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At least 775 records · Page 43

Mobile Thread Task Manager

The Mobile Thread Task Manager (MTTM) is being applied to parallelizing existing flight software to understand the benefits and to develop new techniques and architectural concepts for adapting software to multicore architectures. It allocates and load-balances tasks for a group of threads that migrate across processors to improve cache performance. In order to balance-load across threads, the MTTM augments a basic map-reduce strategy to draw jobs from a global queue. In a multicore processor, memory may be "homed" to the cache of a specific processor and must be accessed from that processor. The MTTB architecture wraps access to data with thread management to move threads to the home processor for that data so that the computation follows the data in an attempt to avoid L2 cache misses. Cache homing is also handled by a memory manager that translates identifiers to processor IDs where the data will be homed (according to rules defined by the user). The user can also specify the number of threads and processors separately, which is important for tuning performance for different patterns of computation and memory access. MTTM efficiently processes tasks in parallel on a multiprocessor computer. It also provides an interface to make it easier to adapt existing software to a multiprocessor environment.

Clement, Bradley J.↗

Reliable and Efficient Distributed Checkpointing System for Grid Environments

In Fine-Grained Cycle Sharing (FGCS) systems, machine owners voluntarily share their unused CPU cycles with guest jobs, as long as their performance degradation is tolerable. However, unpredictable evictions of guest jobs lead to fluctuating completion times. Checkpoint-recovery is an attractive mechanism for recovering from such “failures”. Today’s FGCS systems often use expensive, high-performance dedicated checkpoint servers. However, in geographically distributed clusters, this may incur high checkpoint transfer latencies. Here we present a distributed checkpointing system called FALCON that uses available disk resources of the FGCS machines as shared checkpoint repositories. However, an unavailable storage host may lead to loss of checkpoint data. Therefore, we model the failures of a storage host and develop a prediction algorithm for choosing reliable checkpoint repositories. We experiment with FALCON in the university-wide Condor testbed at Purdue and show improved and consistent performance for guest jobs in the presence of irregular resource availability.

checkpoint↗

Performance of a plasma fluid code on the Intel parallel computers

One approach to improving the real-time efficiency of plasma turbulence calculations is to use a parallel algorithm. A parallel algorithm for plasma turbulence calculations was tested on the Intel iPSC/860 hypercube and the Touchtone Delta machine. Using the 128 processors of the Intel iPSC/860 hypercube, a factor of 5 improvement over a single-processor CRAY-2 is obtained. For the Touchtone Delta machine, the corresponding improvement factor is 16. For plasma edge turbulence calculations, an extrapolation of the present results to the Intel (sigma) machine gives an improvement factor close to 64 over the single-processor CRAY-2.

Lynch, V. E.↗

Efficiency Improvements to the Displacement Based Multilevel Structural Optimization Algorithm

Multilevel Structural Optimization (MSO) continues to be an area of research interest in engineering optimization. In the present project, the weight optimization of beams and trusses using Displacement based Multilevel Structural Optimization (DMSO), a member of the MSO set of methodologies, is investigated. In the DMSO approach, the optimization task is subdivided into a single system and multiple subsystems level optimizations. The system level optimization minimizes the load unbalance resulting from the use of displacement functions to approximate the structural displacements. The function coefficients are then the design variables. Alternately, the system level optimization can be solved using the displacements themselves as design variables, as was shown in previous research. Both approaches ensure that the calculated loads match the applied loads. In the subsystems level, the weight of the structure is minimized using the element dimensions as design variables. The approach is expected to be very efficient for large structures, since parallel computing can be utilized in the different levels of the problem. In this paper, the method is applied to a one-dimensional beam and a large three-dimensional truss. The beam was tested to study possible simplifications to the system level optimization. In previous research, polynomials were used to approximate the global nodal displacements. The number of coefficients of the polynomials equally matched the number of degrees of freedom of the problem. Here it was desired to see if it is possible to only match a subset of the degrees of freedom in the system level. This would lead to a simplification of the system level, with a resulting increase in overall efficiency. However, the methods tested for this type of system level simplification did not yield positive results. The large truss was utilized to test further improvements in the efficiency of DMSO. In previous work, parallel processing was applied to the subsystems level, where the derivative verification feature of the optimizer NPSOL had been utilized in the optimizations. This resulted in large runtimes. In this paper, the optimizations were repeated without using the derivative verification, and the results are compared to those from the previous work. Also, the optimizations were run on both, a network of SUN workstations using the MPICH implementation of the Message Passing Interface (MPI) and on the faster Beowulf cluster at ICASE, NASA Langley Research Center, using the LAM implementation of UP]. The results on both systems were consistent and showed that it is not necessary to verify the derivatives and that this gives a large increase in efficiency of the DMSO algorithm.

Plunkett, C. L.↗

Impact of moderate pump–Stokes chirp on femtosecond coherent anti-Stokes Raman scattering spectra

The effects of inducing moderate chirp in the pump and Stokes beams in chirped-probe-pulse femtosecond coherent anti-Stokes Raman scattering (CARS) spectroscopy are discussed. This is an important issue for measurements in high-pressure systems where the CARS beams must be transmitted through glass of significant thickness to reach the probe volume of interest. The effects were investigated both experimentally, by inserting disks of SF-11 glass into the pump and Stokes beam paths, and theoretically, by incorporating pulse chirp into our time-dependent density matrix (TDDM) simulations. Experimentally, we found that inducing moderate pump and Stokes chirp produced significant spectral narrowing of the nonresonant four-wave mixing contribution to the CARS signal, and this allowed us to control the resonant excitation bandwidth to eliminate interferences from neighboring species. The temperature measurement accuracy and precision were essentially unchanged with respect to the unchirped pump and Stokes case. The effect of moderate pump and Stokes chirp on the narrowing of the Raman excitation efficiency envelope was investigated by solving the full set of TDDM through direct numerical integration. The numerical efficiency of the solutions was enhanced dramatically by developing a parallel version of the TDDM code. The calculated Raman excitation efficiency profile was incorporated in our phenomenological spectral fitting codes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Jagged Tiling for Intra-tile Parallelism and Fine-Grain Multithreading

In this paper, we have developed a novel methodology that takes into consideration multithreaded many-core designs to better utilize memory/processing resources and improve memory residence on tileable applications. It takes advantage of polyhedral analysis and transformation in the form of PLUTO, combined with a highly optimized finegrain tile runtime to exploit parallelism at all levels. The main contributions of this paper include the introduction of multi-hierarchical tiling techniques that increases intra tile parallelism; and a data-flow inspired runtime library that allows the expression of parallel tiles with an efficient synchronization registry. Our current implementation shows performance improvements on an Intel Xeon Phi board up to 32.25% against instances produced by state-of-the-art compiler frameworks for selected stencil applications.

compiler↗

Efficient distributed continual learning for steering experiments in real-time

Deep learning has emerged as a powerful method for extracting valuable information from large volumes of data. However, when new training data arrives continuously (i.e., is not fully available from the beginning), incremental training suffers from catastrophic forgetting (i.e., new patterns are reinforced at the expense of previously acquired knowledge). Training from scratch each time new training data becomes available would result in extremely long training times and massive data accumulation. Rehearsal-based continual learning has shown promise for addressing the catastrophic forgetting challenge, but research to date has not addressed performance and scalability. To fill this gap, we propose an approach based on a distributed rehearsal buffer that efficiently complements data-parallel training on multiple GPUs to achieve high accuracy, short runtime, and scalability. It leverages a set of buffers (local to each GPU) and uses several asynchronous techniques for updating these local buffers in an embarrassingly parallel fashion, all while handling the communication overheads necessary to augment input minibatches using unbiased, global sampling. We further propose a generalization of rehearsal buffers to support both classification and generative learning tasks, as well as more advanced rehearsal strategies (notably Dark Experience Replay, leveraging knowledge distillation). We illustrate this approach with a real-life HPC streaming application from the domain of ptychographic image reconstruction. Furthermore, we run extensive experiments on up to 128 GPUs of the ThetaGPU supercomputer to compare our approach with baselines representative of training-from-scratch (the upper bound in terms of accuracy) and incremental training (the lower bound). Results show that rehearsal-based continual learning achieves a top-5 validation accuracy close to the upper bound, while simultaneously exhibiting a runtime close to the lower bound.

Asynchronous data management↗

A purely Lagrangian method for simulating the shallow water equations on a sphere using smooth particle hydrodynamics

It has long been suggested that a purely Lagrangian solution to global-scale atmospheric/oceanic flows can potentially outperform tradition Eulerian schemes. Meanwhile, a demonstration of a scalable and practical framework remains elusive. Motivated by recent progress in particle-based methods when applied to convection dominated flows, this work presents a fully Lagrangian method for solving the inviscid shallow water equations on a rotating sphere in a smooth particle hydrodynamics framework. To avoid singularities at the poles, the governing equations are solved in Cartesian coordinates, augmented with a Lagrange multiplier to ensure that fluid particles are constrained to the surface of the sphere. An underlying grid in spherical coordinates is used to facilitate efficient neighbor detection and parallelization. The method is applied to a suite of canonical test cases, and conservation, accuracy, and parallel performance are assessed..

Computer Science↗

Calibrated simulation analysis for integration of evaporative cooling and radiant cooling system for different Indian climatic zones

Radiant cooling system (RCS) has proven to be an energy efficient system for meeting a building's cooling requirements. RCS is energy efficient and provides better thermal comfort compared to conventional all-air heating ventilation air conditioning (HVAC) system. To further improve the efficiency of RCS, a parallel evaporative cooling system (cooling tower) is coupled with RCS and analyzed for different climatic condition using calibrated model. A statistical analysis of weather files (based on wet bulb temperature), was used to identify the availability of useful water for cooling tower integration with RCS. A comprehensive simulation feasibility study of the application of cooling tower in RCS was performed for different cities to cover every climatic zones of India. It was found that in summer, the wet bulb temperature (WBT) of different climatic zones, except warm-humid, is suitable for the integration of cooling tower with RCS. An experimental setup was designed and developed for integration of parallel chiller and cooling tower with panel-based RCS for cooling and a dedicated outdoor air system (DOAS) for dehumidification and ventilation. Experiments were conducted for chiller and cooling tower operated RCS in Composite climate of Jaipur, Rajasthan, India. Building Energy Models (BEM) were developed for both the chiller-operated RCS and cooling tower-operated RCS in EnergyPlus and calibrated with the measured data. Using the calibrated models, performance of the system was analyzed for different climatic zones of India. A chiller-operated RCS was considered as a baseline to compare the annual energy saving potential and monthly performance of the cooling tower integrated RCS. Here, in the cooling tower–operated RCS, a total annual savings of 7% in hot and dry climates, 11% in composite climates and 20% in temperate climates was achieved compared to the chiller-operated RCS.

54 ENVIRONMENTAL SCIENCES↗

Efficient Treatment of Large Active Spaces through Multi-GPU Parallel Implementation of Direct Configuration Interaction

In this study, we have extended our graphical processing unit (GPU)-accelerated direct configuration interaction program to multiple devices, reducing iteration times for configuration spaces of 165 million determinants to only 3 s using NVIDIA P100 GPUs. Similar improvements in the one- and two-particle reduced density matrix formation allow for fast analytical energy gradients and electronic properties. Our parallel algorithm enables the calculation of arbitrarily large configuration spaces (limited only by available system memory), with iteration times of 13 min for an active space of 18 electrons in 18 orbitals (2.4 billion determinants) using six consumer grade NVIDIA 1080Ti GPUs. These advances enable routine molecular dynamics simulations, geometry optimizations, and absorption spectrum calculations for molecules with large configuration spaces, a task that has heretofore required massive computational effort. In this work, we demonstrate the utility of our program by generating the absorption spectrum for diphenyl acetylene at the floating occupation molecular orbital complete active space configuration interaction level of theory. Lastly, several active spaces were investigated to assess the dependence of spectral features on orbital space dimension.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Automated “Cells-To-Peptides” Sample Preparation Workflow for High-Throughput, Quantitative Proteomic Assays of Microbes

Mass spectrometry-based quantitative proteomic analysis has proven valuable for clinical and biotechnology-related research and development. Improvements in sensitivity, resolution, and robustness of mass analyzers have also added value. However, manual sample preparation protocols are often a bottleneck for sample throughput and can lead to poor reproducibility, especially for applications where thousands of samples per month must be analyzed. To alleviate these issues, we developed a “cells-to-peptides” automated workflow for Gram-negative bacteria and fungi that includes cell lysis, protein precipitation, resuspension, quantification, normalization, and tryptic digestion. The workflow takes 2 h to process 96 samples from cell pellets to the initiation of the tryptic digestion step and can process 384 samples in parallel. We measured the efficiency of protein extraction from various amounts of cell biomass and optimized the process for standard liquid chromatography–mass spectrometry systems. The automated workflow was tested by preparing 96 Escherichia coli samples and quantifying over 600 peptides that resulted in a median coefficient of variation of 15.8%. Similar technical variance was observed for three other organisms as measured by highly multiplexed LC-MRM–MS acquisition methods. These results show that this automated sample preparation workflow provides robust, reproducible proteomic samples for high-throughput applications.

59 BASIC BIOLOGICAL SCIENCES↗

Solving sparse finite element problems on neuromorphic hardware

The finite element method (FEM) is one of the most important and ubiquitous numerical methods for solving partial differential equations (PDEs) on computers for scientific and engineering discovery. Applying the FEM to larger and more detailed scientific models has driven advances in high-performance computing for decades. Here we demonstrate that scalable spiking neuromorphic hardware can directly implement the FEM by constructing a spiking neural network that solves the large, sparse, linear systems of equations at the core of the FEM. We show that for the Poisson equation, a fundamental PDE in science and engineering, our neural circuit achieves meaningful levels of numerical accuracy and close to ideal scaling on modern, inherently parallel and energy-efficient neuromorphic hardware, specifically Intel’s Loihi 2 neuromorphic platform. We illustrate extensions to irregular mesh geometries in both two and three dimensions as well as other PDEs such as linear elasticity. Our spiking neural network is constructed from a recurrent network model of the brain’s motor cortex and, in contrast to black-box deep artificial neural network-based methods for PDEs, directly translates the well-understood and trusted mathematics of the FEM to a natively spiking neuromorphic algorithm.

Applied mathematics↗

Nonlinear electronic excitations in crystalline solids using meta-generalized gradient approximation and hybrid functional in time-dependent density functional theory

We develop methods to calculate electron dynamics in crystalline solids in real-time time-dependent density functional theory employing exchange-correlation potentials which reproduce band gap energies of dielectrics; a meta-generalized gradient approximation was proposed by Tran and Blaha [Phys. Rev. Lett. 102, 226401 (2009)] (TBm-BJ) and a hybrid functional was proposed by Heyd, Scuseria, and Ernzerhof [J. Chem. Phys. 118, 8207 (2003)] (HSE). In time evolution calculations employing the TB-mBJ potential, we have found it necessary to adopt the predictor-corrector step for a stable time evolution. We have developed a method to evaluate electronic excitation energy without referring to the energy functional which is unknown for the TB-mBJ potential. For the HSE functional, we have developed a method for the operation of the Fock-like term in Fourier space to facilitate efficient use of massive parallel computers equipped with graphic processing units. We compare electronic excitations in silicon and germanium induced by femtosecond laser pulses using the TB-mBJ, HSE, and a simple local density approximation (LDA). At low laser intensities, electronic excitations are found to be sensitive to the band gap energy: they are close to each other using TB-mBJ and HSE and are much smaller in LDA. At high laser intensities close to the damage threshold, electronic excitation energies do not differ much among the three cases.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

SHOCK ACCELERATION OF PARTICLES IN THE NONSTATIONARY EVOLUTION OF COROTATING INTERACTION REGIONS

One-dimensional hybrid simulations are used to investigate the particle energization process during the nonstationary evolution of corotating interaction regions (CIRs) in the heliosphere. The simulation model, where fast and slow solar wind streams interact with each other, allows the formation of a pair (forward/reverse) of shocks at the CIR boundaries and the stream interface interior, which prevents the interchange of both streams. While both shocks are quasi-perpendicular and are not capable of accelerating thermal particles (hundreds of eV) up to a suprathermal energy (tens to hundreds of keV) in the early phase of their development, the reverse shock in the fast wind experiences a transition to a quasi-parallel regime in the later phase. The quasi-parallel reverse shock can efficiently accelerate particles to the suprathermal range. The different timescale of the adiabatic expansion between the fast and slow wind leads to a transition of the shock geometry that can take place more easily in the reverse shock than in the forward shock, where the magnetic field in the fast wind remains more radial to the propagation direction than in the slow wind. The difference in the acceleration efficiency between these shocks follows a well-known observed asymmetry in the profile of the energetic particle fluxes, where the larger intensity increases more in the reverse shock than in the forward shock. The present results suggest that the solar wind thermal plasma, as well as interstellar pickup ions, can contribute to the composition of energetic particles associated with the CIRs.

79 ASTRONOMY AND ASTROPHYSICS↗

LATTE: open-source, high-performance traveltime computation, tomography and source location in acoustic and elastic media

Traveltime-based tomography and source location are fundamental approaches for imaging subsurface structures and understanding the spatiotemporal distribution of seismicity from local to global scales. We present an open-source, high-performance framework integrating eikonal equation solvers and adjoint-state theory for traveltime computation, velocity tomography, source location and joint tomography-location in 2-D/3-D acoustic and elastic media. We introduce novel regularization schemes based on total generalized p-variation, structural similarity and multitask machine learning to enhance the fidelity and interpretability of inverted models and source locations. Key features of our implementation also include the ability to leverage both absolute-difference and double-difference traveltime misfits for high-fidelity velocity tomography and source parameter estimation; support for traveltime computation and inversion in diverse 2-D/3-D scenarios with arbitrary source and receiver distributions; and a perturbation-based optimal step-size estimation method to reduce computational costs. In addition, our implementation employs shared-memory and distributed-memory parallelization to provide an efficient solution for traveltime computation, tomography, and source location. In conclusion, we validate the efficacy and accuracy of our approach through multiple synthetic data examples.

58 GEOSCIENCES↗

Solving Seismic Wave Equations on Variable Velocity Models With Fourier Neural Operator

Here, in the study of subsurface seismic imaging, solving the acoustic wave equation is a pivotal component in existing models. The advancement of deep learning (DL) enables solving partial differential equations (PDEs), including wave equations, by applying neural networks to identify the mapping between the inputs and the solution. This approach can be faster than traditional numerical methods when numerous instances are to be solved. Previous works that concentrate on solving the wave equation by neural networks consider either a single velocity model or multiple simple velocity models, which is restricted in practice. Instead, inspired by the idea of operator learning, this work leverages the Fourier neural operator (FNO) to effectively learn the frequency domain seismic wavefields under the context of variable velocity models. We also propose a new framework paralleled FNO (PFNO) for efficiently training the FNO-based solver given multiple source locations and frequencies. Numerical experiments demonstrate the high accuracy of both FNO and PFNO with complicated velocity models in the OpenFWI datasets. Furthermore, the cross-dataset generalization test verifies that PFNO adapts to out-of-distribution velocity models. Finally, PFNO admits higher computational efficiency on large-scale testing datasets than the traditional finite-difference method. The aforementioned advantages endow the FNO-based solver with the potential to build powerful models for research on seismic waves.

58 GEOSCIENCES↗

Deep Reinforcement Learning-Based Control of Energy Storage for Interarea Oscillation Damping

With the increasing electricity consumption and lack of transmission investment, today's power systems are operated much closer to their limits, raising concerns of inter-area oscillations that deteriorate the system stability. Here, this article presents a novel energy storage placement and control approach for enhanced damping of interarea oscillations. Combining the residual analysis and dominant mode analysis, we are able to identify the advantageous locations for placing energy storage that achieve improved damping performance. To overcome the challenges, such as fixed control parameters and insufficient damping, we propose to use a deep reinforcement learning-based approach for energy storage control. A state-of-the-art guided surrogate-gradient-based evolutionary strategy is used to train a learning agent in a robust, efficient, and reproducible manner. Parallel computing is also adopted to speed up the training process. The proposed strategy has been tested on both medium and large-scale systems. The proposed methods have demonstrated their effectiveness in mitigating various interarea oscillations within a timeframe of 20 s, thereby averting system collapse and enhancing power grid stability effectively.

25 ENERGY STORAGE↗

Distributed seams for gigapixel panoramas

Gigapixel panoramas are an increasingly popular digital image application. They are often created as a mosaic of many smaller images. The mosaic acquisition can take many hours causing the individual images to differ in exposure and lighting conditions. A blending operation is often necessary to give the appearance of a seamless image. The blending quality depends on the magnitude of discontinuity along the image boundaries. Often, new boundaries, or seams, are first computed that minimize this transition. Current techniques based on multi-labeling Graph Cuts are too slow and memory intensive for gigapixel sized panoramas. In this paper, we present a parallel, out-of-core seam computing technique that is fast, has small memory footprint, and is capable of running efficiently on different types of parallel systems. Its maximum memory usage is configurable, in the form of a cache, which can improve performance by reducing redundant disk I/O and computations. It shows near-perfect scaling on symmetric multiprocessing systems and good scaling on clusters and distributed shared memory systems. Lastly, our technique improves the time required to compute seams for gigapixel imagery from many hours (or even days) to just a few minutes, while still producing boundaries with energy that is on-par with Graph Cuts.

97 MATHEMATICS AND COMPUTING↗