Computer simulation of liquids
Computer simulation of liquids
Parallel algorithms in computational science
Parallel algorithms in computational science
Fast parallel algorithms for short-range molecular dynamics
Journal of Computational Physics
MPI versus MPI+OpenMP on IBM SP for the NAS benchmarks
Proceedings of the 2000 ACM/IEEE conference on Supercomputing
Molecular Dynamics Simulation: Elementary Methods
Molecular Dynamics Simulation: Elementary Methods
Terascale spectral element dynamical core for atmospheric general circulation models
Proceedings of the 2001 ACM/IEEE conference on Supercomputing
The Journal of Supercomputing
Automatic performance analysis of hybrid MPI/OpenMP applications
Journal of Systems Architecture: the EUROMICRO Journal - Special issue: Evolutions in parallel distributed and network-based processing
Scalable algorithms for molecular dynamics simulations on commodity clusters
Proceedings of the 2006 ACM/IEEE conference on Supercomputing
Development of mixed mode MPI / OpenMP applications
Scientific Programming
Performance Implications of Cache Affinity on Multicore Processors
Euro-Par '08 Proceedings of the 14th international Euro-Par conference on Parallel Processing
A Microbenchmark Suite for Mixed-Mode OpenMP/MPI
IWOMP '09 Proceedings of the 5th International Workshop on OpenMP: Evolving OpenMP in an Age of Extreme Parallelism
International Journal of High Performance Computing Applications
Microprocessors & Microsystems
ICPPW '09 Proceedings of the 2009 International Conference on Parallel Processing Workshops
Early experiments with the OpenMP/MPI hybrid programming model
IWOMP'08 Proceedings of the 4th international conference on OpenMP in a new era of parallelism
First experiences with intel cluster OpenMP
IWOMP'08 Proceedings of the 4th international conference on OpenMP in a new era of parallelism
Performance analysis of large-scale OpenMP and hybrid MPI/OpenMP applications with VampirNG
IWOMP'05/IWOMP'06 Proceedings of the 2005 and 2006 international conference on OpenMP shared memory parallel programming
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We discuss the computational bottlenecks in molecular dynamics (MD) and describe the challenges in parallelizing the computation-intensive tasks. We present a hybrid algorithm using MPI (Message Passing Interface) with OpenMP threads for parallelizing a generalized MD computation scheme for systems with short range interatomic interactions. The algorithm is discussed in the context of nano-indentation of Chromium films with carbon indenters using the Embedded Atom Method potential for Cr-Cr interaction and the Morse potential for Cr-C interactions. We study the performance of our algorithm for a range of MPI-thread combinations and find the performance to depend strongly on the computational task and load sharing in the multi-core processor. The algorithm scaled poorly with MPI and our hybrid schemes were observed to outperform the pure message passing scheme, despite utilizing the same number of processors or cores in the cluster. Speed-up achieved by our algorithm compared favorably with that achieved by standard MD packages.