Enabling Simulation of High-Dimensional Micro-Macro Biophysical Models through Hybrid CPU and Multi-GPU Parallelism

08/12/2019
by   Steven Cook, et al.
0

Micro-macro models provide a powerful tool to study the relationship between microscale mechanisms and emergent macroscopic behavior. However, the detailed microscopic modeling may require tracking and evolving a high-dimensional configuration space at high computational cost. In this work, we present a parallel algorithm for simulation a high-dimensional micro-macro model of a gliding motility assay. We utilize a holistic approach aligning the data residency and simulation scales with the hybrid CPU and multi-GPU hardware. With a combination of algorithmic modifications, GPU optimizations, and scaling to multiple GPUs, we achieve speedup factors of up to 27 over our previous hybrid CPU-GPU implementation and up to 540 over our single-threaded implementation. This approach enables micro-macro simulations of higher complexity and resolution than would otherwise be feasible.

READ FULL TEXT

Please sign up or login with your details

Forgot password? Click here to reset

Sign in with Google

×

Use your Google Account to sign in to DeepAI

×

Consider DeepAI Pro