Demonstration venue · read-only. Every page can be browsed; the buttons that would change it are switched off. Create an account to run TaxoReview on your own data.

Timothy S. Carpenter

dblp:215/2807 · DBLP profile ↗
← Back
3ranked-venue papers
1as first author
1since 2021 · last 2021
0000-0001-7848-9983ORCID · verified

Domains — the database's venue-derived domains; a paper can count in several

Systems, architecture and hardware · 2 · 1 since 2021Applied, interdisciplinary, general and emerging computing · 1 · 1 first-author

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Computer architecture, parallel and distributed computing, and storage systems
2 papers
High-performance computing · 87% Distributed systems · 13%
Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 100%

Topics — the 4 heaviest of 5, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
High-performance computing
scientific computing systems
0.922021
Generalizable coordination of large multiscale workflows: challenges and learnings at scale · SC 2021
A massively parallel infrastructure for adaptive multiscale simulations: modeling RAS initiation pathway for cancer · SC 2019
Bioinformatics and computational biology › systems biology
multiscale modeling
0.412019
A massively parallel infrastructure for adaptive multiscale simulations: modeling RAS initiation pathway for cancer · SC 2019
Distributed systems
distributed coordination
0.112021
Generalizable coordination of large multiscale workflows: challenges and learnings at scale · SC 2021
Bioinformatics and computational biology › computational oncology
cancer modeling
0.112019
A massively parallel infrastructure for adaptive multiscale simulations: modeling RAS initiation pathway for cancer · SC 2019

Methods — techniques the papers use, named apart from their topics

machine learning · 0.5in situ feedback · 0.5
YearPublicationVenuePosition
2021 Generalizable coordination of large multiscale workflows: challenges and learnings at scale
abstract
The advancement of machine learning techniques and the heterogeneous architectures of most current supercomputers are propelling the demand for large multiscale simulations that can automatically and autonomously couple diverse components and map them to relevant resources to solve complex problems at multiple scales. Nevertheless, despite the recent progress in workflow technologies, current capabilities are limited to coupling two scales. In the first-ever demonstration of using three scales of resolution, we present a scalable and generalizable framework that couples pairs of models using machine learning and in situ feedback. We expand upon the massively parallel Multiscale Machine-Learned Modeling Infrastructure (MuMMI), a recent, award-winning workflow, and generalize the framework beyond its original design. We discuss the challenges and learnings in executing a massive multiscale simulation campaign that utilized over 600,000 node hours on Summit and achieved more than 98% GPU occupancy for more than 83% of the time. We present innovations to enable several orders of magnitude scaling, including simultaneously coordinating 24,000 jobs, and managing several TBs of new data per day and over a billion files in total. Finally, we describe the generalizability of our framework and, with an upcoming open-source release, discuss how the presented framework may be used for new applications.
Harsh Bhatia, Francesco Di Natale, Joseph Y. Moon, Joseph R. Chavez, Fikret Aydin, Christopher B. Stanley, Tomas Oppelstrup, Chris Neale, Sara Kokkila Schumacher, Dong H. Ahn, Stephen Herbein, Timothy S. Carpenter, Sandrasegaram Gnanakaran, Peer-Timo Bremer, James N. Glosli, Felice C. Lightstone, Helgi I. Ingólfsson
SC13
2019 A massively parallel infrastructure for adaptive multiscale simulations: modeling RAS initiation pathway for cancer
abstract
Computational models can define the functional dynamics of complex systems in exceptional detail. However, many modeling studies face seemingly incommensurate requirements: to gain meaningful insights into some phenomena requires models with high resolution (microscopic) detail that must nevertheless evolve over large (macroscopic) length- and time-scales. Multiscale modeling has become increasingly important to bridge this gap. Executing complex multiscale models on current petascale computers with high levels of parallelism and heterogeneous architectures is challenging. Many distinct types of resources need to be simultaneously managed, such as GPUs and CPUs, memory size and latencies, communication bottlenecks, and filesystem bandwidth. In addition, robustness to failure of compute nodes, network, and filesystems is critical.
Francesco Di Natale, Harsh Bhatia, Timothy S. Carpenter, Chris Neale, Sara Kokkila Schumacher, Tomas Oppelstrup, Liam Stanton, Shiv Sundram, Thomas Scogland, Gautham Dharuman, Michael P. Surh, Yue Yang 0034, Claudia Misale, Lars Schneidenbach, Carlos H. A. Costa, Changhoan Kim, Bruce D'Amora, Sandrasegaram Gnanakaran, Dwight V. Nissley, Frederick H. Streitz, Felice C. Lightstone, Peer-Timo Bremer, James N. Glosli, Helgi I. Ingólfsson
SC3
2016 An Electrostatic Funnel in the GABA-Binding Pathway
abstract
The γ-aminobutyric acid type A receptor (GABAA-R) is a major inhibitory neuroreceptor that is activated by the binding of GABA. The structure of the GABAA-R is well characterized, and many of the binding site residues have been identified. However, most of these residues are obscured behind the C-loop that acts as a cover to the binding site. Thus, the mechanism by which the GABA molecule recognizes the binding site, and the pathway it takes to enter the binding site are both unclear. Through the completion and detailed analysis of 100 short, unbiased, independent molecular dynamics simulations, we have investigated this phenomenon of GABA entering the binding site. In each system, GABA was placed quasi-randomly near the binding site of a GABAA-R homology model, and atomistic simulations were carried out to observe the behavior of the GABA molecules. GABA fully entered the binding site in 19 of the 100 simulations. The pathway taken by these molecules was consistent and non-random; the GABA molecules approach the binding site from below, before passing up behind the C-loop and into the binding site. This binding pathway is driven by long-range electrostatic interactions, whereby the electrostatic field acts as a 'funnel' that sweeps the GABA molecules towards the binding site, at which point more specific atomic interactions take over. These findings define a nuanced mechanism whereby the GABAA-R uses the general zwitterionic features of the GABA molecule to identify a potential ligand some 2 nm away from the binding site.
Timothy S. Carpenter, Felice C. Lightstone
PLoS Comput. Biol.1