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Full-Text Articles in Physical Sciences and Mathematics
An Mpi-Enabled Mapreduce Framework For Molecular Dynamics Simulation Applications, Shuju Bai, Ebrahim Khosravi, Seung Jong Park
An Mpi-Enabled Mapreduce Framework For Molecular Dynamics Simulation Applications, Shuju Bai, Ebrahim Khosravi, Seung Jong Park
Computer Science Faculty Research & Creative Works
Computational technologies have been extensively investigated to be applied into many application domains. Since the presence of Hadoop, an implementation of MapReduce framework, scientists have applied it to biological sciences, chemistry, medical sciences, and other areas to efficiently process huge data sets. Although Hadoop is fault-tolerant and processes data in parallel, it does not support MPI in computing. The Map/Reduce tasks in Hadoop have to be serial, which results in inefficient scientific computations wrapped in Map/Reduce tasks. In the real world, many applications require MPI techniques due to their nature. Molecular dynamics simulation is one of them. In our research, …
A Hadoop Approach To Advanced Sampling Algorithms In Molecular Dynamics Simulation On Cloud Computing, Jin Niu, Shuju Bai, Ebrahim Khosravi, Seung Jong Park
A Hadoop Approach To Advanced Sampling Algorithms In Molecular Dynamics Simulation On Cloud Computing, Jin Niu, Shuju Bai, Ebrahim Khosravi, Seung Jong Park
Computer Science Faculty Research & Creative Works
Cloud computing has emerged as a prevalent computing paradigm with the advantages of virtualization, scalability, fault tolerance, and a usage-based pricing model. It has been widely used in various computational research fields. Replica exchange molecular dynamics (REMD) and replica exchange statistical temperature molecular dynamics (RESTMD) are two sampling algorithms in molecular dynamics. Due to the inherent parallel feature of REMD and RESTMD, it is practical to convert them into cloud computing applications. However, the performance of REMD and RESTMD on clouds has not been extensively investigated. In our work, we implemented REMD and RESTMD in cloud computing environment through Hadoop, …