Flexible composition and execution of large scale applications on distributed e-infrastructures

Zasada, Stefan J.; Chang, David C.W.; Haidar, Ali Nasrat; Coveney, Peter V.

doi:10.1016/j.jocs.2013.10.009

Cited by 9 publications

(4 citation statements)

References 24 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In order to do this, it implements a multilayered architecture, shown in figure 2. The first is the client layer, a user portal developed using Google Web Toolkit (GWT) [17]. The user interacts with the BAC system via their web browser.…”

Section: Architecturementioning

confidence: 99%

“…The server layer comprises the server components of the user portal, which are responsible for user login, state management and presentation. This layer either uses a cloud platform provided REST API to set up and control the required Kubernetes infrastructure or, where BAC is run on local, non-cloud resources, builds on an application hosting environment (AHE) [ 18 ]. AHE is designed to hide much of the complexity of dealing with HPC resources from users of such systems, allowing them to interact with applications rather than machines.…”

Section: Architecturementioning

confidence: 99%

See 1 more Smart Citation

Large-scale binding affinity calculations on commodity compute clouds

2020

View full text Add to dashboard Cite

In recent years, it has become possible to calculate binding affinities of compounds bound to proteins via rapid, accurate, precise and reproducible free energy calculations. This is imperative in drug discovery as well as personalized medicine. This approach is based on molecular dynamics (MD) simulations and draws on sequence and structural information of the protein and compound concerned. Free energies are determined by ensemble averages of many MD replicas, each of which requires hundreds of cores and/or GPU accelerators, which are now available on commodity cloud computing platforms; there are also requirements for initial model building and subsequent data analysis stages. To automate the process, we have developed a workflow known as the binding affinity calculator. In this paper, we focus on the software infrastructure and interfaces that we have developed to automate the overall workflow and execute it on commodity cloud platforms, in order to reliably predict their binding affinities on time scales relevant to the domains of application, and illustrate its application to two free energy methods.

show abstract

Section: Architecturementioning

confidence: 99%

Section: Architecturementioning

confidence: 99%

Large-scale binding affinity calculations on commodity compute clouds

2020

View full text Add to dashboard Cite

show abstract

“…The Application Hosting Environment (AHE) [14] is a middleware implementing the Software as a Service paradigm of cloud computing for HPC applications. AHE supports the development of complex simulations based on an integrated workflow engine and eases the transfer of input and output files for applications executed on distributed computing resources.…”

Section: Related Workmentioning

confidence: 99%

Sustainability through flexibility: Building complex simulation programs for distributed computing systems

Hofmann

Rünger

2015

Simulation Modelling Practice and Theory

View full text Add to dashboard Cite

“…We believe that with the right combination of tools and services, the original concept of a distributed e-infrastructure as a provider of transparent and ubiquitous computing power can be realised. To this end, we have developed the Application Hosting Environment [6,7], a lightweight interface layer that provides a higher level of abstraction than many other middleware tools, to allow the user to concentrate on running their applications without having to worry about the minutiae of dealing with every possible combination of compiler, architecture and queuing system.…”

Section: Addressing Users' Problemsmentioning

confidence: 99%

A Distributed Multi-agent Market Place for HPC Compute Cycle Resource Trading

Zasada,

Coveney

2015

Preprint

Self Cite

View full text Add to dashboard Cite

Computer simulation is finding a role in an increasing number of scientific disciplines, concomitant with the rise in available computing power. Realizing this inevitably requires access to computational power beyond the desktop, making use of clusters, supercomputers, data repositories, networks and distributed aggregations of these resources. Accessing one such resource entails a number of usability and security problems; when multiple geographically distributed resources are involved, the difficulty is compounded.This presents the user with the problem of how to gain access to suitable resources to run their workloads as they need them. In this paper we present our solutions to this problem, a resource trading platform that allows users to purchase access to resources within a distributed e-infrastructure. We present the implementation of this Resource Allocation Market Place as a distributed multi-agent system, and show how it provides a highly flexible, efficient tool to schedule workflows across high performance computing resources.

show abstract

Flexible composition and execution of large scale applications on distributed e-infrastructures

Cited by 9 publications

References 24 publications

Large-scale binding affinity calculations on commodity compute clouds

Large-scale binding affinity calculations on commodity compute clouds

Sustainability through flexibility: Building complex simulation programs for distributed computing systems

A Distributed Multi-agent Market Place for HPC Compute Cycle Resource Trading

Contact Info

Product

Resources

About