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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, …
Afcd: An Approximated-Fair And Controlled-Delay Queuing For High Speed Networks, Lin Xue, Suman Kumar, Cheng Cui, Praveenkumar Kondikoppa, Chui Hui Chiu, Seung Jong Park
Afcd: An Approximated-Fair And Controlled-Delay Queuing For High Speed Networks, Lin Xue, Suman Kumar, Cheng Cui, Praveenkumar Kondikoppa, Chui Hui Chiu, Seung Jong Park
Computer Science Faculty Research & Creative Works
High speed networks have characteristics of high bandwidth, long queuing delay, and high burstiness which make it difficult to address issues such as fairness, low queuing delay and high link utilization. Current high-speed networks carry heterogeneous TCP flows which makes it even more challenging to address these issues. Since sender centric approaches do not meet these challenges, there have been several proposals to address them at router level via queue management (QM) schemes. These QM schemes have been fairly successful in addressing either fairness issues or large queuing delay but not both at the same time. We propose a new …
Approximate String Matching By Position Restricted Alignment, Manish Patil, Xuanting Cai, Sharma V. Thankachan, Rahul Shah, Seung Jong Park, David Foltz
Approximate String Matching By Position Restricted Alignment, Manish Patil, Xuanting Cai, Sharma V. Thankachan, Rahul Shah, Seung Jong Park, David Foltz
Computer Science Faculty Research & Creative Works
Given a collection of strings, goal of the approximate string matching is to efficiently find the strings in the collection that are similar to a query string. In this paper, we focus on edit distance as measure to quantify the similarity between two strings. Existing q-gram based methods to address this problem use inverted indexes to index the q-grams of given string collection. These methods begin by generating the q-grams of query string (disjoint or overlapping) and then merge the inverted lists of these q-grams. Several filtering techniques have been proposed so as to segment inverted lists to relatively shorter …