Palabos Sample Clauses

Palabos. Palabos is Lattice Boltzmann Method (LBM) solver, available as open source, and massively parallel. The team of Prof Xxxxxxx Xxxxxxx at University of Geneva (CH) has specialised it to solve a number of relevant biomedical problems, including simulation of blood flow, and bone cement penetration during vertebroplasty. The software has specific features to deal with biomedical problems, reading medical images. Palabos was tested on CADMOS BlueGene/Q (Switzerland), UniGe Baobab (Switzerland). Palabos is actively developed and optimised for emerging exascale systems, and the associated optimisation work is detailed in Section 7 of D5.6 and in D2.3/4. Summarizing the effort done so far, we propose a novel high-performance computational framework for the simulation of fully resolved whole blood flow. The framework models blood constituents like red blood cells (RBCs) and platelets individually, including their detailed non-linear elastic properties and the complex interactions among them. These kinds of simulation are particularly challenging because the large number of blood cells (up to billions) stand in contrast with the major computational requirement of individual constituents. While classical approaches address this challenge through simplified structural modelling of the deformable bodies (e.g., through mass-spring systems), the present framework guarantees accurate physics, desirable numerical properties through a fully featured FEM model and computational efficiency at the same order as more simplified state-of-the-art models. So far, code optimisation was specially focused at the single node level, and HPC-Cloud capabilities were put to a test, from deployment up to managing complex workflows for the optimisation process. Future parallelisation efforts will focus on application of the Replica Computing (RC) pattern (see D2.3), as results obtained from the numerical experiments relies on gathering a statistically relevant number of data from a stochastic process. Computations linked to platelet deposition are suitable for execution on GPU platforms, allowing deployment of these computations on a hybrid supercomputer.

Palabos. Palabos is a lattice-Boltzmann Method (LBM) solver, available as open source, and massively parallel. The team of Prof Xxxxxxx Xxxxxxx at University of Geneva (Switzerland) has specialised it to solve a number of relevant biomedical problems, including simulation of blood flow, and bone cement penetration during vertebroplasty. The software has specific features to deal with biomedical problems including tools to read medical images. Palabos was tested on CADMOS BlueGene/Q (EPFL), Baobab (UNIGE). End-user solution type Please tick one or more Non-clinical research ✔ Clinical research ✔ Clinical decision support ✔ Drug discovery ✔ Design & optimisation ✔ In silico preclinical trials ✔ In silico clinical trials ✔ Personal health forecasting ✔ Provider: UNIGE Contact email: xxxxx.xxxx@xxxxx.xx Number of user organisations (list the top 5): Estimated users at M0: 0 Estimated users at M24: 0 Estimated users at M36: General user base (the software is free for download, users are not tracked individually). Estimated around 100. Access mode: source URL: xxxx://xxx.xxxxxxx.xxx HPC Systems: Baobab (UNIGE), CADMOS (UNIGE), XXXXXX (EPCC), MareNostrum (BSC) HPC motivation: Solve unreducible model, validate reduced-order model, Test model convergence, Larger space-time regions, Uncertainty quantification, Inform surrogate model, Multiscale models, Strongly coupled models. Additional user information: No detailed information available as users are not individually tracked.

Palabos. Application description Palabos is a general software library for computational fluid dynamics using the lattice Boltzmann method. In biomedical research, the main domains of applications are cardiovascular, including the simulation of blood flow in arteries, the investigation of the effect of medical devices such as stents, and cell-level blood simulations to investigate fundamental blood properties. Principal target users are researchers in the biomedical domain and R&D developing new medical devices. The code is open-source and is distributed under the terms of the software license AGPLv3. It can be downloaded from the Web site xxx.xxxxxxx.xxxxx.xx and is straightforward to install, as it depends on no external library (except for an implementation of the MPI communication layer). Technical specifications The Palabos library is written fully in C++ and runs on CPU clusters. It is parallelized with MPI for multi-core CPUs and for CPU clusters, using one MPI task per core (single-run parallelism). Typical memory requirements are 2 GB per core. Pre- and post-processing capabilities are built- in to the Palabos software library. A recommended data visualization tool for Palabos output is the ParaView software. HPC usage and parallel performance The need for HPC is particularly motivated in the field of cell-level blood simulations. Here, an exascale or pre-exascale system is required to simulate a macroscopically significant number of blood cells (of the order of 1 billion cells) while maintaining a detailed description of the physics of each cell. Cell-level simulations are achieved with the Palabos-npFEM coupling. A multi-scale description, i.e., simulation of a large blood volume (a section of an artery) while maintaining the cell-level description, is achieved in the limit of weak scaling, as the blood volume (and the total number of blood cells) scales with the number of available nodes. The figure in Annex 11.1.2 reports the scaling behaviour of the Palabos-npFEM code, as it simulates a coupled fluid – Red Blood Cell system on a heterogeneous platform (fluid on CPU, blood cells on GPU). The graph shows weak scaling, and the size of the simulated blood volume (in micro-meters) is indicated for each data point. Current research focuses on scaling the Palabos-npFEM code to a larger number of nodes, and on porting the full Palabos library to GPU for more efficient large-scale simulations of arterial flows. Porting of the Palabos library to single GPU has ...

Palabos. Scaling behaviour of the Palabos-npFEM code, as it simulates a coupled fluid – Red Blood Cell system on a heterogeneous platform (fluid on CPU, blood cells on GPU). The graph shows weak scaling, and the size of the simulated blood volume (in micro-meters) is indicated for each data point.