TY - GEN
T1 - Performance analysis and optimization of a parallel carbon molecular dynamic code on a Cray T3E
AU - Horoi, Mihai
AU - Enbody, Richard J.
N1 - Publisher Copyright:
© 1998 IEEE.
PY - 1998
Y1 - 1998
N2 - An analysis of the primary factors influencing the performance of a parallel implementation on a Cray T3E of a Carbon Molecular Dynamics code developed at Department of Physics and Astronomy at Michigan State University is presented. We show that classical load-sharing techniques combined with careful analysis of Amdahl's law can be successfully used to significantly increase the performance of the code. This report describes the quantitative analysis of these factors and the solutions used to diminish or eliminate their effects. By slightly modifying the code we reduced its sequential portion to less than 0.1%. We also demonstrate that the MPI collective communications implementation on the Cray T3E dramatically reduces the communication overhead for our code. In the end, a speedup of 170 was obtained using 256 Cray T3E processing elements. These results create the prospect of simulating the dynamics of 1,000-atom nanotubes in the microsecond regime (≈1,000,000 time steps).
AB - An analysis of the primary factors influencing the performance of a parallel implementation on a Cray T3E of a Carbon Molecular Dynamics code developed at Department of Physics and Astronomy at Michigan State University is presented. We show that classical load-sharing techniques combined with careful analysis of Amdahl's law can be successfully used to significantly increase the performance of the code. This report describes the quantitative analysis of these factors and the solutions used to diminish or eliminate their effects. By slightly modifying the code we reduced its sequential portion to less than 0.1%. We also demonstrate that the MPI collective communications implementation on the Cray T3E dramatically reduces the communication overhead for our code. In the end, a speedup of 170 was obtained using 256 Cray T3E processing elements. These results create the prospect of simulating the dynamics of 1,000-atom nanotubes in the microsecond regime (≈1,000,000 time steps).
UR - http://www.scopus.com/inward/record.url?scp=0343427343&partnerID=8YFLogxK
U2 - 10.1109/ICPP.1998.708464
DO - 10.1109/ICPP.1998.708464
M3 - Conference contribution
AN - SCOPUS:0343427343
T3 - Proceedings of the International Conference on Parallel Processing
SP - 62
EP - 69
BT - Proceedings - 1998 International Conference on Parallel Processing, ICPP 1998
A2 - Lai, Ten H.
PB - Institute of Electrical and Electronics Engineers Inc.
T2 - 1998 International Conference on Parallel Processing, ICPP 1998
Y2 - 10 August 1998 through 14 August 1998
ER -