Completing a full replication study of our previously published findings on bluff-body aerodynamics was harder than we thought. Despite the fact that we have good reproducible-research practices, sharing our code and data openly. Here's what we learned from three years, four CFD codes and hundreds of runs.O ur research group prides itself for having adopted Reproducible Research practices. Barba (2012) 1 made a public pledge titled "Reproducibility PI Manifesto" (PI: Principal Investigator), which at the core is a promise to make all research materials and methods open access and discoverable: releasing code, data and analysis/visualization scripts.In 2014, we published a study on Physics of Fluids titled "Lift and wakes of flying snakes". 2 It is a study that used our in-house code for solving the equations of fluid motion in two dimensions (2D), with a solution approach called the "immersed boundary method." The key of such a method for solving the equations is that it exchanges complexity in the mesh generation step for complexity in the application of boundary conditions. It makes it possible to use a simple mesh for discretization (structured Cartesian), but at the cost of an elaborate process that interpolates values of fluid velocity at the boundary points to ensure the no-slip boundary condition (that fluid sticks to a wall). The main finding of our study on wakes of flying snakes was that the 2D section with anatomically correct geometry for the snake's body experiences lift enhancement at a given angle of attack. A previous experimental study 3 had already shown that the lift coefficient of a snake cross section in a wind tunnel gets an extra oomph of lift at 35 degrees angle-of-attack. Our simulations showed the same feature in the plot of lift coefficient. 4 Many detailed observations of the wake (visualized from the fluid-flow solution in terms of the vorticity field in space and time) allowed us to give an explanation of the mechanism providing extra lift. It arises from a vortex on the dorsal side of the body remaining closer to the surface under the effects of interactions with secondary vorticity. The flow around the snake's body cross section adopts a pattern known as a von Karman vortex street. It is a particularly complex flow, because it involves three shear layers: the boundary layer, a separating free shear layer, and the wake. 5 Physically, each of these shear layers is subject to instabilities. The free shear layer can experience 2D Kelvin-Helmholtz instability, while the wake experiences both 2D and 3D instabilities and can show chaotic behavior. Such flows are particularly challenging for computational fluid dynamics (CFD).When a computational research group produces this kind of study with an in-house code, it can take one, two or even three years to write a full research software from scratch, and complete verification and validation. Often, one gets the question: why not use a commercial CFD package? Why not use another research group's opensource code? Doesn't it take much longer to...

No abstract

No abstract

In a new effort to make our research transparent and reproducible by others, we developed a workflow to run and share computational studies on the public cloud Microsoft Azure. It uses Docker containers to create an image of the application software stack. We also adopt several tools that facilitate creating and managing virtual machines on compute nodes and submitting jobs to these nodes. The configuration files for these tools are part of an expanded "reproducibility package" that includes workflow definitions for cloud computing, in addition to input files and instructions. This facilitates re-creating the cloud environment to re-run the computations under the same conditions. Although cloud providers have improved their offerings, many researchers using high-performance computing (HPC) are still skeptical about cloud computing. Thus, we ran benchmarks for tightly coupled applications to confirm that the latest HPC nodes of Microsoft Azure are indeed a viable alternative to traditional on-site HPC clusters. We also show that cloud offerings are now adequate to complete computational fluid dynamics studies with in-house research software that uses parallel computing with GPUs. Finally, we share with the community what we have learned from nearly two years of using Azure cloud to enhance transparency and reproducibility in our computational simulations. ! arXiv:1904.07981v3 [cs.CE]

PetIBM is a C++ library with ready-to-use application codes to solve the two-and three-dimensional incompressible Navier-Stokes equations on fixed structured Cartesian grids with an immersed-boundary method (IBM). PetIBM runs on distributed-memory architectures and can be used to compute the flow around multiple moving rigid immersed boundaries (with prescribed kinematics).