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At least 271 records · Page 15

Parallelizing autotuning for HPC applications: Unveiling the potential of the speculation strategy in Bayesian optimization

In the exascale computing era, tuning High-Performance Computing (HPC) applications has become a significant computational challenge. Although Bayesian optimization (BO) has emerged as a promising tool for HPC performance tuning, the BO workflow is inherently sequential (i.e., one function evaluation at a time) and cannot leverage the huge amount of parallel resources present in modern supercomputers, resulting in a considerable underutilization of their computational capabilities. This paper explores the trade-off between search quality and parallelism in BO, investigating a diverse set of methods. Building upon both previous approaches from the literature and novel methodologies introduced in this work, our study provides a deep analysis to accelerate BO performance tuning. By examining a set of synthetic functions and practical HPC applications, our exploration analyzes the interaction among various BO methods for parallelization, the quantity of parallel resources, the runtime distribution of target HPC applications, and the costs associated with different search orchestration mechanisms that have been overlooked in previous studies. Compared to sequential BO, our novel methodology achieves comparable quality while demonstrating robust scalability in search time as the amount of parallel resources increases; it also outperforms a state-of-the-art tuner, which supports parallelization, achieving up to 3.67x faster search time. We provide high-value insights for practitioners seeking to leverage the power of parallel computing for efficient HPC application tuning. Additionally, to further assist researchers in accelerating the performance tuning of their HPC applications, we provide an extension of an existing open-source tuning framework that incorporates our methods.

Bayesian optimization↗

Evaluation of 2 cognitive abilities tests in a dual-task environment

Most real world operators are required to perform multiple tasks simultaneously. In some cases, such as flying a high performance aircraft or trouble shooting a failing nuclear power plant, the operator's ability to time share or process in parallel" can be driven to extremes. This has created interest in selection tests of cognitive abilities. Two tests that have been suggested are the Dichotic Listening Task and the Cognitive Failures Questionnaire. Correlations between these test results and time sharing performance were obtained and the validity of these tests were examined. The primary task was a tracking task with dynamically varying bandwidth. This was performed either alone or concurrently with either another tracking task or a spatial transformation task. The results were: (1) An unexpected negative correlation was detected between the two tests; (2) The lack of correlation between either test and task performance made the predictive utility of the tests scores appear questionable; (3) Pilots made more errors on the Dichotic Listening Task than college students.

Vidulich, M. A.↗

Parallel CE/SE Computations via Domain Decomposition

This paper describes the parallelization strategy and achieved parallel efficiency of an explicit time-marching algorithm for solving conservation laws. The Space-Time Conservation Element and Solution Element (CE/SE) algorithm for solving the 2D and 3D Euler equations is parallelized with the aid of domain decomposition. The parallel efficiency of the resultant algorithm on a Silicon Graphics Origin 2000 parallel computer is checked.

Himansu, Ananda↗

Improving Resource Selection and Scheduling Using Predictions

The introduction of computational grids has resulted in several new problems in the area of scheduling that can be addressed using predictions. The first problem is selecting where to run an application on the many resources available in a grid. Our approach to help address this problem is to provide predictions of when an application would start to execute if submitted to specific scheduled computer systems. The second problem is gaining simultaneous access to multiple computer systems so that distributed applications can be executed. We help address this problem by investigating how to support advance reservations in local scheduling systems. Our approaches to both of these problems are based on predictions for the execution time of applications on space- shared parallel computers. As a side effect of this work, we also discuss how predictions of application run times can be used to improve scheduling performance.

Smith, Warren↗

Benchmark Comparison of Cloud Analytics Methods Applied to Earth Observations

Earth Observation data are a vital resource for studying long term changes, but the large data volumes can be challenging to analyze. Time series analysis in particular is hampered by the typical thin-time-slice file organization. We examine several potential solutions inspired in large part by the data-parallel methods that have arisen with cloud computing. These solutions include various combinations of data re-organization, spatial indexing, distributed storage and pre-computation that we term "Analytics Optimized Data Stores" (AODS). We find that even simple solutions (such as a data cube) produce more than an order of magnitude improvement; the best provide two to three orders of magnitude improvement. The most performant solutions have tradeoffs in terms of generality or storage footprint, but may nonetheless be useful components in data analytics frameworks where performance is critical.

parallel processing (computers)↗

A Parallelized Oxidation-Driven Surface Recession Framework in DSMC Code, SPARTA

Spacecrafts rely on ablative thermal protection systems (TPS) made of composites consisting of a carbon-based reinforcement and a polymeric matrix. These materials are designed to withstand high-temperature oxidation and surface recession during re-entry into the Earth's atmosphere. However, ablation occurs due to a complex interplay of thermal, mechanical, and chemical factors, making it challenging to determine the individual impact of each on the TPS's overall degradation. In this study, we have developed an ablation model that can leverage a finite rate carbon oxidation model to predict material recession and surface states more accurately. Stochastic PArallel Rarified-gas Time-accurate Analyzer (SPARTA), a direct-simulation Monte Carlo (DSMC) code, is modified to allow oxidation-driven ablation of implicitly defined carbon surfaces. In SPARTA, implicit surfaces are generated from the grid corner point values via a marching cubes algorithm, therefore creating a new set of surface elements every time ablation is performed. The finite-rate oxidation model developed by Gopalan et. al can perform both gas-surface and pure-surface reactions and is now adapted to tally surface data on a per grid cell basis. The ablation functionality was also adjusted so once the reactions have occurred, the number of reactions leading to CO formation can be converted to corner point reduction values; therefore, carbon removal is directly proportional to surface recession. We also briefly discuss some unique challenges associated with parallelizing this dynamic surface state and geometry. Finally, we analyze the performance of this parallelized implicit chemistry model with simple 2D and 3D benchmark cases by producing surface state statistics, area changes over time, and visualization across a range of surface temperatures and processors with and without load-balancing.

DSMC↗

A real-time blade element helicopter simulation for handling qualities analysis

A simulation model which utilizes parallel processing platforms is described in terms of its contributions to improved real-time helicopter simulation. The FLIGHTLAB parallel processing environment is explained, and the relative advantages of the blade element and rotor map models for rigid and elastic articulated blades are discussed. A UH-60 simulation is conducted by means of a rigid model with 14 degrees of freedom, as well as an elastic model with 26 degrees of freedom, to compare trim conditions, longitudinal static margins, and longitudinal and lateral frequency responses. The FLIGHTLAB system is shown to facilitate restructuring for parallel processing as well as the systematic comparison of a variety of models. The system can facilitate the comparison of rigid and elastic blade element rotor models at NASA-Ames and other research facilities.

Du Val, Ronald W.↗

Scalability of a Low-Cost Multi-Teraflop Linux Cluster for High-End Classical Atomistic and Quantum Mechanical Simulations

Scalability of a low-cost, Intel Xeon-based, multi-Teraflop Linux cluster is tested for two high-end scientific applications: Classical atomistic simulation based on the molecular dynamics method and quantum mechanical calculation based on the density functional theory. These scalable parallel applications use space-time multiresolution algorithms and feature computational-space decomposition, wavelet-based adaptive load balancing, and spacefilling-curve-based data compression for scalable I/O. Comparative performance tests are performed on a 1,024-processor Linux cluster and a conventional higher-end parallel supercomputer, 1,184-processor IBM SP4. The results show that the performance of the Linux cluster is comparable to that of the SP4. We also study various effects, such as the sharing of memory and L2 cache among processors, on the performance.

Kikuchi, Hideaki↗

The relation of scalability and execution time

Scalability has been used extensively as a de facto performance criterion for evaluating parallel algorithms and architectures. However, for many, scalability has theoretical interests only since it does not reveal execution time. In this paper, the relation between scalability and execution time is carefully studied. Results show that the isospeed scalability well characterizes the variation of execution time: smaller scalability leads to larger execution time, the same scalability leads to the same execution time, etc. Three algorithms from scientific computing are implemented on an Intel Paragon and an IBM SP2 parallel computer. Experimental and theoretical results show that scalability is an important, distinct metric for parallel and distributed systems, and may be as important as execution time in a scalable parallel and distributed environment.

Sun, Xian-He↗

IMS Rapid Response 2024 Summary Report: A Machine Learning Potential for the Periodic Table

Stockpile stewardship and nuclear waste remediation are inherently chemically complex, involving practically the full diversity of the periodic table, but existing methods are too expensive or not functional for a large diversity of atom types. Overall, the field of machine learning interatomic potentials (MLIPs) has advanced dramatically in 2024 with large high-accuracy datasets existing for bulk, surface, and organic chemical systems and new online leaderboards for diverse chemistry. To participate in, and bring LANL interests into this ecosystem, here, we have built upon existing technologies created by LANL to create a framework capable of creating machine learning interatomic potentials (MLIPs) for over 90 atom types. Our results have created a massively diverse coordination complex training dataset more than 3 times the size of existing datasets, parallelized MLIP training over multiple GPUs, enabling the training of an MLIP spanning the periodic table at 20 times the speed of prior training on 32 GPUs. These advances are substantial towards creation on foundational MLIPs for LANL-specific application areas.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Performance Evaluation in Network-Based Parallel Computing

Network-based parallel computing is emerging as a cost-effective alternative for solving many problems which require use of supercomputers or massively parallel computers. The primary objective of this project has been to conduct experimental research on performance evaluation for clustered parallel computing. First, a testbed was established by augmenting our existing SUNSPARCs' network with PVM (Parallel Virtual Machine) which is a software system for linking clusters of machines. Second, a set of three basic applications were selected. The applications consist of a parallel search, a parallel sort, a parallel matrix multiplication. These application programs were implemented in C programming language under PVM. Third, we conducted performance evaluation under various configurations and problem sizes. Alternative parallel computing models and workload allocations for application programs were explored. The performance metric was limited to elapsed time or response time which in the context of parallel computing can be expressed in terms of speedup. The results reveal that the overhead of communication latency between processes in many cases is the restricting factor to performance. That is, coarse-grain parallelism which requires less frequent communication between processes will result in higher performance in network-based computing. Finally, we are in the final stages of installing an Asynchronous Transfer Mode (ATM) switch and four ATM interfaces (each 155 Mbps) which will allow us to extend our study to newer applications, performance metrics, and configurations.

Dezhgosha, Kamyar↗

Mapping unstructured grid computations to massively parallel computers

Investigated here is this mapping problem: assign the tasks of a parallel program to the processors of a parallel computer such that the execution time is minimized. First, a taxonomy of objective functions and heuristics used to solve the mapping problem is presented. Next, we develop a highly parallel heuristic mapping algorithm, called Cyclic Pairwise Exchange (CPE), and discuss its place in the taxonomy. CPE uses local pairwise exchanges of processor assignments to iteratively improve an initial mapping. A variety of initial mapping schemes are tested and recursive spectral bipartitioning (RSB) followed by CPE is shown to result in the best mappings. For the test cases studied here, problems arising in computational fluid dynamics and structural mechanics on unstructured triangular and tetrahedral meshes, RSB and CPE outperform methods based on simulated annealing. Much less time is required to do the mapping and the results obtained are better. Compared with random and naive mappings, RSB and CPE reduce the communication time two fold for the test problems used. Finally, we use CPE in two applications on a CM-2. The first application is a data parallel mesh-vertex upwind finite volume scheme for solving the Euler equations on 2-D triangular unstructured meshes. CPE is used to map grid points to processors. The performance of this code is compared with a similar code on a Cray-YMP and an Intel iPSC/860. The second application is parallel sparse matrix-vector multiplication used in the iterative solution of large sparse linear systems of equations. We map rows of the matrix to processors and use an inner-product based matrix-vector multiplication. We demonstrate that this method is an order of magnitude faster than methods based on scan operations for our test cases.

Hammond, Steven Warren↗

Parallel Computation of the Jacobian Matrix for Nonlinear Equation Solvers Using MATLAB

Demonstrating speedup for parallel code on a multicore shared memory PC can be challenging in MATLAB due to underlying parallel operations that are often opaque to the user. This can limit potential for improvement of serial code even for the so-called embarrassingly parallel applications. One such application is the computation of the Jacobian matrix inherent to most nonlinear equation solvers. Computation of this matrix represents the primary bottleneck in nonlinear solver speed such that commercial finite element (FE) and multi-body-dynamic (MBD) codes attempt to minimize computations. A timing study using MATLAB's Parallel Computing Toolbox was performed for numerical computation of the Jacobian. Several approaches for implementing parallel code were investigated while only the single program multiple data (spmd) method using composite objects provided positive results. Parallel code speedup is demonstrated but the goal of linear speedup through the addition of processors was not achieved due to PC architecture.

Rose, Geoffrey K.↗

Parametric binary dissection

Binary dissection is widely used to partition non-uniform domains over parallel computers. This algorithm does not consider the perimeter, surface area, or aspect ratio of the regions being generated and can yield decompositions that have poor communication to computation ratio. Parametric Binary Dissection (PBD) is a new algorithm in which each cut is chosen to minimize load + lambda x(shape). In a 2 (or 3) dimensional problem, load is the amount of computation to be performed in a subregion and shape could refer to the perimeter (respectively surface) of that subregion. Shape is a measure of communication overhead and the parameter permits us to trade off load imbalance against communication overhead. When A is zero, the algorithm reduces to plain binary dissection. This algorithm can be used to partition graphs embedded in 2 or 3-d. Load is the number of nodes in a subregion, shape the number of edges that leave that subregion, and lambda the ratio of time to communicate over an edge to the time to compute at a node. An algorithm is presented that finds the depth d parametric dissection of an embedded graph with n vertices and e edges in O(max(n log n, de)) time, which is an improvement over the O(dn log n) time of plain binary dissection. Parallel versions of this algorithm are also presented; the best of these requires O((n/p) log(sup 3)p) time on a p processor hypercube, assuming graphs of bounded degree. How PBD is applied to 3-d unstructured meshes and yields partitions that are better than those obtained by plain dissection is described. Its application to the color image quantization problem is also discussed, in which samples in a high-resolution color space are mapped onto a lower resolution space in a way that minimizes the color error.

Bokhari, Shahid H.↗

Galerkin/Runge-Kutta discretizations for parabolic equations with time dependent coefficients

A new class of fully discrete Galerkin/Runge-Kutta methods is constructed and analyzed for linear parabolic initial boundary value problems with time dependent coefficients. Unlike any classical counterpart, this class offers arbitrarily high order convergence while significantly avoiding what has been called order reduction. In support of this claim, error estimates are proved, and computational results are presented. Additionally, since the time stepping equations involve coefficient matrices changing at each time step, a preconditioned iterative technique is used to solve the linear systems only approximately. Nevertheless, the resulting algorithm is shown to preserve the original convergence rate while using only the order of work required by the base scheme applied to a linear parabolic problem with time independent coefficients. Furthermore, it is noted that special Runge-Kutta methods allow computations to be performed in parallel so that the final execution time can be reduced to that of a low order method.

Keeling, Stephen L.↗

Galerkin/Runge-Kutta discretizations for parabolic equations with time-dependent coefficients

A new class of fully discrete Galerkin/Runge-Kutta methods is constructed and analyzed for linear parabolic initial boundary value problems with time dependent coefficients. Unlike any classical counterpart, this class offers arbitrarily high order convergence while significantly avoiding what has been called order reduction. In support of this claim, error estimates are proved, and computational results are presented. Additionally, since the time stepping equations involve coefficient matrices changing at each time step, a preconditioned iterative technique is used to solve the linear systems only approximately. Nevertheless, the resulting algorithm is shown to preserve the original convergence rate while using only the order of work required by the base scheme applied to a linear parabolic problem with time independent coefficients. Furthermore, it is noted that special Runge-Kutta methods allow computations to be performed in parallel so that the final execution time can be reduced to that of a low order method.

Keeling, Stephen L.↗

Parametric Study of a YAV-8B Harrier in Ground Effect using Time-Dependent Navier-Stokes Computations

A process is described which enables the generation of 35 time-dependent viscous solutions for a YAV-8B Harrier in ground effect in one week. Overset grids are used to model the complex geometry of the Harrier aircraft and the interaction of its jets with the ground plane and low-speed ambient flow. The time required to complete this parametric study is drastically reduced through the use of process automation, modern computational platforms, and parallel computing. Moreover, a dual-time-stepping algorithm is described which improves solution robustness. Unsteady flow visualization and a frequency domain analysis are also used to identify and correlated key flow structures with the time variation of lift.

Pandya, Shishir↗

High-resolution turbulent simulations using the Connection Machine-2

The spectral method provides an efficient algorithm for solving the 3D incompressible Navier-Stokes equations in periodic boundaries. Most people, so far, have used vectorized machines, such as the CRAY-2, to implement fast Fourier transformations and time integrations in the spectral calculations. In this paper, new results are presented using the spectral calculations on the Connection Machine-2 with a parallel algorithm. The large memory of the Connection Machine-2 and the parallel algorithm allows, of the first time, to implement a 512-cubed mesh resolution for high Reynolds number flows. The computational speed of the present code is about 30 percent faster than the fastest CRAY-2 simulations with four processors. Parallel machines, such as the Connection Machine-2, will possibly provide new computational power for understanding the intermittency and cascade mechanism in fluid turbulence.

Chen, Shiyi↗