Empirical Study of Molecular Dynamics Workflow Data Movement: DYAD Vs. Traditional I/O Systems

This experimental work examines data movement in molecular dynamics (MD) workflows, comparing the Dynamic and Asynchronous Data Streamliner (DYAD) middleware with traditional, industry-standard I/O systems such as XFS and Lustre. DYAD moves MD simulation frames to analytics processes, providing enhanced flexibility and efficiency for dynamic data transfers and in situ analytics. At the same time, traditional I/O storage systems provide durability and scalability for high-performance computing (HPC) systems. The study integrates MD workflows with common simulation codes, facilitating immediate capture and transfer of MD frames to a staging area. It explores various molecular models, from simple to complex, assessing data management performance and scalability. Different producer-consumer pairs, molecular models, and data transaction frequency enable testing across small to large-scale HPC scenarios, from single-node configurations to large, distributed environments. The findings reveal that adaptive mechanisms for minimizing synchronization, direct network communication between producer and consumer processes, and optimizations of both data movement and synchronization are crucial for performance and scalability in MD workflows.