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The Community is the Infrastructure: A Short Discussion of the PETSc User Community [article]

Mark Adams, Satish Balay, Jed Brown, Victor Eijkhout, Jacob Faibussowitsch, Fande Kong, Matthew Knepley, Scott Kruger, Oana Marin, Richard Mills, Todd Munson, Patrick Sanan (+3 others)
2021 figshare.com  
This paper describes the development community for the Portable, Extensible Toolkit for Scientific Computing (PETSc), a suite of data structures and routines for the scalable (parallel) solution of scientific  ...  Whitepaper submitted to the 2021 Collegeville Workshop Series on Scientific Software, which focused on the theme of "software teams".  ...  The PETSc community as infrastructure PETSc, apart from being a popular library for scientific computing, is a group of people dedicated to developing, extending, maintaining, and using the library to  ... 
doi:10.6084/m9.figshare.16523043.v1 fatcat:7hsmm4a3fram7eo65mv2rz4bqu

xSDK Foundations: Toward an Extreme-scale Scientific Software Development Kit

2017 Supercomputing Frontiers and Innovations  
The Extreme-scale Scientific Software Development Kit (xSDK) defines community policies to improve code quality and compatibility across independently developed packages (hypre, PETSc, SuperLU, Trilinos  ...  Combining software developed by independent groups is imperative: no single team has resources for all predictive science and decision support capabilities.  ...  infrastructure.  ... 
doi:10.14529/jsfi170104 fatcat:yrtuqdq6vza2vbw3u77unbdtim

xSDK Foundations: Toward an Extreme-scale Scientific Software Development Kit [article]

Roscoe Bartlett, Irina Demeshko, Todd Gamblin, Glenn Hammond, Michael Heroux, Jeffrey Johnson, Alicia Klinvex, Xiaoye Li, Lois Curfman McInnes, J. David Moulton, Daniel Osei-Kuffuor, Jason Sarich (+3 others)
2017 arXiv   pre-print
The Extreme-scale Scientific Software Development Kit (xSDK) defines community policies to improve code quality and compatibility across independently developed packages (hypre, PETSc, SuperLU, Trilinos  ...  Combining software developed by independent groups is imperative: no single team has resources for all predictive science and decision support capabilities.  ...  infrastructure.  ... 
arXiv:1702.08425v1 fatcat:jxslsupy7bc7pao7nx6xugjxea

Using PETSc to develop scalable applications for next-generation power grid

Shrirang Abhyankar, Barry Smith, Hong Zhang, Alexander Flueck
2011 Proceedings of the first international workshop on High performance computing, networking and analytics for the power grid - HiPCNA-PG '11  
The goal of this paper is to introduce the high performance computing library PETSc and motivate using such high performance computing libraries for developing existing and future power system applications  ...  Using high performance computing libraries for developing power system applications is not yet done in the power system community but well-explored by researchers doing PDE simulations.  ...  Smart Grid is bringing a new meaning to how communication and control is done.  ... 
doi:10.1145/2096123.2096138 fatcat:vvvhz62xovgyndgsswwixkq5s4

An overview of the Advanced CompuTational Software (ACTS) collection

L. A. Drummond, O. A. Marques
2005 ACM Transactions on Mathematical Software  
ACTS interactions within the computational science community ACKNOWLEDGMENT  ...  Lastly, we present a vision of the ACTS project for deployment of the ACTS Collection by the computational sciences community.  ...  Although its parallel implementation is based on MPI, PETSc users rarely need to invoke MPI because the communication is efficiently and transparently handled inside the PETSc routines.  ... 
doi:10.1145/1089014.1089016 fatcat:7pgu5tetu5hwpoflrfwyyzobwa

PETSc and Overture: Lessons Learned Developing an Interface between Components [chapter]

Kristopher R. Buschelman, William D. Gropp, Lois C. McInnes, Barry F. Smith
2001 IFIP Advances in Information and Communication Technology  
We compare three basic approaches to developing the internal interface between Overture and PETSc, the final one of which is a peerto-peer model.  ...  We consider two software packages that" interact with each other as components: Overture and PETSc.  ...  Acknowledgments We express our thanks for the invaluable assistance of Satish Balay who helped us overcome many of the technical problems associated with software interaction and software development.  ... 
doi:10.1007/978-0-387-35407-1_4 fatcat:3pwqomqux5e6lm6cmcah6gzfgy

Toward Performance-Portable PETSc for GPU-based Exascale Systems [article]

Richard Tran Mills, Mark F. Adams, Satish Balay, Jed Brown, Alp Dener, Matthew Knepley, Scott E. Kruger, Hannah Morgan, Todd Munson, Karl Rupp, Barry F. Smith, Stefano Zampini (+2 others)
2021 arXiv   pre-print
A blueprint for using GPUs from PETSc-based codes is provided, and case studies emphasize the flexibility and high performance achieved on current GPU-based systems.  ...  PETSc design for performance portability addresses fundamental GPU accelerator challenges and stresses flexibility and extensibility by separating the programming model used by the application from that  ...  , in support of the nation's exascale computing imperative, and by the Austrian Science Fund (FWF) under grant P29119-N30.  ... 
arXiv:2011.00715v2 fatcat:j5kitlnnlnbkppunuf7c5g5uum

The PetscSF Scalable Communication Layer [article]

Junchao Zhang, Jed Brown, Satish Balay, Jacob Faibussowitsch, Matthew Knepley, Oana Marin, Richard Tran Mills, Todd Munson, Barry F. Smith, Stefano Zampini
2021 arXiv   pre-print
PetscSF, the communication component of the Portable, Extensible Toolkit for Scientific Computation (PETSc), is designed to provide PETSc's communication infrastructure suitable for exascale computers  ...  An efficient and portable model for network and intra-node communication is essential for implementing large-scale applications.  ...  ACKNOWLEDGMENTS We thank Akhil Langer and Jim Dinan from the NVIDIA NVSHMEM team for their assistance. This work was supported by the Exascale Computing Project  ... 
arXiv:2102.13018v2 fatcat:wwdkuu74bzferbic3cngw4bcpa

The MedIGrid PSE in an LCG/gLite environment

Almerico Murli, Vania Boccia, Luisa Carracciuolo, Luisa D'Amore, Giuliano Laccetti, Marco Lapegna
2008 2008 IEEE International Symposium on Parallel and Distributed Processing with Applications  
In this paper we are concerned with improvements and enhancements of a medical imaging grid-enabled infrastructure, named MedIGrid, oriented to the transparent use of resource-intensive applications for  ...  We'll mainly focus on how to exploit the features of the new middleware environment to improve the efficiency and the services reliability of the PSE; further, some comments will be devoted to how to modify  ...  The GRID infrastructure As cited before, the testbed we used is mainly the SCoPE infrastructure, essentially based on the integration of the LCG/gLite and SCOPE-toolkit middlewares.  ... 
doi:10.1109/ispa.2008.65 dblp:conf/ispa/MurliBCDLL08 fatcat:nw52o56x7jgd5lfrtuv4dqheli

Optimizing Sparse Matrix Assembly in Finite Element Solvers with One-Sided Communication [chapter]

Niclas Jansson
2013 Lecture Notes in Computer Science  
We here address this issue by using our own stack based representation of the sparse matrix, and a hybrid parallel programming model combining traditional message passing with one-sided communication.  ...  In parallel finite element solvers, sparse matrix assembly is often a bottleneck.  ...  Acknowledgments The author would like to acknowledge the financial support from the Swedish Foundation for Strategic Research and is also grateful for the large amount of computer time given on Lindgren  ... 
doi:10.1007/978-3-642-38718-0_15 fatcat:6mwavdob5bcwxlo263mgr4vie4

ACTS – A COLLECTION OF HIGH PERFORMING SOFTWARE TOOLS FOR SCIENTIFIC COMPUTING

L.A. DRUMMOND, O.A. MARQUES
2003 Realizing Teracomputing  
During the past decades there has been a continuous growth in the number of physical and societal problems that have been successfully studied and solved by means of computational modeling and simulation  ...  It also highlight the tools that are in demand by Climate and Weather modelers.  ...  Acknowledgements The ACTS Collection project is funded by the US Department of Energy, office of Mathematical, Information and Computation Science. LADrummond-2002 submitted to  ... 
doi:10.1142/9789812704832_0016 fatcat:3sjml3yfr5cpjmke2gjbxzqthy

Scalable Delft3D Flexible Mesh for Efficient Modelling of Shallow Water and Transport Processes

M. Mogé, M. J. Russcher, A. Emerson, M. Genseberger
2019 Zenodo  
D-Flow Flexible Mesh ("D-Flow FM") [1] is the hydrodynamic module of the Delft3D Flexible Mesh Suite [2].  ...  The parallelisation is based on mesh decomposition and the use of deep halo regions may lead to significant mesh imbalance.  ...  Acknowledgements This work was financially supported by the PRACE project funded in part by the EU's Horizon 2020 Research and Innovation programme (2014-2020) under grant agreement 730913.  ... 
doi:10.5281/zenodo.3527660 fatcat:qvgdt4twv5cs5gqrcfziwifwc4

Using DOE Math Libraries: Introducing the xSDK [article]

Lois Curfman McInnes, Jim Willenbring, Ulrike Meier Yang, All XSDK Developers
2018 Figshare  
The Extreme-scale Scientific Software Development Kit (xSDK) provides infrastructure for a collection of related and complementary software elements—developed by diverse, independent teams throughout the  ...  Finally, we will provide the opportunity for breakout discussions and hands-on sessions with developers of the individual member packages (hypre, MAGMA, MFEM, PETSc, SUNDIALS, SuperLU, Trilinos), focusing  ...  Acknowledgements • This work was supported by the U.S.  ... 
doi:10.6084/m9.figshare.6015977.v1 fatcat:4fn4sy5dbbbkzhzym57dtecu3m

Blending Extensibility and Performance in Dense and Sparse Parallel Data Management

Javier Fresno, Arturo Gonzalez-Escribano, Diego R. Llanos
2014 IEEE Transactions on Parallel and Distributed Systems  
of the programmer.  ...  Our experimental results in different parallel environments show that this new approach combines the flexibility obtained when the programmer handles all the details with a performance comparable to the  ...  Area -Research Infrastructures Initiative.  ... 
doi:10.1109/tpds.2013.248 fatcat:ecciaa4e6razpmy24z7lefzutq

CIG Perspectives on 14 Years of Sustaining Software and a Community of Practice in Computational Geodynamics [article]

Lorraine Hwang, Louise H. Kellogg
2019 Figshare  
Who we are… The Computational Infrastructure for Geodynamics (CIG) is a community-driven organization that advances Earth science by developing and disseminating software for geophysics and related fields  ...  , computational, & domain expertise Software Development Community Contributed Entirely CIG funded Successful CIG codes mix community and CIG development and support deal.II PETSc ASH  ... 
doi:10.6084/m9.figshare.7792235.v1 fatcat:ehoxndnnnvapbbzwqbe35otgay
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