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Evaluation of Emerging Energy-Efficient Heterogeneous Computing Platforms for Biomolecular and Cellular Simulation Workloads

John E. Stone, Michael J. Hallock, James C. Phillips, Joseph R. Peterson, Zaida Luthey-Schulten, Klaus Schulten
2016 2016 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW)  
We describe early experiences adapting several biomolecular simulation and analysis applications for emerging heterogeneous computing platforms that combine power-efficient system-onchip multi-core CPUs  ...  We compare the performance and energy efficiency of scientific applications running on emerging platforms with results obtained on traditional platforms, identify hardware and algorithmic performance bottlenecks  ...  ACKNOWLEDGMENT The authors wish to acknowledge support of the CUDA Center of Excellence at the University of Illinois, and NIH funding through grants 9P41GM104601, 5R01GM098243-02 and PHS 5 T32 GM008276  ... 
doi:10.1109/ipdpsw.2016.130 pmid:27516922 pmcid:PMC4978513 dblp:conf/ipps/StoneHPPLS16 fatcat:bs7d25eh5fhi7fxkliu4gkkfyu

Bioexcel Deliverable 1.3 - Roadmap Of Future Hardware And Long-Term Development Plan For Each Pilot Application

Rossen Apostolov, Mark Abraham, Erwin Laure, Erik Lindahl, Alexandre Bonvin, Bert de Groot, Emiliano Ippoliti
2017 Zenodo  
Upcoming extreme-scale compute platforms will offer great opportunities for tackling important, large-scale scientific questions.  ...  In this document we analyze from the viewpoint of biomolecular applications the requirements for different Exascale aspects such as HPC architectures, software management, programming environments, I/O  ...  data movement between compute units, and improve energy efficiency, and also permit simulations to run faster on less costly hardware.  ... 
doi:10.5281/zenodo.574605 fatcat:tyevo2n3vbbeto4agkn7uouiiq

ATIP/A*CRC Workshop on Accelerator Technologies for High-Performance Computing: Does Asia Lead the Way? Programme Handbook [article]

Michalewicz Marek, Kahaner David
2012 Zenodo  
Information Program (ATIP) and the Agency for Science, Technology and Research (A*STAR) Computational Resource Centre (A*CRC), this workshop in Singapore focus on the practical aspects of scientific and  ...  With support from the United States National Science Foundation (NSF) and in cooperation with the HPC Special Interest Group (HPC SIG) of the Association for Computing Machinery (ACM), the Asian Technology  ...  Many computing applications at OIST, like gene sequencing, are very data intense and this data needs to be accessible from many different platforms (Windows PCs, HPC cluster, Mac OS).  ... 
doi:10.5281/zenodo.3977457 fatcat:v2aftckqinasxk5ugdw27vinpa

Understanding ML driven HPC: Applications and Infrastructure [article]

Geoffrey Fox, Shantenu Jha
2019 arXiv   pre-print
In this paper, which is part of the Learning Everywhere series, we discuss "how" learning methods and HPC simulations are being integrated to enhance effective performance of computations.  ...  A primary driver of such coupling is the promise that Machine Learning (ML) will give major performance improvements for traditional HPC simulations.  ...  Acknowledgement This work was partially supported by NSF CIF21 DIBBS 1443054 and nanoBIO 1720625. SJ was partially supported by ExaLearn -a DOE Exascale Computing project.  ... 
arXiv:1909.02363v1 fatcat:zuipze66ebaf3nz2uwgf763zte

Why High-Performance Modelling and Simulation for Big Data Applications Matters [chapter]

Clemens Grelck, Ewa Niewiadomska-Szynkiewicz, Marco Aldinucci, Andrea Bracciali, Elisabeth Larsson
2019 Msphere  
Unfortunately, big data problems are often not easily amenable to efficient and effective use of High Performance Computing (HPC) facilities and technologies.  ...  Modelling and Simulation (M&S) offer adequate abstractions to manage the complexity of analysing big data in scientific and engineering domains.  ...  This work was supported by the ICT COST Action IC1406 High-Performance Modelling and Simulation for Big Data Applications.  ... 
doi:10.1007/978-3-030-16272-6_1 fatcat:3zyj3266mzhffeic5rlqqe7mx4

Defense Advanced Research Projects Agency (Darpa) Fiscal Year 2015 Budget Estimates

Department Of Defense Comptroller's Office
2014 Zenodo  
Neurotechnology for Emerging Therapies (SUBNETS)) and better data management.  ...  The budget request details the proposed investments $80 million to develop new sets of tools for imaging and analytics of neural and synaptic brain activities that will improve diagnosis and care of wounded  ...  , 10 -100 times higher computational energy efficiency, scalability of technologies to sub-10 nanometer dimensions, development of novel computing architectures, and highly energy-efficient information  ... 
doi:10.5281/zenodo.1215345 fatcat:fjzhmynqjbaafk67q2ckcblj2m

Defense Advanced Research Projects Agency (Darpa) Fiscal Year 2016 Budget Estimates

Department Of Defense Comptroller's Office
2015 Zenodo  
switches, 10 -100 times higher computational energy efficiency, scalability of technologies to sub-10 nanometer dimensions, development of novel computing architectures, and highly energy-efficient information  ...  Simulation results outperform state-of-the-art server and GPU systems by 100x in performance and 1000x in energy efficiency.  ... 
doi:10.5281/zenodo.1215366 fatcat:cqn5tyfixjanzp5x3tgfkpedri

D2.4: Stakeholder Management in PRACE 2.0

Jean-Philippe Nominé, Philippe Segers
2017 Zenodo  
of research infrastructures, H2020 projects etc.); user communities including new or emerging areas; funding agencies and policy makers; SMEs for which PRACE SHAPE programme offered an HPC adoption strong  ...  The recent launching of a Digital Single Market (DSM) strategy for Europe, announced by the EC in April 2016, provides a new horizon with an extended and strengthened need and interest for HPC.  ...  Energy oriented Centre of Excellence for computer applications; • BioExcel -Centre of Excellence for Biomolecular Research; • NoMaD -The Novel Materials Discovery Laboratory; • MaX -Materials design at  ... 
doi:10.5281/zenodo.6801676 fatcat:5z7huwaa5vg57go37wtxbkz6iu

Nanosystems, Edge Computing, and the Next Generation Computing Systems

Ali Passian, Neena Imam
2019 Sensors  
We survey the qualitative figures of merit of technologies of current interest for the next generation computing with an emphasis on edge computing.  ...  the range from macroscopic device sizes and kW energies to atomic domains and single-photon energies.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/s19184048 fatcat:rtjffajkj5h4vfa4v7yuevhdzi

Web and Grid Technologies in Bioinformatics, Computational and Systems Biology: A Review

Natalio Krasnogor, Azhar Shah, Daniel Barthel, Piotr Lukasiak, Jacek Blazewicz
2008 Current Bioinformatics  
CellML [53] Cell Markup Language http://www.cellml.org/ Storage and exchange of computerbased mathematical models for biomolecular simulations OBO [54] Open Biomedical Ontology http://obo.sourceforge.net  ...  The use of computational and networking resources is thus unavoidable.  ...  The evaluation of these methods show that both methods perform similarly in terms of efficiency e.g. on a database of about 500,000 protein sequences (205 MB) each method takes about 60 seconds for downloading  ... 
doi:10.2174/157489308783329850 fatcat:thpj6eywwvg5tfdqvbw5nch3ty

Biological and Medical Sciences

Detlev W. Bronk, Carl-Goran Heden, C. H. Waddington
1971 Annals of the New York Academy of Sciences  
The percentage of applied and translational activities is, however, increasing.  ...  Figure 31 illustrates an estimate of the contribution of each individual BMS RI to research activities across this spectrum, from basic medical/ biological research and innovation activities to activities  ...  working platform during the process of evaluation.  ... 
doi:10.1111/j.1749-6632.1971.tb41309.x fatcat:6zdkjtuojrdwhib3lpdzoq7i3u

Biological and Medical Sciences

G. J. Kennedy
1989 The gerontologist  
The percentage of applied and translational activities is, however, increasing.  ...  Figure 31 illustrates an estimate of the contribution of each individual BMS RI to research activities across this spectrum, from basic medical/ biological research and innovation activities to activities  ...  working platform during the process of evaluation.  ... 
doi:10.1093/geront/29.1.137a fatcat:32k4evfphzhdddo3ikpfvbwcgi

Genome sequencing and next-generation sequence data analysis: A comprehensive compilation of bioinformatics tools and databases

Jose C. Jimenez-Lopez, Emma W. Gachomo, Sweta Sharma, Simeon O. Kotchoni
2013 American Journal of Molecular Biology  
We focus on their potential applications for efficient collection, storage, and analysis of genetic data/information from a wide range of gene banks.  ...  In this paper, we provide an overview of major advances in bioinformatics and computational biology in genome sequencing and next-generation sequence data analysis.  ...  As acquisition of genomic data becomes increasingly cost-efficient, genomic data sets are accumulating at an exponential rate and new types of genetic data are emerging.  ... 
doi:10.4236/ajmb.2013.32016 fatcat:qqfycymt2fh6pl6ifudliybm2q

第57回年会予稿集

2019 Seibutsu Butsuri  
However, the computational cost of the QM based MD simulation is very large. Furthermore, there are few assessment of the energy conservation for the DFTB-MD simulations.  ...  In recent years, the emergence of thermometric methodologies for and insights into the thermal response of cellular organelles has opened a door for thermal biology at the single cell level.  ...  thermal properties surrounding the nanoparticle. 3Pos184 粒子フィルター MD シミュレーションによる高速 AFM データからの分子動態推定 Biomolecular dynamics inferred from high-speed AFM data via particle-filter MD simulations Suguru Kato  ... 
doi:10.2142/biophys.59.s1 fatcat:rsudhlmaanetrhmdxjgsiyorme

D7.2.2 Exploitation of HPC Tools and Techniques

Michael Lysaght, Bjorn Lindi, Vit Vondrak, John Donners, Marc Tajchman
2014 Zenodo  
The objective of PRACE-3IP Work Package 7 (WP7) 'Application Enabling and Support' is to provide applications enabling support for HPC applications codes which are important for European researchers to  ...  For a more detailed description of each of the exploitation projects summarised here, we refer the reader to the PRACE-3IP whitepaper associated with each of the 17 projects.  ...  Such a technique can be efficiently employed to evaluate accurately the electrostatic contribution to the free energy, for modeling of biomolecular titration states, computation of the electrostatic potential  ... 
doi:10.5281/zenodo.6575525 fatcat:5y3cjsculrdejllndosbjpcgiq
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