SEARCH · Engineering Papers

Results for “software development framework”

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.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,531 records · Page 85

All sources NASA NTRS DOE OSTI

DOE OSTI2025

Calibrating a finite-strain phase-field model of fracture for bonded granular materials with uncertainty quantification

To study the mechanical behavior of mock high explosives, an experimental and simulation program was developed to calibrate, with quantified uncertainty, a material model of the bonded granular material Idoxuridine and nitroplasticized Estane-5703. This paper reports on the efficacy of such a framework as a generalizable methodology for calibrating material models against experimental data with uncertainty quantification. Additionally, this paper studies the effect of two manufacturing temperatures and three initial granular configurations on the unconfined compressive behavior of the resulting bonded granular materials. In each of these cases, the same calibration framework was used; in that, hundreds of high-fidelity direct numerical simulations using a new, graphics processing unit-enabled, high-performance finite element method software, Ratel, were run to calibrate a finite-strain phase-field fracture model against experimental data. It was found that manufacturing temperature influenced the elastic response of the mock high explosives, with higher temperatures yielding a stiffer response. By contrast, it was found that the initial configuration of the grains had a negligible impact on the overall behavior of the mock high explosives though it remains possible that local damage accumulation within the specimens could be altered by the initial configurations. Overall, the calibration framework was successful at creating well-calibrated models, showing its usefulness as an engineering and scientific tool.

36 MATERIALS SCIENCE↗

DOE OSTI2013

Hierarchical Petascale Simulation Framework For Stress Corrosion Cracking

A number of major accomplishments resulted from the project. These include: • Data Structures, Algorithms, and Numerical Methods for Reactive Molecular Dynamics. We have developed a range of novel data structures, algorithms, and solvers (amortized ILU, Spike) for use with ReaxFF and charge equilibration. • Parallel Formulations of ReactiveMD (Purdue ReactiveMolecular Dynamics Package, PuReMD, PuReMD-GPU, and PG-PuReMD) for Messaging, GPU, and GPU Cluster Platforms. We have developed efficient serial, parallel (MPI), GPU (Cuda), and GPU Cluster (MPI/Cuda) implementations. Our implementations have been demonstrated to be significantly better than the state of the art, both in terms of performance and scalability. • Comprehensive Validation in the Context of Diverse Applications. We have demonstrated the use of our software in diverse systems, including silica-water, silicon-germanium nanorods, and as part of other projects, extended it to applications ranging from explosives (RDX) to lipid bilayers (biomembranes under oxidative stress). • Open Source Software Packages for Reactive Molecular Dynamics. All versions of our soft- ware have been released over the public domain. There are over 100 major research groups worldwide using our software. • Implementation into the Department of Energy LAMMPS Software Package. We have also integrated our software into the Department of Energy LAMMPS software package.

36 MATERIALS SCIENCE↗

DOE OSTI2014

Numerical Implementation of Time-Dependent Density Functional Theory for Extended Systems in Extreme Environments

In recent years, DFT-MD has been shown to be a useful computational tool for exploring the properties of WDM. These calculations achieve excellent agreement with shock compression experiments, which probe the thermodynamic parameters of the Hugoniot state. New X-ray Thomson Scattering diagnostics promise to deliver independent measurements of electronic density and temperature, as well as structural information in shocked systems. However, they require the development of new levels of theory for computing the associated observables within a DFT framework. The experimentally observable x-ray scattering cross section is related to the electronic density-density response function, which is obtainable using TDDFT - a formally exact extension of conventional DFT that describes electron dynamics and excited states. In order to develop a capability for modeling XRTS data and, more generally, to establish a predictive capability for first principles simulations of matter in extreme conditions, real-time TDDFT with Ehrenfest dynamics has been implemented in an existing PAW code for DFT-MD calculations. The purpose of this report is to record implementation details and benchmarks as the project advances from software development to delivering novel scientific results. Results range from tests that establish the accuracy, efficiency, and scalability of our implementation, to calculations that are verified against accepted results in the literature. Aside from the primary XRTS goal, we identify other more general areas where this new capability will be useful, including stopping power calculations and electron-ion equilibration.

97 MATHEMATICS AND COMPUTING↗

NASA NTRSDate not supplied

Evaluation of Precision Landing Performance Using A Generalized Aerospace Simulation in Simulink Framework

NASA’s science and exploration goals to return to the Moon and beyond will need to perform precision landings to place humans and cargo supplies near places of scientific interest, surface resources, or pre-established basecamps. With the maturation of new navigation technology, such as terrain relative navigation, precision landing is now feasible, enabling new exploration sites, such as the lunar poles. However, verification of precision landing performance becomes crucial since not reaching the designated landing site would have a high risk of loss of mission. Therefore, having a high-fidelity simulation platform to evaluate six degrees of freedom vehicle performance during high-risk phases of flight such landing is a fundamental part of the system verification and risk reduction. The NASA Marshall Space Flight Center has developed the GeneraLized Aerospace Simulation in Simulink® (GLASS) tool which incorporates guidance, navigation, and control algorithms, as well as vehicle and environmental models, such as gravity, vehicle mass properties, navigation sensors, propulsion, and terrain models. GLASS uses the MathWorks® Simulink® environment which provides a model-based design framework that allows the incorporation of vehicle models in a modular architecture. The Simulink® environment provides seamless integration with all the MathWorks® capabilities and toolboxes, such as control design toolboxes and Simscape™ Multibody™ dynamics toolbox. The MathWorks® environment also allows for guidance, navigation, and control algorithms to be auto coded in C language, enabling quick software and hardware in the loop testing. This paper provides an overview of GLASS capabilities for analyzing precision landing performance, including navigation trades applied to a NASA human lander reference design architecture.

Guidance↗

DOE OSTI2015

Evolving the Land Information System into a Cloud Computing Service

The Land Information System (LIS) was developed to use advanced flexible land surface modeling and data assimilation frameworks to integrate extremely large satellite- and ground-based observations with advanced land surface models to produce continuous high-resolution fields of land surface states and fluxes. The resulting fields are extremely useful for drought and flood assessment, agricultural planning, disaster management, weather and climate forecasting, water resources assessment, and the like. We envisioned transforming the LIS modeling system into a scientific cloud computing-aware web and data service that would allow clients to easily setup and configure for use in addressing large water management issues. The focus of this Phase 1 project was to determine the scientific, technical, commercial merit and feasibility of the proposed LIS-cloud innovations that are currently barriers to broad LIS applicability. We (a) quantified the barriers to broad LIS utility and commercialization (high performance computing, big data, user interface, and licensing issues); (b) designed the proposed LIS-cloud web service, model-data interface, database services, and user interfaces; (c) constructed a prototype LIS user interface including abstractions for simulation control, visualization, and data interaction, (d) used the prototype to conduct a market analysis and survey to determine potential market size and competition, (e) identified LIS software licensing and copyright limitations and developed solutions, and (f) developed a business plan for development and marketing of the LIS-cloud innovation. While some significant feasibility issues were found in the LIS licensing, overall a high degree of LIS-cloud technical feasibility was found.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2017

Developing EGS Collab Site Geologic Framework Models at the Sanford Underground Research Facility, Lead, South Dakota

The ongoing DOE/GTO funded EGS Collab project aims to stimulate and conduct inter-well flow tests at an intermediate (~10-20 m) in an underground mine in Lead, South Dakota. It is a collaborative initiative where several national laboratories, universities, and other institutions are working together to develop experimental, instrumentation, characterization, and monitoring tools and concepts that could be later employed at a full-scale EGS demonstration FORGE site. In this paper, we describe the development and workflow approach and some preliminary results of earth modeling task for EGS Collab project. We are creating earth models at three different domain scales – EGS Collab, Intermediate, and Large area – using RockWorks 17 software. Local geology, drifts/shafts, and 4850 L boreholes are incorporated in these models. Similarly, available and applicable physical/mechanical properties are also planned to be included in the earth models. Besides providing visualization of the local geology, mine architecture, and bore holes in the test site, the earth modeling task also envision to develop a series of 3-D block models (ASCII files for scattered data/point clouds in the form of X, Y, Z, g) for various physical/mechanical properties of rock. These 3-D block models will provide a consistent baseline value for a parameter of interest to all modeling/simulation groups involved in the EGS Collab project. For this task, we have assembled a preliminary suite of physical/mechanical properties of rocks. Some of the earth modeling results (3-D block models) have been tested by some modeling/simulation team members to test their applicability and for developing additional modeling capability or modifications in RockWorks exported 3-D block models. It is expected that the earth modeling results will be helpful for achieving the overall EGS Collab project objectives.

15 GEOTHERMAL ENERGY↗

DOE OSTI2026

Feasibility Study on Implementing a Staggered-Grid Finite Volume Method for System Analysis Code Development Under the MOOSE Framework

Here, this work summarizes a feasibility study on testing numerical algorithms that are suitable and efficient for advanced system analysis code development under the mutli-physics framework, MOOSE. The key to the test bed is the implementation of high-order one-dimensional staggered-grid finite volume method (SG-FVM), and its direct interaction with the linear/nonlinear solver, PETSc. The test bed utilized a more flexible code structure to enable the finite volume method implementation and direct interacting with the solver package, instead of using the natively supported finite element method by the framework. Using a suite of selected test problems with different problem sizes and levels of complexity, the implemented SG-FVM demonstrated superior performance improvement against a direct finite element method implementation through MOOSE. On two computer systems, the speedup was observed to be significant, with at least one order of magnitude of solving time reduction. For a complex reactor model, transient simulation was performed using the newly developed finite volume method code, the results of which agree very well with the reference results from the finite element method code. Overall, this study demonstrates a successful feasibility study on the proposed numerical algorithms and software structure to support advanced system analysis tool development.

MOOSE↗

NASA NTRS2019

Uncertainty Quantification of a Rotorcraft Conceptual Sizing Toolsuite

A computational framework to support the quantification of system uncertainties and sensitivities for rotorcraft applications is presented using the NASA Design and Analysis of Rotorcraft (NDARC) conceptual sizing tool. A 90 passenger conceptual tiltrotor configuration was used for case demonstration in the modeling of uncertainties in NDARCs emission module. A non-intrusive forward propagation uncertainty quantification approach was applied to ensemble simulations using a Monte Carlo methodology with stratified Latin hypercube sampling. An off-the-shelf software, DAKOTA, which supports trade studies and design space exploration, including optimization, surrogate modeling and uncertainty analysis was used to address the research goals. A toolsuite was further developed incorporating DAKOTA with automated design processes and methods using function wrappers to execute program routines including support for data post-processing. Uncertainties in rotorcraft emissions modeling using the Average Temperature Response metric for a set mission profile were studied. It was shown that for the current study, using the base-line best estimate modeling parameters for the Average Temperature Response metric, NDARC under-estimates the effects of emissions when compared with results from Monte Carlo simulations. A global sensitivity analysis was further undertaken to quantify the contribution of the various emission species on output sensitivity, hence uncertainty. The work demonstrates that the developed toolsuite is robust and will support the quantification of system uncertainties and sensitivities in future rotorcraft design efforts.

Rotorcraft↗

DOE OSTI2015

A paradigm shift - the key to optimal, defensible and transparent waste management, disposal and remediation decisions - 15236

Current methods for structuring nuclear waste management, disposal, and remediation decisions are subject to three major limitations. First, they are based on a series of extraordinarily conservative assumptions. The dominant way of thinking is that, for example, conservative models yield better, safer decisions. Second, they lack methods to meaningfully address and incorporate the 'human dimension'. The dominant way of thinking is that the current approach is sufficient to bring together the values and interests of both internal and external stakeholders in making a decision. And third, they lack a formal method through which both internal and external stakeholders are encouraged collectively to 'think through' complex problems that contain multiple competing objectives so that wise, socially acceptable, and scientifically-defensible decisions are made. To overcome these limitations, a paradigm shift is needed towards a holistic, integrated approach to structure nuclear waste management, disposal and remediation decisions. The first requirement of this paradigm shift is the realization and recognition that the problems faced are decision problems, and that there is a formal theory of decision analysis that can, and should, be used to support finding the best solutions. Decision analysis, very simply, is formalized common sense. The reason it is needed for complex problems is that there are too many moving parts (variables) for humans to manage with out the formalism. Decision analysis leads to addressing problem solving using a combination of a science-based model and a costs/values model. Expectation ('realism') and uncertainty are addressed in the science-based models, whereas stakeholder values, preferences, and desires are addressed when modeling costs and value judgments. Science-based modeling tools have been developed, improved, and used since the current regulatory setting was introduced about 30 years ago. However, modeling of costs and value judgments has not often been addressed using any formal approach, despite the openings that exist in regulations (e.g., CERCLA's modifying criteria and the concept of 'as low as reasonably achievable' referenced in DOE Orders). A discussion of the need and rationale for this paradigm shift is presented, followed by a description of the technical basics of this approach to decision modeling, and ending with an explanation of the steps that are taken in this approach to structured decision-making. A software framework program called Guided Interactive Statistical Decision Tools (GiSdT - pronounced 'gist') is introduced that supports this paradigm shift. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2023

Virtual Engineering Software Framework for Integrated Biomass Conversion Modeling

This presentation covers the design and implementation of a software tool to systematically connect computational models of unit operations to simulate an integrated process of low-temperature conversion of biomass to fuel. This virtual engineering (VE) software was designed with the overarching goal of connecting unit models written in various programming languages and requiring different computational resources within a single, flexible framework. The models and features currently considered for the VE library include mechanistic models for pretreatment, enzymatic hydrolysis, and aerobic bioreaction; high-fidelity computational fluid dynamics (CFD) simulations for enzymatic hydrolysis and aerobic bioreaction; and the capability to perform techno-economic analyses (TEA) using Aspen Plus, a commercial software package. The CFD models require access to high-performance computing (HPC) resources, so in addition to handling multiple programming languages and interfaces, the VE software must also be capable of interacting with an HPC scheduler to submit, run, and post-process jobs. Using the Python programming language, a new VE software package has been developed that contains functionality to manage the input-output communication between various unit models, schedule simulations to run on NREL's HPC and analyze those results, and interface with existing TEA software workflows. A Jupyter-notebook GUI was also created to solicit user input and provide documentation. In cases where multiple models for a particular unit-operation exist, selection between models is accomplished through a simple checkbox, with the appropriate inputs and outputs being parsed and converted seamlessly in the background. Each operation makes use of a different programming language, but the flow of information from pretreatment to enzymatic hydrolysis to bioreaction is managed with an intuitive, centralized file-communication strategy. In this talk, the programming approach and implementation details of the notebook are presented for multiple possibilities of the conversion process, including a demonstration of the ability to manage HPC resources. Additionally, an example of a sensitivity study of treatment parameters governing the overall conversion outcome is shown which highlights the ease of defining new problems using the VE Notebook workflow and leads into a discussion of ongoing work to enable outer-loop optimization studies.

biofuel↗

NASA NTRS2006

Mission Control Technologies: A New Way of Designing and Evolving Mission Systems

Current mission operations systems are built as a collection of monolithic software applications. Each application serves the needs of a specific user base associated with a discipline or functional role. Built to accomplish specific tasks, each application embodies specialized functional knowledge and has its own data storage, data models, programmatic interfaces, user interfaces, and customized business logic. In effect, each application creates its own walled-off environment. While individual applications are sometimes reused across multiple missions, it is expensive and time consuming to maintain these systems, and both costly and risky to upgrade them in the light of new requirements or modify them for new purposes. It is even more expensive to achieve new integrated activities across a set of monolithic applications. These problems impact the lifecycle cost (especially design, development, testing, training, maintenance, and integration) of each new mission operations system. They also inhibit system innovation and evolution. This in turn hinders NASA's ability to adopt new operations paradigms, including increasingly automated space systems, such as autonomous rovers, autonomous onboard crew systems, and integrated control of human and robotic missions. Hence, in order to achieve NASA's vision affordably and reliably, we need to consider and mature new ways to build mission control systems that overcome the problems inherent in systems of monolithic applications. The keys to the solution are modularity and interoperability. Modularity will increase extensibility (evolution), reusability, and maintainability. Interoperability will enable composition of larger systems out of smaller parts, and enable the construction of new integrated activities that tie together, at a deep level, the capabilities of many of the components. Modularity and interoperability together contribute to flexibility. The Mission Control Technologies (MCT) Project, a collaboration of multiple NASA Centers, led by NASA Ames Research Center, is building a framework to enable software to be assembled from flexible collections of components and services.

Trimble, Jay↗

DOE OSTI2024

Path-Integrated Stereo X-Ray Digital Image Correlation: Resolving the Violation of Conservation of Intensity

In this study, x-ray imaging addresses many challenges with visible light imaging in extreme environments, where optical diagnostics such as digital image correlation (DIC) and particle image velocimetry (PIV) suffer biases from index of refraction changes and/or cannot penetrate visibly occluded objects. However, conservation of intensity—the fundamental principle of optical image correlation algorithms—may be violated if ancillary components in the X-ray path besides the surface or fluid of interest move during the test. The test series treated in this work sought to characterize the safe use of fiber-epoxy composites in aerospace and aviation industries during fire accident scenarios. Stereo X-ray DIC was employed to measure test unit deformation in an extreme thermal environment involving a visibly occluded test unit, incident surface heating to temperatures above 600°C, and flames and soot from combusting epoxy decomposition gasses. The objective of the current work is to evaluate two solutions to resolve the violation of conservation of intensity that resulted from both the test unit and the thermal chamber deforming during the test. The first solution recovered conservation of intensity by pre-processing the path-integrated X-ray images to isolate the DIC pattern of the test unit from the thermal chamber components. These images were then correlated with standard, optical DIC software. The second solution, called Path-Integrated Digital Image Correlation (PI-DIC), modified the fundamental matching criterion of DIC to account for multiple, independently-moving components contributing to the final image intensity. The PI-DIC algorithm was extended from a 2D framework to a stereo framework and implemented in a custom DIC software. Both solutions accurately measured the cylindrical shape of the undeformed test unit, recovering radii values of R = 76.20±0.12 mm compared to the theoretical radius of R theor = 76.20 mm. During the test, the test unit bulged asymmetrically as decomposition gasses pressurized the interior and eventually burned in a localized jet. Both solutions measured the heterogeneous radius of this bulge, which reached a maximum of approximately R = 91 mm, with a discrepancy of 2–3% between the two solutions. Two solutions that resolve the violation of conservation of intensity for path-integrated X-ray images were developed. Both were successfully employed in a stereo X-ray DIC configuration to measure deformation of an aluminum-skinned, fiber-epoxy composite test unit in a fire accident scenario.

47 OTHER INSTRUMENTATION↗

DOE OSTI2024

Boosting RDataFrame performance with transparent bulk event processing

RDataFrame is ROOT’s high-level interface for Python and C++ data analysis. Since it first became available, RDataFrame adoption has grown steadily and it is now poised to be a major component of analysis software pipelines for LHC Run 3 and beyond. Thanks to its design inspired by declarative programming principles, RDataFrame enables the development of highperformance, highly parallel analyses without requiring expert knowledge of multi-threading and I/O: user logic is expressed in terms of self-contained, small computation kernels tied together by a high-level API. This design completely decouples analysis logic from its actual execution, and opens several interesting avenues for workflow optimization. In particular, in this work we explore the benefits of moving internal data processing from an event-by-event to a bulkby-bulk loop. This refactoring dramatically reduces the framework’s runtime overheads; in collaboration with the I/O layer it improves data access patterns; it exposes information that optimizing compilers might use to auto-vectorize the invocation of user-defined computations; finally, while existing user-facing interfaces remain unaffected, it becomes possible to additionally offer interfaces that explicitly expose bulks of events, useful e.g. for the injection of GPU kernels into the analysis workflow. In order to inform similar future R&D, design challenges will be presented, as well as an investigation of the relevant timememory trade-off backed by novel performance benchmarks.

Guiraud, Enrico↗

DOE OSTI2012

Framework Application for Core Edge Transport Simulations (FACETS) Performance Analysis (Final Report)

The goal of the FACETS project (Framework Application for Core-Edge Transport Simulations) was to provide a multiphysics, parallel framework application (FACETS) that will enable whole-device modeling for the U.S. fusion program, to provide the modeling infrastructure needed for ITER, the next step fusion confinement device. Through use of modern computational methods, including component technology and object oriented design, FACETS is able to switch from one model to another for a given aspect of the physics in a flexible manner. This enables use of simplified models for rapid turnaround or high-fidelity models that can take advantage of the largest supercomputer hardware. FACETS does so in a heterogeneous parallel context, where different parts of the application execute in parallel by utilizing task farming, domain decomposition, and/or pipelining as needed and applicable. ParaTools, Inc. was tasked with supporting the performance analysis and tuning of the FACETS components and framework in order to achieve the parallel scaling goals of the project. The TAU Performance System® was used for instrumentation, measurement, archiving, and profile / tracing analysis. ParaTools, Inc. also assisted in FACETS performance engineering efforts. Through the use of the TAU Performance System, ParaTools provided instrumentation, measurement, analysis and archival support for the FACETS project. Performance optimization of key components has yielded significant performance speedups. TAU was integrated into the FACETS build for both the full coupled application and the UEDGE component. The performance database provided archival storage of the performance regression testing data generated by the project, and helped to track improvements in the software development.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Integration of Waveform Simulation Methods

The generation of synthetic seismograms through simulation is a fundamental tool of seismology required to run quantitative hypothesis tests. A variety of approaches have been developed throughout the seismological community and each has their own specific user interface based on their implementation. This causes a challenge to researchers who will need to learn new interfaces with each new software they wish to use and create substantial challenges when attempting to compare results from different tools. Here we provide a unified interface that facilitates interoperability amongst several simulation tools through a modern containerized Python package. Further, this package includes post-processing analysis modules designed to facilitate end-to-end analysis of synthetic seismograms. In this report we present the conceptual guidance and an example implementation of the new Waveform Simulation Framework.

58 GEOSCIENCES↗

DOE OSTI2021

Towards Automatic and Agile AI/ML Accelerator Design with End-to-End Synthesis

Domain-specific designs offer greater energy efficiency and performance gain than general-purpose processors. For this reason, modern system-on-chips have a significant portion of their silicon area with custom accelerators. However, designing hardware by hand is laborious and time-consuming, given the large design space and the performance, power, and area constraints that are not realized in the software. Moreover, domain-specific algorithms (e.g., machine learning models) are evolving quickly, challenging the accelerator design further. To address these issues, this paper presents SODA Synthesizer, an automated open-source high-level ML framework to Verilog modular compiler targeting AI/ML Application-Specific Integrated Circuits (ASICs) accelerators. SODA tightly couples the Multi- Level Intermediate Representation (MLIR) compiler infrastructure [24] and open-source HLS approaches. Thus, SODA can support various ML frameworks and algorithms and can perform optimizations that combine specialized architecture templates and conventional HLS to generate the hardware modules. In addition, SODA’s closed-loop design space exploration (DSE) engine allows developers to perform end-to-end design space explorations on different metrics and technology nodes.

Zhang, Jeff↗

DOE OSTI2015

Assessment of grid-friendly collective optimization framework for distributed energy resources

Distributed energy resources have the potential to provide services to facilities and buildings at lower cost and environmental impact in comparison to traditional electric-gridonly services. The reduced cost could result from a combination of higher system efficiency and exploitation of electricity tariff structures. Traditionally, electricity tariffs are designed to encourage the use of ‘off peak’ power and discourage the use of ‘onpeak’ power, although recent developments in renewable energy resources and distributed generation systems (such as their increasing levels of penetration and their increased controllability) are resulting in pressures to adopt tariffs of increasing complexity. Independently of the tariff structure, more or less sophisticated methods exist that allow distributed energy resources to take advantage of such tariffs, ranging from simple pre-planned schedules to Software-as-a-Service schedule optimization tools. However, as the penetration of distributed energy resources increases, there is an increasing chance of a ‘tragedy of the commons’ mechanism taking place, where taking advantage of tariffs for local benefit can ultimately result in degradation of service and higher energy costs for all. In this work, we use a scheduling optimization tool, in combination with a power distribution system simulator, to investigate techniques that could mitigate the deleterious effect of ‘selfish’ optimization, so that the high-penetration use of distributed energy resources to reduce operating costs remains advantageous while the quality of service and overall energy cost to the community is not affected.

Pensini, Alessandro↗

DOE OSTI2014

SWAP-Assembler: scalable and efficient genome assembly towards thousands of cores

Background: There is a widening gap between the throughput of massive parallel sequencing machines and the ability to analyze these sequencing data. Traditional assembly methods requiring long execution time and large amount of memory on a single workstation limit their use on these massive data. Results: This paper presents a highly scalable assembler named as SWAP-Assembler for processing massive sequencing data using thousands of cores, where SWAP is an acronym for Small World Asynchronous Parallel model. In the paper, a mathematical description of multi-step bi-directed graph (MSG) is provided to resolve the computational interdependence on merging edges, and a highly scalable computational framework for SWAP is developed to automatically preform the parallel computation of all operations. Graph cleaning and contig extension are also included for generating contigs with high quality. Experimental results show that SWAP-Assembler scales up to 2048 cores on Yanhuang dataset using only 26 minutes, which is better than several other parallel assemblers, such as ABySS, Ray, and PASHA. Results also show that SWAP-Assembler can generate high quality contigs with good N50 size and low error rate, especially it generated the longest N50 contig sizes for Fish and Yanhuang datasets. Conclusions: In this paper, we presented a highly scalable and efficient genome assembly software, SWAPAssembler. Compared with several other assemblers, it showed very good performance in terms of scalability and contig quality. This software is available at: https://sourceforge.net/projects/swapassembler

59 BASIC BIOLOGICAL SCIENCES↗