Fast parallel algorithms for short-range molecular dynamics
Journal of Computational Physics
Improving memory hierarchy performance for irregular applications
ICS '99 Proceedings of the 13th international conference on Supercomputing
Noncontiguous I/O Accesses Through MPI-IO
CCGRID '03 Proceedings of the 3st International Symposium on Cluster Computing and the Grid
Noncontiguous I/O through PVFS
CLUSTER '02 Proceedings of the IEEE International Conference on Cluster Computing
Data Sieving and Collective I/O in ROMIO
FRONTIERS '99 Proceedings of the The 7th Symposium on the Frontiers of Massively Parallel Computation
PVFS: a parallel file system for linux clusters
ALS'00 Proceedings of the 4th annual Linux Showcase & Conference - Volume 4
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This article analyzes the impact of different solutions of I/O performance problem on Molecular Dynamics (MD) simulation. MD accesses data in a non-contiguous way, with unpredictable patterns that change as the simulation progresses. Such application drastically affect the performance of Parallel File Systems. We show that there is a strong relation between the distribution of the atoms on the simulation space and MD I/O performance. We propose a variant of data sieving approach that uses the symmetry of the MD’s access pattern to minimize the number of I/O operations, and behaves considerably better than other tested solutions.