Michela Taufer

Affiliations:
  • University of Tennesee, Knoxville, Knoxville, TN, USA
  • University of Delaware, USA


According to our database1, Michela Taufer authored at least 147 papers between 1996 and 2022.

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Bibliography

2022
VPIC 2.0: Next Generation Particle-in-Cell Simulations.
IEEE Trans. Parallel Distributed Syst., 2022

Designing an Interactive, Notebook-Embedded, Tree Visualization to Support Exploratory Performance Analysis.
CoRR, 2022

2021
Identifying Degree and Sources of Non-Determinism in MPI Applications Via Graph Kernels.
IEEE Trans. Parallel Distributed Syst., 2021

A Graphic Encoding Method for Quantitative Classification of Protein Structure and Representation of Conformational Changes.
IEEE ACM Trans. Comput. Biol. Bioinform., 2021

ANACIN-X: A software framework for studying non-determinism in MPI applications.
Softw. Impacts, 2021

A lightweight method for evaluating <i>in situ</i> workflow efficiency.
J. Comput. Sci., 2021

Reproducing GW150914: The First Observation of Gravitational Waves From a Binary Black Hole Merger.
Comput. Sci. Eng., 2021

Cybercosm: New Foundations for a Converged Science Data Ecosystem.
CoRR, 2021

PEng4NN: An Accurate Performance Estimation Engine for Efficient Automated Neural Network Architecture Search.
CoRR, 2021

Assessing Resource Provisioning and Allocation of Ensembles of In Situ Workflows.
Proceedings of the ICPP Workshops 2021: 50th International Conference on Parallel Processing, 2021

Optimize Memory Usage in Vector Particle-In-Cell (VPIC) to Break the 10 Trillion Particle Barrier in Plasma Simulations.
Proceedings of the Computational Science - ICCS 2021, 2021

AI4IO: A Suite of Ai-Based Tools for IO-Aware HPC Resource Management.
Proceedings of the 28th IEEE International Conference on High Performance Computing, 2021

A Roadmap to Robust Science for High-throughput Applications: The Scientists' Perspective.
Proceedings of the 17th IEEE International Conference on eScience, 2021

A Case Study in Scientific Reproducibility from the Event Horizon Telescope (EHT).
Proceedings of the 17th IEEE International Conference on eScience, 2021

A Roadmap to Robust Science for High-throughput Applications: The Developers' Perspective.
Proceedings of the IEEE International Conference on Cluster Computing, 2021

2020
Memory-Efficient and Skew-Tolerant MapReduce Over MPI for Supercomputing Systems.
IEEE Trans. Parallel Distributed Syst., 2020

Building a Vision for Reproducibility in the Cyberinfrastructure Ecosystem: Leveraging Community Efforts.
Supercomput. Front. Innov., 2020

Spatial Gap-Filling of ESA CCI Satellite-Derived Soil Moisture Based on Geostatistical Techniques and Multiple Regression.
Remote. Sens., 2020

Flux: Overcoming scheduling challenges for exascale workflows.
Future Gener. Comput. Syst., 2020

Reproducing GW150914: the first observation of gravitational waves from a binary black hole merger.
CoRR, 2020

Building Containerized Environments for Reproducibility and Traceability of Scientific Workflows.
CoRR, 2020

Usability and Performance Improvements in Hatchet.
Proceedings of the IEEE/ACM International Workshop on HPC User Support Tools and Workshop on Programming and Performance Visualization Tools, 2020

CanarIO: Sounding the Alarm on IO-Related Performance Degradation.
Proceedings of the 2020 IEEE International Parallel and Distributed Processing Symposium (IPDPS), 2020

A Novel Metric to Evaluate In Situ Workflows.
Proceedings of the Computational Science - ICCS 2020, 2020

2019
Creating a portable, high-level graph analytics paradigm for compute and data-intensive applications.
Int. J. High Perform. Comput. Netw., 2019

A three-phase workflow for general and expressive representations of nondeterminism in HPC applications.
Int. J. High Perform. Comput. Appl., 2019

SOMOSPIE: A modular SOil MOisture SPatial Inference Engine based on data driven decision.
CoRR, 2019

Studying the Impact of Power Capping on MapReduce-based, Data-intensive Mini-applications on Intel KNL and KNM Architectures.
CoRR, 2019

Characterization of Power Usage and Performance in Data-Intensive Applications Using MapReduce over MPI.
Proceedings of the Parallel Computing: Technology Trends, 2019

Session details: Reliability and Variability.
Proceedings of the 28th International Symposium on High-Performance Parallel and Distributed Computing, 2019

Initial Thoughts on Cybersecurity And Reproducibility.
Proceedings of the 2nd International Workshop on Practical Reproducible Evaluation of Computer Systems, 2019

Applicability Study of the PRIMAD Model to LIGO Gravitational Wave Search Workflows.
Proceedings of the 2nd International Workshop on Practical Reproducible Evaluation of Computer Systems, 2019

Characterizing In Situ and In Transit Analytics of Molecular Dynamics Simulations for Next-Generation Supercomputers.
Proceedings of the 15th International Conference on eScience, 2019

SOMOSPIE: A Modular SOil MOisture SPatial Inference Engine Based on Data-Driven Decisions.
Proceedings of the 15th International Conference on eScience, 2019

2018
Record-and-Replay Techniques for HPC Systems: A Survey.
Supercomput. Front. Innov., 2018

The future of scientific workflows.
Int. J. High Perform. Comput. Appl., 2018

Modeling the Next-Generation High Performance Schedulers.
Proceedings of the 2018 ACM SIGSIM Conference on Principles of Advanced Discrete Simulation, 2018

PRIONN: Predicting Runtime and IO using Neural Networks.
Proceedings of the 47th International Conference on Parallel Processing, 2018

KeyBin2: Distributed Clustering for Scalable and In-Situ Analysis.
Proceedings of the 47th International Conference on Parallel Processing, 2018

On the Power of Combiner Optimizations in MapReduce Over MPI Workflows.
Proceedings of the 24th IEEE International Conference on Parallel and Distributed Systems, 2018

Leveraging In Situ Data Analysis to Enable Computational Steering of Brain's Neocortex Simulations with GENESIS.
Proceedings of the 20th IEEE International Conference on High Performance Computing and Communications; 16th IEEE International Conference on Smart City; 4th IEEE International Conference on Data Science and Systems, 2018

Graphic Encoding of Macromolecules for Efficient High-Throughput Analysis.
Proceedings of the 2018 ACM International Conference on Bioinformatics, 2018

2017
Enabling scalable and accurate clustering of distributed ligand geometries on supercomputers.
Parallel Comput., 2017

<i>In situ</i> data analytics and indexing of protein trajectories.
J. Comput. Chem., 2017

Scheduling DAG-based workflows on single cloud instances: High-performance and cost effectiveness with a static scheduler.
Int. J. High Perform. Comput. Appl., 2017

Mimir: Memory-Efficient and Scalable MapReduce for Large Supercomputing Systems.
Proceedings of the 2017 IEEE International Parallel and Distributed Processing Symposium, 2017

Bloomfish: A Highly Scalable Distributed K-mer Counting Framework.
Proceedings of the 23rd IEEE International Conference on Parallel and Distributed Systems, 2017

Data analytics for modeling soil moisture patterns across united states ecoclimatic domains.
Proceedings of the 2017 IEEE International Conference on Big Data (IEEE BigData 2017), 2017

2016
Special Issue on Cluster Computing.
Parallel Comput., 2016

Performance characterization of irregular I/O at the extreme scale.
Parallel Comput., 2016

Resource Management for Running HPC Applications in Container Clouds.
Proceedings of the High Performance Computing - 31st International Conference, 2016

HYPPO: A Hybrid, Piecewise Polynomial Modeling Technique for Non-Smooth Surfaces.
Proceedings of the 28th International Symposium on Computer Architecture and High Performance Computing, 2016

Scheduling Matters: Area-Oriented Heuristic for Resource Management.
Proceedings of the 28th International Symposium on Computer Architecture and High Performance Computing, 2016

Study of Neocortex Simulations with GENESIS on High Performance Computing Resources.
Proceedings of the 22nd IEEE International Conference on Parallel and Distributed Systems, 2016

Who is Afraid of I/O?: Exploring I/O Challenges and Opportunities at the Exascale.
Proceedings of the ACM 7th Workshop on Scientific Cloud Computing, 2016

Scalable I/O-Aware Job Scheduling for Burst Buffer Enabled HPC Clusters.
Proceedings of the 25th ACM International Symposium on High-Performance Parallel and Distributed Computing, 2016

Machine Learning Predictions of Runtime and IO Traffic on High-End Clusters.
Proceedings of the 2016 IEEE International Conference on Cluster Computing, 2016

Development of a Scalable Method for Creating Food Groups Using the NHANES Dataset and MapReduce.
Proceedings of the 7th ACM International Conference on Bioinformatics, 2016

2015
Free energetics of carbon nanotube association in aqueous inorganic NaI salt solutions: Temperature effects using all-atom molecular dynamics simulations.
J. Comput. Chem., 2015

It-Situ Data Analysis of Protein Folding Trajectories.
CoRR, 2015

AsHES Keynote.
Proceedings of the 2015 IEEE International Parallel and Distributed Processing Symposium Workshop, 2015

HiCOMB 2015 Keynote and Invited Talks.
Proceedings of the 2015 IEEE International Parallel and Distributed Processing Symposium Workshop, 2015

A Testing Engine for High-Performance and Cost-Effective Workflow Execution in the Cloud.
Proceedings of the 44th International Conference on Parallel Processing, 2015

A Genetic Programming Approach to Design Resource Allocation Policies for Heterogeneous Workflows in the Cloud.
Proceedings of the 21st IEEE International Conference on Parallel and Distributed Systems, 2015

Performance Tuning of MapReduce Jobs Using Surrogate-based Modeling.
Proceedings of the International Conference on Computational Science, 2015

From HPC Performance to Climate Modeling: Transforming Methods for HPC Predictions into Models of Extreme Climate Conditions.
Proceedings of the 11th IEEE International Conference on e-Science, 2015

Dynamic CPU Resource Allocation in Containerized Cloud Environments.
Proceedings of the 2015 IEEE International Conference on Cluster Computing, 2015

A Two-Tiered Approach to I/O Quality of Service in Docker Containers.
Proceedings of the 2015 IEEE International Conference on Cluster Computing, 2015

Network Quality of Service in Docker Containers.
Proceedings of the 2015 IEEE International Conference on Cluster Computing, 2015

On the Need for Reproducible Numerical Accuracy through Intelligent Runtime Selection of Reduction Algorithms at the Extreme Scale.
Proceedings of the 2015 IEEE International Conference on Cluster Computing, 2015

Accurate Scoring of Drug Conformations at the Extreme Scale.
Proceedings of the 15th IEEE/ACM International Symposium on Cluster, 2015

2014
Pursuing Coordinated Trajectory Progression and Efficient Resource Utilization of GPU-Enabled Molecular Dynamics Simulations.
IEEE Des. Test, 2014

Bandwidth Modeling in Large Distributed Systems for Big Data Applications.
Proceedings of the 15th International Conference on Parallel and Distributed Computing, 2014

Enabling In-Situ Data Analysis for Large Protein-Folding Trajectory Datasets.
Proceedings of the 2014 IEEE 28th International Parallel and Distributed Processing Symposium, 2014

Benchmarking the Performance of Scientific Applications with Irregular I/O at the Extreme Scale.
Proceedings of the 43rd International Conference on Parallel Processing Workshops, 2014

Using surrogate-based modeling to predict optimal I/O parameters of applications at the extreme scale.
Proceedings of the 20th IEEE International Conference on Parallel and Distributed Systems, 2014

Study of the Network Impact on Earthquake Early Warning in the Quake-catcher Network Project.
Proceedings of the International Conference on Computational Science, 2014

Gender and volunteer computing: A survey study.
Proceedings of the IEEE Frontiers in Education Conference, 2014

Applying frequency analysis techniques to dag-based workflows to benchmark and predict resource behavior on non-dedicated clusters.
Proceedings of the 2014 IEEE International Conference on Cluster Computing, 2014

2013
On the powerful use of simulations in the Quake-Catcher Network to efficiently position low-cost earthquake sensors.
Future Gener. Comput. Syst., 2013

GPU-Enabled Macromolecular Simulation: Challenges and Opportunities.
Comput. Sci. Eng., 2013

Secondary Structure Predictions for Long RNA Sequences Based on Inversion Excursions and MapReduce.
Proceedings of the 2013 IEEE International Symposium on Parallel & Distributed Processing, 2013

Performance Dissection of a Molecular Dynamics Code across CUDA and GPU Generations.
Proceedings of the 2013 IEEE International Symposium on Parallel & Distributed Processing, 2013

Efficient SDS Simulations on Multi-GPU Nodes of XSEDE High-End Clusters.
Proceedings of the 9th IEEE International Conference on eScience, 2013

Benchmarking Gender Differences in Volunteer Computing Projects.
Proceedings of the 9th IEEE International Conference on eScience, 2013

On Efficiently Capturing Scientific Properties in Distributed Big Data without Moving the Data: A Case Study in Distributed Structural Biology Using MapReduce.
Proceedings of the 16th IEEE International Conference on Computational Science and Engineering, 2013

Performance Impact of I/O on QMCPack Simulations at the Petascale and Beyond.
Proceedings of the 16th IEEE International Conference on Computational Science and Engineering, 2013

2012
Hierarchical fractional-step approximations and parallel kinetic Monte Carlo algorithms.
J. Comput. Phys., 2012

A scalable and accurate method for classifying protein-ligand binding geometries using a MapReduce approach.
Comput. Biol. Medicine, 2012

On the Cost of a General GPU Framework: The Strange Case of CUDA 4.0 vs. CUDA 5.0.
Proceedings of the 2012 SC Companion: High Performance Computing, 2012

On the effectiveness of application-aware self-management for scientific discovery in volunteer computing systems.
Proceedings of the SC Conference on High Performance Computing Networking, 2012

Reengineering High-throughput Molecular Datasets for Scalable Clustering Using MapReduce.
Proceedings of the 14th IEEE International Conference on High Performance Computing and Communication & 9th IEEE International Conference on Embedded Software and Systems, 2012

ExSciTecH: Expanding volunteer computing to Explore Science, Technology, and Health.
Proceedings of the 8th IEEE International Conference on E-Science, 2012

A modularized MapReduce framework to support RNA secondary structure prediction and analysis workflows.
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2012

Secondary structure predictions for long RNA sequences based on inversion excursions: preliminary results.
Proceedings of the ACM International Conference on Bioinformatics, 2012

2011
Protein Docking.
Proceedings of the Encyclopedia of Parallel Computing, 2011

Evaluation of Several Two-Step Scoring Functions Based on Linear Interaction Energy, Effective Ligand Size, and Empirical Pair Potentials for Prediction of Protein-Ligand Binding Geometry and Free Energy.
J. Chem. Inf. Model., 2011

Structural, dynamic, and electrostatic properties of fully hydrated DMPC bilayers from molecular dynamics simulations accelerated with graphical processing units (GPUs).
J. Comput. Chem., 2011

Molecular dynamics simulations of aqueous ions at the liquid-vapor interface accelerated using graphics processors.
J. Comput. Chem., 2011

Special issue of computer communications on information and future communication security.
Comput. Commun., 2011

Poster: study of protein-ligand binding geometries using a scalable and accurate octree-based algorithm in mapReduce.
Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis, 2011

FENZI: GPU-Enabled Molecular Dynamics Simulations of Large Membrane Regions Based on the CHARMM Force Field and PME.
Proceedings of the 25th IEEE International Symposium on Parallel and Distributed Processing, 2011

Providing Quality of Science in Volunteer Computing.
Proceedings of the 13th IEEE International Conference on High Performance Computing & Communication, 2011

Simulating Application Resilience at Exascale.
Proceedings of the Euro-Par 2011: Parallel Processing Workshops - CCPI, CGWS, HeteroPar, HiBB, HPCVirt, HPPC, HPSS, MDGS, ProPer, Resilience, UCHPC, VHPC, Bordeaux, France, August 29, 2011

On the Powerful Use of Simulations in the Quake-Catcher Network to Efficiently Position Low-cost Earthquake Sensors.
Proceedings of the IEEE 7th International Conference on E-Science, 2011

2010
Parallelization of tau-leap coarse-grained Monte Carlo simulations on GPUs.
Proceedings of the 24th IEEE International Symposium on Parallel and Distributed Processing, 2010

Improving numerical reproducibility and stability in large-scale numerical simulations on GPUs.
Proceedings of the 24th IEEE International Symposium on Parallel and Distributed Processing, 2010

A Dynamic Programming Algorithm for Finding the Optimal Segmentation of an RNA Sequence in Secondary Structure Predictions.
Proceedings of the ISCA 2nd International Conference on Bioinformatics and Computational Biology, 2010

Accelerating HMMER on GPUs by implementing hybrid data and task parallelism.
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, 2010

Automatic selection of near-native protein-ligand conformations using a hierarchical clustering and volunteer computing.
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, 2010

2009
PseudoBase++: an extension of PseudoBase for easy searching, formatting and visualization of pseudoknots.
Nucleic Acids Res., 2009

Performance Prediction and Analysis of BOINC Projects: An Empirical Study with EmBOINC.
J. Grid Comput., 2009

EmBOINC: An emulator for performance analysis of BOINC projects.
Proceedings of the 23rd IEEE International Symposium on Parallel and Distributed Processing, 2009

MNEMONIC: A Network Environment for Automatic Optimization and Tuning of Data Movement over Advanced Networks.
Proceedings of the 18th International Conference on Computer Communications and Networks, 2009

Balancing Scientist Needs and Volunteer Preferences in Volunteer Computing Using Constraint Optimization.
Proceedings of the Computational Science, 2009

Modeling Job Lifespan Delays in Volunteer Computing Projects.
Proceedings of the 9th IEEE/ACM International Symposium on Cluster Computing and the Grid, 2009

Towards Large-Scale Molecular Dynamics Simulations on Graphics Processors.
Proceedings of the Bioinformatics and Computational Biology, 2009

2008
A distributed evolutionary method to design scheduling policies for volunteer computing.
SIGMETRICS Perform. Evaluation Rev., 2008

RNAVLab: A virtual laboratory for studying RNA secondary structures based on grid computing technology.
Parallel Comput., 2008

On the Effectiveness of Rebuilding RNA Secondary Structures from Sequence Chunks.
Proceedings of the 22nd IEEE International Symposium on Parallel and Distributed Processing, 2008

2007
Evaluation of IEEE 754 floating-point arithmetic compliance across a wide range of heterogeneous computers.
Proceedings of the Richard Tapia Celebration of Diversity in Computing Conference 2007, 2007

SimBA: A Discrete Event Simulator for Performance Prediction of Volunteer Computing Projects.
Proceedings of the 21st International Workshop on Principles of Advanced and Distributed Simulation, 2007

Topaz: Extending Firefox to Accommodate the GridFTP Protocol.
Proceedings of the 21th International Parallel and Distributed Processing Symposium (IPDPS 2007), 2007

RNAVLab: A unified environment for computational RNA structure analysis based on grid computing technology.
Proceedings of the 21th International Parallel and Distributed Processing Symposium (IPDPS 2007), 2007

Moving Volunteer Computing towards Knowledge-Constructed, Dynamically-Adaptive Modeling and Scheduling.
Proceedings of the 21th International Parallel and Distributed Processing Symposium (IPDPS 2007), 2007

2006
Predictor@Home: A "Protein Structure Prediction Supercomputer' Based on Global Computing.
IEEE Trans. Parallel Distributed Syst., 2006

Poster reception - SimBA: a discrete event simulator for performance prediction of volunteer computing projects.
Proceedings of the ACM/IEEE SC2006 Conference on High Performance Networking and Computing, 2006

compPknots: A Framework for Parallel Prediction and Comparison of RNA Secondary Structures with Pseudoknots.
Proceedings of the Frontiers of High Performance Computing and Networking, 2006

A systematic multi-step methodology for performance analysis of communication traces of distributed applications based on hierarchical clustering.
Proceedings of the 20th International Parallel and Distributed Processing Symposium (IPDPS 2006), 2006

The Effectiveness of Threshold-Based Scheduling Policies in BOINC Projects.
Proceedings of the Second International Conference on e-Science and Grid Technologies (e-Science 2006), 2006

2005
DGMonitor: A Performance Monitoring Tool for Sandbox-Based Desktop Grid Platforms.
J. Supercomput., 2005

The Computational Chemistry Prototyping Environment.
Proc. IEEE, 2005

Study of a highly accurate and fast protein-ligand docking method based on molecular dynamics.
Concurr. Comput. Pract. Exp., 2005

Predictor@Home: A "Protein Structure Prediction Supercomputer" Based on Public-Resource Computing.
Proceedings of the 19th International Parallel and Distributed Processing Symposium (IPDPS 2005), 2005

Homogeneous Redundancy: a Technique to Ensure Integrity of Molecular Simulation Results Using Public Computing.
Proceedings of the 19th International Parallel and Distributed Processing Symposium (IPDPS 2005), 2005

Metrics for Effective Resource Management in Global Computing Environments.
Proceedings of the First International Conference on e-Science and Grid Technologies (e-Science 2005), 2005

2004
Study of a Highly Accurate and Fast Protein-Ligand Docking Algorithm Based on Molecular Dynamics.
Proceedings of the 18th International Parallel and Distributed Processing Symposium (IPDPS 2004), 2004

Characterizing and Evaluating Desktop Grids: An Empirical Study.
Proceedings of the 18th International Parallel and Distributed Processing Symposium (IPDPS 2004), 2004

2003
Implementation and Characterization of Protein Folding on a Desktop Computational Grid - Is CHARMM a Suitable Candidate for the United Devices MetaProcessor?
Proceedings of the 17th International Parallel and Distributed Processing Symposium (IPDPS 2003), 2003

A Performance Monitor Based on Virtual Global Time for Clusters of PCs.
Proceedings of the 2003 IEEE International Conference on Cluster Computing (CLUSTER 2003), 2003

Combining Task- and Data Parallelism to Speed up Protein Folding on a Desktop Grid Platform.
Proceedings of the 3rd IEEE International Symposium on Cluster Computing and the Grid (CCGrid 2003), 2003

2002
Inverting middleware: performance analysis of layered application codes in high performance distributed computing.
PhD thesis, 2002

Scalability and resource usage of an OLAP benchmark on clusters of PCs.
Proceedings of the Fourteenth Annual ACM Symposium on Parallel Algorithms and Architectures, 2002

Performance Characterization of a Molecular Dynamics Code on PC Clusters: Is There Any Easy Parallelism in CHARMM?.
Proceedings of the 16th International Parallel and Distributed Processing Symposium (IPDPS 2002), 2002

On the Migration of the Scientific Code Dyana from SMPs to Clusters of PCs and on to the Grid.
Proceedings of the 2nd IEEE International Symposium on Cluster Computing and the Grid (CCGrid 2002), 2002

1998
Accurate Performance Evaluation, Modelling and Prediction of a Message Passing Simulation Code based on Middleware.
Proceedings of the ACM/IEEE Conference on Supercomputing, 1998

1996
Molecular Dynamics Simulations on Cray Clusters using the SCIDDLE-PVM environment.
Proceedings of the Parallel Virtual Machine, 1996


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