title: Real-Time Agent-Based Modeling Simulation with in-situ Visualization of Complex Biological Systems: A Case Study on Vocal Fold Inflammation and Healing.
abstract: We present an efficient and scalable scheme for implementing agent-based modeling (ABM) simulation with In Situ visualization of large complex systems on heterogeneous computing platforms. The scheme is designed to make optimal use of the resources available on a heterogeneous platform consisting of a multicore CPU and a GPU, resulting in minimal to no resource idle time. Furthermore, the scheme was implemented under a client-server paradigm that enables remote users to visualize and analyze simulation data as it is being generated at each time step of the model. Performance of a simulation case study of vocal fold inflammation and wound healing with 3.8 million agents shows 35× and 7× speedup in execution time over single-core and multi-core CPU respectively. Each iteration of the model took less than 200 ms to simulate, visualize and send the results to the client. This enables users to monitor the simulation in real-time and modify its course as needed.
authors.affiliation: Department of Electrical and Computer Engineering - University of Maryland-College Park, Maryland, USA.
authors.forename: Nuttiiya
authors.initials: N
authors.lastname: Seekhao
authors.affiliation: Department of Mechanical Engineering - McGill University, Montreal, Canada.
authors.forename: Caroline
authors.initials: C
authors.lastname: Shung
authors.affiliation: Department of Electrical and Computer Engineering - University of Maryland-College Park, Maryland, USA.
authors.forename: Joseph
authors.initials: J
authors.lastname: JaJa
authors.affiliation: Department of Mechanical Engineering - McGill University, Montreal, Canada.
authors.forename: Luc
authors.initials: L
authors.lastname: Mongeau
authors.affiliation: School of Communication Sciences and Disorders - McGill University, Montreal, Canada.
authors.forename: Nicole Y K
authors.initials: NY
authors.lastname: Li-Jessen
keywords: ABMs; HPC; Heterogeneous Platform; In Situ Visualization; Systems Biology; component