SeisNoise.jl: Ambient Seismic Noise Cross Correlation on the CPU and GPU in Julia

2020 ◽  
Vol 92 (1) ◽  
pp. 517-527
Author(s):  
Timothy Clements ◽  
Marine A. Denolle
Keyword(s):  
Seismic Noise ◽  
High Performance ◽  
Cross Correlation ◽  
Graphic Processing Unit ◽  
Ambient Seismic Noise ◽  
Processing Unit ◽  
Central Processing ◽  
And Performance ◽  
Noise Cross Correlation ◽  
Performance Computing

Abstract We introduce SeisNoise.jl, a library for high-performance ambient seismic noise cross correlation, written entirely in the computing language Julia. Julia is a new language, with syntax and a learning curve similar to MATLAB (see Data and Resources), R, or Python and performance close to Fortran or C. SeisNoise.jl is compatible with high-performance computing resources, using both the central processing unit and the graphic processing unit. SeisNoise.jl is a modular toolbox, giving researchers common tools and data structures to design custom ambient seismic cross-correlation workflows in Julia.

scholarly journals Imaging New Zealand's Crustal Structure Using Ambient Seismic Noise Recordings from Permanent and Temporary Instruments

2021 ◽  
Author(s):  
◽  
Yannik Behr
Keyword(s):  
Seismic Noise ◽  
Cross Correlation ◽  
Velocity Structure ◽  
Shear Velocity ◽  
Ambient Seismic Noise ◽  
Uppermost Mantle ◽  
Noise Sources ◽  
Noise Field ◽  
Rayleigh And Love Waves ◽  
Noise Cross Correlation

<p>We use ambient seismic noise to image the crust and uppermost mantle, and to determine the spatiotemporal characteristics of the noise field itself, and examine the way in which those characteristics may influence imaging results. Surface wave information extracted from ambient seismic noise using cross-correlation methods significantly enhances our knowledge of the crustal and uppermost mantle shear-velocity structure of New Zealand. We assemble a large dataset of three-component broadband continuous seismic data from temporary and permanent seismic stations, increasing the achievable resolution of surface wave velocity maps in comparison to a previous study. Three-component data enables us to examine both Rayleigh and Love waves using noise cross-correlation functions. Employing a Monte Carlo inversion method, we invert Rayleigh and Love wave phase and group velocity dispersion curves separately for spatially averaged isotropic shear velocity models beneath the Northland Peninsula. The results yield first-order radial anisotropy estimates of 2% in the upper crust and up to 15% in the lower crust, and estimates of Moho depth and uppermost mantle velocity compatible with previous studies. We also construct a high-resolution, pseudo-3D image of the shear-velocity distribution in the crust and uppermost mantle beneath the central North Island using Rayleigh and Love waves. We document, for the first time, the lateral extent of low shear-velocity zones in the upper and mid-crust beneath the highly active Taupo Volcanic Zone, which have been reported previously based on spatially confined 1D shear-velocity profiles. Attributing these low shear-velocities to the presence of partial melt, we use an empirical relation to estimate an average percentage of partial melt of < 4:2% in the upper and middle crust. Analysis of the ambient seismic noise field in the North Island using plane wave beamforming and slant stacking indicates that higher mode Rayleigh waves can be detected, in addition to the fundamental mode. The azimuthal distributions of seismic noise sources inferred from beamforming are compatible with high near-coastal ocean wave heights in the period band of the secondary microseism (~7 s). Averaged over 130 days, the distribution of seismic noise sources is azimuthally homogeneous, indicating that the seismic noise field is well-suited to noise cross-correlation studies. This is underpinned by the good agreement of our results with those from previous studies. The effective homogeneity of the seismic noise field and the large dataset of noise cross-correlation functions we here compiled, provide the cornerstone for future studies of ambient seismic noise and crustal shear velocity structure in New Zealand.</p>

scholarly journals Controllers: An abstraction to ease the use of hardware accelerators

2017 ◽  
Vol 32 (6) ◽  
pp. 838-853 ◽  
Author(s):  
Ana Moreton–Fernandez ◽  
Hector Ortega–Arranz ◽  
Arturo Gonzalez–Escribano
Keyword(s):  
Graphics Processing Units ◽  
High Performance ◽  
Abstract Entity ◽  
Hardware Accelerators ◽  
Processing Unit ◽  
Central Processing ◽  
Computing Platforms ◽  
Graphics Processing ◽  
Performance Computing ◽  
Selection Of

Nowadays the use of hardware accelerators, such as the graphics processing units or XeonPhi coprocessors, is key in solving computationally costly problems that require high performance computing. However, programming solutions for an efficient deployment for these kind of devices is a very complex task that relies on the manual management of memory transfers and configuration parameters. The programmer has to carry out a deep study of the particular data that needs to be computed at each moment, across different computing platforms, also considering architectural details. We introduce the controller concept as an abstract entity that allows the programmer to easily manage the communications and kernel launching details on hardware accelerators in a transparent way. This model also provides the possibility of defining and launching central processing unit kernels in multi-core processors with the same abstraction and methodology used for the accelerators. It internally combines different native programming models and technologies to exploit the potential of each kind of device. Additionally, the model also allows the programmer to simplify the proper selection of values for several configuration parameters that can be selected when a kernel is launched. This is done through a qualitative characterization process of the kernel code to be executed. Finally, we present the implementation of the controller model in a prototype library, together with its application in several case studies. Its use has led to reductions in the development and porting costs, with significantly low overheads in the execution times when compared to manually programmed and optimized solutions which directly use CUDA and OpenMP.

scholarly journals Comparative evaluation of performance and scalability of convolutional neural network implementations on a multisystem HPC architecture

2021 ◽  
Vol 2062 (1) ◽  
pp. 012008
Author(s):  
Sunil Pandey ◽  
Naresh Kumar Nagwani ◽  
Shrish Verma
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
High Performance ◽  
Processing Unit ◽  
Neural Network Training ◽  
Central Processing ◽  
Network Training ◽  
Hot Rolled ◽  
Hot Rolled Steel ◽  
Performance Computing

Abstract The convolutional neural network training algorithm has been implemented for a central processing unit based high performance multisystem architecture machine. The multisystem or the multicomputer is a parallel machine model which is essentially an abstraction of distributed memory parallel machines. In actual practice, this model corresponds to high performance computing clusters. The proposed implementation of the convolutional neural network training algorithm is based on modeling the convolutional neural network as a computational pipeline. The various functions or tasks of the convolutional neural network pipeline have been mapped onto the multiple nodes of a central processing unit based high performance computing cluster for task parallelism. The pipeline implementation provides a first level performance gain through pipeline parallelism. Further performance gains are obtained by distributing the convolutional neural network training onto the different nodes of the compute cluster. The two gains are multiplicative. In this work, the authors have carried out a comparative evaluation of the computational performance and scalability of this pipeline implementation of the convolutional neural network training with a distributed neural network software program which is based on conventional multi-model training and makes use of a centralized server. The dataset considered for this work is the North Eastern University’s hot rolled steel strip surface defects imaging dataset. In both the cases, the convolutional neural networks have been trained to classify the different defects on hot rolled steel strips on the basis of the input image. One hundred images corresponding to each class of defects have been used for the training in order to keep the training times manageable. The hyperparameters of both the convolutional neural networks were kept identical and the programs were run on the same computational cluster to enable fair comparison. Both the convolutional neural network implementations have been observed to train to nearly 80% training accuracy in 200 epochs. In effect, therefore, the comparison is on the time taken to complete the training epochs.

scholarly journals BLVector: Fast BLAST-Like Algorithm for Manycore CPU With Vectorization

2021 ◽  
Vol 12 ◽  
Author(s):  
Sergio Gálvez ◽  
Federico Agostini ◽  
Javier Caselli ◽  
Pilar Hernandez ◽  
Gabriel Dorado
Keyword(s):  
Amino Acids ◽  
Execution Time ◽  
High Performance ◽  
Protein Sequences ◽  
Processing Unit ◽  
Central Processing ◽  
Real Scenario ◽  
High Level ◽  
Performance Computing ◽  
Comprehensive Study

New High-Performance Computing architectures have been recently developed for commercial central processing unit (CPU). Yet, that has not improved the execution time of widely used bioinformatics applications, like BLAST+. This is due to a lack of optimization between the bases of the existing algorithms and the internals of the hardware that allows taking full advantage of the available CPU cores. To optimize the new architectures, algorithms must be revised and redesigned; usually rewritten from scratch. BLVector adapts the high-level concepts of BLAST+ to the x86 architectures with AVX-512, to harness their capabilities. A deep comprehensive study has been carried out to optimize the approach, with a significant reduction in time execution. BLVector reduces the execution time of BLAST+ when aligning up to mid-size protein sequences (∼750 amino acids). The gain in real scenario cases is 3.2-fold. When applied to longer proteins, BLVector consumes more time than BLAST+, but retrieves a much larger set of results. BLVector and BLAST+ are fine-tuned heuristics. Therefore, the relevant results returned by both are the same, although they behave differently specially when performing alignments with low scores. Hence, they can be considered complementary bioinformatics tools.

scholarly journals High-performance computing in water resources hydrodynamics

2020 ◽  
Vol 22 (5) ◽  
pp. 1217-1235 ◽  
Author(s):  
M. Morales-Hernández ◽  
M. B. Sharif ◽  
S. Gangrade ◽  
T. T. Dullo ◽  
S.-C. Kao ◽  
...  
Keyword(s):  
Water Resources ◽  
High Performance Computing ◽  
Graphics Processing Units ◽  
High Performance ◽  
Large Scale ◽  
Test Case ◽  
Processing Unit ◽  
Central Processing ◽  
Graphics Processing ◽  
Performance Computing

Abstract This work presents a vision of future water resources hydrodynamics codes that can fully utilize the strengths of modern high-performance computing (HPC). The advances to computing power, formerly driven by the improvement of central processing unit processors, now focus on parallel computing and, in particular, the use of graphics processing units (GPUs). However, this shift to a parallel framework requires refactoring the code to make efficient use of the data as well as changing even the nature of the algorithm that solves the system of equations. These concepts along with other features such as the precision for the computations, dry regions management, and input/output data are analyzed in this paper. A 2D multi-GPU flood code applied to a large-scale test case is used to corroborate our statements and ascertain the new challenges for the next-generation parallel water resources codes.

scholarly journals Imaging New Zealand's Crustal Structure Using Ambient Seismic Noise Recordings from Permanent and Temporary Instruments

2021 ◽  
Author(s):  
◽  
Yannik Behr
Keyword(s):  
Seismic Noise ◽  
Cross Correlation ◽  
Velocity Structure ◽  
Shear Velocity ◽  
Ambient Seismic Noise ◽  
Uppermost Mantle ◽  
Noise Sources ◽  
Noise Field ◽  
Rayleigh And Love Waves ◽  
Noise Cross Correlation

<p>We use ambient seismic noise to image the crust and uppermost mantle, and to determine the spatiotemporal characteristics of the noise field itself, and examine the way in which those characteristics may influence imaging results. Surface wave information extracted from ambient seismic noise using cross-correlation methods significantly enhances our knowledge of the crustal and uppermost mantle shear-velocity structure of New Zealand. We assemble a large dataset of three-component broadband continuous seismic data from temporary and permanent seismic stations, increasing the achievable resolution of surface wave velocity maps in comparison to a previous study. Three-component data enables us to examine both Rayleigh and Love waves using noise cross-correlation functions. Employing a Monte Carlo inversion method, we invert Rayleigh and Love wave phase and group velocity dispersion curves separately for spatially averaged isotropic shear velocity models beneath the Northland Peninsula. The results yield first-order radial anisotropy estimates of 2% in the upper crust and up to 15% in the lower crust, and estimates of Moho depth and uppermost mantle velocity compatible with previous studies. We also construct a high-resolution, pseudo-3D image of the shear-velocity distribution in the crust and uppermost mantle beneath the central North Island using Rayleigh and Love waves. We document, for the first time, the lateral extent of low shear-velocity zones in the upper and mid-crust beneath the highly active Taupo Volcanic Zone, which have been reported previously based on spatially confined 1D shear-velocity profiles. Attributing these low shear-velocities to the presence of partial melt, we use an empirical relation to estimate an average percentage of partial melt of < 4:2% in the upper and middle crust. Analysis of the ambient seismic noise field in the North Island using plane wave beamforming and slant stacking indicates that higher mode Rayleigh waves can be detected, in addition to the fundamental mode. The azimuthal distributions of seismic noise sources inferred from beamforming are compatible with high near-coastal ocean wave heights in the period band of the secondary microseism (~7 s). Averaged over 130 days, the distribution of seismic noise sources is azimuthally homogeneous, indicating that the seismic noise field is well-suited to noise cross-correlation studies. This is underpinned by the good agreement of our results with those from previous studies. The effective homogeneity of the seismic noise field and the large dataset of noise cross-correlation functions we here compiled, provide the cornerstone for future studies of ambient seismic noise and crustal shear velocity structure in New Zealand.</p>

scholarly journals HYPERDOCK: Improving virtual screening through parallel hyperheuristics

2019 ◽  
Vol 34 (1) ◽  
pp. 30-41
Author(s):  
Baldomero Imbernón ◽  
Antonio Llanes ◽  
José-Matías Cutillas-Lozano ◽  
Domingo Giménez
Keyword(s):  
Virtual Screening ◽  
High Performance ◽  
Graphics Processing Unit ◽  
Processing Unit ◽  
Central Processing ◽  
Pharmacological Targets ◽  
Graphics Processing ◽  
Computational Systems ◽  
Performance Computing ◽  
Different Levels

Virtual screening (VS) methods aid clinical research by predicting the interaction of ligands with pharmacological targets. The computational requirements of VS, along with the size of the databases, propitiate the use of high-performance computing. METADOCK is a tool for the application of metaheuristics to VS in heterogeneous clusters of computers based on central processing unit (CPU) and graphics processing unit (GPU). HYPERDOCK represents a step forward; the exploration for satisfactory metaheuristics is systematically approached by means of hyperheuristics working on top of the metaheuristic schema of METADOCK. Multiple metaheuristics are explored, so the process is computationally demanding. HYPERDOCK exploits the parallelism of METADOCK and includes parallelism at its own level. The different levels of parallelism can be used to exploit the parallelism offered by computational systems composed of multicore CPU + multi-GPUs. The efficient exploitation of these systems enables HYPERDOCK to improve ligand–receptor binding.

scholarly journals Performance Evaluation of SW Algorithm on NVIDIA GeForce GTX TITAN X Graphic Processing Unit (GPU)

2018 ◽  
Vol 12 (2) ◽  
pp. 670
Author(s):  
Ahmad Hasif Azman ◽  
Syed Abdul Mutalib Al Junid ◽  
Abdul Hadi Abdul Razak ◽  
Mohd Faizul Md Idros ◽  
Abdul Karimi Halim ◽  
...  
Keyword(s):  
Performance Evaluation ◽  
Dna Sequence ◽  
Sequence Alignment ◽  
High Performance ◽  
Graphic Processing Unit ◽  
Processing Unit ◽  
Central Processing ◽  
Dna Sequence Alignment ◽  
Algorithm Implementation ◽  
Graphic Processing

Nowadays, the requirement for high performance and sensitive alignment tools have increased after the advantage of the Deoxyribonucleic Acid (DNA) and molecular biology has been figured out through Bioinformatics study. Therefore, this paper reports the performance evaluation of parallel Smith-Waterman Algorithm implementation on the new NVIDIA GeForce GTX Titan X Graphic Processing Unit (GPU) compared to the Central Processing Unit (CPU) running on Intel® CoreTM i5-4440S CPU 2.80GHz. Both of the design were developed using C-programming language and targeted to the respective platform. The code for GPU was developed and compiled using NVIDIA Compute Unified Device Architecture (CUDA). It clearly recorded that, the performance of GPU based computational is better compared to the CPU based. These results indicate that the GPU based DNA sequence alignment has a better speed in accelerating the computational process of DNA sequence alignment.

scholarly journals High Performance Computing Environment using General Purpose Computations on Graphics Processing Unit

2021 ◽  
Vol 7 (2) ◽  
Author(s):  
Andreas Widjaja ◽  
Tjatur Kandaga Gautama ◽  
Sendy Ferdian Sujadi ◽  
Steven Rumanto Harnandy
Keyword(s):  
High Performance Computing ◽  
High Performance ◽  
Graphics Processing Unit ◽  
General Purpose ◽  
Superior Performance ◽  
Processing Unit ◽  
Development Phase ◽  
And Performance ◽  
Graphics Processing ◽  
Performance Computing

Here a report of a development phase of an environment of high performance computing (HPC) using general purpose computations on the graphics processing unit (GPGPU) is presented. The HPC environment accommodates computational tasks which demand massive parallelisms or multi-threaded computations. For this purpose, GPGPU is utilized because such tasks require many computing cores running in parallel. The development phase consists of several stages, followed by testing its capabilities and performance. For starters, the HPC environment will be served for computational projects of students and members of the Faculty of Information Technology, Universitas Kristen Maranatha. The goal of this paper is to show a design of a HPC which is capable of running complex and multi-threaded computations. The test results of the HPC show that the GPGPU numerical computations have superior performance than the CPU, with the same level of precision.

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