E. scolopes is a species of small squids, commonly known as the Hawaiian bobtail squid, living off the coast of Hawaii. Early in its life cycle, it forms a life-long symbiosis with bacteria Vibrio fischeri . The squids need the bioluminescent bacteria for a form of camouflage called counter-illumination, which helps the squid blend in with the moonlit … More Modeling Bacterial War
Fluid-structure interactions (FSI) are ubiquitous in nature, laboratory, and industrial setting. For example, animal locomotion, fluid flowing through porous media, or cheese being stirred and pumped through a cheese making machine. However, FSI problems are challenging to solve analytically or simulate numerically, due to their nonlinear, multi-physics nature. In particular, it is difficult to reconcile … More Simulating Fluid–Structure Interactions
This past week, some of us from the Rycroft group attended SIAM CSE 19 at Spokane, WA. One of the presentations I gave is a poster on GPU application performance profiling. This is part of the summer CSGF practicum project I did at LBNL with CCSE group. The applications are written using AMReX framework, and … More Performance study on GPU offloading via CUDA, OpenACC, and OpenMP in AMReX
Multigrid is an iterative method that is particularly suited for solving large, sparse linear systems, in the form of . When we have a sparse matrix at hand, direct methods, such as LU decomposition, for solving the equation becomes undesirable, because we might lose the sparsity and end up with a dense matrix. The best … More Multigrid in a nutshell
Equations for fluid dynamics In one of my research projects, I study numerical methods for fluid-structure interaction (FSI) problems. Examples of this type of problems are ubiquitous in nature, industries, and laboratories. For instance, as organisms swim in a liquid, the parts that generate propulsion, such as flagella and fins, are the solid structures that … More Multigrid applied to Incompressible Navier-Stokes Equation
Many problems in computational sciences require solving linear systems, in the form of . Examples includes integrating an system of ordinary differential equations (ODEs) or solving partial differential equations (PDEs), image processing and analysis, etc. When the problems become large, direct methods, such as LU decomposition, become inefficient. This makes using an iterative method, such … More Hybrid parallelized multigrid with OpenMP, GPU acceleration, and MPI
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