In this work, we describe the CRIMSON (CardiovasculaR Integrated Modelling and SimulatiON) software environment. CRIMSON provides a powerful, customizable and user-friendly system for performing three-dimensional and reduced-order computational haemodynamics studies via a pipeline which involves: 1) segmenting vascular structures from medical images; 2) constructing analytic arterial and venous geometric models; 3) performing finite element mesh generation; 4) designing, and 5) applying boundary conditions; 6) running incompressible Navier-Stokes simulations of blood flow with fluid-structure interaction capabilities; and 7) post-processing and visualizing the results, including velocity, pressure and wall shear stress fields. A key aim of CRIMSON is to create a software environment that makes powerful computational haemodynamics tools accessible to a wide audience, including clinicians and students, both within our research laboratories and throughout the community. The overall philosophy is to leverage best-in-class open source standards for medical image processing, parallel flow computation, geometric solid modelling, data assimilation, and mesh generation. It is actively used by researchers in Europe, North and South America, Asia, and Australia. It has been applied to numerous clinical problems; we illustrate applications of CRIMSON to real-world problems using examples ranging from pre-operative surgical planning to medical device design optimization.

Summary Reliable mesh‐based simulations are needed to solve complex engineering problems. Mesh adaptivity can increase reliability by reducing discretization errors but requires multiple software components to exchange information. Often, components exchange information by reading and writing a common file format. This file‐based approach becomes a problem on massively parallel computers where filesystem bandwidth is a critical performance bottleneck. Our approach using data streams and component interfaces avoids the filesystem bottleneck. In this paper, we present these techniques and their use for coupling mesh adaptivity to the PHASTA computational fluid dynamics solver, the Albany multi‐physics framework, and the Omega3P linear accelerator frequency analysis applications. Performance results are reported on up to 16,384 cores of an Intel Knights Landing‐based system.

This paper introduces a general-purpose communication package built on top of MPI which is aimed at improving inter-processor communications for parallel computations characterized by large numbers of messages. The current library provides a utility for such applications based on two key attributes that are: (i) explicit consideration of the neighborhood communication pattern to avoid many-to-many calls and to reduce the number of collective calls and (ii) use of non-blocking MPI functions along with message packing to reduce actual communications in number and time. The introduction of the neighborhood communications leads to substantial reductions in the data exchange cost.

Implicit methods for partial differential equations using unstructured meshes allow for an efficient solution strategy for many real-world problems (e.g., simulation-based virtual surgical planning). Scalable solvers employing these methods not only enable solution of extremely-large practical problems but also lead to dramatic compression in time-to-solution. We present a parallelization paradigm and associated procedures that enable our implicit, unstructured flow-solver to achieve strong scalability.