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At least 109 records · Page 6

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↗

Scalable Light Module for Low-Cost, High-Efficiency Light- Emitting Diode Luminaires

During this two-year program Cree developed a scalable, modular optical architecture for low-cost, high-efficacy light emitting diode (LED) luminaires. Stated simply, the goal of this architecture was to efficiently and cost-effectively convey light from LEDs (point sources) to broad luminaire surfaces (area sources). By simultaneously developing warm-white LED components and low-cost, scalable optical elements, a high system optical efficiency resulted. To meet program goals, Cree evaluated novel approaches to improve LED component efficacy at high color quality while not sacrificing LED optical efficiency relative to conventional packages. Meanwhile, efficiently coupling light from LEDs into modular optical elements, followed by optimally distributing and extracting this light, were challenges that were addressed via novel optical design coupled with frequent experimental evaluations. Minimizing luminaire bill of materials and assembly costs were two guiding principles for all design work, in the effort to achieve luminaires with significantly lower normalized cost ($/klm) than existing LED fixtures. Chief project accomplishments included the achievement of >150 lm/W warm-white LEDs having primary optics compatible with low-cost modular optical elements. In addition, a prototype Light Module optical efficiency of over 90% was measured, demonstrating the potential of this scalable architecture for ultra-high-efficacy LED luminaires. Since the project ended, Cree has continued to evaluate optical element fabrication and assembly methods in an effort to rapidly transfer this scalable, cost-effective technology to Cree production development groups. The Light Module concept is likely to make a strong contribution to the development of new cost-effective, high-efficacy luminaries, thereby accelerating widespread adoption of energy-saving SSL in the U.S.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Development, Verification and Validation of Parallel, Scalable Volume of Fluid CFD Program for Propulsion Applications

There are many instances involving liquid/gas interfaces and their dynamics in the design of liquid engine powered rockets such as the Space Launch System (SLS). Some examples of these applications are: Propellant tank draining and slosh, subcritical condition injector analysis for gas generators, preburners and thrust chambers, water deluge mitigation for launch induced environments and even solid rocket motor liquid slag dynamics. Commercially available CFD programs simulating gas/liquid interfaces using the Volume of Fluid approach are currently limited in their parallel scalability. In 2010 for instance, an internal NASA/MSFC review of three commercial tools revealed that parallel scalability was seriously compromised at 8 cpus and no additional speedup was possible after 32 cpus. Other non-interface CFD applications at the time were demonstrating useful parallel scalability up to 4,096 processors or more. Based on this review, NASA/MSFC initiated an effort to implement a Volume of Fluid implementation within the unstructured mesh, pressure-based algorithm CFD program, Loci-STREAM. After verification was achieved by comparing results to the commercial CFD program CFD-Ace+, and validation by direct comparison with data, Loci-STREAM-VoF is now the production CFD tool for propellant slosh force and slosh damping rate simulations at NASA/MSFC. On these applications, good parallel scalability has been demonstrated for problems sizes of tens of millions of cells and thousands of cpu cores. Ongoing efforts are focused on the application of Loci-STREAM-VoF to predict the transient flow patterns of water on the SLS Mobile Launch Platform in order to support the phasing of water for launch environment mitigation so that vehicle determinantal effects are not realized.

West, Jeff↗

Memory Scalability and Efficiency Analysis of Parallel Codes

Memory scalability is an enduring problem and bottleneck that plagues many parallel codes. Parallel codes designed for High Performance Systems are typically designed over the span of several, and in some instances 10+, years. As a result, optimization practices which were appropriate for earlier systems may no longer be valid and thus require careful optimization consideration. Specifically, parallel codes whose memory footprint is a function of their scalability must be carefully considered for future exa-scale systems. In this paper we present a methodology and tool to study the memory scalability of parallel codes. Using our methodology we evaluate an application s memory footprint as a function of scalability, which we coined memory efficiency, and describe our results. In particular, using our in-house tools we can pinpoint the specific application components which contribute to the application s overall memory foot-print (application data- structures, libraries, etc.).

Janjusic, Tommy↗

Scalable In Situ Computation of Lagrangian Representations via Local Flow Maps

In situ computation of Lagrangian flow maps to enable post hoc time-varying vector field analysis has recently become an active area of research. However, the current literature is largely limited to theoretical settings and lacks a solution to address scalability of the technique in distributed memory. To improve scalability, we propose and evaluate the benefits and limitations of a simple, yet novel, performance optimization. Our proposed optimization is a communication-free model resulting in local Lagrangian flow maps, requiring no message passing or synchronization between processes, intrinsically improving scalability, and thereby reducing overall execution time and alleviating the encumbrance placed on simulation codes from communication overheads. To evaluate our approach, we computed Lagrangian flow maps for four time-varying simulation vector fields and investigated how execution time and reconstruction accuracy are impacted by the number of GPUs per compute node, the total number of compute nodes, particles per rank, and storage intervals. Our study consisted of experiments computing Lagrangian flow maps with up to 67M particle trajectories over 500 cycles and used as many as 2048 GPUs across 512 compute nodes. In all, our study contributes an evaluation of a communication-free model as well as a scalability study of computing distributed Lagrangian flow maps at scale using in situ infrastructure on a modern supercomputer.

Sane, Sudhanshu↗

Scalable and efficient learning from crowds with Gaussian processes

Over the last few years, multiply-annotated data has become a very popular source of information. Online platforms such as Amazon Mechanical Turk have revolutionized the labelling process needed for any classification task, sharing the effort between a number of annotators (instead of the classical single expert). This crowdsourcing approach has introduced new challenging problems, such as handling disagreements on the annotated samples or combining the unknown expertise of the annotators. Probabilistic methods, such as Gaussian Processes (GP), have proven successful to model this new crowdsourcing scenario. However, GPs do not scale up well with the training set size, which makes them prohibitive for medium-to-large datasets (beyond 10K training instances). This constitutes a serious limitation for current real-world applications. In this work, we introduce two scalable and efficient GP-based crowdsourcing methods that allow for processing previously-prohibitive datasets. The first one is an efficient and fast approximation to GP with squared exponential (SE) kernel. The second allows for learning a more flexible kernel at the expense of a heavier training (but still scalable to large datasets). Since the latter is not a GP-SE approximation, it can be also considered as a whole new scalable and efficient crowdsourcing method, useful for any dataset size. Both methods use Fourier features and variational inference, can predict the class of new samples, and estimate the expertise of the involved annotators. A complete experimentation compares them with state-of-the-art probabilistic approaches in synthetic and real crowdsourcing datasets of different sizes. Finally, they stand out as the best performing approach for large scale problems. Moreover, the second method is competitive with the current state-of-the-art for small datasets.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Scalable and Resilient Etched Metallic Micro- and Nanostructured Surfaces for Enhanced Flow Boiling

Flow boiling and evaporation in tubes and channels occur in a wide variety of energy systems, such as refrigeration, air conditioning, power generation, electronics cooling, distillation, and purification. In this work, we demonstrate remarkably increased heat transfer coefficients of 270% during refrigerant flow boiling in scalable microstructured (~40 µm), industrial-scale (~1 m long) aluminum (Al) tubes, when compared to smooth unstructured Al tubes. To achieve scalable nanomanufacturing, we create highly conformal and durable structured surfaces by relying on hydrochloric acid Al etching. Flow boiling tests were conducted in 6.35 mm diameter Al tubes using R134a refrigerant as the working fluid. To benchmark our approach and to elucidate the effect of the structure length scale, we also fabricated ultrascalable boehmite (AlO(OH)) nanostructured (~300 nm) Al tubes, showing that etched microscale features are necessary and key to enhancement. Durability tests conducted using a 28 day long continual flow boiling experiment demonstrated negligible degradation of the etched surfaces. The scalable and cost-effective techniques used to create these durable, etched-Al microstructures may significantly reduce manufacturing cost when contrasted with current enhancement approaches such as extrusion, drawing, and welding.

36 MATERIALS SCIENCE↗

Scalable continuous flow synthesis of ZnO nanorod arrays in 3-D ceramic honeycomb substrates for low-temperature desulfurization

Scalable and cost-effective synthesis and assembly of technologically important nanostructures in three-dimensional (3D) substrates hold keys to bridge the demonstrated nanotechnologies in academia with industrially relevant scalable manufacturing. In this paper, using ZnO nanorod arrays as an example, a hydrothermal-based continuous flow synthesis (CFS) method is successfully used to integrate the nano-arrays in multi-channeled monolithic cordierite. Compared to the batch process, CFS enhances the average growth rate of nano-arrays by 125%, with the average length increasing from 2 μm to 4.5 μm within the same growth time of 4 hours. The precursor utilization efficiency of CFS is enhanced by 9 times compared to that of batch process by preserving the majority of precursors in recyclable solution. Computational fluid dynamic simulation suggests a steady-state solution flow and mass transport inside the channels of honeycomb substrates, giving rise to steady and consecutive growth of ZnO nano-arrays with an average length of 10 μm in 12 h. The monolithic ZnO nano-array-integrated cordierite obtained through CFS shows enhanced low-temperature (200 °C) desulfurization capacity and recyclability in comparison to ZnO powder wash-coated cordierite. This can be attributed to exposed ZnO {101¯0} planes, better dispersion and stronger interactions between sorbent and reactant in the ZnO nanorod arrays, as well as the sintering-resistance of nano-array configurations during sulfidation–regeneration cycles. Finally, with the demonstrated scalable synthesis and desulfurization performance of ZnO nano-arrays, a promising, industrially relevant integration strategy is provided to fabricate metal oxide nano-array-based monolithic devices for various environmental and energy applications.

36 MATERIALS SCIENCE↗

Scalable Deep Learning via I/O Analysis and Optimization

Scalable deep neural network training has been gaining prominence because of the increasing importance of deep learning in a multitude of scientific and commercial domains. Consequently, a number of researchers have investigated techniques to optimize deep learning systems. Much of the prior work has focused on runtime and algorithmic enhancements to optimize the computation and communication. Despite these enhancements, however, deep learning systems still suffer from scalability limitations, particularly with respect to data I/O. This situation is especially true for training models where the computation can be effectively parallelized, leaving I/O as the major bottleneck. In fact, our analysis shows that I/O can take up to 90% of the total training time. Thus, in this article, we first analyze LMDB, the most widely used I/O subsystem of deep learning frameworks, to understand the causes of this I/O inefficiency. Based on our analysis, we propose LMDBIO—an optimized I/O plugin for scalable deep learning. LMDBIO includes six novel optimizations that together address the various shortcomings in existing I/O for deep learning. Lastly, our experimental results show that LMDBIO significantly outperforms LMDB in all cases and improves overall application performance by up to 65-fold on a 9,216-core system.

97 MATHEMATICS AND COMPUTING↗

Enhancing scalability of a matrix-free eigensolver for studying many-body localization

We propose several techniques to enhance the parallel scalability of a matrix-free eigensolver designed for studying many-body localization (MBL) of quantum spin chain models with nearest-neighbor interactions and on-site disorder. This type of problem is computationally challenging because the dimension of the associated Hamiltonian matrix grows exponentially with respect to the number of spins L, and we need to average over different realizations of the random disorder to obtain relevant statistical behavior. For each disorder realization, we need to compute eigenvalues from different regions of the spectrum and their corresponding eigenvectors. In previous work, the interior eigenstates for a single eigenvalue problem are computed via the shift-and-invert Lanczos algorithm. Due to the extremely high memory footprint of the LU factorizations, this technique is not well suited for large L’s. For example, we need thousands of compute nodes on modern high performance computing infrastructures to go beyond L = 24. The matrix-free approach does not suffer from this memory bottleneck, however, its scalability is limited by a computation and communication load imbalance. To reduce this imbalance and to significantly enhance the scalability of the matrix-free eigensolver, we reorder the matrix and leverage the consistent space runtime, CSPACER. We also show its efficiency in managing irregular communication patterns at scale compared to optimized MPI non-blocking two-sided and one-sided RMA implementation variants. This effort enables us to study MBL for spin chains with a larger number of spins. The efficiency and effectiveness of the proposed algorithm is demonstrated by computing eigenstates on a massively parallel many-core high performance computer.

METIS↗

Scalable Al 2 O 3 –TiO 2 Conductive Oxide Interfaces as Defect Reservoirs for Resistive Switching Devices

Abstract Resistive switching devices herald a transformative technology for memory and computation, offering considerable advantages in performance and energy efficiency. Here, a simple and scalable material system of conductive oxide interfaces is employed, and their unique properties are leveraged for a new type of resistive switching device. An Al 2 O 3 –TiO 2 ‐based valence‐change resistive switching device, where the conductive oxide interface serves both as the bottom electrode and as a reservoir of defects for switching, is demonstrated. The amorphous–polycrystalline Al 2 O 3 –TiO 2 conductive interface is obtained following the technological path of simplifying the fabrication of the 2D electron gases (2DEGs), making them scalable for practical mass integration. Physical analysis of the device chemistry and microstructure with comprehensive electrical analysis of its switching behavior and performance is combined. The origin of the resistive switching is pinpointed to the conductive oxide interface, which serves both as the bottom electrode and as a reservoir of oxygen vacancies. The latter plays a key role in valence‐change resistive switching devices. The new device, based on scalable and complementary metal–oxide–semiconductor (CMOS)‐technology‐compatible fabrication processes, opens new design spaces toward increased tunability and simplification of the device selection challenge.

36 MATERIALS SCIENCE↗

A Novel and Scalable Method for Microencapsulating Salt Hydrate Phase Change Materials in Core–Shell Fibers

Phase change materials (PCMs) are in high demand for applications such as thermal energy storage in buildings, electronics cooling, and thermal management of electric vehicle batteries and data centers. Among these materials, salt hydrate PCMs are particularly attractive due to their high thermal energy storage capacity and low cost. However, they suffer from two major issues: leakage in the melted phase and phase segregation during phase transitions. Microencapsulation is the primary process capable of addressing both of these challenges. However, there is no reliable or scalable method available for microencapsulating salt hydrate PCMs. As a result, the full potential of salt hydrates for building and data center applications has yet to be realized. In this work, we present an innovative method for the microencapsulation of salt hydrate PCMs using a co‐axial pushing technique. This process creates core–shell fibers, with the salt hydrate as the core and a polymer as the shell. Our approach demonstrates strong potential for scalable microencapsulation of salt hydrate PCMs. In conclusion, achieving scalability could enable their widespread use in applications such as data center cooling, battery thermal management, and building climate control.

Sharma, Jaswinder [Oak Ridge National Laboratory (↗

Predicting Low Toxicity and Scalable Solvent Systems for High–Speed Roll–to–Roll Perovskite Manufacturing

Printed lead-based perovskite photovoltaics (PV) have gained interest due to their potential to be manufactured with scalable roll-to-roll techniques. In industrial scale-up, toxicity of inks can constrain roll-to-roll manufacturing due to the added cost of managing toxic effluents. Due to solvent toxicity, few perovskite solution chemistries in published works are scalable to gigawatt production capacity at low cost. Herein, it is shown that for scalable PV production, the use of aprotic polar solvents should be avoided due to their overall toxicity. Compliance with worldwide worker safety regulations for solvent exposure limits could require additional air handling requirements for some solvents, which in turn would affect cost-effectiveness. It is shown that costs associated with handling of hazardous substances can be significant and estimate an added cost of ¢3.7/W for dimethylformamide (DMF)-based inks. To solve this problem, a new perovskite ink solvent system is developed that is composed entirely of ether and alcohol, which has an effective exposure limit 14× higher than DMF, making it suitable for industrial coating processes. Here, it is shown that the new ink solvent system is capable of fabricating high-efficiency perovskite solar cells processed in 1 min on a standard roll-to-roll system.

36 MATERIALS SCIENCE↗

Scalable Representation Learning for Long-Term Augmented Reality-Based Information Delivery in Collaborative Human-Robot Perception

Augmented reality (AR)-based information delivery has been attracting an increasing attention in the past few years to improve com- munication in human-robot teaming. In the long-term use of AR systems for collaborative human-robot perception, one of the biggest challenges is to perform place and scene matching under long-term environmental changes, such as dramatic variations in lighting, weather and vegetation across di erent times of the day, months, and seasons. To address this challenge, we introduce a novel representation learning approach that learns a scalable long-term representation model that can be used for place and scene matching in various long-term conditions. Our approach is formulated as a regularized optimization problem, which selects the most representative scene templates in di erent scenarios to construct a scalable representation of the same place that can exhibit signi cant long-term environment changes. Our approach adaptively learns to select a small subset of the templates to construct the representation model, based on a user-de ned representativeness threshold, which makes the learned model highly scalable to the long-term variations in real-world applications. To solve the formulated optimization problem, a new algo- rithmic solver is designed, which is theoretically guaranteed to converge to the global optima. Experiments are conducted using two large-scale benchmark datasets, which have demonstrated the superior performance of our approach for long-term place and scene matching.

42 ENGINEERING↗

Scalable Data Management of the Uintah Simulation Framework for Next-Generation Engineering Problems with Radiation

The need to scale next-generation industrial engineering problems to the largest computational platforms presents unique challenges. This paper focuses on data management related problems faced by the Uintah simulation framework at a production scale of 260K processes. Uintah provides a highly scalable asynchronous many-task runtime system, which in this work is used for the modeling of a 1000 megawatt electric (MWe) ultra-supercritical (USC) coal boiler. At 260K processes, we faced both parallel I/O and visualization related challenges, e.g., the default file-per-process I/O approach of Uintah did not scale on Mira. In this paper we present a simple to implement, restructuring based parallel I/O technique. We impose a restructuring step that alters the distribution of data among processes. The goal is to distribute the dataset such that each process holds a larger chunk of data, which is then written to a file independently. This approach finds a middle ground between two of the most common parallel I/O schemes–file per process I/O and shared file I/O–in terms of both the total number of generated files, and the extent of communication involved during the data aggregation phase. To address scalability issues when visualizing the simulation data, we developed a lightweight renderer using OSPRay, which allows scientists to visualize the data interactively at high quality and make production movies. Finally, this work presents a highly efficient and scalable radiation model based on the sweeping method, which significantly outperforms previous approaches in Uintah, like discrete ordinates. The integrated approach allowed the USC boiler problem to run on 260K CPU cores on Mira.

97 MATHEMATICS AND COMPUTING↗

Scalable electric-field-assisted fabrication of vertically aligned carbon nanotube membranes with flow enhancement

In this work, we report a solution-based approach for fabricating vertically aligned carbon-nanotube (VACNT) membranes, which improves on the unaligned nature of CNT mixed-matrix membranes. This approach addresses important challenges regarding scalability and incorporation of different types and sizes of nanotube as pores in a membrane. In a new, solvent-deposition approach, CNTs are dispersed and then aligned and concentrated via electro-deposition from an organic solvent, using a composite AC + DC electric field to form aligned CNT arrays. This enables VACNT number densities that are two orders-of-magnitude higher than possible from direct suspension of CNTs in the liquid oligomer. The solvent is then replaced by a UV-curable oligomer, which is selectively cured to form macroscopic membranes of highly controlled thickness. After plasma etching to open pores, the VACNT membranes are shown to be permeable, and to have pore sizes consistent with flow through internal channels of the CNTs. In a first for field-aligned, solution-fabricated VACNT membranes, the pores show substantial, 100–300 × , gas-flow enhancement compared to theory, similar to membranes fabricated via less scalable methods (i.e., by CVD growth of already aligned CNT forests). The solution-based, electric-field-assisted approach aligns nanotubes of different sizes and types grown by any means, and is scalable to the efficient fabrication of large-area VACNT membranes for a variety of important applications.

36 MATERIALS SCIENCE↗

Scalable implicit incompressible resistive MHD with stabilized FE and fully-coupled Newton–Krylov-AMG

Here, we discuss that the computational solution of the governing balance equations for mass, momentum, heat transfer and magnetic induction for resistive magnetohydrodynamics (MHD) systems can be extremely challenging. These difficulties arise from both the strong nonlinear, nonsymmetric coupling of fluid and electromagnetic phenomena, as well as the significant range of time- and length-scales that the interactions of these physical mechanisms produce. This paper explores the development of a scalable, fully-implicit stabilized unstructured finite element (FE) capability for 3D incompressible resistive MHD. The discussion considers the development of a stabilized FE formulation in context of the variational multiscale (VMS) method, and describes the scalable implicit time integration and direct-to-steady-state solution capability. The nonlinear solver strategy employs Newton–Krylov methods, which are preconditioned using fully-coupled algebraic multilevel preconditioners. These preconditioners are shown to enable a robust, scalable and efficient solution approach for the large-scale sparse linear systems generated by the Newton linearization. Verification results demonstrate the expected order-of-accuracy for the stabilized FE discretization. The approach is tested on a variety of prototype problems, that include MHD duct flows, an unstable hydromagnetic Kelvin–Helmholtz shear layer, and a 3D island coalescence problem used to model magnetic reconnection. Initial results that explore the scaling of the solution methods are also presented on up to 128K processors for problems with up to 1.8B unknowns on a CrayXK7.

97 MATHEMATICS AND COMPUTING↗

Toucan: A performance portable, scalable implementation of the DECA algorithm

In the field of additive manufacturing (AM), cellular automata (CA) is extensively used to simulate microstructural evolution during solidification. However, while traditional CA approaches are relatively fast, they still require a substantial number of time steps, are limited to moderate volumes, and are relatively difficult to improve through parallelism due to the highly localized nature of the solidification front. Here, to address these issues of time to solution and load balancing, we introduce Toucan, a parallel, performance-portable, and scalable code written in C++ with the Kokkos library that leverages the discrete event inspired cellular automata (DECA) algorithm to perform parallel-in-time (PinT) grain growth simulations. Toucan effectively mitigates load balancing issues by distributing the computational workload more evenly across processors, enhancing scalability and efficiency. We conduct both strong and weak scaling studies on up to 64 GPUs on the Frontier supercomputer, demonstrating that Toucan significantly outperforms the current state-of-the-art, time-stepped CA code, ExaCA, on both single and multi-GPU simulations. Even in AM-specific weak scaling scenarios, Toucan maintains near-ideal scaling, in contrast to the linear increase observed with ExaCA due to the moving laser raster pattern. This study highlights Toucan’s potential to transform microstructural simulations in AM by radically improving both efficiency and scalability over existing methods.

36 MATERIALS SCIENCE↗