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RepEx: A Flexible Framework for Scalable Replica Exchange Molecular Dynamics Simulations [article]

Antons Treikalis, Andre Merzky, Haoyuan Chen, Tai-Sung Lee, Darrin M. York, Shantenu Jha
2016 arXiv   pre-print
Replica Exchange (RE) simulations have emerged as an important algorithmic tool for the molecular sciences.  ...  In this paper, we propose the RepEx framework which address these aforementioned shortcomings of existing approaches, while striking the balance between flexibility (any RE scheme) and scalability (tens  ...  We acknowledge allocation TG-MCB090174 for computing time on XSEDE allocated resources. We acknowledge NSF ACI 1516469 and ACI 1515572 (Cheatham) for time on Blue Waters machine.  ... 
arXiv:1601.05439v1 fatcat:vn5ahfz4bzfrbelxyfkwhqbz2q

Case Studies in Designing Elastic Applications

D. Rajan, A. Thrasher, B. Abdul-Wahid, J. A. Izaguirre, S. Emrich, D. Thain
2013 2013 13th IEEE/ACM International Symposium on Cluster, Cloud, and Grid Computing  
This is especially appealing to scientific applications that require a very large scale to compete in the research space.  ...  In this paper, we present case studies of several elastic applications built using the Work Queue programming framework.  ...  Replica exchange simulations (REPEX) work by creating multiple replicas of a protein molecule at different temperature configurations and simulating their dynamics over multiple time steps.  ... 
doi:10.1109/ccgrid.2013.46 dblp:conf/ccgrid/RajanTAIET13 fatcat:aviqmwf4vvecbozewaxbbkzgpy

Middleware Building Blocks for Workflow Systems [article]

Matteo Turilli, Vivek Balasubramanian, Andre Merzky, Ioannis Paraskevakos, Shantenu Jha
2019 arXiv   pre-print
workflows on high performance computing machines; (ii) illustrating a set of building blocks that enable multiple points of integration, which results in design flexibility and functional extensibility  ...  This paper describes a building blocks approach to the design of scientific workflow systems.  ...  We thank Daniel Smith, Levi Naden and Sam Ellis (MolSSI) for useful discussions and insight. This was was supported primarily by NSF 1440677 and DOE ASCR de-sc0016280.  ... 
arXiv:1903.10057v1 fatcat:vvlkcxkuebhdxcp5bcqrcwu4tu

A Framework For Replica Exchange Simulations

Antons Treikalis
OF THE THESIS A Framework For Replica Exchange Simulations By ANTONS TREIKALIS Thesis Director: Shantenu Jha Replica Exchange (RE) simulations have emerged as an important algorithmic tool for the molecular  ...  We propose the RepEx framework which addresses the aforementioned limitations, while striking the balance between flexibility (RE pattern) and scalability (several thousand replicas) over a diverse range  ...  Chapter 3 RADICAL-Pilot RepEx framework In this chapter we present our framework for REMD simulations.  ... 

TOWARDS AN ERROR DETECTION TEST FRAMEWORK FOR MOLECULAR DYNAMICS APPLICATIONS Towards an Error Detection Test Framework for Molecular Dynamics Applications

Suvigya Tripathi, Suvigya Tripathi, Shantenu Jha
2016 unpublished
There are several applications in the field of chemical sciences for Molecular Dynamics (MD) simulations.  ...  The EnsembleMD toolkit and RepEx facilitates a simple framework for MD applications, but they lack the feature of testing their functionality during Software Development Life Cycle (SDLC).  ...  RADICAL RepEx Framework RepEx is a framework for replica exchange molecular dynamics simulations over multiple dimensions.  ... 

Principles for the Design and Operation of Elastic Scientific Applications on Distributed Systems

Dinesh Rajan Pandiarajan
So operating parameters such as the number of partitions and the instances to provision for execution must be determined at runtime for efficient operation.  ...  In effect, the presented techniques create self-operating elastic applications that dynamically determine the partitions of their workloads and the scale of resources to utilize.  ...  In this chapter, we consider the construction of replica exchange molecular dynamics simulation as an elastic application.  ... 
doi:10.7274/kh04dn42580 fatcat:mrebptzpuvbqnfc3tnh5w532ta

A programming model and execution system for adaptive ensemble applications on high performance computing systems

Vivekanandan Balasubramanian
Depending on the scientific problem, a task of an ensemble can be any type of a program: from a molecular simulation, to a data analysis or a machine learning model.  ...  HPC systems are increasingly displaying performance dynamism and fluctuations due to aggressive thermal management and throttling. Tog [...]  ...  Relationships between current and past forecasts from the Weather Research and Replica Exchange Replica Exchange is a class of methods [50] that is popularly used to enhance sampling in molecular simulations  ... 
doi:10.7282/t3-0yx8-xx61 fatcat:z3rwncac5vckrgjnllp2ytlwiy

Multiscale simulation of RNA catalysis

Haoyuan Chen
Molecular simulations have become an essential part in modern chemistry research.  ...  Finally, in Chapter 6, method developments on an advanced sampling method called the multi-dimensional replica exchange method is presented and applied to two prototypical problems in biochemistry.  ...  Figure 5 . 5 12: All the free energy profiles generated in bootstrapping. demonstrate a new framework that enables highly flexible multi-dimensional replica exchange molecular dynamics (REMD) simulations  ... 
doi:10.7282/t35141nf fatcat:pduvb472rrgf7hhynnyuor5p2q