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This software contains the code artifacts for the Supercomputing 2025 paper titled "C.A.T.S.: Memory and Control Flow Tracing for Whole-Program Performance Analysis". The included code contains analysis passes, dynamic program instrumentation, runtime, examples, and tests.
Nowcasts, or near-real-time (NRT) forecasts, of soil moisture based on the Soil Moisture Active and Passive (SMAP) mission could provide substantial value for a range of applications including hazards monitoring and agricultural planning. To provide such a NRT forecast with high fidelity, we enhanced a time series deep learning architecture, long short-term memory (LSTM), with a novel data integration (DI) kernel to assimilate the most recent SMAP observations as soon as they become available. The kernel is adaptive in that it can accommodate irregular observational schedules. Testing over the CONUS, this NRT forecast product showcases predictions with unprecedented accuracy when evaluated against subsequent SMAP retrievals. It showed smaller error than NRT forecasts reported in the literature, especially at longer forecast latency. The comparative advantage was due to LSTM’s structural improvements, as well as its ability to utilize more input variables and more training data. The DI-LSTM was compared to the original LSTM model that runs without data integration, referred to as the projection model here. We found that the DI procedure removed the autocorrelated effects of forcing errors and errors due to processes not represented in the inputs, for example, irrigation and floodplain/lake inundation, as well as mismatches due to unseen forcing conditions. The effects of this purely data-driven DI kernel are discussed for the first time in the geosciences. Furthermore, this work presents an upper-bound estimate for the random component of the SMAP retrieval error.
In this article, we present the ExaScale PaRallel finite element tearing and interconnecting SOlver (ESPRESO) finite element method (FEM) library, which includes an FEM toolbox with interfaces to professional and open-source simulation tools, and a massively parallel hybrid total finite element tearing and interconnecting (HTFETI) solver which can fully utilize the Oak Ridge Leadership Computing Facility Titan supercomputer and achieve superlinear scaling. This article presents several new techniques for finite element tearing and interconnecting (FETI) solvers designed for efficient utilization of supercomputers with a focus on (i) performance—we present a fivefold reduction of solver runtime for the Laplace equation by redesigning the FETI solver and offloading the key workload to the accelerator. We compare Intel Xeon Phi 7120p and Tesla K80 and P100 accelerators to Intel Xeon E5-2680v3 and Xeon Phi 7210 central processing units; and (ii) memory efficiency—we present two techniques which increase the efficiency of the HTFETI solver 1.8 times and push the limits of the largest possible problem ESPRESO that can solve from 124 to 223 billion unknowns for problems with unstructured meshes. Finally, we show that by dynamically tuning hardware parameters, we can reduce energy consumption by up to 33%.
Abstract Background Pacific Biosciences HiFi read technology is currently the industry standard for high accuracy long-read sequencing that has been widely adopted by large sequencing and assembly initiatives for generation of de novo assemblies in non-model organisms. Though adapter contamination filtering is routine in traditional short-read analysis pipelines, it has not been widely adopted for HiFi workflows. Results Analysis of 55 publicly available HiFi datasets revealed that a read-sanitation step to remove sequence artifacts derived from PacBio library preparation from read pools is necessary as adapter sequences can be erroneously integrated into assemblies. Conclusions Here we describe the nature of adapter contaminated reads, their consequences in assembly, and present HiFiAdapterFilt, a simple and memory efficient solution for removing adapter contaminated reads prior to assembly.
A critical figure of merit (FoM) for electro-optic (EO) modulators is the transmission change per voltage, d T / d V . Conventional approaches in wave-guided modulators maximize d T / d V via a high EO coefficient or longer light-material interaction lengths but are ultimately limited by material losses and nonlinearities. Optical and RF resonances improve d T / d V at the cost of spectral non-uniformity, especially for high- Q optical cavity resonances. Here, we introduce an EO modulator based on piezo-strain-concentration of a photonic crystal cavity to address both trade-offs: (i) it eliminates the trade-off between d T / d V and waveguide loss—i.e., enhancement of the resonance tuning efficiency d v c / d V for the fixed EO coefficient, waveguide length, and cavity Q —and (ii) at high DC strains it exhibits a non-volatile (NV) cavity tuning Δ v c ,NV for passive memory and programming of multiple devices into resonance despite fabrication variations. The device is fabricated on a scalable silicon nitride-on-aluminum nitride platform. We measure d v c / d V =177±1MHz/V, corresponding to Δ v c =40±0.32GHz for a voltage spanning ±120V with an energy consumption of δ U /Δ v c =0.17nW/GHz. The modulation bandwidth is flat up to ω BW,3dB /2 π =3.2±0.07MHz for broadband DC-AC and 142±17MHz for resonant operation near a 2.8 GHz mechanical resonance. Optical extinction up to 25 dB is obtained via Fano-type interference. Strain-induced beam-buckling modes are programmable under a “read-write” protocol with a continuous, repeatable tuning range of 5±0.25GHz, allowing for storage and retrieval, which we quantify with mutual information of 2.4 bits and a maximum non-volatile excursion of 8 GHz. Using a full piezo-optical finite-element-model (FEM) we identify key design principles for optimizing strain-based modulators and chart a path towards achieving performance comparable to lithium niobate-based modulators and the study of high strain physics on-chip.
This data package supports the publication “Fire-altered Carbon Pools Create Disturbance Memory in Stream Dissolved Organic Carbon” by Li et al. (2026). The package contains processed model inputs, configuration files, restart files, simulation outputs, scripts, and visualization products used to evaluate post-fire dissolved organic carbon (DOC) dynamics in the Naches River Watershed, Washington, USA, following the 2021 Schneider Springs Fire. The modeling workflow couples ELM-BGC, the biogeochemistry-enabled Energy Exascale Earth System Model Land Model; ATS, the Advanced Terrestrial Simulator for integrated surface-subsurface hydrology; and PFLOTRAN, a reactive transport model for multicomponent aqueous geochemistry. Together, these models simulate how wildfire-induced changes in vegetation, litter, coarse woody debris, and soil organic matter influence DOC production, transport, and reaction from burned hillslopes to stream networks. The archive includes preprocessed meteorological, geospatial, hydrologic, and biogeochemical forcing data; ELM-BGC-derived DOC source terms; ATS mesh files; PFLOTRAN reactive-transport inputs; model configuration files; spin-up and transient restart files; watershed-scale diagnostic outputs; stream concentration time series; and figures or visualization files used to inspect and reproduce key results. File types include Hierarchical Data Format 5 (HDF5) files for gridded forcing and model-coupling data, model input and configuration files for ELM-BGC, ATS, and PFLOTRAN, restart and simulation-output files generated by the modeling workflow, tabular or time-series diagnostic outputs, scripts for post-processing and figure generation, and image or visualization products associated with the manuscript. Use of the package depends on the intended task. Re-running the simulations requires the relevant modeling software, including ELM-BGC, ATS, and PFLOTRAN as ATS's geochemical engine. Inspecting outputs and reproducing figures requires Python with scientific plotting libraries such as Matplotlib, and three-dimensional model outputs may be viewed with ParaView. Geographic information system files or maps may be inspected with ArcGIS Pro or comparable GIS software. The data package is intended to enable traceability, reuse, and partial reproduction of the coupled land-to-watershed hydro-biogeochemical modeling workflow used to test how wildfire disturbance affects terrestrial carbon pools and downstream DOC dynamics.
This document serves as a detailed companion to the powerpoint slides presented as part of the ASC L2 milestone review for Integrated Codes milestone #4782 titled “Assess Newly Emerging Programming and Memory Models for Advanced Architectures on Integrated Codes”, due on 9/30/2014, and presented for formal program review on 9/12/2014. The program review committee is represented by Mike Zika (A Program Project Lead for Kull), Brian Pudliner (B Program Project Lead for Ares), Scott Futral (DEG Group Lead in LC), and Mike Glass (Sierra Project Lead at Sandia). This document, along with the presentation materials, and a letter of completion signed by the review committee will act as proof of completion for this milestone.
The objective of this proposal is to develop tools and techniques (in the compiler) to manage data of a task and communication among tasks on the scratch pad memory (SPM) of the core, so that any application (a set of tasks) can be executed efficiently on an SPM based manycore architecture.
This was a collaborative effort between The Regents of the University of California, Lawrence Livermore National Laboratory (LLNL) and Sierra Interventions, LLC, to develop shape memory polymer foam devices for treating hemorrhagic stroke.
The Multiphysics Object Oriented Simulation Environment (MOOSE) framework has been developed to solve a variety of complex simulations ranging from groundwater flows to full reactor simulations. MOOSE excels at solving fully-implicit, fully-coupled, highly nonlinear models using the Jacobian Free Newton-Krylov (JFNK) method relying on years of expertise in several dependent packages including PETSc, libMesh, Hypre and many others. The modular design of MOOSE enables the rapid development of new physics models that can be coupled with relative ease within the framework for building up simulations of different levels of complexity. With the ongoing adoption of MOOSE to new application areas along with streamlining of existing simulations, the priorities must be adjusted to include code optimizations. This includes both execution speed and the memory footprint of MOOSE-based simulations. These two categories can be further broken down into ''micro-optimizations'' or source code optimizations and algorithmic optimizations where source code is restructured to accomplish the same tasks through a more efficient means. However, before any code optimizations can occur, one must have robust way of measuring these critical simulation properties to identify the best candidates for optimizations along with having a way to identify the effectiveness of proposed optimizations to the framework. This report discusses the preliminary work towards the implementation of a robust execution baseline of the framework and derivative applications under a variety of different simulations. In addition, several potential optimization target areas in both the MOOSE framework and dependent libraries have been identified. An implementation strategy and potential benefits are discussed.
In this Program, a team of industry and academic experts in optical interconnect design have come together to develop optical components and network architectures for the next generation high-bandwidth memory modules for DOE relevant high-performance computing applications.
Pattern recognition associative memory (PRAM) devices are parallel processing engines which are used to tackle the complex combinatorics of track nding algorithms, particularly for silicon based tracking triggers. PRAM development has been mostly limited to the realm of ASICs, which often leads to lengthy and expensive design cycles. FPGAs allow for quick iterations, making them an ideal hardware platform for designing and evaluating new PRAM features before committing to silicon. In this paper we present our FPGA-based PRAM designs and discuss how logic blocks which were originally developed for ASICs have been redesigned to take advantage of modern FPGA architectures.
This work investigated pulsed laser deposition of Cr-doped AlN thin films for use as ferromagnetic layers in memory cells for superconducting electronics. The film morphology, crystalline structure, and magnetization were investigated as a function of laser fluence on the target and background N 2 pressure during deposition. Higher laser fluence resulted in films composed of a smooth underlayer with a high density of poorly adhered, rough crystallites at the surface. Lower laser fluence reduced the density of surface crystallites significantly. X-ray diffraction showed that films grown at high laser fluence show crystalline peaks associated with AlN. Both types of films showed hysteretic magnetization curves consistent with films grown by other deposition techniques.
Hyde Memorial State Park has lost grid supplied power and has been running on a diesel generator for some time now. The powerline that feeds the park is a state owned, 5 mile underground extension from the PNM service connection point. The line has decayed over the past 30 plus years and due to the location (much of it running under the road) the cost of repair and the logistics of closing the road are not good options. In June 2019 through a state contractor, the State of New Mexico Energy, Minerals and Natural Resources Department completed a renewable energy microgrid feasibility study to see if it was technically and economically feasible to operate the park without future grid power. The study looked at solar plus battery storage and a propane generator as a possible option. New Mexico State Parks Division has indicated their wish to move forward with the microgrid project which will now go out to one of the state’s energy services performance contractors. The contractor will have to finalize the feasibility study and develop a complete list of construction costs. Given, the lack of long-term O&M data on the battery, as part of the next phase of the project the State of New Mexico Energy, Minerals and Natural Resources Department asked Los Alamos National Laboratory to preliminary examine the potential for pumped hydro as an alternative to batteries.
Project Goal: Use parametric Machine Learning methods in order to reduce memory requirements at checkpointing & restarting in the IMC simulations of Thermal Radiative Transfer using: Expectation Maximization and Weighted Gaussian Mixture Model-based approach for `particle-data compression', introduced in Plasma Physics to model Maxwellian particle distributions by Luis Chacon and Guangye Chen; Expectation Maximization with Weighted Hyper-Erlang Model in order to compress isotropic IMC particle data in the frequency domain; and Expectation Maximization and von Mises-Fisher Mixture Model for compression of anisotropic IMC particle data in the angular domain (work-in-progress).
High-temperature advanced reactors under development, such as sodium fast reactors (SFR) and molten salt cooled reactors (MSCR), are expected to offer lower levelized cost of energy (LCOE) compared to existing light water reactor (LWR’s). In the existing light water reactors (LWR’s), operation and maintenance (O&M) expenses constitute the largest fraction of the total operating cost. Some of the O&M costs are related maintenance of sensors which can fail due to exposure to harsh environment in a reactor. The O&M costs of Advanced Reactor (AR)’s are expected to constitute a significant fraction of the total cost as well, because of high temperature and radiation level in AR are likely to cause material fatigue and premature failure of sensors and components. The O&M costs in AR’s could be reduced through integration of advanced informatics of performance-related sensors into a digital twin designed for reactor monitoring. For example, machine learning (ML) could be employed for real-time validation and correction of performance-related sensors, and reducing the number of performance-related physical sensor units through virtual sensing. As part of the effort, we investigate real-time validation of thermal hydraulic sensors through one-step ahead forecasting of sensor values using long short-term memory (LSTM) recurrent neural networks (RNN). The sensors are installed in a flow loop containing a thermal mixing tee, which is a common experimental model to study thermal fatigue in a thermal hydraulic loop. In addition, nonlinear transients generated in a thermal mixing tee constitute a good challenge data set for training and validation of ML algorithms. Sensors in this study include thermocouples, flow meters, and optical fibers for distributed temperature sensing. In one experiment, measurement data sets were obtained for a loop was filled with water, and in another experiment, measurements were performed on a loop filled with liquid metal Galinstan. We have also conducted preliminary investigation of one-step ahead prediction of fiber optics-based distributed temperature sensing with LSTM networks. In predicting fiber-based temperature measurements, we treated each gauge pitch of the fiber as an independent sensor. Accuracy of one-step ahead forecasting was estimated by calculating root mean square error (RMSE) for the test segment of time series of each sensor. RMSE’s for temperature sensors in water loop were, for the most part, lower than for the same sensors in Galinstan loop. The RMSE’s for flow meters were similar for both loops. The RMSE’s for distributed temperature measured with the fiber optic sensor were similar to those of the point sensors. Results of this study demonstrated the capability of LSTM one-step ahead forecasting with RMSE comparable to uncertainty in sensor measurements.
In the last 3 years, we have worked on both the nanoscale and microscale understanding of TMPT, defect formation and evolution, and plasticity in SMFOs, specifically in YSTZ. The validated computational investigations have provided unmatched insights into the deformation and shape memory behaviors of SMFOs that could not be obtained from experiments.
We theoretically studied the feasibility of building a long-term read-write quantum memory using the principle of parity-time (PT) symmetry, which has already been demonstrated for classical systems. The design consisted of a two-resonator system. Although both resonators would feature intrinsic loss, the goal was to apply a driving signal to one of the resonators such that it would become an amplifying subsystem, with a gain rate equal and opposite to the loss rate of the lossy resonator. Consequently, the loss and gain probabilities in the overall system would cancel out, yielding a closed quantum system. Upon performing detailed calculations on the impact of a driving signal on a lossy resonator, our results demonstrated that an amplifying resonator is physically unfeasible, thus forestalling the possibility of PT-symmetric quantum storage. Our finding serves to significantly narrow down future research into designing a viable quantum hard drive.