Exploiting Parallel R in the Cloud with SPRINT

Piotrowski, Michał; McGilvary, Gary A.; Sloan, Terence; Mewissen, Muriel; Lloyd, Ashley; Forster, Thorsten; Mitchell, Lawrence; Ghazal, Peter

doi:10.3414/me11-02-0039

Cited by 4 publications

(3 citation statements)

References 26 publications

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“…As so-called focus themes, seven areas of research were highlighted and discussed: Recent developments in boosting methodology (e.g., [13], [14], [15]), intelligent data analysis for knowledge discovery, patient monitoring, and quality assessment (e.g., [16], [17] [18]), grid and cloud computing in biomedical research (19, [20], [21], [22]), two topics of medical imaging, one of high performance methods ( [23], [24]) and another one on image analysis and modelling (e.g., [25], [26], [27]), health information search, combining text, visual Information, and knowledge bases (e.g., [28], [29], [30]), and web science in medicine and health care ( [31], [32], [33]). Most of these themes have also been addressed in other publications, outside these focus themes.…”

Section: Major Topics Discussed In Mimmentioning

confidence: 99%

From Bed to Bench: Bridging from Informatics Practice to Theory

Haux

Lehmann

2014

Appl Clin Inform

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SummaryBackground: In 2009, Applied Clinical Informatics (ACI) -focused on applications in clinical informatics -was launched as a companion journal to Methods of Information in Medicine (MIM). Both journals are official journals of the International Medical Informatics Association. Objectives: To explore which congruencies and interdependencies exist in publications from theory to practice and from practice to theory and to determine existing gaps. Major topics discussed in ACI and MIM were analyzed. We explored if the intention of publishing companion journals to provide an information bridge from informatics theory to informatics practice and vice versa could be supported by this model. In this manuscript we will report on congruencies and interdependences from practice to theory and on major topics in MIM. Methods: Retrospective, prolective observational study on recent publications of ACI and MIM. All publications of the years 2012 and 2013 were indexed and analyzed. Results: Hundred and ninety-six publications were analyzed (ACI 87, MIM 109). In MIM publications, modelling aspects as well as methodological and evaluation approaches for the analysis of data, information, and knowledge in biomedicine and health care were frequently raised -and often discussed from an interdisciplinary point of view. Important themes were ambient-assisted living, anatomic spatial relations, biomedical informatics as scientific discipline, boosting, coding, computerized physician order entry, data analysis, grid and cloud computing, health care systems and services, health-enabling technologies, health information search, health information systems, imaging, knowledge-based decision support, patient records, signal analysis, and web science. Congruencies between journals could be found in themes, but with a different focus on content. Interdependencies from practice to theory, found in these publications, were only limited. Conclusions: Bridging from informatics theory to practice and vice versa remains a major component of successful research and practice as well as a major challenge.

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Section: Major Topics Discussed In Mimmentioning

confidence: 99%

From Bed to Bench: Bridging from Informatics Practice to Theory

Haux

Lehmann

2014

Appl Clin Inform

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“…2) Case Study: SPRINT-R: To illustrate that V-BOINC can not only execute standalone applications and to also show the performance achieved of a real use case applica-tion, we execute the Simple Parallel R INTerface (SPRINT) [19], which has MPI and the statistical package R as dependencies, on V-BOINC. SPRINT is a package providing parallel functions of R allowing data to be analysed over multiple processors rather than performing the computation on a single node and was chosen as it already is in wide use on computing clusters.…”

Section: A Boinc Vs V-boincmentioning

confidence: 99%

V-BOINC: The Virtualization of BOINC

McGilvary

Barker

Lloyd

et al. 2013

2013 13th IEEE/ACM International Symposium on Cluster, Cloud, and Grid Computing

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Abstract-The Berkeley Open Infrastructure for Network Computing (BOINC) is an open source client-server middleware system created to allow projects with large computational requirements, usually set in the scientific domain, to utilize a technically unlimited number of volunteer machines distributed over large physical distances. However various problems exist deploying applications over these heterogeneous machines using BOINC: applications must be ported to each machine architecture type, the project server must be trusted to supply authentic applications, applications that do not regularly checkpoint may lose execution progress upon volunteer machine termination and applications that have dependencies may find it difficult to run under BOINC.To solve such problems we introduce virtual BOINC, or V-BOINC, where virtual machines are used to run computations on volunteer machines. Application developers can then compile their applications on a single architecture, checkpointing issues are solved through virtualization API's and many security concerns are addressed via the virtual machine's sandbox environment. In this paper we focus on outlining a unique approach on how virtualization can be introduced into BOINC and demonstrate that V-BOINC offers acceptable computational performance when compared to regular BOINC. Finally we show that applications with dependencies can easily run under V-BOINC in turn increasing the computational potential volunteer computing offers to the general public and project developers.

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“…Piotrowski et al [16] provide a discussion of high performance computing in the cloud. Genomic analyses, for example, require high performance computing infrastructure and massive parallelization.…”

Section: Grid and Cloud Computingmentioning

confidence: 99%