4 Search Results for "Ahern, Sean"

Document
DOI: 10.4230/OASIcs.PARMA-DITAM.2026.3
High Performance Visualization with VisIVO Across Cloud and HPC

Authors: Umer Arshad, Eva Sciacca, Nicola Tuccari, Fabio Pitari, and Giuseppa Muscianisi

Published in: OASIcs, Volume 141, 17th Workshop on Parallel Programming and Run-Time Management Techniques for Many-Core Architectures and 15th Workshop on Design Tools and Architectures for Multicore Embedded Computing Platforms (PARMA-DITAM 2026)

Abstract
The rapid growth of data in Astrophysics and Cosmology creates significant challenges that require scalable computing and advanced visualization solutions. Cineca is Italy’s largest supercomputing center and a leading global provider of high-performance computing (HPC) services. This paper shows that the integration of the VisIVO scientific visualization framework is with the cloud-based InterActive Computing (IAC) service at Cineca. This integration enables GPU-accelerated, real-time visualization on HPC resources via a Jupyter interface in their browser. A new dedicated Python wrapper and a custom Jupyter kernel enable VisIVO to run smoothly from interactive notebooks, avoid command-line operations, and visualize data directly on HPC compute nodes. Furthermore, we enabled cloud-oriented RESTful APIs, built with the Flask framework, to perform VisIVO operations remotely via simple web services. This setup hides the backend’s complexity and simplifies connections with other applications. Our framework increases system accessibility, ensures reproducibility of results, and supports rapid data exploration for large astrophysical simulations. The system was evaluated using real-world cases, including visual analysis of cosmological simulations generated using the OpenGadget3 code. Results indicate that the system is scalable and reliable, and that it facilitates interactive scientific discovery on high-performance computing (HPC) infrastructures.
Cite as

Umer Arshad, Eva Sciacca, Nicola Tuccari, Fabio Pitari, and Giuseppa Muscianisi. High Performance Visualization with VisIVO Across Cloud and HPC. In 17th Workshop on Parallel Programming and Run-Time Management Techniques for Many-Core Architectures and 15th Workshop on Design Tools and Architectures for Multicore Embedded Computing Platforms (PARMA-DITAM 2026). Open Access Series in Informatics (OASIcs), Volume 141, pp. 3:1-3:11, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

Copy BibTex To Clipboard

@InProceedings{arshad_et_al:OASIcs.PARMA-DITAM.2026.3,
  author =	{Arshad, Umer and Sciacca, Eva and Tuccari, Nicola and Pitari, Fabio and Muscianisi, Giuseppa},
  title =	{{High Performance Visualization with VisIVO Across Cloud and HPC}},
  booktitle =	{17th Workshop on Parallel Programming and Run-Time Management Techniques for Many-Core Architectures and 15th Workshop on Design Tools and Architectures for Multicore Embedded Computing Platforms (PARMA-DITAM 2026)},
  pages =	{3:1--3:11},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-416-1},
  ISSN =	{2190-6807},
  year =	{2026},
  volume =	{141},
  editor =	{Baroffio, Davide and Busia, Paola and Denisov, Lev and Shukla, Nitin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.PARMA-DITAM.2026.3},
  URN =		{urn:nbn:de:0030-drops-256700},
  doi =		{10.4230/OASIcs.PARMA-DITAM.2026.3},
  annote =	{Keywords: High-performance computing, HPC, VisIVO, Scientific visualization, Interactive visualization, Cloud computing, Jupyter, Flask, REST API}
}
Document
DOI: 10.4230/OASIcs.NINeS.2026.21
Accio: Rethinking OS-Architecture Co-Design for Next-Gen I/O

Authors: Amirmohammad Nazari, Rajit Manohar, and Robert Soulé

Published in: OASIcs, Volume 139, 1st New Ideas in Networked Systems (NINeS 2026)

Abstract
In this paper, we propose a novel software/hardware design to improve I/O performance while maintaining existing POSIX-standard APIs. Our approach stands in contrast to existing kernel-bypass strategies that improve performance at the expense of abandoning familiar programming abstractions. Our key insight is that navigating the performance-functionality trade-off requires changes to the processor; it cannot be done without support of the CPU micro-architecture. Our design, called Accio, includes: dedicated hardware for interrupt management, a hardware assist for thread scheduling, tables in hardware that manage I/O state, and modifications to the operating system to support the new hardware. Our evaluation demonstrates that Accio saturates the bus bandwidth, reduces CPU usage by up to 66% compared to state-of-the-art kernel-bypass systems, and reduces latency to 1/12th of that of the Linux kernel, matching that of kernel-bypass systems.
Cite as

Amirmohammad Nazari, Rajit Manohar, and Robert Soulé. Accio: Rethinking OS-Architecture Co-Design for Next-Gen I/O. In 1st New Ideas in Networked Systems (NINeS 2026). Open Access Series in Informatics (OASIcs), Volume 139, pp. 21:1-21:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

Copy BibTex To Clipboard

@InProceedings{nazari_et_al:OASIcs.NINeS.2026.21,
  author =	{Nazari, Amirmohammad and Manohar, Rajit and Soul\'{e}, Robert},
  title =	{{Accio: Rethinking OS-Architecture Co-Design for Next-Gen I/O}},
  booktitle =	{1st New Ideas in Networked Systems (NINeS 2026)},
  pages =	{21:1--21:24},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-414-7},
  ISSN =	{2190-6807},
  year =	{2026},
  volume =	{139},
  editor =	{Argyraki, Katerina and Panda, Aurojit},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.NINeS.2026.21},
  URN =		{urn:nbn:de:0030-drops-256063},
  doi =		{10.4230/OASIcs.NINeS.2026.21},
  annote =	{Keywords: Networks, Operating Systems, I/O Optimization}
}
Document
DOI: 10.4230/LIPIcs.DNA.31.4
Differentiable Programming of Indexed Chemical Reaction Networks and Reaction-Diffusion Systems

Authors: Inhoo Lee, Salvador Buse, and Erik Winfree

Published in: LIPIcs, Volume 347, 31st International Conference on DNA Computing and Molecular Programming (DNA 31) (2025)

Abstract
Many molecular systems are best understood in terms of prototypical species and reactions. The central dogma and related biochemistry are rife with examples: gene i is transcribed into RNA i, which is translated into protein i; kinase n phosphorylates substrate m; protein p dimerizes with protein q. Engineered nucleic acid systems also often have this form: oligonucleotide i hybridizes to complementary oligonucleotide j; signal strand n displaces the output of seesaw gate m; hairpin p triggers the opening of target q. When there are many variants of a small number of prototypes, it can be conceptually cleaner and computationally more efficient to represent the full system in terms of indexed species (e.g. for dimerization, M_p, D_pq) and indexed reactions (M_p + M_q → D_pq). Here, we formalize the Indexed Chemical Reaction Network (ICRN) model and describe a Python software package designed to simulate such systems in the well-mixed and reaction-diffusion settings, using a differentiable programming framework originally developed for large-scale neural network models, taking advantage of GPU acceleration when available. Notably, this framework makes it straightforward to train the models’ initial conditions and rate constants to optimize a target behavior, such as matching experimental data, performing a computation, or exhibiting spatial pattern formation. The natural map of indexed chemical reaction networks onto neural network formalisms provides a tangible yet general perspective for translating concepts and techniques from the theory and practice of neural computation into the design of biomolecular systems.
Cite as

Inhoo Lee, Salvador Buse, and Erik Winfree. Differentiable Programming of Indexed Chemical Reaction Networks and Reaction-Diffusion Systems. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 4:1-4:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

Copy BibTex To Clipboard

@InProceedings{lee_et_al:LIPIcs.DNA.31.4,
  author =	{Lee, Inhoo and Buse, Salvador and Winfree, Erik},
  title =	{{Differentiable Programming of Indexed Chemical Reaction Networks and Reaction-Diffusion Systems}},
  booktitle =	{31st International Conference on DNA Computing and Molecular Programming (DNA 31)},
  pages =	{4:1--4:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-399-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{347},
  editor =	{Schaeffer, Josie and Zhang, Fei},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.31.4},
  URN =		{urn:nbn:de:0030-drops-238534},
  doi =		{10.4230/LIPIcs.DNA.31.4},
  annote =	{Keywords: Differentiable Programming, Chemical Reaction Networks, Reaction-Diffusion Systems}
}
Document
DOI: 10.4230/DFU.Vol2.SciViz.2011.59
Comparative Visualization Using Cross-Mesh Field Evaluations and Derived Quantities

Authors: Hank Childs, Sean Ahern, Jeremy Meredith, Mark Miller, and Kenneth I. Joy

Published in: Dagstuhl Follow-Ups, Volume 2, Scientific Visualization: Interactions, Features, Metaphors (2011)

Abstract
We present a data-level comparative visualization system that utilizes two key pieces of technology: (1) cross-mesh field evaluation - algorithms to evaluate a field from one mesh onto another - and (2) a highly flexible system for creating new derived quantities. In contrast to previous comparative visualization efforts, which focused on "A-B" comparisons, our system is able to compare many related simulations in a single analysis. Types of possible novel comparisons include comparisons of ensembles of data generated through parameter studies, or comparisons of time-varying data. All portions of the system have been parallelized and our results are applicable to petascale data sets.
Cite as

Hank Childs, Sean Ahern, Jeremy Meredith, Mark Miller, and Kenneth I. Joy. Comparative Visualization Using Cross-Mesh Field Evaluations and Derived Quantities. In Scientific Visualization: Interactions, Features, Metaphors. Dagstuhl Follow-Ups, Volume 2, pp. 59-72, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2011)

Copy BibTex To Clipboard

@InCollection{childs_et_al:DFU.Vol2.SciViz.2011.59,
  author =	{Childs, Hank and Ahern, Sean and Meredith, Jeremy and Miller, Mark and Joy, Kenneth I.},
  title =	{{Comparative Visualization Using Cross-Mesh Field Evaluations and Derived Quantities}},
  booktitle =	{Scientific Visualization: Interactions, Features, Metaphors},
  pages =	{59--72},
  series =	{Dagstuhl Follow-Ups},
  ISBN =	{978-3-939897-26-2},
  ISSN =	{1868-8977},
  year =	{2011},
  volume =	{2},
  editor =	{Hagen, Hans},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DFU.Vol2.SciViz.2011.59},
  URN =		{urn:nbn:de:0030-drops-32870},
  doi =		{10.4230/DFU.Vol2.SciViz.2011.59},
  annote =	{Keywords: Comparative Visualization, Cross-Mesh Field Evaluation, Derived Quantity}
}
  • Refine by Type
  • 4 Document/PDF
  • 3 Document/HTML

  • Refine by Publication Year
  • 2 2026
  • 1 2025
  • 1 2011

  • Refine by Author
  • 1 Ahern, Sean
  • 1 Arshad, Umer
  • 1 Buse, Salvador
  • 1 Childs, Hank
  • 1 Joy, Kenneth I.
  • Show More...

  • Refine by Series/Journal
  • 1 LIPIcs
  • 2 OASIcs
  • 1 DFU

  • Refine by Classification
  • 1 Computer systems organization → Molecular computing
  • 1 Computer systems organization → Processors and memory architectures
  • 1 Computing methodologies
  • 1 Hardware → Networking hardware
  • 1 Software and its engineering → Operating systems

  • Refine by Keyword
  • 1 Chemical Reaction Networks
  • 1 Cloud computing
  • 1 Comparative Visualization
  • 1 Cross-Mesh Field Evaluation
  • 1 Derived Quantity
  • Show More...

Any Issues?
X

Feedback on the Current Page

CAPTCHA

Thanks for your feedback!

Feedback submitted to Dagstuhl Publishing

Could not send message

Please try again later or send an E-mail
© 2023-2026 Schloss Dagstuhl – LZI GmbH Schloss Dagstuhl – LZI GmbH About DROPS Imprint Privacy Contact