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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
ABSTRACT:
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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