371,457 research outputs found
Dynamic Smagorinsky Modeled Large-Eddy Simulations of Turbulence Using Tetrahedral Meshes
Eddy-resolving numerical computations of turbulent flows are emerging as viable alternatives to Reynolds Averaged Navier-Stokes (RANS) calculations for flows with an intrinsically steady mean state due to the advances in large-scale parallel computing. In these computations, medium to large turbulent eddies are resolved by the numerics while the smaller or subgrid scales are either modeled or taken care of by the inherent numerical dissipation. To advance the state of the art of unstructured-mesh turbulence simulation capabilities, large eddy simulations (LES) using the dynamic Smagorinsky model (DSM) on tetrahedral meshes are carried out with the space-time conservation element, solution element (CESE) method. In contrast to what has been reported in the literature, the present implementation of dynamic models allows for active backscattering without any ad-hoc limiting of the eddy viscosity calculated from the subgrid-scale model. For the benchmark problems involving compressible isotropic turbulence decay as well as the shock/turbulent boundary layer interaction benchmark problems, no numerical instability associated with kinetic energy growth is observed and the volume percentage of the backscattering portion accounts for about 38-40% of the simulation domain. A slip-wall model in conjunction with the implemented DSM is used to simulate a relatively high Reynolds number Mach 2.85 turbulent boundary layer over a 30 ramp with several tetrahedral meshes and a wall-normal spacing of either & = 10 or & = 20. The computed mean wall pressure distribution, separation region size, mean velocity profiles, and Reynolds stress agree reasonably well with experimental data
Automating Fault Tolerance in High-Performance Computational Biological Jobs Using Multi-Agent Approaches
Background: Large-scale biological jobs on high-performance computing systems
require manual intervention if one or more computing cores on which they
execute fail. This places not only a cost on the maintenance of the job, but
also a cost on the time taken for reinstating the job and the risk of losing
data and execution accomplished by the job before it failed. Approaches which
can proactively detect computing core failures and take action to relocate the
computing core's job onto reliable cores can make a significant step towards
automating fault tolerance.
Method: This paper describes an experimental investigation into the use of
multi-agent approaches for fault tolerance. Two approaches are studied, the
first at the job level and the second at the core level. The approaches are
investigated for single core failure scenarios that can occur in the execution
of parallel reduction algorithms on computer clusters. A third approach is
proposed that incorporates multi-agent technology both at the job and core
level. Experiments are pursued in the context of genome searching, a popular
computational biology application.
Result: The key conclusion is that the approaches proposed are feasible for
automating fault tolerance in high-performance computing systems with minimal
human intervention. In a typical experiment in which the fault tolerance is
studied, centralised and decentralised checkpointing approaches on an average
add 90% to the actual time for executing the job. On the other hand, in the
same experiment the multi-agent approaches add only 10% to the overall
execution time.Comment: Computers in Biology and Medicin
Parallel load balancing strategy for Volume-of-Fluid methods on 3-D unstructured meshes
© 2016. This version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/l Volume-of-Fluid (VOF) is one of the methods of choice to reproduce the interface motion in the simulation of multi-fluid flows. One of its main strengths is its accuracy in capturing sharp interface geometries, although requiring for it a number of geometric calculations. Under these circumstances, achieving parallel performance on current supercomputers is a must. The main obstacle for the parallelization is that the computing costs are concentrated only in the discrete elements that lie on the interface between fluids. Consequently, if the interface is not homogeneously distributed throughout the domain, standard domain decomposition (DD) strategies lead to imbalanced workload distributions. In this paper, we present a new parallelization strategy for general unstructured VOF solvers, based on a dynamic load balancing process complementary to the underlying DD. Its parallel efficiency has been analyzed and compared to the DD one using up to 1024 CPU-cores on an Intel SandyBridge based supercomputer. The results obtained on the solution of several artificially generated test cases show a speedup of up to similar to 12x with respect to the standard DD, depending on the interface size, the initial distribution and the number of parallel processes engaged. Moreover, the new parallelization strategy presented is of general purpose, therefore, it could be used to parallelize any VOF solver without requiring changes on the coupled flow solver. Finally, note that although designed for the VOF method, our approach could be easily adapted to other interface-capturing methods, such as the Level-Set, which may present similar workload imbalances. (C) 2014 Elsevier Inc. Allrights reserved.Peer ReviewedPostprint (author's final draft
Revisiting Matrix Product on Master-Worker Platforms
This paper is aimed at designing efficient parallel matrix-product algorithms
for heterogeneous master-worker platforms. While matrix-product is
well-understood for homogeneous 2D-arrays of processors (e.g., Cannon algorithm
and ScaLAPACK outer product algorithm), there are three key hypotheses that
render our work original and innovative:
- Centralized data. We assume that all matrix files originate from, and must
be returned to, the master.
- Heterogeneous star-shaped platforms. We target fully heterogeneous
platforms, where computational resources have different computing powers.
- Limited memory. Because we investigate the parallelization of large
problems, we cannot assume that full matrix panels can be stored in the worker
memories and re-used for subsequent updates (as in ScaLAPACK).
We have devised efficient algorithms for resource selection (deciding which
workers to enroll) and communication ordering (both for input and result
messages), and we report a set of numerical experiments on various platforms at
Ecole Normale Superieure de Lyon and the University of Tennessee. However, we
point out that in this first version of the report, experiments are limited to
homogeneous platforms
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