Multiscale Universal Interface: A concurrent framework for coupling heterogeneous solvers

Tang, Yuhang; Kudo, Shuhei; Bian, Xin; Li, Zhen; Karniadakis, George Em

doi:10.1016/j.jcp.2015.05.004

Cited by 75 publications

(56 citation statements)

References 32 publications

(42 reference statements)

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“…OpenRBC is written in C++ using features from the C++11 standard. To maximize portability and allow easy integration into other software systems [18], the project is organized as a headeronly library with no external dependencies. The software implements SIMD vectorization [19] and OpenMP shared memory parallelization, and was specifically optimized toward making efficient use of large numbers of simultaneous hardware threads.…”

Section: Software Overviewmentioning

confidence: 99%

OpenRBC: A Fast Simulator of Red Blood Cells at Protein Resolution

Tang

et al. 2017

Biophysical Journal

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We present OpenRBC, a coarse-grained molecular dynamics code, which is capable of performing an unprecedented in silico experiment-simulating an entire mammal red blood cell lipid bilayer and cytoskeleton as modeled by multiple millions of mesoscopic particles-using a single shared memory commodity workstation. To achieve this, we invented an adaptive spatial-searching algorithm to accelerate the computation of short-range pairwise interactions in an extremely sparse three-dimensional space. The algorithm is based on a Voronoi partitioning of the point cloud of coarse-grained particles, and is continuously updated over the course of the simulation. The algorithm enables the construction of the key spatial searching data structure in our code, i.e., a lattice-free cell list, with a time and space cost linearly proportional to the number of particles in the system. The position and the shape of the cells also adapt automatically to the local density and curvature. The code implements OpenMP parallelization and scales to hundreds of hardware threads. It outperforms a legacy simulator by almost an order of magnitude in time-to-solution and >40 times in problem size, thus providing, to our knowledge, a new platform for probing the biomechanics of red blood cells.

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Section: Software Overviewmentioning

confidence: 99%

OpenRBC: A Fast Simulator of Red Blood Cells at Protein Resolution

Tang

et al. 2017

Biophysical Journal

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“…Tang et al (2015) recently introduced the multiscale universal interface (MUI), which is a headeronly library that takes most of the programming-related issues off the user's hands. A data sampler, derived from texture sampling concepts, is implemented which allows for spatial data interpolation between descriptions.…”

Section: Discussionmentioning

confidence: 99%

Progress in particle-based multiscale and hybrid methods for flow applications

Teschner

Könözsy

Jenkins

2016

Microfluid Nanofluid

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“…The concurrent coupling of two independent solvers requires robust on-the-fly data transfer. For the examples shown here, we used a light weight library called Multiscale Universal Interface [40], or MUI for short, to bridge the solvers.…”

Section: Methodsmentioning

confidence: 99%

Supervised parallel-in-time algorithm for long-time Lagrangian simulations of stochastic dynamics: Application to hydrodynamics

Blumers

Karniadakis

2019

Journal of Computational Physics

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Lagrangian particle methods based on detailed atomic and molecular models are powerful computational tools for studying the dynamics of microscale and nanoscale systems. However, the maximum time step is limited by the smallest oscillation period of the fastest atomic motion, rendering long-time simulations very expensive. To resolve this bottleneck, we propose a supervised parallel-in-time algorithm for stochastic dynamics (SPASD) to accelerate long-time Lagrangian particle simulations. Our method is inspired by bottom-up coarse-graining projections that yield mean-field hydrodynamic behavior in the continuum limit. Here as an example, we use the dissipative particle dynamics (DPD) as the Lagrangian particle simulator that is supervised by its macroscopic counterpart, i.e., the Navier-Stokes simulator. The low-dimensional macroscopic system (here, the Navier-Stokes solver) serves as a predictor to supervise the high-dimensional Lagrangian simulator, in a predictor-corrector type algorithm. The results of the Lagrangian simulation then correct the mean-field prediction and provide the proper microscopic details (e.g., consistent fluctuations, correlations, etc.). The unique feature that sets SPASD apart from other multiscale methods is the use of a low-fidelity macroscopic model as a predictor. The macro-model can be approximate and even inconsistent with the microscale description, but SPASD anticipates the deviation and corrects it internally to recover the true dynamics. We first present the algorithm and analyze its theoretical speedup, and subsequently we present the accuracy and convergence of the algorithm for the timedependent plane Poiseuille flow, demonstrating that SPASD converges exponentially fast over iterations, irrespective of the accuracy of the predictor. Moreover, the fluctuating characteristics of the stochastic dynamics are identical to the unsupervised (serial in time) DPD simulation. We also compare the performance of SPASD to the conventional spatial decomposition method, which is one of the most parallel-efficient methods for particle simulations. We find that the parallel efficiency of SPASD and the conventional spatial decomposition method are similar for a small number of computing cores, but for a large number of cores the performance of SPASD is superior. Furthermore, SPASD can be used in conjunction with spatial decomposition for enhanced performance. Lastly, we simulate a two-dimensional cavity flow that requires more iterations to converge compared to the Poiseuille flow, and we observe that SPASD converges to the correct solution. Although a DPD solver is used to demonstrate the results, SPASD is a general framework and can be readily applied to other Lagrangian approaches including molecular dynamics and Langevin dynamics.A. Blumers et al. / arXiv.org (2019) 1-18 2 therefore Lagrangian methods based on detailed atomic and molecular models are required [2]. However, because the atomistic details are explicitly modeled, the maximum time step is limited by the smallest oscillation ...

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Multiscale Universal Interface: A concurrent framework for coupling heterogeneous solvers

Cited by 75 publications

References 32 publications

OpenRBC: A Fast Simulator of Red Blood Cells at Protein Resolution

OpenRBC: A Fast Simulator of Red Blood Cells at Protein Resolution

Progress in particle-based multiscale and hybrid methods for flow applications

Supervised parallel-in-time algorithm for long-time Lagrangian simulations of stochastic dynamics: Application to hydrodynamics

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