Analyzing and Modeling the Performance of the HemeLB Lattice-Boltzmann Simulation Environment

We investigate the performance of the HemeLB lattice-Boltzmann simulator for cerebrovascular blood flow, aimed at providing timely and clinically relevant assistance to neurosurgeons. HemeLB is optimised for sparse geometries, supports interactive use, and scales well to 32,768 cores for problems with ~81 million lattice sites. We obtain a maximum performance of 29.5 billion site updates per second, with only an 11% slowdown for highly sparse problems (5% fluid fraction). We present steering and visualisation performance measurements and provide a model which allows users to predict the performance, thereby determining how to run simulations with maximum accuracy within time constraints.Comment: Accepted by the Journal of Computational Science. 33 pages, 16 figures, 7 table

Supercomputing with MPI meets the Common Workflow Language standards: an experience report

Use of standards-based workflows is still somewhat unusual by high-performance computing users. In this paper we describe the experience of using the Common Workflow Language (CWL) standards to describe the execution, in parallel, of MPI-parallelised applications. In particular, we motivate and describe the simple extension to the specification which was required, as well as our implementation of this within the CWL reference runner. We discuss some of the unexpected benefits, such as simple use of HPC-oriented performance measurement tools, and CWL software requirements interfacing with HPC module systems. We close with a request for comment from the community on how these features could be adopted within versions of the CWL standards.Comment: Submitted to 15th Workshop on Workflows in Support of Large-Scale Science (WORKS20

PolNet:A Tool to Quantify Network-Level Cell Polarity and Blood Flow in Vascular Remodeling

In this article, we present PolNet, an open-source software tool for the study of blood flow and cell-level biological activity during vessel morphogenesis. We provide an image acquisition, segmentation, and analysis protocol to quantify endothelial cell polarity in entire in vivo vascular networks. In combination, we use computational fluid dynamics to characterize the hemodynamics of the vascular networks under study. The tool enables, to our knowledge for the first time, a network-level analysis of polarity and flow for individual endothelial cells. To date, PolNet has proven invaluable for the study of endothelial cell polarization and migration during vascular patterning, as demonstrated by two recent publications. Additionally, the tool can be easily extended to correlate blood flow with other experimental observations at the cellular/molecular level. We release the source code of our tool under the Lesser General Public License

Exploring the origins of the power-law properties of energy landscapes: An egg-box model

Multidimensional potential energy landscapes (PELs) have a Gaussian distribution for the energies of the minima, but at the same time the distribution of the hyperareas for the basins of attraction surrounding the minima follows a power-law. To explore how both these features can simultaneously be true, we introduce an ``egg-box'' model. In these model landscapes, the Gaussian energy distribution is used as a starting point and we examine whether a power-law basin area distribution can arise as a natural consequence through the swallowing up of higher-energy minima by larger low-energy basins when the variance of this Gaussian is increased sufficiently. Although the basin area distribution is substantially broadened by this process,it is insufficient to generate power-laws, highlighting the role played by the inhomogeneous distribution of basins in configuration space for actual PELs.Comment: 7 pages, 8 figure

A Bespoke Workflow Management System for Data-Driven Urgent HPC

In this paper we present a workflow management system which permits the kinds of data-driven workflows required by urgent computing, namely where new data is integrated into the workflow as a disaster progresses in order refine the predictions as time goes on. This allows the workflow toadapt to new data at runtime, a capability that most workflow management systems do not possess. The workflow management system was developed for the EU-funded VESTEC project, which aims to fuse HPC with real-time data for supporting urgent decision making. We first describe an example workflow from the VESTEC project, and show why existing workflow technologies do not meet the needs of the project. We then go on to present the design of our Workflow Management System, describe how it is implemented into the VESTEC system, and provide an example of the workflow system in use for a test case

Role of Correlations in the Collective Behavior of Microswimmer Suspensions

International audienceIn this Letter, we study the collective behavior of a large number of self-propelled microswimmers immersed in a fluid. Using unprecedentedly large-scale lattice Boltzmann simulations, we reproduce the transition to bacterial turbulence. We show that, even well below the transition, swimmers move in a correlated fashion that cannot be described by a mean-field approach. We develop a novel kinetic theory that captures these correlations and is nonperturbative in the swimmer density. To provide an experimentally accessible measure of correlations, we calculate the diffusivity of passive tracers and reveal its nontrivial density dependence. The theory is in quantitative agreement with the lattice Boltzmann simulations and captures the asymmetry between pusher and puller swimmers below the transition to turbulence

Impact of blood rheology on wall shear stress in a model of the middle cerebral artery

Perturbations to the homeostatic distribution of mechanical forces exerted by blood on the endothelial layer have been correlated with vascular pathologies including intracranial aneurysms and atherosclerosis. Recent computational work suggests that in order to correctly characterise such forces, the shear-thinning properties of blood must be taken into account. To the best of our knowledge, these findings have never been compared against experimentally observed pathological thresholds. In the current work, we apply the three-band diagram (TBD) analysis due to Gizzi et al. to assess the impact of the choice of blood rheology model on a computational model of the right middle cerebral artery. Our results show that, in the model under study, the differences between the wall shear stress predicted by a Newtonian model and the well known Carreau-Yasuda generalized Newtonian model are only significant if the vascular pathology under study is associated with a pathological threshold in the range 0.94 Pa to 1.56 Pa, where the results of the TBD analysis of the rheology models considered differs. Otherwise, we observe no significant differences.Comment: 14 pages, 6 figures, published at Interface Focu

Choice of boundary condition for lattice-Boltzmann simulation of moderate-Reynolds-number flow in complex domains

Modeling blood flow in larger vessels using lattice-Boltzmann methods comes with a challenging set of constraints: a complex geometry with walls and inlet/outlets at arbitrary orientations with respect to the lattice, intermediate Reynolds number, and unsteady flow. Simple bounce-back is one of the most commonly used, simplest, and most computationally efficient boundary conditions, but many others have been proposed. We implement three other methods applicable to complex geometries (Guo, Zheng and Shi, Phys Fluids (2002); Bouzdi, Firdaouss and Lallemand, Phys. Fluids (2001); Junk and Yang Phys. Rev. E (2005)) in our open-source application \HemeLB{}. We use these to simulate Poiseuille and Womersley flows in a cylindrical pipe with an arbitrary orientation at physiologically relevant Reynolds (1--300) and Womersley (4--12) numbers and steady flow in a curved pipe at relevant Dean number (100--200) and compare the accuracy to analytical solutions. We find that both the Bouzidi-Firdaouss-Lallemand and Guo-Zheng-Shi methods give second-order convergence in space while simple bounce-back degrades to first order. The BFL method appears to perform better than GZS in unsteady flows and is significantly less computationally expensive. The Junk-Yang method shows poor stability at larger Reynolds number and so cannot be recommended here. The choice of collision operator (lattice Bhatnagar-Gross-Krook vs.\ multiple relaxation time) and velocity set (D3Q15 vs.\ D3Q19 vs.\ D3Q27) does not significantly affect the accuracy in the problems studied.Comment: Submitted to Phys. Rev. E, 14 pages, 6 figures, 5 table

Computer simulations reveal complex distribution of haemodynamic forces in a mouse retina model of angiogenesis.

There is currently limited understanding of the role played by haemodynamic forces on the processes governing vascular development. One of many obstacles to be overcome is being able to measure those forces, at the required resolution level, on vessels only a few micrometres thick. In this paper, we present an in silico method for the computation of the haemodynamic forces experienced by murine retinal vasculature (a widely used vascular development animal model) beyond what is measurable experimentally. Our results show that it is possible to reconstruct high-resolution three-dimensional geometrical models directly from samples of retinal vasculature and that the lattice-Boltzmann algorithm can be used to obtain accurate estimates of the haemodynamics in these domains. We generate flow models from samples obtained at postnatal days (P) 5 and 6. Our simulations show important differences between the flow patterns recovered in both cases, including observations of regression occurring in areas where wall shear stress (WSS) gradients exist. We propose two possible mechanisms to account for the observed increase in velocity and WSS between P5 and P6: (i) the measured reduction in typical vessel diameter between both time points and (ii) the reduction in network density triggered by the pruning process. The methodology developed herein is applicable to other biomedical domains where microvasculature can be imaged but experimental flow measurements are unavailable or difficult to obtain