CSE Seminar By:
Edmond Chow
Computer Science Generalist,
D. E. Shaw Research, New York, NY

Title: Load-Balanced Bonded Force Calculations on Anton

Abstract:
Molecular dynamics (MD) simulations of biological molecules involve the calculation of "bonded" force terms due to covalent bonds. On parallel computers, this calculation is normally not load balanced because the data partitioning required for load balance is in conflict with the partitioning needed for the much more expensive "nonbonded" (electrostatic and van der Waals) force calculation. On Anton, a specialized parallel machine for MD calculations, the situation has changed: the nonbonded component of the calculation has been dramatically accelerated and the remaining bonded component can often be a non-negligible determinant of overall performance. This talk describes the challenges in load balancing the bonded force calculations on Anton. In addition to the usual considerations of balancing load and minimizing communication across processors, we consider balancing the storage required per node, to allow larger chemical systems to be simulated. This interesting combinatorial problem arises because many bond terms share the same parameter data and this data does not need to be duplicated within a node. We also consider the hierarchical problem of partitioning the data among Anton nodes and its relation to partitioning the data within each node for computation by multiple cores. Additional resource limitations at this level also lead to interesting (and messy!) combinatorial problems for load balance.