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Improving Molecular Dynamics Simulation Performance on Low-Cost Systems
May-June 2013 (vol. 15 no. 3)
pp. 64-70
Teong Han Chew, Universiti Teknologi Malaysia
Kwee Hong Joyce-Tan, Universiti Kebangsaan Malaysia
Zeti Azura Mohamed Hussein, Universiti Kebangsaan Malaysia
Pek Iee Elizabeth-Chia, Universiti Teknologi Malaysia
Mohd Shahir Shamsir, Universiti Teknologi Malaysia
For simulation-based work, researchers often have limited hardware capacities and budgets, so they create a low-cost parallel computing platform using PCs and commodity hardware, assembled and configured as a Beowulf-class computing cluster. Here, an astute approach (for a molecular dynamics simulation example) greatly improves performance through hardware upgrades and other tricks.
Index Terms:
Scientific computing,Performance evaluation,Costs,Simulation,Parallel processing,Molecular computing,scientific computing,molecular dynamics,performance tuning,performance comparison,low-cost system,Gromacs,NAMD
Teong Han Chew, Kwee Hong Joyce-Tan, Zeti Azura Mohamed Hussein, Pek Iee Elizabeth-Chia, Mohd Shahir Shamsir, "Improving Molecular Dynamics Simulation Performance on Low-Cost Systems," Computing in Science and Engineering, vol. 15, no. 3, pp. 64-70, May-June 2013, doi:10.1109/MCSE.2013.61
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