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At least 1,747 records · Page 97

Adventures in Parallel Processing: Entry, Descent and Landing Simulation for the Genesis and Stardust Missions

This paper will describe the Entry, Descent and Landing simulation tradeoffs and techniques that were used to provide the Monte Carlo data required to approve entry during a critical period just before entry of the Genesis Sample Return Capsule. The same techniques will be used again when Stardust returns on January 15, 2006. Only one hour was available for the simulation which propagated 2000 dispersed entry states to the ground. Creative simulation tradeoffs combined with parallel processing were needed to provide the landing footprint statistics that were an essential part of the Go/NoGo decision that authorized release of the Sample Return Capsule a few hours before entry.

Lyons, Daniel T.↗

Improved Impact of Atmospheric Infrared Sounder (AIRS) Radiance Assimilation in Numerical Weather Prediction

Improvements to global and regional numerical weather prediction (NWP) have been demonstrated through assimilation of data from NASA s Atmospheric Infrared Sounder (AIRS). Current operational data assimilation systems use AIRS radiances, but impact on regional forecasts has been much smaller than for global forecasts. Retrieved profiles from AIRS contain much of the information that is contained in the radiances and may be able to reveal reasons for this reduced impact. Assimilating AIRS retrieved profiles in an identical analysis configuration to the radiances, tracking the quantity and quality of the assimilated data in each technique, and examining analysis increments and forecast impact from each data type can yield clues as to the reasons for the reduced impact. By doing this with regional scale models individual synoptic features (and the impact of AIRS on these features) can be more easily tracked. This project examines the assimilation of hyperspectral sounder data used in operational numerical weather prediction by comparing operational techniques used for AIRS radiances and research techniques used for AIRS retrieved profiles. Parallel versions of a configuration of the Weather Research and Forecasting (WRF) model with Gridpoint Statistical Interpolation (GSI) that mimics the analysis methodology, domain, and observational datasets for the regional North American Mesoscale (NAM) model run at the National Centers for Environmental Prediction (NCEP)/Environmental Modeling Center (EMC) are run to examine the impact of each type of AIRS data set. The first configuration will assimilate the AIRS radiance data along with other conventional and satellite data using techniques implemented within the operational system; the second configuration will assimilate AIRS retrieved profiles instead of AIRS radiances in the same manner. Preliminary results of this study will be presented and focus on the analysis impact of the radiances and profiles for selected cases.

Zavodsky, Bradley↗

High Performance Parallel Architectures

Traditional remote sensing instruments are multispectral, where observations are collected at a few different spectral bands. Recently, many hyperspectral instruments, that can collect observations at hundreds of bands, have been operational. Furthermore, there have been ongoing research efforts on ultraspectral instruments that can produce observations at thousands of spectral bands. While these remote sensing technology developments hold great promise for new findings in the area of Earth and space science, they present many challenges. These include the need for faster processing of such increased data volumes, and methods for data reduction. Dimension Reduction is a spectral transformation, aimed at concentrating the vital information and discarding redundant data. One such transformation, which is widely used in remote sensing, is the Principal Components Analysis (PCA). This report summarizes our progress on the development of a parallel PCA and its implementation on two Beowulf cluster configuration; one with fast Ethernet switch and the other with a Myrinet interconnection. Details of the implementation and performance results, for typical sets of multispectral and hyperspectral NASA remote sensing data, are presented and analyzed based on the algorithm requirements and the underlying machine configuration. It will be shown that the PCA application is quite challenging and hard to scale on Ethernet-based clusters. However, the measurements also show that a high- performance interconnection network, such as Myrinet, better matches the high communication demand of PCA and can lead to a more efficient PCA execution.

El-Ghazawi, Tarek↗

Performance Assessment of OVERFLOW on Distributed Computing Environment

The aerodynamic computer code, OVERFLOW, with a multi-zone overset grid feature, has been parallelized to enhance its performance on distributed and shared memory paradigms. Practical application benchmarks have been set to assess the efficiency of code's parallelism on high-performance architectures. The code's performance has also been experimented with in the context of the distributed computing paradigm on distant computer resources using the Information Power Grid (IPG) toolkit, Globus. Two parallel versions of the code, namely OVERFLOW-MPI and -MLP, have developed around the natural coarse grained parallelism inherent in a multi-zonal domain decomposition paradigm. The algorithm invokes a strategy that forms a number of groups, each consisting of a zone, a cluster of zones and/or a partition of a large zone. Each group can be thought of as a process with one or multithreads assigned to it and that all groups run in parallel. The -MPI version of the code uses explicit message-passing based on the standard MPI library for sending and receiving interzonal boundary data across processors. The -MLP version employs no message-passing paradigm; the boundary data is transferred through the shared memory. The -MPI code is suited for both distributed and shared memory architectures, while the -MLP code can only be used on shared memory platforms. The IPG applications are implemented by the -MPI code using the Globus toolkit. While a computational task is distributed across multiple computer resources, the parallelism can be explored on each resource alone. Performance studies are achieved with some practical aerodynamic problems with complex geometries, consisting of 2.5 up to 33 million grid points and a large number of zonal blocks. The computations were executed primarily on SGI Origin 2000 multiprocessors and on the Cray T3E. OVERFLOW's IPG applications are carried out on NASA homogeneous metacomputing machines located at three sites, Ames, Langley and Glenn. Plans for the future will exploit the distributed parallel computing capability on various homogeneous and heterogeneous resources and large scale benchmarks. Alternative IPG toolkits will be used along with sophisticated zonal grouping strategies to minimize the communication time across the computer resources.

Djomehri, M. Jahed↗

Improvements to a Batch Pentadiagonal Solver on NVIDIA GPUs

This poster presents the recent work in OVERFLOW to port the batched pentadiagonal solver to NVIDIA GPUs. There are five pentadiagonal systems for each pencil in the grid but three of these systems share the same LHS. Our first simple approach for porting the pentadiagonal solver to the GPUs was to take advantage of the shared LHS by assigning three threads to the three LHS of each pencil. We demonstrated that this custom solver was 92% faster than the NVIDIA batched pentadiagonal library implementation on a V100 GPU due to the lower memory bandwidth requirements. The second approach treated each pentadiagonal system as a 2x2 block tridiagonal system and used a variant of the parallel cyclic reduction algorithm to solve the problem. One benefit of this approach is that it does not require interleaving the data between each system. We demonstrated that this algorithm is 2.18x faster than the NVIDIA library implementation for the same amount of work. If we take advantage of our shared LHS, this approach is 2.58x faster than the library implementation on a V100 GPU.

GPU Programming↗

PHASM: A Toolkit for Creating AI Surrogate Models within Legacy Codebases

PHASM (“Parallel Hardware viA Surrogate Models”) is a software toolkit for creating AI-based surrogate models of scientific code. AI-based surrogate models are widely used for creating fast and inverse simulations. PHASM anticipates an additional future use case: adapting legacy code to modern hardware. While data centers are investing in heterogeneous hardware such as GPUs and FPGAs, many established scientific codebases remain unable to take advantage of the hardware’s higher parallelism without undergoing a costly rewrite. An alternative is to train a AI-based surrogate model to mimic computationally intensive functions in the code, and run the surrogate instead. PHASM formalizes a development lifecycle for such surrogate models, including discovering functions amenable to replacement with a surrogate model, predicting the resulting performance, identifying the function’s space of inputs and outputs, binding the model to the code, and managing model versions. A suite of software tools for facilitating these steps was written and validated against a set of model problems.

97 MATHEMATICS AND COMPUTING↗

Algorithms and programming tools for image processing on the MPP, part 2

A number of algorithms were developed for image warping and pyramid image filtering. Techniques were investigated for the parallel processing of a large number of independent irregular shaped regions on the MPP. In addition some utilities for dealing with very long vectors and for sorting were developed. Documentation pages for the algorithms which are available for distribution are given. The performance of the MPP for a number of basic data manipulations was determined. From these results it is possible to predict the efficiency of the MPP for a number of algorithms and applications. The Parallel Pascal development system, which is a portable programming environment for the MPP, was improved and better documentation including a tutorial was written. This environment allows programs for the MPP to be developed on any conventional computer system; it consists of a set of system programs and a library of general purpose Parallel Pascal functions. The algorithms were tested on the MPP and a presentation on the development system was made to the MPP users group. The UNIX version of the Parallel Pascal System was distributed to a number of new sites.

Reeves, Anthony P.↗

Phase transformation path in Aluminum under ramp compression; simulation and experimental study

Abstract We present a framework based on non-equilibrium molecular dynamics (NEMD) to reproduce the phase transformation event of Aluminum under ramp compression loading. The simulated stress-density response, virtual x-ray diffraction patterns, and structure analysis are compared against the previously observed experimental laser-driven ramp compression in-situ x-ray diffraction data. The NEMD simulations show the solid–solid phase transitions are consistent to experimental observations with a close-packed face-centered cubic (fcc) (111), hexagonal close-packed (hcp) structure (002), and body-centered cubic bcc (110) planes remaining parallel. The atomic-level analysis of NEMD simulations identifiy the exact phase transformation pathway happening via Bain transformation while the previous in situ x-ray diffraction data did not provide sufficient information for deducing the exact phase transformation path.

36 MATERIALS SCIENCE↗

Operationally Efficient Propulsion System Study (OEPSS) Data Book: Integrated Booster Propulsion Module (BPM) Engine Start Dynamics - Volume 8

A fluid-dynamic, digital-transient computer model of an integrated, parallel propulsion system was developed for the CDC mainframe and the SUN workstation computers. Since all STME component designs were used for the integrated system, computer subroutines were written characterizing the performance and geometry of all the components used in the system, including the manifolds. Three transient analysis reports were completed. The first report evaluated the feasibility of integrated engine systems in regards to the start and cutoff transient behavior. The second report evaluated turbopump out and combined thrust chamber/turbopump out conditions. The third report presented sensitivity study results in staggered gas generator spin start and in pump performance characteristics.

Kemp, Victoria R.↗

Vibrational Dependence of Line Coupling and Line Mixing in Self-Broadened Parallel Bands of NH3

Line coupling and line mixing effects have been calculated for several self-broadened NH3 lines in parallel bands involving an excited v2 mode. It is well known that once the v2 mode is excited, the inversion splitting quickly increases as this quantum number increases. In the present study, we have shown that the v2 dependence of the inversion splitting plays a dominant role in the calculated line-shape parameters. For the v2 band with a 36 cm-1 splitting, the intra-doublet couplings practically disappear and for the 2v2 and 2v2 - v2 bands with much higher splitting values, they are completely absent. With respect to the inter-doublet coupling, it becomes the most efficient coupling mechanism for the v2 band, but it is also completely absent for bands with higher v2 quantum numbers. Because line mixing is caused by line coupling, the above conclusions on line coupling are also applicable for line mixing. Concerning the check of our calculated line mixing effects, while the present formalism has well explained the line mixing signatures observed in the v1 band, there are large discrepancies between the measured Rosenkranz mixing parameters and our calculated results for the v2 and 2v2 bands. In order to clarify these discrepancies, we propose to make some new measurements. In addition, we have calculated self-broadened half-widths in the v2 and 2v2 bands and made comparisons with several measurements and with the values listed in HITRAN 2012. In general, the agreements with measurements are very good. In contrast, the agreement with HITRAN 2012 is poor, indicating that the empirical formula used to predict the HITRAN 2012 data has to be updated.

Parallel bands↗

Scalable line and plane relaxation in a parallel structured multigrid solver

The efficient solution of sparse, linear systems that arise through the discretization of partial differential equations remains a key challenge for a range of high performance scientific simulations. One approach for reducing data movement and improving performance is by exposing and exploiting structure in a problem through the use of robust structured multilevel solvers. By choosing coarsening that preserves the structure of the problem, these methods maintain efficient structured computation and communication throughout the multigrid hierarchy. However, when coarsening is not permitted to be dependent on the operator, anisotropy must be addressed by the smoother — producing error compatible for coarse-grid correction with structured coarsening. Here, the components required in a scalable parallel structured solver are described with a focus on memory and communication efficiency of robust smoothers. While the implementation of communication and memory reduction techniques in smoothers integrated in a complete 3D solver present a significant engineering challenge, a novel approach is proposed that addresses these challenges systematically through a change to the solver’s execution model. Enabled by user-level threading paired with a set of data and communication abstractions, this approach permits seamless aggregation of communication in plane smoothers — directly reusing code for a 2D distributed multilevel cycle. Results show an effective reduction in communication costs for coarse-grid problems, and result in a speedup of 8.7x in smoothing routines shown in Fig. 12 using this approach. This produces a significant improvement to strong scalability while maintaining favorable weak scaling behavior. Finally, a parallel scaling study using a series of refined meshes is included that demonstrates the effectiveness of this approach in an application of interest.

97 MATHEMATICS AND COMPUTING↗

Run-time scheduling and execution of loops on message passing machines

Sparse system solvers and general purpose codes for solving partial differential equations are examples of the many types of problems whose irregularity can result in poor performance on distributed memory machines. Often, the data structures used in these problems are very flexible. Crucial details concerning loop dependences are encoded in these structures rather than being explicitly represented in the program. Good methods for parallelizing and partitioning these types of problems require assignment of computations in rather arbitrary ways. Naive implementations of programs on distributed memory machines requiring general loop partitions can be extremely inefficient. Instead, the scheduling mechanism needs to capture the data reference patterns of the loops in order to partition the problem. First, the indices assigned to each processor must be locally numbered. Next, it is necessary to precompute what information is needed by each processor at various points in the computation. The precomputed information is then used to generate an execution template designed to carry out the computation, communication, and partitioning of data, in an optimized manner. The design is presented for a general preprocessor and schedule executer, the structures of which do not vary, even though the details of the computation and of the type of information are problem dependent.

Crowley, Kay↗

Run-time scheduling and execution of loops on message passing machines

Sparse system solvers and general purpose codes for solving partial differential equations are examples of the many types of problems whose irregularity can result in poor performance on distributed memory machines. Often, the data structures used in these problems are very flexible. Crucial details concerning loop dependences are encoded in these structures rather than being explicitly represented in the program. Good methods for parallelizing and partitioning these types of problems require assignment of computations in rather arbitrary ways. Naive implementations of programs on distributed memory machines requiring general loop partitions can be extremely inefficient. Instead, the scheduling mechanism needs to capture the data reference patterns of the loops in order to partition the problem. First, the indices assigned to each processor must be locally numbered. Next, it is necessary to precompute what information is needed by each processor at various points in the computation. The precomputed information is then used to generate an execution template designed to carry out the computation, communication, and partitioning of data, in an optimized manner. The design is presented for a general preprocessor and schedule executer, the structures of which do not vary, even though the details of the computation and of the type of information are problem dependent.

Saltz, Joel↗

Field-Programmable Gate Array Computer in Structural Analysis: An Initial Exploration

This paper reports on an initial assessment of using a Field-Programmable Gate Array (FPGA) computational device as a new tool for solving structural mechanics problems. A FPGA is an assemblage of binary gates arranged in logical blocks that are interconnected via software in a manner dependent on the algorithm being implemented and can be reprogrammed thousands of times per second. In effect, this creates a computer specialized for the problem that automatically exploits all the potential for parallel computing intrinsic in an algorithm. This inherent parallelism is the most important feature of the FPGA computational environment. It is therefore important that if a problem offers a choice of different solution algorithms, an algorithm of a higher degree of inherent parallelism should be selected. It is found that in structural analysis, an 'analog computer' style of programming, which solves problems by direct simulation of the terms in the governing differential equations, yields a more favorable solution algorithm than current solution methods. This style of programming is facilitated by a 'drag-and-drop' graphic programming language that is supplied with the particular type of FPGA computer reported in this paper. Simple examples in structural dynamics and statics illustrate the solution approach used. The FPGA system also allows linear scalability in computing capability. As the problem grows, the number of FPGA chips can be increased with no loss of computing efficiency due to data flow or algorithmic latency that occurs when a single problem is distributed among many conventional processors that operate in parallel. This initial assessment finds the FPGA hardware and software to be in their infancy in regard to the user conveniences; however, they have enormous potential for shrinking the elapsed time of structural analysis solutions if programmed with algorithms that exhibit inherent parallelism and linear scalability. This potential warrants further development of FPGA-tailored algorithms for structural analysis.

Singleterry, Robert C., Jr.↗

Integrated hydrogeophysical modelling and data assimilation for geoelectrical leak detection

Time-lapse electrical resistivity tomography (ERT) measurements provide indirect observations of hydrological processes in the Earth's shallow subsurface at high spatial and temporal resolution. ERT has been used in the past decades to detect leaks and monitor the evolution of associated contaminant plumes. Specifically, inverted resistivity images allow visualization of the dynamic changes in the structure of the plume. However, existing methods do not allow the direct estimation of leak parameters (e.g. leak rate, location, etc.) and their uncertainties. We propose an ensemble-based data assimilation framework that evaluates proposed hydrological models against observed time-lapse ERT measurements without directly inverting for the resistivities. Each proposed hydrological model is run through the parallel coupled hydro-geophysical simulation code PFLOTRAN-E4D to obtain simulated ERT measurements. The ensemble of model proposals is then updated using an iterative ensemble smoother. In this paper, we demonstrate the proposed framework on synthetic and field ERT data from controlled tracer injection experiments. Our results show that the approach allows joint identification of contaminant source location, initial release time, and solute loading from the cross-borehole time-lapse ERT data, alongside with an assessment of uncertainties in these estimates. We demonstrate a reduction in site-wide uncertainty by comparing the prior and posterior plume mass discharges at a selected image plane. This framework is particularly attractive to sites that have previously undergone extensive geological investigation (e.g., nuclear sites). It is well suited to complement ERT imaging and we discuss practical issues in its application to field problems.

58 GEOSCIENCES↗

Advancing specialized biofoundries via automated adaptive laboratory evolution

Adaptive laboratory evolution (ALE) is a powerful strategy for improving microbial phenotypes by harnessing natural selection under defined environmental conditions. Through applying selection regimes, beneficial mutations accumulate, enabling the generation of strains with enhanced properties. However, conventional ALE is labor-intensive and difficult to scale, limiting reproducibility and broader discovery of evolutionary principles. Recent advances in robotics, automation, and computational infrastructure are transforming ALE into a scalable, data-rich experimental paradigm. Automated platforms enable standardized and complex protocols, real-time monitoring, and highly parallel evolution campaigns, improving consistency while generating longitudinal datasets that reveal convergent adaptive mechanisms. Here, we discuss the role of specialized biofoundries in advancing automated ALE and enabling large-scale evolutionary engineering. We review major automated ALE formats and outline key design principles for effective ALE biofoundries, highlighting how automated ALE can support autonomous experimentation and AI-guided strain engineering.

59 BASIC BIOLOGICAL SCIENCES↗

Dataset of simulated vibrational density of states and X-ray diffraction profiles of mechanically deformed and disordered atomic structures in Gold, Iron, Magnesium, and Silicon

This dataset is comprised of a library of atomistic structure files and corresponding X-ray diffraction (XRD) profiles and vibrational density of states (VDoS) profiles for bulk single crystal silicon (Si), gold (Au), magnesium (Mg), and iron (Fe) with and without disorder introduced into the atomic structure and with and without mechanical loading. Included with the atomistic structure files are descriptor files that measure the stress state, phase fractions, and dislocation content of the microstructures. All data was generated via molecular dynamics or molecular statics simulations using the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) code. This dataset can inform the understanding of how local or global changes to a materials microstructure can alter their spectroscopic and diffraction behavior across a variety of initial structure types (cubic diamond, face-centered cubic (FCC), hexagonal close-packed (HCP), and body-centered cubic (BCC) for Si, Au, Mg, and Fe, respectively) and overlapping changes to the microstructure (i.e., both disorder insertion and mechanical loading).

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Evaluation of a pair-based, joint-likelihood association approach for regional infrasound event identification

SUMMARY A Bayesian framework for the association of infrasonic detections is presented and evaluated for analysis at regional propagation scales. A pair-based, joint-likelihood association approach is developed that identifies events by computing the probability that individual detection pairs are attributable to a hypothetical common source and applying hierarchical clustering to identify events from the pair-based analysis. The framework is based on a Bayesian formulation introduced for infrasonic source localization and utilizes the propagation models developed for that application with modifications to improve the numerical efficiency of the analysis. Clustering analysis is completed using hierarchical analysis via weighted linkage for a non-Euclidean distance matrix defined by the negative log-joint-likelihood values. The method is evaluated using regional synthetic data with propagation distances of hundreds of kilometres in order to study the sensitivity of the method to uncertainties and errors in backazimuth and time of arrival. The method is found to be robust and stable for typical uncertainties, able to effectively distinguish noise detections within the data set from those in events, and can be made numerically efficient due to its ease of parallelization.

58 GEOSCIENCES↗