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SCHEDULE: NOV 15-20, 2015

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Task-Based Parallel Computation of the Density Matrix in Quantum-Based Molecular Dynamics Using Graph Partitioning

SESSION: Regular & ACM Student Research Competition Poster Reception

EVENT TYPE: Posters, Receptions, ACM Student Research Competition

EVENT TAG(S): HPC Beginner Friendly, Regular Poster

TIME: 5:15PM - 7:00PM

SESSION CHAIR(S): Michela Becchi, Manish Parashar, Dorian C. Arnold

AUTHOR(S):Sergio Pino, Matthew Kroonblawd, Purnima Ghale, Georg Hahn, Vivek Sardeshmukh, Guangjie Shi, Hristo Djidjev, Christian Negre, Robert Pavel, Benjamin Bergen, Susan Mniszewski, Christoph Junghans

ROOM:Level 4 - Lobby


Quantum molecular dynamics(QMD) simulations are highly accurate, but they are computationally expensive due to the calculation of the ground-state electronic density matrix P via an O(N^3) diagonalization. Second-order spectral projection(SP2) is an efficient O(N) alternative to obtain P from a Hamiltonian matrix H. This poster presents a data-parallel version of the SP2 algorithm that uses an undirected graph representation of the matrix P to divide the computation into smaller independent partitions. These partitions can give rise to undesirable load imbalances in standard MPI/OpenMP-based implementations, as they are often of unequal sizes. The load-balancing problem is addressed by using task-based programming models to schedule parallel computations during runtime. We present CnC and Charm++ implementations that can be integrated into existing QMD codes. Our approach is applied to QMD simulations of representative biological protein systems with more than 10,000 atoms, exceeding size limitations of diagonalization by more than an order of magnitude.

Chair/Author Details:

Michela Becchi, Manish Parashar, Dorian C. Arnold (Chair) - University of Missouri|Rutgers University|University of New Mexico|

Sergio Pino - Los Alamos National Laboratory

Matthew Kroonblawd - Los Alamos National Laboratory

Purnima Ghale - Los Alamos National Laboratory

Georg Hahn - Los Alamos National Laboratory

Vivek Sardeshmukh - Los Alamos National Laboratory

Guangjie Shi - Los Alamos National Laboratory

Hristo Djidjev - Los Alamos National Laboratory

Christian Negre - Los Alamos National Laboratory

Robert Pavel - Los Alamos National Laboratory

Benjamin Bergen - Los Alamos National Laboratory

Susan Mniszewski - Los Alamos National Laboratory

Christoph Junghans - Los Alamos National Laboratory

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