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At least 109 records · Page 6

[Earth Science Technology Office's Computational Technologies Project]

This grant supported the effort to characterize the problem domain of the Earth Science Technology Office's Computational Technologies Project, to engage the Beowulf Cluster Computing Community as well as the High Performance Computing Research Community so that we can predict the applicability of said technologies to the scientific community represented by the CT project and formulate long term strategies to provide the computational resources necessary to attain the anticipated scientific objectives of the CT project. Specifically, the goal of the evaluation effort is to use the information gathered over the course of the Round-3 investigations to quantify the trends in scientific expectations, the algorithmic requirements and capabilities of high-performance computers to satisfy this anticipated need.

Fischer, James↗

Computational Approaches to Simulation and Optimization of Global Aircraft Trajectories

This study examines three possible approaches to improving the speed in generating wind-optimal routes for air traffic at the national or global level. They are: (a) using the resources of a supercomputer, (b) running the computations on multiple commercially available computers and (c) implementing those same algorithms into NASA’s Future ATM Concepts Evaluation Tool (FACET) and compares those to a standard implementation run on a single CPU. Wind-optimal aircraft trajectories are computed using global air traffic schedules. The run time and wait time on the supercomputer for trajectory optimization using various numbers of CPUs ranging from 80 to 10,240 units are compared with the total computational time for running the same computation on a single desktop computer and on multiple commercially available computers for potential computational enhancement through parallel processing on the computer clusters. This study also re-implements the trajectory optimization algorithm for further reduction of computational time through algorithm modifications and integrates that with FACET to facilitate the use of the new features which calculate time-optimal routes between worldwide airport pairs in a wind field for use with existing FACET applications. The implementations of trajectory optimization algorithms use MATLAB, Python, and Java programming languages. The performance evaluations are done by comparing their computational efficiencies and based on the potential application of optimized trajectories. The paper shows that in the absence of special privileges on a supercomputer, a cluster of commercially available computers provides a good option for computing wind-optimal trajectories for national and global air traffic system studies.

Ng, Hok K.↗

Construction of Blaze at the University of Illinois at Chicago: A Shared, High-Performance, Visual Computer for Next-Generation Cyberinfrastructure-Accelerated Scientific, Engineering, Medical and Public Policy Research

The Blaze high-performance visual computing system serves the high-performance computing research and education needs of University of Illinois at Chicago (UIC). Blaze consists of a state-of-the-art, networked, computer cluster and ultra-high-resolution visualization system called CAVE2(TM) that is currently not available anywhere in Illinois. This system is connected via a high-speed 100-Gigabit network to the State of Illinois' I-WIRE optical network, as well as to national and international high speed networks, such as the Internet2, and the Global Lambda Integrated Facility. This enables Blaze to serve as an on-ramp to national cyberinfrastructure, such as the National Science Foundation’s Blue Waters petascale computer at the National Center for Supercomputing Applications at the University of Illinois at Chicago and the Department of Energy’s Argonne Leadership Computing Facility (ALCF) at Argonne National Laboratory. DOE award # DE-SC005067, leveraged with NSF award #CNS-0959053 for “Development of the Next-Generation CAVE Virtual Environment (NG-CAVE),” enabled us to create a first-of-its-kind high-performance visual computing system. The UIC Electronic Visualization Laboratory (EVL) worked with two U.S. companies to advance their commercial products and maintain U.S. leadership in the global information technology economy. New applications are being enabled with the CAVE2/Blaze visual computing system that is advancing scientific research and education in the U.S. and globally, and help train the next-generation workforce.

47 OTHER INSTRUMENTATION↗

SU-E-T-314: The Application of Cloud Computing in Pencil Beam Scanning Proton Therapy Monte Carlo Simulation

Purpose: Monte Carlo simulation plays an important role for proton Pencil Beam Scanning (PBS) technique. However, MC simulation demands high computing power and is limited to few large proton centers that can afford a computer cluster. We study the feasibility of utilizing cloud computing in the MC simulation of PBS beams. Methods: A GATE/GEANT4 based MC simulation software was installed on a commercial cloud computing virtual machine (Linux 64-bits, Amazon EC2). Single spot Integral Depth Dose (IDD) curves and in-air transverse profiles were used to tune the source parameters to simulate an IBA machine. With the use of StarCluster software developed at MIT, a Linux cluster with 2–100 nodes can be conveniently launched in the cloud. A proton PBS plan was then exported to the cloud where the MC simulation was run. Results: The simulated PBS plan has a field size of 10×10cm{sup 2}, 20cm range, 10cm modulation, and contains over 10,000 beam spots. EC2 instance type m1.medium was selected considering the CPU/memory requirement and 40 instances were used to form a Linux cluster. To minimize cost, master node was created with on-demand instance and worker nodes were created with spot-instance. The hourly cost for the 40-node cluster was $0.63 and the projected cost for a 100-node cluster was $1.41. Ten million events were simulated to plot PDD and profile, with each job containing 500k events. The simulation completed within 1 hour and an overall statistical uncertainty of < 2% was achieved. Good agreement between MC simulation and measurement was observed. Conclusion: Cloud computing is a cost-effective and easy to maintain platform to run proton PBS MC simulation. When proton MC packages such as GATE and TOPAS are combined with cloud computing, it will greatly facilitate the pursuing of PBS MC studies, especially for newly established proton centers or individual researchers.

07 ISOTOPE AND RADIATION SOURCES↗

A Study of Parallel Scalability and Dynamic Workload Balancing in GlennICE

The Glenn Icing Computational Environment (GlennICE) is a computational tool designed to calculate ice growth on complex three-dimensional geometries. It utilizes user-supplied computational fluid dynamics solutions for the geometry of interest. Key developments include advancements in convergence of collection efficiency, trajectory optimization, and refinement methodology. These improvements have significantly enhanced GlennICE’s efficiency for practical engineering applications. A recent study focused on benchmarking GlennICE’s scalability in a parallel environment using static scheduling. Findings indicated a potential twofold increase in efficiency through workload balance enhancements. This paper presents an analysis of the solver’s new workload balancing improvements, incorporating shared memory and dynamic scheduling routines. Results demonstrate a highly efficient and consistent algorithm across high-performance computing clusters.

Computational Icing↗

Architecture-Adaptive Computing Environment: A Tool for Teaching Parallel Programming

Recently, networked and cluster computation have become very popular. This paper is an introduction to a new C based parallel language for architecture-adaptive programming, aCe C. The primary purpose of aCe (Architecture-adaptive Computing Environment) is to encourage programmers to implement applications on parallel architectures by providing them the assurance that future architectures will be able to run their applications with a minimum of modification. A secondary purpose is to encourage computer architects to develop new types of architectures by providing an easily implemented software development environment and a library of test applications. This new language should be an ideal tool to teach parallel programming. In this paper, we will focus on some fundamental features of aCe C.

Dorband, John E.↗

Hydraulic Study of the South Carolina DOT Catch Basin Type 25

Proper design of surface drainage of both rural and urban highways is essential to minimize flooding and provide traffic safety. Inlets collect the excess storm water from a roadway and discharge it to storm drains. Knowing the performance of inlets (or hydraulic efficiency), defined as the percentage of intercepted flow to the total street flow, is necessary in the design of inlet spacing. The location of inlets can be determined such that the system can transport all or a majority of the road surface flow during rain events. A new type of a catch basin with an inlet grate, Type 25 (CB25), to use as drainage on South Carolina’s freeways was designed by the South Carolina Department of Transportation engineers. Because it is a new design, a study was necessary to establish the hydraulic capacity of the grate. Computational fluid dynamics (CFD) modeling was chosen for this purpose, instead of more expensive and time consuming laboratory testing. CFD has been widely used in design of new transportation infrastructure, as well as performance analysis of the existing structures. Three dimensional computational fluid dynamic simulations were developed by scientists at Argonne’s Transportation Research and Analysis Computing Center with the use of high performance cluster computing. The work was performed under an inter-agency agreement between the U.S. Department of Transportation and the U.S Department of Energy and funded by the South Carolina Department of Transportation.

42 ENGINEERING↗

Cyber-Infrastructure for Data-Intensive Geospatial Computing

With the recent advent of heterogeneous High-performance Computing (HPC) to handle EO “Big Data” workloads, there is a need for a unified Cyber-infrastructure (CI) platform that can bridge the best of many HPC worlds. In this chapter, we discuss such a CI platform being developed at Geographic Information Science and Technology (GIST) group using novel and innovative techniques, and emerging technologies that are scalable to large-scale supercomputers. The CI platform utilizes a wide variety of computing such as GPGPU, distributed, real-time and cluster computing, which are being brought together architecturally to enable data-driven analysis, scientific understanding of earth system models, and research collaboration. This development addresses the need for close integration of EO and other geospatial information in the face of growing volumes of the data, and facilitates spatio-temporal analysis of disparate and dynamic data streams. Horizontal scalability and linear throughput are supported in the heart of the platform itself. It is being used to support very broad application areas, ranging from high-resolution settlement mapping, national bioenergy infrastructure to urban information and mobility systems. The platform provides spatio-temporal decision support capabilities in planning, policy and operational missions for US federal agencies. Also, the platform is designed to be functionally and technologically sustainable for continued support of the US energy and environment mission for the coming decades.

Karthik, Rajasekar↗

GPU accelerated fully space and time resolved numerical simulations of self-focusing laser beams in SBS-active media

A computer cluster equipped with Graphics Processing Units (GPUs) is used for simulating nonlinear optical wave packets undergoing Kerr self-focusing and stimulated Brillouin scattering in fused silica. We first recall the model equations in full (3+1) dimensions. These consist of two coupled nonlinear Schrödinger equations for counterpropagating optical beams closed with a source equation for light-induced acoustic waves seeded by thermal noise. Compared with simulations on a conventional cluster of Central Processing Units (CPUs), GPU-based computations allow us to use a significant (16 times) larger number of mesh points within similar computation times. Reciprocally, simulations employing the same number of mesh points are between 3 and 20 times faster on GPUs than on the same number of classical CPUs. Performance speedups close to 45 are reported for isolated functions evaluating, e.g., the optical nonlinearities. Since the field intensities may reach the ionization threshold of silica, the action of a defocusing electron plasma is also addressed.

97 MATHEMATICS AND COMPUTING↗

Reconstruction of Thermal Protection System Aeroheating using a Green’s Function Approach

Inverse heat transfer (IHT) techniques are often used to reconstruct the surface heating conditions on spacecraft thermal protection systems (TPS) during atmospheric entry. Current IHT techniques for entry spacecraft applications, however, demand substantial computational resources, and are impractical for analyses such as uncertainty quantification and real-time health monitoring. In this paper, a Green’s function sensor fusion approach is used to reconstruct the TPS surface aeroheating conditions on experimental spaceflight and ground test systems from collocated temperature and heat flux sensors embedded in the TPS. The algorithm leverages Green’s functions to model the heat conduction within the spacecraft TPS and stabilizes the recovery of the surface heating condition using the direct heat flux sensor measurement. The algorithm is validated using arc-jet ground test data and applied to the reconstruction of the Mars 2020 backshell heating during Martian atmospheric entry. The performance of the algorithm is benchmarked against a current state-of-the-art IHT framework, FIAT_Opt. The Green’s function-based reconstruction algorithm recovers the net hot-wall heat flux absorbed by the TPS and the incident heat flux from the atmospheric entry environment in close agreement with FIAT_Opt. Notably, computation of the surface heating condition is completed in three orders of magnitude less time with the Green’s function sensor fusion approach using a consumer-grade PC, versus with FIAT_Opt running on a high performance computer cluster. The efficiency of the algorithm is leveraged to compute the uncertainty contributions of input parameters to the total uncertainty in reconstructed Mars 2020 backshell heating for the full atmospheric entry heat pulse. The sensitivity analysis uncovers that, at different times throughout the entry heat pulse, uncertainties in the TPS specific heat, thermal conductivity, and emissivity are all dominant drivers of the reconstruction uncertainty. These results demonstrate Green’s functions and sensor-fusion techniques as promising IHT approaches to reconstruct atmospheric entry environments from TPS-embedded measurements, and highlight how these techniques may give access to post-flight analyses previously hindered by the prohibitive cost of current methods.

Kenneth McAfee↗

Reconstruction of Thermal Protection System Aeroheating using a Green’s Function Approach

Inverse heat transfer (IHT) techniques are often used to reconstruct the surface heating conditions on spacecraft thermal protection systems (TPS) during atmospheric entry. Current IHT techniques for entry spacecraft applications, however, demand substantial computational resources, and are impractical for analyses such as uncertainty quantification and real-time health monitoring. In this paper, a Green’s function sensor fusion approach is used to reconstruct the TPS surface aeroheating conditions on experimental spaceflight and ground test systems from collocated temperature and heat flux sensors embedded in the TPS. The algorithm leverages Green’s functions to model the heat conduction within the spacecraft TPS and stabilizes the recovery of the surface heating condition using the direct heat flux sensor measurement. The algorithm is validated using arc-jet ground test data and applied to the reconstruction of the Mars 2020 backshell heating during Martian atmospheric entry. The performance of the algorithm is benchmarked against a current state-of-the-art IHT framework, FIAT_Opt. The Green’s function-based reconstruction algorithm recovers the net hot-wall heat flux absorbed by the TPS and the incident heat flux from the atmospheric entry environment in close agreement with FIAT_Opt. Notably, computation of the surface heating condition is completed in three orders of magnitude less time with the Green’s function sensor fusion approach using a consumer-grade PC, versus with FIAT_Opt running on a high performance computer cluster. The efficiency of the algorithm is leveraged to compute the uncertainty contributions of input parameters to the total uncertainty in reconstructed Mars 2020 backshell heating for the full atmospheric entry heat pulse. The sensitivity analysis uncovers that, at different times throughout the entry heat pulse, uncertainties in the TPS specific heat, thermal conductivity, and emissivity are all dominant drivers of the reconstruction uncertainty. These results demonstrate Green’s functions and sensor-fusion techniques as promising IHT approaches to reconstruct atmospheric entry environments from TPS-embedded measurements, and highlight how these techniques may give access to post-flight analyses previously hindered by the prohibitive cost of current methods.

Kenneth McAfee↗

DMINDA: an integrated web server for DNA motif identification and analyses

DMINDA (DNA motif identification and analyses) is an integrated web server for DNA motif identification and analyses, which is accessible at http: //csbl.bmb.uga.edu/DMINDA/. This web site is freely available to all users and there is no login requirement. This server provides a suite of cis-regulatory motif analysis functions on DNA sequences, which are important to elucidation of the mechanisms of transcriptional regulation: (i) de novo motif finding for a given set of promoter sequences along with statistical scores for the predicted motifs derived based on information extracted from a control set, (ii) scanning motif instances of a query motif in provided genomic sequences, (iii) motif comparison and clustering of identified motifs, and (iv) co-occurrence analyses of query motifs in given promoter sequences. The server is powered by a backend computer cluster with over 150 computing nodes, and is particularly useful for motif prediction and analyses in prokaryotic genomes. We believe that DMINDA, as a new and comprehensive web server for cis-regulatory motif finding and analyses, will benefit the genomic research community in general and prokaryotic genome researchers in particular.

59 BASIC BIOLOGICAL SCIENCES↗

Autonomic Cluster Management System (ACMS): A Demonstration of Autonomic Principles at Work

Cluster computing, whereby a large number of simple processors or nodes are combined together to apparently function as a single powerful computer, has emerged as a research area in its own right. The approach offers a relatively inexpensive means of achieving significant computational capabilities for high-performance computing applications, while simultaneously affording the ability to. increase that capability simply by adding more (inexpensive) processors. However, the task of manually managing and con.guring a cluster quickly becomes impossible as the cluster grows in size. Autonomic computing is a relatively new approach to managing complex systems that can potentially solve many of the problems inherent in cluster management. We describe the development of a prototype Automatic Cluster Management System (ACMS) that exploits autonomic properties in automating cluster management.

Baldassari, James D.↗

DNS and LES of turbulent flow in a closed channel featuring a pattern of hemispherical roughness elements

Three mesh adaptivity algorithms were developed to facilitate and expedite the use of the CADIS and FW-CADIS hybrid Monte Carlo/deterministic techniques in accurate full-scale neutronics simulations of fusion energy systems with immense sizes and complicated geometries. First, a macromaterial approach enhances the fidelity of the deterministic models without changing the mesh. Second, a deterministic mesh refinement algorithm generates meshes that capture as much geometric detail as possible without exceeding a specified maximum number of mesh elements. Finally, a weight window coarsening algorithm decouples the weight window mesh and energy bins from the mesh and energy group structure of the deterministic calculations in order to remove the memory constraint of the weight window map from the deterministic mesh resolution. The three algorithms were used to enhance an FW-CADIS calculation of the prompt dose rate throughout the ITER experimental facility and resulted in a 23.3% increase in the number of mesh tally elements in which the dose rates were calculated in a 10-day Monte Carlo calculation. Additionally, because of the significant increase in the efficiency of FW-CADIS simulations, the three algorithms enabled this difficult calculation to be accurately solved on a regular computer cluster, eliminating the need for a world-class super computer.

Nuclear Science & Technology↗

Automatic mesh adaptivity for hybrid Monte Carlo/deterministic neutronics modeling of difficult shielding problems

The CADIS and FW-CADIS hybrid Monte Carlo/deterministic techniques dramatically increase the efficiency of neutronics modeling, but their use in the accurate design analysis of very large and geometrically complex nuclear systems has been limited by the large number of processors and memory requirements for their preliminary deterministic calculations and final Monte Carlo calculation. Three mesh adaptivity algorithms were developed to reduce the memory requirements of CADIS and FW-CADIS without sacrificing their efficiency improvement. First, a macromaterial approach enhances the fidelity of the deterministic models without changing the mesh. Second, a deterministic mesh refinement algorithm generates meshes that capture as much geometric detail as possible without exceeding a specified maximum number of mesh elements. Finally, a weight window coarsening algorithm decouples the weight window mesh and energy bins from the mesh and energy group structure of the deterministic calculations in order to remove the memory constraint of the weight window map from the deterministic mesh resolution. The three algorithms were used to enhance an FW-CADIS calculation of the prompt dose rate throughout the ITER experimental facility. Using these algorithms resulted in a 23.3% increase in the number of mesh tally elements in which the dose rates were calculated in a 10-day Monte Carlo calculation and, additionally, increased the efficiency of the Monte Carlo simulation by a factor of at least 3.4. The three algorithms enabled this difficult calculation to be accurately solved using an FW-CADIS simulation on a regular computer cluster, eliminating the need for a world-class super computer.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Automatic mesh adaptivity for CADIS and FW-CADIS neutronics modeling of difficult shielding problems

The CADIS and FW-CADIS hybrid Monte Carlo/deterministic techniques dramatically increase the efficiency of neutronics modeling, but their use in the accurate design analysis of very large and geometrically complex nuclear systems has been limited by the large number of processors and memory requirements for their preliminary deterministic calculations and final Monte Carlo calculation. Three mesh adaptivity algorithms were developed to reduce the memory requirements of CADIS and FW-CADIS without sacrificing their efficiency improvement. First, a macro-material approach enhances the fidelity of the deterministic models without changing the mesh. Second, a deterministic mesh refinement algorithm generates meshes that capture as much geometric detail as possible without exceeding a specified maximum number of mesh elements. Finally, a weight window coarsening algorithm de-couples the weight window mesh and energy bins from the mesh and energy group structure of the deterministic calculations in order to remove the memory constraint of the weight window map from the deterministic mesh resolution. The three algorithms were used to enhance an FW-CADIS calculation of the prompt dose rate throughout the ITER experimental facility. Using these algorithms resulted in a 23.3% increase in the number of mesh tally elements in which the dose rates were calculated in a 10-day Monte Carlo calculation and, additionally, increased the efficiency of the Monte Carlo simulation by a factor of at least 3.4. The three algorithms enabled this difficult calculation to be accurately solved using an FW-CADIS simulation on a regular computer cluster, obviating the need for a world-class super computer. (authors)

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Containers on Switches: A Cluster School Experience

Network switches, such as those from Arista and Mellanox, often have underutilized computational resources in the form of built-in processors and memory. By leveraging these untapped resources, we can optimize functionality and efficiency of computational cluster networks. Our research focuses on deploying containers directly onto these switches to execute various auxiliary tasks ranging from metric logging to system-wide management via post-boot configuration. By doing so, we can significantly enchance the capabilities of the cluster without the need for additional dedicated hardware. Our research involved five distinct scenarios where switch utilization could have a profound impact on HPC Clusters: run cloud-init services via link-local connection; configuring a Telegraf container to export metrics; deploying a caching proxy; creating a reconfigurable IPv6 DHCP/DNS provider for VLAN; and implementing a client detection with Magellan discovery. These scenarios were containerized with podman and docker, and tested both physically on the switch virtually on a QEMU VM both running SONiC OS. Testing and findings indicate that network switches can indeed be used for these scenarios. They offer a wide range of possibilities beyond these applications. They run as expected as containers on the switches, and although there were some minor issues, work-arounds were implemented. Overall, this is a positive result that can be further explored with more scenarios.

97 MATHEMATICS AND COMPUTING↗