknown cost, also employs a safety filter based on an analytically unknown control barrier function (CBF) safety metric. Tuning is necessitated by accelerators being large complex systems, with many drifting parameters due to thermal effects and degradation. At the same time, safe operation (the maintenance of state constraints) is crucial, as damage brings astronomical costs, both financially and in operation downtime. Our measured (but analytically unknown) safety metric is the beam current. We perform multivariable Safe ES on three accelerator applications, in which we adapt 4, 6, and 3 magnet strength parameters, respectively. Two of the three applications are for validated simulation models of beamlines at LANSCE: the first for the proton radiography (pRad) beamline of 800-MeV protons for spot size tuning; the second on a high-performance code, HPSim, for tuning the low-energy beam transport (LEBT) region that contains a beam of 750-keV protons. The third is an experimental tuning of the steering magnets in the LEBT at LANSCE.

43 PARTICLE ACCELERATORS↗

A fast implicit solver for semiconductor models in one space dimension

Several different approaches are proposed for solving fully implicit discretizations of a simplified Boltzmann-Poisson system with a linear relaxation-type collision kernel. This system models the evolution of free electrons in semiconductor devices under a low-density assumption. At each implicit time step, the discretized system is formulated as a fixed-point problem, which can then be solved with a variety of methods. A key algorithmic component in all the approaches considered here is a recently developed sweeping algorithm for Vlasov-Poisson systems. A synthetic acceleration scheme has been implemented to accelerate the convergence of iterative solvers by using the solution to a drift-diffusion equation as a preconditioner. The performance of four iterative solvers and their accelerated variants has been compared on problems modeling semiconductor devices with various electron mean-free-path.

97 MATHEMATICS AND COMPUTING↗

Cloud Services Enable Efficient AI-Guided Simulation Workflows across Heterogeneous Resources

Applications which fuse machine learning and simulation are rarely best served by a single computing resource. Highly parallel simulation codes are best deployed on super- computers, while AI tasks used to decide which simulations to perform may be best suited to specialized accelerators. Here we present a Function-as-a-Service (FaaS) system for executing complex, distributed computational campaigns that achieves performance parity with conventional workflow systems without the complexities of secure network connections between compute providers. One innovation enabling high performance is a subsystem that directly moves task data between sites, separate from the cloud-hosted FaaS system used to distribute task instructions. We also introduce a flexible scheduling system that allows us access factor of 2 trade offs between the amount of resources required to solve a problem at each compute site. We anticipate that this system will upgrade multi-site applications from demonstration projects to routine practice in computational science.

Ward, Logan↗

Computationally efficient evaluation of optimum homogeneous charge compression ignition operating range with accelerated multizone engine cycle simulation

The very intensive calculations necessary to define a performance map requiring evaluation of over a hundred individual operating points can be efficiently conducted with accelerated multizone for engine cycle simulation, leading to a definition of regions of acceptable and optimum homogeneous charge compression ignition operation. Accelerated multizone for engine cycle simulation has the virtue of enabling accurate evaluation of many operating conditions based on thermal stratification data from a single fluid mechanics run at motored conditions. This is possible because thermal stratification is more sensitive to engine geometry than to operating conditions. In this article, accuracy of accelerated multizone for engine cycle simulation is demonstrated by comparison with experimental data for iso-octane homogeneous charge compression ignition operation over a broad range of lean equivalence ratios (0.14–0.28). The validated accelerated multizone for engine cycle simulation model is then applied to generating a performance map for an engine controlled by appropriately adjusting equivalence ratio and internal exhaust gas recirculation. Regions of acceptable and optimum combustion are identified. It is finally demonstrated that while indicated mean effective pressure remains low for optimum homogeneous charge compression ignition operation (1–4 bar), this is sufficient for a large fraction of typical driving in light-duty vehicles. Much driving including idle can therefore be done in homogeneous charge compression ignition mode at high efficiency and low (essentially zero) NOx and particulate matter emissions.

30 DIRECT ENERGY CONVERSION↗

Modeled Results of Four Residential Energy Efficiency Measure Packages for Deriving Advanced Building Construction Research Targets

The Advanced Building Construction (ABC) Initiative from the U.S. Department of Energy Building Technologies Office is working to accelerate industrialized construction innovations for decarbonizing buildings. To inform performance and cost targets for research under the ABC Initiative, this analysis used the ResStock™ tool to evaluate the energy savings, utility bill impacts, and carbon emissions impacts of four simulated upgrade packages with specific target performance levels on a large sample of residential dwelling units (approximately 550,000) representative of the U.S. housing stock.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Accelerating Thermochemical Equilibrium Calculations for Nuclear Reactor Applications

Thermochemical properties play a key role in modeling and simulation of several key phenomena in nuclear reactors. There has been an increasing interest in incorporating CALPHAD-based formulations in multiphysics simulations including for Molten Salt Reactors where knowledge of phase evolution of the salt and the chemical potentials of various elements are of utmost importance in source term analyses and redox control. However, the size of such simulations is often limited by the high computational cost of full thermodynamic equilibrium calculations. This work discusses the current efforts aimed at accelerating thermochemical equilibrium calculations for multiphysics simulations performed using the open-source finite element / finite volume code Multiphysics Object Oriented Simulation Environment (MOOSE) [1]. While several methods have been proposed for accelerating phase equilibrium calculations [2], most focus on relatively small systems and often rely on a- priori knowledge of the state-space of the system. Nuclear materials, however, are often multi-component systems owing to the evolution of composition under irradiation and an approach based on a-priori mapping of phase diagram is often not enough. This work is aimed at demonstrating an on-the-fly surrogate modeling framework that uses active learning to reduce the number of full equilibrium calculations that must be performed. By combining with efficient coupling approaches, the surrogate framework helps in reducing the computational cost of thermodynamic equilibrium informed multiphysics simulations of nuclear materials. The performance is benchmarked against full coupling with the thermochemistry library Thermochimica [3]. This work uses a machine learning based approach for constructing surrogate models to predict the stable phases in a multicomponent system. The surrogates were constructed using neural networks and Gaussian process classification. In this work, we compare the relative performance of the two methods. We also demonstrate the use of caching previous calculations by interpolating the values from nearest neighbors. References [1] Lindsay, A.D., et al. "2.0 – MOOSE: Enabling massively parallel multiphysics simulation", SoftwareX, 20 (2022): 101202. [2] Roos, W.A. and Zietsman J.H. "Accelerating complex chemical equilibrium calculations – A Review", Calphad, 77 (2022): 102380. [3] Piro, M.H.A., et al. "The thermochemistry library Thermochimica", Computational Materials Science, 67 (2013): 266-272.

36 MATERIALS SCIENCE↗

Application of Superconducting Cavities as Ultra-Sensitive RF Photon Detectors

Superconducting radio frequency (SRF) cavities are the world’s most efficient engineered oscillators, and they have long been employed for extremely high efficiency transfer of energy to beams of charged particles. Decades of R&D for particle accelerators have led to modern treatments for SRF cavities that achieve higher performance than was previously possible. Advanced SRF cavities using particle accelerator technology are now being used to search for new physics, including dark matter and gravitational waves. The extremely high Q makes it possible to search for very small signals from photons in the radio frequency range, and the extremely high electric fields makes it possible to perform experiments that involve pumping one mode of a cavity in order to search for power transfer mediated by new physics. This talk will present novel experiments that employ SRF cavities, including searches for axions and dark photons dark matter, light-shining-through-walls, and high frequency gravitational waves. Results to be presented include searches with world record sensitivity.

43 PARTICLE ACCELERATORS↗

A GPU-Accelerated Population Generation, Sorting, and Mutation Kernel for an Optimization-Based Causal Inference Model

We develop a GPU-accelerated machine learning generative adversarial network model that can be used with observational data for the purpose of constructing causal inferences. The theoretical basis of our machine learning model is novel and is conceptualized to be operable and scalable for high performance computing platforms. Our GPU-accelerated code enables large-scale parallelization of the computation within a common and accessible computing environment. This will expand the reach of our model and empower research in new substantive domains while maintaining the underlying theoretical properties.

Cho, Wendy K. Tam↗

Stereoscopic detection of hot spots in superfluid 4 He (He II) for accelerator-cavity diagnosis

Superconducting radio-frequency (SRF) cavities cooled by superfluid 4He (He II) are building blocks of many modern particle accelerators due to their high quality factor. However, Joule heating from sub-millimeter surface defects on cavities can lead to cavity quenching, which limits the maximum acceleration gradient of the accelerators. Developing a non-contacting detection technology to accurately locate these surface hot spots is the key to improve the performance of SRF cavities and hence the accelerators. In a recent proof-of-concept experiment, we demonstrated that a molecular tagging velocimetry (MTV) technique based on the tracking of a He molecular tracer line created nearby a surface hot spot in He II can be utilized to locate the hot spot. In order to make this technique practically useful, here we describe our further development of a stereoscopic MTV setup for tracking the tracer line’s motion in three-dimensional (3D) space. We simulate a quench spot by applying a transient voltage pulse to a small heater mounted on a substrate plate. Images of the drifted tracer line, taken with two cameras from orthogonal directions, are used to reconstruct the line profile in 3D space. Here, a new algorithm for analyzing the 3D line profile is developed, which incorporates the finite size effect of the heater. We show that the center location of the heater can be reproduced on the substrate surface with an uncertainty of only a few hundred microns, thereby proving the practicability of this method.

43 PARTICLE ACCELERATORS↗

Conversion of the LLNL/CAMS 1 MV biomedical AMS system to a semi-automated natural abundance 14C spectrometer: system optimization and performance evaluation

The Lawrence Livermore National Laboratory – Center for Accelerator Mass Spectrometry compact 1 MV biomedical accelerator mass spectrometer was repurposed and optimized for the semi-automated radiocarbon measurement of natural abundance environmental samples. Here we present results from 15 months of routine system operation and evaluate the system performance based on 30 sample wheels measured with consistent operating conditions over 7 months from August 2019 to March 2020. Additionally, the average measurement precision was 2.7 ± 0.7‰. System accuracy was assessed with measurements of 14 C-free materials, standard materials with 14 C-content spanning 0.5 to 1.5 F 14 C, and by comparison to split samples measured with the 10 MV AMS system. Overall, this system can routinely measure samples as small as 300 µgC and less than 33000 years without the need for size-specific correction protocols.

43 PARTICLE ACCELERATORS↗

GPU-friendly surface model for Monte-Carlo detector simulations

The demands for Monte-Carlo simulation are drastically increasing with the Large Hadron Collider’s high-luminosity upgrade, and are expected to exceed the currently available compute resources. At the same time, modern high-performance computing has adopted powerful hardware accelerators, particularly GPUs. The AdePT and Celeritas projects aim to address the demanding computational needs by leveraging these heterogeneous computing architectures. While both have successfully ported realistic detector simulations to GPUs using the VecGeom library, the complexity of geometry modeling emerged as a bottleneck. Thread divergence and high register usage were degrading the GPU performance. Therefore, a new, GPU-friendly surface-based model has been introduced in the VecGeom library that decomposes the divergent code of the 3D primitive solids into simpler and more balanced surface algorithms. In this work, we present the latest developments, focusing on the additions required to efficiently model complex setups like the CMS Phase-2 geometry. This includes memory reduction techniques, and adding accelerating structures for faster traversal.

Diederichs, Severin [CERN]↗

cuAlign: Scalable Network Alignment on GPU Accelerators

Given two graphs, the objective of network alignment is to find the best one-to-one mapping of vertices in one graph (??) to vertices in the other (??), such that the number of overlaps is maximized. We say that edges(??, ??) ???and(??', ??') ??? are overlapped if ?? is mapped to ??' and ?? is mapped to??'. Network alignment is an important optimization problem with several applications in bioinformatics, computer vision and ontology matching. Since it is an NP-hard problem, efficient heuristics and scalable implementations are necessary. In this work, we introduce a new framework that combines the concepts of intra-network proximity using vertex embedding,Belief Propagation (BP) and approximate weighted matching, and provides qualitative improvements up to22%over state-of-the-art approaches. We also provide scalable implementations on GPU accelerators, demonstrating up to19×speedup for Belief Propagation and 3× speedup for approximate weighted matching relative to previous multithreaded implementation. A combination of combinatorial and algebraic kernels within the network alignment algorithm poses significant hurdles for parallelization. Load imbalance and irregular DRAM traffic limit achievable performance on GPUs. Our novel approach identifies and exploits unique structural proper-ties of the BP-based algorithm and employs code fusion to reduce data movement between different steps of the algorithm. Using a diverse set of inputs, we demonstrate qualitative improvements of our algorithms, and performance gains of our GPU-accelerated implementation. We believe that our work will enable algorithmic improvements and practical applications of network alignment.

Xiang, Lizhi↗