Renato N. Elias

Exploring many task computing in scientific workflows

One of the main advantages of using a scientific workflow management system (SWfMS) to orchestrate data flows among scientific activities is to control and register the whole workflow execution. The execution of activities within a workflow with high performance computing (HPC) presents challenges in SWfMS execution control. Current solutions leave the scheduling to the HPC queue system. Since the workflow execution engine does not run on remote clusters, SWfMS are not aware of the parallel strategy of the workflow execution. Consequently, remote execution control and provenance registry of the parallel activities is very limited from the SWfMS side. This work presents a set of components to be included on the workflow specification of any SWMfS to control parallelization of activities as MTC. In addition, these components can gather provenance data during remote workflow execution. Through these MTC components, the parallelization strategy can be registered and reused, and provenance data can be uniformly queried. We have evaluated our approach by performing parameter sweep parallelization in solving the incompressible 3D Navier-Stokes equations. Experimental results show the performance gains with the additional benefits of distributed provenance support.

Parallel edge-based inexact newton solution of steady incompressible 3D navier-stokes equations

The parallel edge-based solution of 3D incompressible Navier-Stokes equations is presented. The governing partial differential equations are discretized using the SUPG/PSPG stabilized finite element method [5] on unstructured grids. The resulting fully coupled nonlinear system of equations is solved by the inexact Newton-Krylov method [1]. Matrix-vector products within GMRES are computed edge-by-edge, diminishing flop counts and memory requirements. The non-linear solver parallel implementation is based in message passing interface (MPI). Performance tests on several computers, such as the SGI Altix, the Cray XD1 and a mini-wireless cluster were carried out in representative problems and results have shown that edge-based schemes require less CPU time and memory than element-based solutions.

Uncertainty quantification in numerical simulation of particle-laden flows

Numerical models can help to push forward the knowledge about complex dynamic physical systems. Modern approaches employ detailed mathematical models, taking into consideration inherent uncertainties on input parameters (phenomenological parameters or boundary and initial conditions, among others). Particle-laden flows are complex physical systems found in nature, generated due to the (possible small) spatial variation on the fluid density promoted by the carried particles. They are one of the main mechanisms responsible for the deposition of sediments on the seabed. A detailed understanding of particle-laden flows, often referred to as turbidity currents, helps geologists to understand the mechanisms that give rise to reservoirs, strategic in oil exploration. Uncertainty quantification (UQ) provides a rational framework to assist in this task, by combining sophisticated computational models with a probabilistic perspective in order to deepen the knowledge about the physics of the problem and to access the reliability of the results obtained with numerical simulations. This work presents a stochastic analysis of sediment deposition resulting from a turbidity current considering uncertainties on the initial sediment concentrations and particles settling velocities. The statistical moments of the deposition mapping, like other important features of the currents, are approximated by a Sparse Grid Stochastic Collocation method that employ a parallel flow solver for the solution of the deterministic problems associated to the grid points. The whole procedure is supported and steered by a scientific workflow management engine designed for high performance computer applications.

Computational Techniques for Stabilized Edge-Based Finite Element Simulation of Nonlinear Free-Surface Flows

Free-surface flows occur in several problems in hydrodynamics, such as fuel or water sloshing in tanks, waves breaking in ships, offshore platforms, harbors, and coastal areas. The computation of such highly nonlinear flows is challenging, since free-surfaces commonly present merging, fragmentation, and breaking parts, leading to the use of interface-capturing Eulerian approaches. In such methods the surface between two fluids is captured by the use of a marking function, which is transported in a flow field. In this work we discuss computational techniques for efficient implementation of 3D incompressible streamline-upwind/Petrov–Galerkin (SUPG)/pressure-stabilizing/Petrov–Galerkin finite element methods to cope with free-surface problems with the volume-of-fluid method (Elias, and Coutinho, 2007, “Stabilized Edge-Based Finite Element Simulation of Free-Surface Flows,” Int. J. Numer. Methods Fluids, 54, pp. 965–993). The pure advection equation for the scalar marking function was solved by a fully implicit parallel edge-based SUPG finite element formulation. Global mass conservation is enforced, adding or removing mass proportionally to the absolute value of the normal velocity of the interface. We introduce parallel edge-based data structures, a parallel dynamic deactivation algorithm to solve the marking function equation only in a small region around the interface. The implementation is targeted to distributed memory systems with cache-based processors. The performance and accuracy of the proposed solution method is tested in the simulation of the water impact on a square cylinder and in the propagation of a solitary wave.

Evaluation of message passing communication patterns in finite element solution of coupled problems

This work presents a performance evaluation of single node and subdomain communication schemes available in EdgeCFD, an implicit edge-based coupled fluid flow and transport code for solving large scale problems in modern clusters. A natural convection flow problem is considered to assess performance metrics. Tests, focused in single node multi-core performance, show that past Intel Xeon processors dramatically suffer when large workloads are imposed to a single node. However, the problem seems to be mitigated in the newest Intel Xeon processor. We also observe that MPI nonblocking point-to-point interface sub-domain communications, although more difficult to implement, are more effective than collective interface subdomain communications.

Inexact Newton-type methods for non-linear problems arising from the SUPG/PSPG solution of steady incompressible navier-stokes equations

Equations finite element discretization of the incompress ible steady-state Navier-Stokes equations yields a non-linear problem, due to the c onvective terms in the momentum equations. Several methods may be used to solve thi s non-linear problem. In this work we study Inexact Newton-type methods, associated with the SUPG/PSPG stabilized finite element formulation. The resulting systems of equat ions are solved iteratively by a preconditioned Krylov-space method such as GMRES. N umerical experiments are shown to validate our approach. Performance of the nonlin ear strategies is accessed by numerical tests. We concluded that Inexact Newton-t ype methods are more efficient than conventional Newton-type methods.

Edgepack: a parallel vertex and node reordering package for optimizing edge-based computations in unstructured grids

A new and simple method is proposed to choose the best data configuration in terms of processing phase time according to previous probing of edge-based matrix-vector products for codes using iterative solvers in unstructured grid problems. This method is realized as a suite of routines named EdgePack, acting during both pre-solution and solution phase, based on data locality optimization techniques and variations of matrix-vector product algorithm. Results have been demonstrating the great flexibility and simplicity of this method, which is suitable for distributed memory platforms in which different data configurations can coexist.

EdgeCFD-ALE: A Stabilized Finite Element System for Fluid-Structure Interaction in Offshore Engineering

This work presents the development of EdgeCFD-ALE, a finite element system for complex fluid-structure interactions designed for offshore hydrodynamics. Sloshing of liquids in tanks, wave breaking in ships, offshore platforms motions and green water on decks are important examples of these problems. The software uses edge-based parallel stabilized finite elements for the Navier-Stokes equations and the Volume-Of-Fluid method for the free-surface, both described by an Arbitrary Lagrangian Eulerian (ALE) formulation. Turbulence in is treated by a Smagorinsky model. Mesh updating is accomplished by a parallel edge-based solution of a non-homogeneous scalar diffusion problem in each spatial coordinate. Boundary conditions involve the motion of the immersed body’s surface, i.e., the fluid-structure interface, taken as the Lagrangian portion of the domain in the overall problem. The simulation capabilities of the present software are demonstrated in the solution of two problems, the interaction of two cylinders in tandem and the free fall of a sphere.Copyright

A Stabilized Edge-Based Finite Element Approach to Wave-Structure Interaction Assessment

Complex flows involving waves and free-surfaces occur in several problems in hydrodynamics, such as fuel or water sloshing in tanks, waves breaking in ships, offshore platforms motions, wave action on harbors and coastal areas. The computation of such highly nonlinear flows is challenging since waves and free-surfaces commonly present merging, fragmentation and cusps, leading to the use of interface capturing Arbitrary Lagrangian-Eulerian (ALE) approaches. In such methods the interface between the two fluids is captured by the use of a marking function that is transported in a flow field. In this work we simulate these problems with a 3D incompressible SUPG/PSPG parallel edge-based finite element flow solver associated to the Volume-of-Fluid (VOF) method. The hyperbolic equation for the transport of the marking function is also solved by a fully implicit parallel edge-based SUPG finite element formulation. Global mass conservation is enforced adding or removing mass proportionally to the absolute value of the normal velocity at the interface. All those techniques were successfully implemented in a computational code, which has been suitably used to carry out several studies. The performance and accuracy of the proposed solution method is tested in the simulation waves and in the interaction between waves and a semisubmersible structure. Results count on the establishment of a relaxation zone close to the domain outflow, which partially absorbs incoming waves, avoiding their reflection.Copyright

COMPUTATIONAL SIMULATION OF FREE SURFACE FLOWS USING STABILIZED EDGE-BASED FINITE ELEMENT METHOD

Flows involving waves and free-surfaces occur in several problems in hydrodynamics, such as sloshing in tanks, waves breaking in ship and motions of offshore platforms. The computation of such wave problems is challenging since the water/air interface (or free-surface) commonly present merging, fragmentation and cusps, leading to the use of interface capturing Arbitrary Lagrangian-Eulerian (ALE) approaches. In such methods the interface between the two fluids is captured by the use of a marking function which is transported in a flow field. In this work we simulate these problems with a 3D incompressible SUPG/PSPG parallel edge-based finite element flow solver associated to the Volume-of-Fluid (VOF) method [1]. The hyperbolic equation for the transport of the marking function is also solved by a fully implicit parallel edge-based SUPG finite element formulation. Global mass conservation is enforced adding or removing mass proportionally to the absolute value of the normal velocity at the interface. The performance and accuracy of the proposed solution method is tested in the simulation of pulse wave and the interaction of a fixed square cylinder with a progressive wave.Copyright