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Simplifying the Development, Use and Sustainability of HPC Software [article]

Jeremy Cohen, Chris Cantwell, Neil Chue Hong, David Moxey, Malcolm Illingworth, Andrew Turner, John Darlington, Spencer Sherwin
2013 arXiv   pre-print
The use of such frameworks has implications for the sustainability of scientific software.  ...  require more support from computer scientists and resource providers to develop efficient code and make optimal use of the resources available to them.  ...  Software efforts, such as in the area of workflows, aim to simplify the use of multiple codes or tools that may previously have been scripted locally and to enable the use of distributed services in place  ... 
arXiv:1309.1101v1 fatcat:qzwvhmoz7jfjlbethmhdcb2zlm

Simplifying the Development, Use and Sustainability of HPC Software

2014 Journal of Open Research Software  
(HPC), scientists require more support from computer scientists and resource providers to develop efficient code that offers long-term sustainability and makes optimal use of the resources available to  ...  In this updated version of our submission to the WSSSPE13 workshop at SuperComputing 2013 we set out our approach to simplifying access to HPC applications and resources for end-users through the use of  ...  Acknowledgements The authors would like to thank the UK Engineering and Physical Sciences Research Council (EPSRC) for funding the libhpc: Intelligent Component-based Development of HPC Applications stage  ... 
doi:10.5334/jors.az fatcat:5drhtsjkafg3zhheuv56q6hrma

A Modern Approach to CI for HPC Projects (SIAM CSE21) [article]

Harmen Stoppels
2021 figshare.com  
A talk presented at the SIAM CSE21 conference, MS30: Software Productivity and Sustainability for CSEA major difficulty in developing C, C++ and Fortran packages for HPC is the vast amount of different  ...  Given the current maturity of the Spack package manager, this talk presents how Spack can effectively be used centrally in package development itself.  ...  APIs you might want to test Spack 13 ▪ Package manager tailored to HPC ▪ Wraps 5000+ packages ▪ Increasingly popular as a development tool ▪ Supports installing from local sources ▪ Supports running package  ... 
doi:10.6084/m9.figshare.14130380.v1 fatcat:xftgw5oiz5fixjqjc7u7u5z2x4

How a Community Software Ecosystem Perspective Helps to Advance Science Goals in the Exascale Computing Project [article]

Lois Curfman McInnes
2021 figshare.com  
E4S represents a portfolio-driven effort to collect, test, and deliver the latest in reusable open-source HPC software products, as driven by the common needs of applications.  ...  A key lesson learned is the need for close collaboration between teams developing applications and reusable software technologies, as well as the need for crosscutting strategies to increase developer  ...  00033-y Application Development (AD) Software Technology (ST) Hardware and Integration (HI) Integrated delivery of ECP products on targeted systems at leading DOE HPC facilities 6 US HPC vendors  ... 
doi:10.6084/m9.figshare.14120930.v2 fatcat:erhhkvll55gxjddlsolwhvjrki

How a Community Software Ecosystem Perspective Helps to Advance Science Goals in the Exascale Computing Project [article]

Lois Curfman McInnes
2021 figshare.com  
E4S represents a portfolio-driven effort to collect, test, and deliver the latest in reusable open-source HPC software products, as driven by the common needs of applications.  ...  A key lesson learned is the need for close collaboration between teams developing applications and reusable software technologies, as well as the need for crosscutting strategies to increase developer  ...  Stoyanov Developer Productivity & Software Sustainability Report https://exascaleproject.  ... 
doi:10.6084/m9.figshare.14120930.v1 fatcat:gnfherkpivcdhefriq6yv6jyje

Developing a High-Performance Computing/Numerical Analysis Roadmap

Anne Trefethen, Nick Higham, Iain Duff, Peter Coveney
2009 The international journal of high performance computing applications  
A roadmap activity in the UK has leveraged US and European efforts for identifying the challenges and barriers in the development of high-performance computing (HPC) algorithms and software.  ...  Algorithms and software that application developers can reuse in the form of high-quality, high performance, sustained software components, libraries and modules 2.  ...  The activity has benefitted from the work of the team at OeRC and in particular Mark Hylton and Stef Salvini.  ... 
doi:10.1177/1094342009347710 fatcat:75sv6a3d45gg3bjzyklgyxnvzm

CHAMP is a HPC Access and Metadata Portal

Christopher Cave-Ayland, Michael Bearpark, Charles Romain, Henry Rzepa
2022 Journal of Open Source Software  
Acknowledgments We acknowledge the extensive contributions of Dr. Matthew Harvey for work on version 1 of this software.  ...  The recent 2.0 release is a ground up rewrite to facilitate its publication as an open-source package, to modernise the code base and to address isues of portability and sustainability.  ...  and publication. It provides a web based interface allowing submission of HPC workloads and subsequent one-click publication of the results to data repositories such as Zenodo.  ... 
doi:10.21105/joss.03824 fatcat:e5xdalpp75ghln3u6rhjrziepm

Beyond Performance Tools: Measuring and Modeling Productivity in HPC

Michael O. McCracken, Nicole Wolter, Allan Snavely
2007 Third International Workshop on Software Engineering for High Performance Computing Applications (SE-HPC '07)  
The common measure of merit widely put forward in High-Performance Computing (HPC), high computational performance as measured in floating-point operations per second (FLOPs), does not account for many  ...  In this paper we discuss these bottlenecks, show an approach to analyzing productivity based on measurement and modeling of HPC workflow, and present plans for measurement and experimentation tools to  ...  We defined models for workflow in HPC and have proposed tools that use those models to help users analyze their productivity and cope with the challenges of using HPC for research.  ... 
doi:10.1109/se-hpc.2007.2 fatcat:tjskmamesfedpddz4zvaaftjdu

Packaging, containerization, and virtualization of computational omics methods: Advances, challenges, and opportunities [article]

Mohammed Alser, Sharon Waymost, Ram Ayyala, Brendan Lawlor, Richard J. Abdill, Neha Rajkumar, Nathan LaPierre, Jaqueline Brito, Andre M. Ribeiro-dos-Santos, Can Firtina, Nour Almadhoun, Varuni Sarwal (+7 others)
2022 arXiv   pre-print
We outline the challenges, advantages, and limitations of each approach and some of the most widely used platforms from the perspectives of users, software developers, and system administrators.  ...  We also propose principles to make packaging, virtualization, and containerization of omics software more sustainable and robust to increase the reproducibility of biomedical and life science research.  ...  We thank Thiago Mosqueiro (Amazon.com) for the fruitful discussion and feedback. M.A. dedicates this paper to the memory of his father, who passed away on 9th March 2022.  ... 
arXiv:2203.16261v1 fatcat:5gagale4xzcdpm2kpym4pidy3m

Bioexcel Deliverable 5.1 - Initial Business Plan

Holger Noack, Ian Harrow, Alexandre Bonvin, Adam Carter, Rossen Apostolov, Erwin Laure
2016 Zenodo  
The key value that we provide is the enhancement of efficiency, scalability and usability of open-source software important to the biomolecular community.  ...  Section three gives a brief overview of the HPC ecosystem.  ...  The goal of the software development is to improve the efficiency, scalability and ease of use of BioExcel's flagship software, and to provide workflows and interfaces to match the possibilities provided  ... 
doi:10.5281/zenodo.263932 fatcat:zaisc6fj7nhzbm7cumcnh2pyl4

HPC Cloud for Scientific and Business Applications

Marco A. S. Netto, Rodrigo N. Calheiros, Eduardo R. Rodrigues, Renato L. F. Cunha, Rajkumar Buyya
2018 ACM Computing Surveys  
Moreover, the discussion on the right pricing and contractual models to fit small and large users is relevant for the sustainability of HPC clouds.  ...  This paper brings a survey and taxonomy of efforts in HPC cloud and a vision on what we believe is ahead of us, including a set of research challenges that, once tackled, can help advance businesses and  ...  ACKNOWLEDGMENTS We thank the anonymous reviewers for their helpful comments in the preparation of this article. This work has been partially supported by FINEP/MCTI under grant no. 03.14.0062.00.  ... 
doi:10.1145/3150224 fatcat:o76lya7e2nb2tdom54oshgd5qe

First Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE): Submission and Peer-Review Process, and Results [article]

Daniel S. Katz and Gabrielle Allen and Neil Chue Hong and Manish Parashar and David Proctor
2014 arXiv   pre-print
This technical report discusses the submission and peer-review process used by the First Workshop on on Sustainable Software for Science: Practice and Experiences (WSSSPE) and the results of that process  ...  It is intended to record both this alternative model as well as the papers associated with the workshop that resulted from that process.  ...  Simplifying the Development, Use and Sustainability of HPC Software [12] • Jaroslaw Slawinski, Vaidy Sunderam. Towards Semi-Automatic Deployment of Scientific Anshu Dubey, S. Brandt, R. Brower, M.  ... 
arXiv:1311.3523v3 fatcat:gjqnln33cjheln45m4r2ujj2y4

HEP-Frame: A Software Engineered Framework to Aid the Development and Efficient Multicore Execution of Scientific Code

Andre Pereira, Antonio Onofre, Alberto Proenca
2015 2015 International Conference on Computational Science and Computational Intelligence (CSCI)  
This communication presents an evolutionary software prototype of a user-centered Highly Efficient Pipelined Framework, HEP-Frame, to aid the development of sustainable parallel scientific code with a  ...  a wide set of multicore systems, with both HPC and HTC techniques.  ...  of the application requirements and (iii) adequate design of sustainable software, both the algorithms and the data structures, to be efficiently executed on a wide range of HPC/HTC computing environments  ... 
doi:10.1109/csci.2015.42 fatcat:64a3dcpaozcptlcrolqpkvngk4

Easy Access to HPC Resources through the Application GUI

2016 Supercomputing Frontiers and Innovations  
In order to simplify the access, we have developed an interface between the applications and the clusters, that automates the transfer of input data and job submission to the clusters and also the retrieval  ...  KAUST hosts the tenth fastest supercomputer in the world (Shaheen II) and several HPC clusters.  ...  This paper is distributed under the terms of the Creative Commons Attribution-Non Commercial 3.0 License which permits non-commercial use, reproduction and distribution of the work without further permission  ... 
doi:10.14529/jsfi160302 fatcat:mf64ogmj6jeqzkmqbtc3bxpdcu

A Perspective on the SPPEXA Collaboration from Japan [chapter]

Takayuki Aoki
2020 Lecture Notes in Computational Science and Engineering  
at the University of Tokyo developed ppOpen-HPC, which is an open source infrastructure for the development and execution of optimized and reliable simulation code on post-peta-scale (pp) parallel computers  ...  To highlight the success of the Japanese collaboration with SPPEXA, we have a brief look at two working groups. ppOpen-HPC and ESSEX-II As a part of Post-Peta CREST projects between 2011 and 2015, a group  ...  The Role of Japan in HPC Collaborations The SPPEXA program was unique in the sense that it established sustainable connections in the field of HPC between France, Germany, and Japan.  ... 
doi:10.1007/978-3-030-47956-5_3 fatcat:h5flbynq25hlxcia474fyuwryi
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