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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

Addressing Global Data Dependencies in Heterogeneous Asynchronous Runtime Systems on GPUs

Large-scale parallel applications with complex global data dependencies beyond those of reductions pose significant scalability challenges in an asynchronous runtime system. Internodal challenges include identifying the all-to-all communication of data dependencies among the nodes. Intranodal challenges include gathering together these data dependencies into usable data objects while avoiding data duplication. This paper addresses these challenges within the context of a large-scale, industrial coal boiler simulation using the Uintah asynchronous many-task runtime system on GPU architectures. We show significant reduction in time spent analyzing data dependencies through refinements in our dependency search algorithm. Multiple task graphs are used to eliminate subsequent analysis when task graphs change in predictable and repeatable ways. Using a combined data store and task scheduler redesign reduces data dependency duplication ensuring that problems fit within host and GPU memory. Furthermore, these modifications did not require any changes to application code or sweeping changes to the Uintah runtime system. We report results running on the DOE Titan system on 119K CPU cores and 7.5K GPUs simultaneously. Our solutions can be generalized to other task dependency problems with global dependencies among thousands of nodes which must be processed efficiently at large scale.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

Analysis of Time Dependent Data and PRA

In the past decades, several numerical simulation codes have been employed to simulate accident dynamics (e.g., RELAP5-3D, MELCOR, MAAP). In order to evaluate the impact of uncertainties into accident dynamics, several stochastic methodologies have been coupled with these codes. These stochastic methods range from classical Monte-Carlo and Latin Hypercube sampling to stochastic polynomial methods. Similar approaches have been introduced into the risk and safety community where stochastic methods (such as RAVEN, ADAPT, MCDET, ADS) have been coupled with safety analysis codes in order to evaluate the safety impact of timing and sequencing of events. These approaches are usually called Dynamic PRA or simulation-based PRA methods. These uncertainties and safety methods usually generate a large number of simulation runs (database storage may be on the order of gigabytes or higher). The scope of this paper is to present a broad overview of methods and algorithms that can be used to analyze and extract information from large data sets containing time dependent data. In this context, 'extracting information' means constructing input-output correlations, finding commonalities, and identifying outliers. Some of the algorithms presented here have been developed or are under development within the RAVEN statistical framework. (authors)

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2017

WIREFRAME: Supporting Data-dependent Parallelism through Dependency Graph Execution in GPUs

GPUs lack fundamental support for data-dependent parallelism and synchronization. While CUDA Dynamic Parallelism signals progress in this direction, many limitations and challenges still re-main. This paper introducesWireframe, a hardware-software solution that enables generalized support for data-dependent parallelism and synchronization. Wireframe enables applications to naturally express execution dependencies across different thread blocks through a dependency graph abstraction at run-time, which is sent to the GPU hardware at kernel launch. At run-time, the hardware enforces the dependencies specified in the dependency graph through a dependency-aware thread block scheduler. Overall, Wireframe is able to improve total execution time up to 65.20% with an average of 45.07%.

Abdolrashidi, AmirAli↗
DOE OSTI2018

Spectral Methods in Time-dependent Data Analysis

We aim to create a new model for time-dependent data analysis, named dynamical learning, that integrates data-driven manifold learning techniques with operator-theoretic methods from dynamical systems theory. This approach has the potential to deliver more efficient methods for analyzing time-dependent data, such as video streams, by naturally separating out the temporal and spatial features of the data. We aim to apply the newly developed methods to video surveillance data related to Sandia mission applications, and particularly focus on the problems of image segmentation and object tracking. This project ended early due to the departure of the PI from Sandia about 18 months into the project. Therefore, this document reports on partial progress towards the initial goals of the project. In addition, this document reports on part of the work conducted during the project; see the Appendix for a summary of all the work conducted during the 18 months.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

AutoCheck: Automatically Identifying Variables for Checkpointing by Data Dependency Analysis

Checkpoint/Restart (C/R) has been widely deployed in numerous HPC systems, Clouds, and industrial data centers, which are typically operated by system engineers. Nevertheless, there is no existing approach that helps system engineers without domain expertise and domain scientists without system fault tolerance knowledge identify those critical variables accounted for correct application execution restoration in a failure for C/R. To address this problem, we propose an analytical model and a tool (AutoCheck) that can automatically identify critical variables to checkpoint for C/R. AutoCheck relies on first, analytically tracking and optimizing data dependency between variables and other application execution state, and second, a set of heuristics that identify critical variables for checkpointing from the refined data dependency graph (DDG). AutoCheck allows programmers to pinpoint critical variables to checkpoint quickly within a few minutes. We evaluate AutoCheck on 13 representative HPC benchmarks, demonstrating that AutoCheck can efficiently identify correct critical variables to checkpoint.

HPC↗
DOE OSTI2020

Trainability of ReLU networks and Data-dependent Initialization

Here, in this paper, we study the trainability of rectified linear unit (ReLU) networks at initialization. A ReLU neuron is said to be dead if it only outputs a constant for any input. Two death states of neurons are introduced–tentative and permanent death. A network is then said to be trainable if the number of permanently dead neurons is sufficiently small for a learning task. We refer to the probability of a randomly initialized network being trainable as trainability. We show that a network being trainable is a necessary condition for successful training, and the trainability serves as an upper bound of training success rates. In order to quantify the trainability, we study the probability distribution of the number of active neurons at initialization. In many applications, overspecified or overparameterized neural networks are successfully employed and shown to be trained effectively. With the notion of trainability, we show that overparameterization is both a necessary and a sufficient condition for achieving a zero training loss. Furthermore, we propose a data-dependent initialization method in an overparameterized setting. Numerical examples are provided to demonstrate the effectiveness of the method and our theoretical findings.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

Identifying Urinary and Serum Exosome Biomarkers for Radiation Exposure Using a Data Dependent Acquisition and SWATH-MS Combined Workflow

Purpose: Early and accurate assessment of radiation injury by radiation-responsive biomarkers is critical for triage and early intervention. Biofluids such as urine and serum are convenient for such analysis. Recent research has also suggested that exosomes are a reliable source of biomarkers in disease progression. In the present study, we analyzed total urine proteome and exosomes isolated from urine or serum for potential biomarkers of acute and persistent radiation injury in mice exposed to lethal whole body irradiation (WBI). Methods and Materials: For feasibility studies, the mice were irradiated at 10.4 Gy WBI, and urine and serum samples were collected 24 and 72 hours after irradiation. Exosomes were isolated and analyzed using liquid chromatography mass spectrometry/mass spectrometry-based workflow for radiation exposure signatures. A data dependent acquisition and SWATH-MS combined workflow approach was used to identify significantly exosome biomarkers indicative of acute or persistent radiation-induced responses. For the validation studies, mice were exposed to 3, 6, 8, or 10 Gy WBI, and samples were analyzed for comparison. Results: A comparison between total urine proteomics and urine exosome proteomics demonstrated that exosome proteomic analysis was superior in identifying radiation signatures. Feasibility studies identified 23 biomarkers from urine and 24 biomarkers from serum exosomes after WBI. Urinary exosome signatures identified different physiological parameters than the ones obtained in serum exosomes. Exosome signatures from urine indicated injury to the liver, gastrointestinal, and genitourinary tracts. In contrast, serum showed vascular injuries and acute inflammation in response to radiation. Selected urinary exosomal biomarkers also showed changes at lower radiation doses in validation studies. Conclusions: Exosome proteomics revealed radiation- and time-dependent protein signatures after WBI. A total of 47 differentially secreted proteins were identified in urinary and serum exosomes. Together, these data showed the feasibility of defining biomarkers that could elucidate tissue-associated and systemic response caused by high-dose ionizing radiation. This is the first report using an exosome proteomics approach to identify radiation signatures.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2019

SAD phasing of XFEL data depends critically on the error model

A nonlinear least-squares method for refining a parametric expression describing the estimated errors of reflection intensities in serial crystallographic (SX) data is presented. This approach, which is similar to that used in the rotation method of crystallographic data collection at synchrotrons, propagates error estimates from photon-counting statistics to the merged data. Here, it is demonstrated that the application of this approach to SX data provides better SAD phasing ability, enabling the autobuilding of a protein structure that had previously failed to be built. Estimating the error in the merged reflection intensities requires the understanding and propagation of all of the sources of error arising from the measurements. One type of error, which is well understood, is the counting error introduced when the detector counts X-ray photons. Thus, if other types of random errors (such as readout noise) as well as uncertainties in systematic corrections (such as from X-ray attenuation) are completely understood, they can be propagated along with the counting error, as appropriate. In practice, most software packages propagate as much error as they know how to model and then include error-adjustment terms that scale the error estimates until they explain the variance among the measurements. If this is performed carefully, then during SAD phasing likelihood-based approaches can make optimal use of these error estimates, increasing the chance of a successful structure solution. In serial crystallography, SAD phasing has remained challenging, with the few examples of de novo protein structure solution each requiring many thousands of diffraction patterns. Here, the effects of different methods of treating the error estimates are estimated and it is shown that using a parametric approach that includes terms proportional to the known experimental uncertainty, the reflection intensity and the squared reflection intensity to improve the error estimates can allow SAD phasing even from weak zinc anomalous signal.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Multiple marker abundance profiling: combining selected reaction monitoring and data-dependent acquisition for rapid estimation of organelle abundance in subcellular samples

Measuring changes in protein or organelle abundance in the cell is an essential, but challenging aspect of cell biology. Frequently-used methods for determining organelle abundance typically rely on detection of a very few marker proteins, so are unsatisfactory. In silico estimates of protein abundances from publicly available protein spectra can provide useful standard abundance values but contain only data from tissue proteomes, and are not coupled to organelle localization data. A new protein abundance score, the normalized protein abundance scale (NPAS), expands on the number of scored proteins and the scoring accuracy of lower-abundance proteins in Arabidopsis. NPAS was combined with subcellular protein localization data, facilitating quantitative estimations of organelle abundance during routine experimental procedures. A suite of targeted proteomics markers for subcellular compartment markers was developed, enabling independent verification of in silico estimates for relative organelle abundance. Estimation of relative organelle abundance was found to be reproducible and consistent over a range of tissues and growth conditions. In silico abundance estimations and localization data have been combined into an online tool, multiple marker abundance profiling, available in the SUBA4 toolbox (http://suba.live).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Time Dependent Data Mining in RAVEN

RAVEN is a generic software framework to perform parametric and probabilistic analysis based on the response of complex system codes. The goal of this type of analyses is to understand the response of such systems in particular with respect their probabilistic behavior, to understand their predictability and drivers or lack of thereof. Data mining capabilities are the cornerstones to perform such deep learning of system responses. For this reason static data mining capabilities were added last fiscal year (FY 15). In real applications, when dealing with complex multi-scale, multi-physics systems it seems natural that, during transients, the relevance of the different scales, and physics, would evolve over time. For these reasons the data mining capabilities have been extended allowing their application over time. In this writing it is reported a description of the new RAVEN capabilities implemented with several simple analytical tests to explain their application and highlight the proper implementation. The report concludes with the application of those newly implemented capabilities to the analysis of a simulation performed with the Bison code.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Numerical eigen-spectrum slicing, accurate orthogonal eigen-basis, and mixed-precision eigenvalue refinement using OpenMP data-dependent tasks and accelerator offload

Performing a variety of numerical computations efficiently and, at the same time, in a portable fashion requires both an overarching design followed by a number of implementation strategies. All of these are exemplified below as we present transitioning the PLASMA numerical library from relying on dependence-driven large tasks to achieving utilization of fine grain tasking and offload to hardware accelerators while keeping its core dependence sets: OpenMP source code pragmas and runtime for most system-level functionality and basic low-level numerical kernels provided directly by hardware vendors or open source projects with vendor contributions. We also present new algorithmic methods and their efficient parallel implementations including fine grained tasking for eigen-spectrum slicing and offload for mixed-precision eigenvalue refinement. We provide performance, scaling, and numerical results showing sizable gains over the available solutions from either the open source and vendor-provided packages.

Luszczek, Piotr↗
DOE OSTI2022

POSTER: Automatic Differentiation of Parallel Loops with Formal Methods

The accompanying poster to this short paper presents a combination of reverse mode AD and formal methods to enable efficient differentiation of (or backpropagation through) shared-memory parallel code. Compared to the state of the art, our approach can more often avoid the need for atomic updates or private data copies during the parallel derivative computation, even in the presence of unstructured or data-dependent data access patterns. This is achieved by gathering information about the memory access patterns from the input program, which is assumed to be correctly parallelized. This information is then used to build a model of assertions in a theorem prover, which can be used to check the safety of shared memory accesses during the parallel derivative computation

Automatic Differentiation↗
DOE OSTI2016

On the Impact of Widening Vector Registers on Sequence Alignment

Vector extensions, such as SSE, have been part of the x86 since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. In this paper, we demonstrate that the trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. We present a practically efficient SIMD implementation of a parallel scan based sequence alignment algorithm that can better exploit wider SIMD units. We conduct comprehensive workload and use case analyses to characterize the relative behavior of the striped and scan approaches and identify the best choice of algorithm based on input length and SIMD width.

Needleman-Wunsch↗
DOE OSTI2018

Time-dependent behavioral data from zebrafish reveals novel signatures of chemical toxicity using point of departure analysis

High-content imaging of embryonic zebrafish behavior can be used as a screening approach to rapidly evaluate the relative potential for chemicals to cause toxicity. However, most statistical methods applied to these data so far transform movement values to incidence-based “hits” and calculate lowest effect levels (LELs), which loses individual fish resolution of behavior and defies hazard ranking due to reliance on applied dose levels. Here, we have developed and parallelized a workflow to calculate benchmark dose (BMD) values from dynamic, high-content zebrafish behavior data that scales for high-throughput chemical screening. To appropriately capture the dynamics of zebrafish response from light to dark stimulus, we summarized time-dependent data using both area under the curve and immediate change at the transition point into two novel metrics that characterized abnormal behavior as a function of chemical concentration. The BMD workflow was applied to calculate BMD 10 values of 1,060 ToxCast chemicals for 24 zebrafish endpoints, including behavior, mortality and morphology. The BMD 10 values provided better precision and separation than LELs for clustering chemicals since they were derived from models that best-fit their concentration-response curves. Clustering analysis revealed behavioral signatures as the most sensitive endpoints. High concordance in chemical activity was observed between ToxCast assays and zebrafish behavioral endpoints, however ToxPi analysis indicated that rankings based on in vitro data was not a reliable predictor of in vivo rankings for lower potency chemicals. The methods developed in this work will enable the use of high-content zebrafish behavioral screening data for BMD analysis in toxicological hazard assessment.

59 BASIC BIOLOGICAL SCIENCES↗