Algorithm 1016

2021 ◽  
Vol 47 (2) ◽  
pp. 1-22
Author(s):  
Jens Hahne ◽  
Stephanie Friedhoff ◽  
Matthias Bolten
Keyword(s):  
Message Passing ◽  
Message Passing Interface ◽  
Space Time ◽  
Point Of View ◽  
Multiple Time ◽  
Relaxation Schemes ◽  
Time Integrators ◽  
Parallel Tests ◽  
Time Dependent Problems ◽  
Different Levels

In this article, we introduce the Python framework PyMGRIT, which implements the multigrid-reduction-in-time (MGRIT) algorithm for solving (non-)linear systems arising from the discretization of time-dependent problems. The MGRIT algorithm is a reduction-based iterative method that allows parallel-in-time simulations, i.e., calculating multiple time steps simultaneously in a simulation, using a time-grid hierarchy. The PyMGRIT framework includes many different variants of the MGRIT algorithm, ranging from different multigrid cycle types and relaxation schemes, various coarsening strategies, including time-only and space-time coarsening, and the ability to utilize different time integrators on different levels in the multigrid hierachy. The comprehensive documentation with tutorials and many examples and the fully documented code allow an easy start into the work with the package. The functionality of the code is ensured by automated serial and parallel tests using continuous integration. PyMGRIT supports serial runs suitable for prototyping and testing of new approaches, as well as parallel runs using the Message Passing Interface (MPI). In this manuscript, we describe the implementation of the MGRIT algorithm in PyMGRIT and present the usage from both a user and a developer point of view. Three examples illustrate different aspects of the package itself, especially running tests with pure time parallelism, as well as space-time parallelism through the coupling of PyMGRIT with PETSc or Firedrake.

scholarly journals Simulation of the performance and scalability of message passing interface (MPI) communications of atmospheric models running on exascale supercomputers

2018 ◽  
Vol 11 (8) ◽  
pp. 3409-3426 ◽  
Author(s):  
Yongjun Zheng ◽  
Philippe Marguinaud
Keyword(s):  
Message Passing ◽  
Message Passing Interface ◽  
Grid Point ◽  
Routing Algorithm ◽  
Point Of View ◽  
Atmospheric Models ◽  
Innovative Methods ◽  
Spectral Models ◽  
Communication Time ◽  
Better Than

Abstract. In this study, we identify the key message passing interface (MPI) operations required in atmospheric modelling; then, we use a skeleton program and a simulation framework (based on SST/macro simulation package) to simulate these MPI operations (transposition, halo exchange, and allreduce), with the perspective of future exascale machines in mind. The experimental results show that the choice of the collective algorithm has a great impact on the performance of communications; in particular, we find that the generalized ring-k algorithm for the alltoallv operation and the generalized recursive-k algorithm for the allreduce operation perform the best. In addition, we observe that the impacts of interconnect topologies and routing algorithms on the performance and scalability of transpositions, halo exchange, and allreduce operations are significant. However, the routing algorithm has a negligible impact on the performance of allreduce operations because of its small message size. It is impossible to infinitely grow bandwidth and reduce latency due to hardware limitations. Thus, congestion may occur and limit the continuous improvement of the performance of communications. The experiments show that the performance of communications can be improved when congestion is mitigated by a proper configuration of the topology and routing algorithm, which uniformly distribute the congestion over the interconnect network to avoid the hotspots and bottlenecks caused by congestion. It is generally believed that the transpositions seriously limit the scalability of the spectral models. The experiments show that the communication time of the transposition is larger than those of the wide halo exchange for the semi-Lagrangian method and the allreduce in the generalized conjugate residual (GCR) iterative solver for the semi-implicit method below 2×105 MPI processes. The transposition whose communication time decreases quickly with increasing number of MPI processes demonstrates strong scalability in the case of very large grids and moderate latencies. The halo exchange whose communication time decreases more slowly than that of transposition with increasing number of MPI processes reveals its weak scalability. In contrast, the allreduce whose communication time increases with increasing number of MPI processes does not scale well. From this point of view, the scalability of spectral models could still be acceptable. Therefore it seems to be premature to conclude that the scalability of the grid-point models is better than that of spectral models at the exascale, unless innovative methods are exploited to mitigate the problem of the scalability presented in the grid-point models.

Multi-level Parallelization of Genotype Imputation on Supercomputers

2020 ◽  
Vol 15 ◽  
Author(s):  
Weiwen Zhang ◽  
Long Wang ◽  
Theint Theint Aye ◽  
Juniarto Samsudin ◽  
Yongqing Zhu
Keyword(s):  
Association Study ◽  
Message Passing ◽  
High Performance ◽  
Message Passing Interface ◽  
Genome Wide Association Study ◽  
Job Scheduling ◽  
Genotype Imputation ◽  
Job Level ◽  
Multi Level ◽  
High Performance Requirement

Background: Genotype imputation as a service is developed to enable researchers to estimate genotypes on haplotyped data without performing whole genome sequencing. However, genotype imputation is computation intensive and thus it remains a challenge to satisfy the high performance requirement of genome wide association study (GWAS). Objective: In this paper, we propose a high performance computing solution for genotype imputation on supercomputers to enhance its execution performance. Method: We design and implement a multi-level parallelization that includes job level, process level and thread level parallelization, enabled by job scheduling management, message passing interface (MPI) and OpenMP, respectively. It involves job distribution, chunk partition and execution, parallelized iteration for imputation and data concatenation. Due to the design of multi-level parallelization, we can exploit the multi-machine/multi-core architecture to improve the performance of genotype imputation. Results: Experiment results show that our proposed method can outperform the Hadoop-based implementation of genotype imputation. Moreover, we conduct the experiments on supercomputers to evaluate the performance of the proposed method. The evaluation shows that it can significantly shorten the execution time, thus improving the performance for genotype imputation. Conclusion: The proposed multi-level parallelization, when deployed as an imputation as a service, will facilitate bioinformatics researchers in Singapore to conduct genotype imputation and enhance the association study.

scholarly journals Management of Intraoperative Mechanical Ventilation to Prevent Postoperative Complications after General Anesthesia: A Narrative Review

2021 ◽  
Vol 10 (12) ◽  
pp. 2656
Author(s):  
Alberto Fogagnolo ◽  
Federica Montanaro ◽  
Lou’i Al-Husinat ◽  
Cecilia Turrini ◽  
Michela Rauseo ◽  
...  
Keyword(s):  
Mechanical Ventilation ◽  
Tidal Volume ◽  
Pulmonary Complications ◽  
Point Of View ◽  
Whole Body ◽  
Positive End Expiratory Pressure ◽  
Ventilation Strategies ◽  
Harmful Effects ◽  
Ventilation Induced Lung Injury ◽  
Different Levels

Mechanical ventilation (MV) is still necessary in many surgical procedures; nonetheless, intraoperative MV is not free from harmful effects. Protective ventilation strategies, which include the combination of low tidal volume and adequate positive end expiratory pressure (PEEP) levels, are usually adopted to minimize the ventilation-induced lung injury and to avoid post-operative pulmonary complications (PPCs). Even so, volutrauma and atelectrauma may co-exist at different levels of tidal volume and PEEP, and therefore, the physiological response to the MV settings should be monitored in each patient. A personalized perioperative approach is gaining relevance in the field of intraoperative MV; in particular, many efforts have been made to individualize PEEP, giving more emphasis on physiological and functional status to the whole body. In this review, we summarized the latest findings about the optimization of PEEP and intraoperative MV in different surgical settings. Starting from a physiological point of view, we described how to approach the individualized MV and monitor the effects of MV on lung function.

scholarly journals Distributed Singular Value Decomposition Method for Fast Data Processing in Recommendation Systems

Energies ◽  
2021 ◽  
Vol 14 (8) ◽  
pp. 2284
Author(s):  
Krzysztof Przystupa ◽  
Mykola Beshley ◽  
Olena Hordiichuk-Bublivska ◽  
Marian Kyryk ◽  
Halyna Beshley ◽  
...  
Keyword(s):  
Distributed Systems ◽  
Singular Value Decomposition ◽  
Data Processing ◽  
Message Passing ◽  
Message Passing Interface ◽  
Recommendation Systems ◽  
Singular Value ◽  
Singular Value Decomposition Method ◽  
Value Decomposition ◽  
Svd Method

The problem of analyzing a big amount of user data to determine their preferences and, based on these data, to provide recommendations on new products is important. Depending on the correctness and timeliness of the recommendations, significant profits or losses can be obtained. The task of analyzing data on users of services of companies is carried out in special recommendation systems. However, with a large number of users, the data for processing become very big, which causes complexity in the work of recommendation systems. For efficient data analysis in commercial systems, the Singular Value Decomposition (SVD) method can perform intelligent analysis of information. With a large amount of processed information we proposed to use distributed systems. This approach allows reducing time of data processing and recommendations to users. For the experimental study, we implemented the distributed SVD method using Message Passing Interface, Hadoop and Spark technologies and obtained the results of reducing the time of data processing when using distributed systems compared to non-distributed ones.

scholarly journals E-Commerce Calls for Cyber-Security and Sustainability: How European Citizens Look for a Trusted Online Environment

2021 ◽  
Vol 13 (12) ◽  
pp. 6752
Author(s):  
Idiano D’Adamo ◽  
Rocío González-Sánchez ◽  
Maria Sonia Medina-Salgado ◽  
Davide Settembre-Blundo
Keyword(s):  
Cyber Security ◽  
Theoretical Perspective ◽  
Point Of View ◽  
Decision Makers ◽  
European Countries ◽  
Business Strategies ◽  
Public Authorities ◽  
Regulatory Policies ◽  
Critical Issues ◽  
Different Levels

The pandemic has changed the citizens’ behavior, inducing them to avoid any real contact. This has given an incredible impulse to e-commerce; however, the complexity of the topic has not yet been adequately explored in the literature. To fill this gap, this study has a twofold purpose: (1) to investigate how European countries comparatively perform in e-commerce, and (2) to describe what are the most important challenges for the further expansion of e-commerce. To this end, we adopted a hybrid methodology based on multi-criteria decision analysis (MCDA) and a Likert scale survey. The first method allows to us rank the e-commerce performance of different European countries, while the second one looks at the problems and barriers that characterize online shopping. The results of the study show that European countries have different sensitivities to the issue of cyber-security, and among them it is possible to identify three groups with different levels of attention to the critical issues of e-commerce. The Netherlands, Sweden and Denmark belong to the group of countries most responsive to e-commerce. This request is part of a broader framework of transition toward sustainable development, i.e., a reliable digital environment where citizens and businesses can exercise their rights and freedoms in complete security. Finally, from a theoretical perspective, this paper adds a new baseline to the literature on the state of the art of e-commerce in Europe that addresses the effects of the pandemic. From a managerial point of view, decision makers can find in the results of this analysis a support for the setting of business strategies for the expansion of firms in certain markets and guidance for public authorities when defining regulatory policies for e-commerce.

A high-performance, portable implementation of the MPI message passing interface standard

1996 ◽  
Vol 22 (6) ◽  
pp. 789-828 ◽  
Author(s):  
William Gropp ◽  
Ewing Lusk ◽  
Nathan Doss ◽  
Anthony Skjellum
Keyword(s):  
Message Passing ◽  
High Performance ◽  
Message Passing Interface

Based on Numerical Simulation of High-Performance Parallel Machine Muffler Experimental Calibration

2013 ◽  
Vol 718-720 ◽  
pp. 1645-1650
Author(s):  
Gen Yin Cheng ◽  
Sheng Chen Yu ◽  
Zhi Yong Wei ◽  
Shao Jie Chen ◽  
You Cheng
Keyword(s):  
Numerical Simulation ◽  
Finite Element ◽  
Boundary Element ◽  
Message Passing ◽  
High Performance ◽  
Message Passing Interface ◽  
Parallel Machine ◽  
Simulation Software ◽  
Experimental Calibration ◽  
The Cost

Commonly used commercial simulation software SYSNOISE and ANSYS is run on a single machine (can not directly run on parallel machine) when use the finite element and boundary element to simulate muffler effect, and it will take more than ten days, sometimes even twenty days to work out an exact solution as the large amount of numerical simulation. Use a high performance parallel machine which was built by 32 commercial computers and transform the finite element and boundary element simulation software into a program that can running under the MPI (message passing interface) parallel environment in order to reduce the cost of numerical simulation. The relevant data worked out from the simulation experiment demonstrate that the result effect of the numerical simulation is well. And the computing speed of the high performance parallel machine is 25 ~ 30 times a microcomputer.

scholarly journals A lightweight approach to performance portability with targetDP

2016 ◽  
Vol 32 (2) ◽  
pp. 288-301
Author(s):  
Alan Gray ◽  
Kevin Stratford
Keyword(s):  
Particle Physics ◽  
Message Passing ◽  
Graphics Processing Units ◽  
High Performance ◽  
Large Scale ◽  
Message Passing Interface ◽  
Graphics Processing Unit ◽  
Processing Unit ◽  
Performance Portability ◽  
Graphics Processing

Leading high performance computing systems achieve their status through use of highly parallel devices such as NVIDIA graphics processing units or Intel Xeon Phi many-core CPUs. The concept of performance portability across such architectures, as well as traditional CPUs, is vital for the application programmer. In this paper we describe targetDP, a lightweight abstraction layer which allows grid-based applications to target data parallel hardware in a platform agnostic manner. We demonstrate the effectiveness of our pragmatic approach by presenting performance results for a complex fluid application (with which the model was co-designed), plus separate lattice quantum chromodynamics particle physics code. For each application, a single source code base is seen to achieve portable performance, as assessed within the context of the Roofline model. TargetDP can be combined with Message Passing Interface (MPI) to allow use on systems containing multiple nodes: we demonstrate this through provision of scaling results on traditional and graphics processing unit-accelerated large scale supercomputers.

DESITTER GAUGE THEORY OF GRAVITATION

2003 ◽  
Vol 14 (01) ◽  
pp. 41-48 ◽  
Author(s):  
G. ZET ◽  
V. MANTA ◽  
S. BABETI
Keyword(s):  
Gauge Theory ◽  
Riemann Tensor ◽  
Space Time ◽  
Point Of View ◽  
Field Equations ◽  
Minkowski Space Time ◽  
Strength Tensor ◽  
Group A ◽  
Theory Of Gravitation ◽  
Tensor Formula

A deSitter gauge theory of gravitation over a spherical symmetric Minkowski space–time is developed. The "passive" point of view is adapted, i.e., the space–time coordinates are not affected by group transformations; only the fields change under the action of the symmetry group. A particular ansatz for the gauge fields is chosen and the components of the strength tensor are computed. An analytical solution of Schwarzschild–deSitter type is obtained in the case of null torsion. It is concluded that the deSitter group can be considered as a "passive" gauge symmetry for gravitation. Because of their complexity, all the calculations, inclusive of the integration of the field equations, are performed using an analytical program conceived in GRTensorII for MapleV. The program allows one to compute (without using a metric) the strength tensor [Formula: see text], Riemann tensor [Formula: see text], Ricci tensor [Formula: see text], curvature scalar [Formula: see text], field equations, and the integration of these equations.

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