Michela Taufer

Publications

• ANACIN-X: A software framework for studying non-determinism in MPI applications
• Analysis of Vector Particle-In-Cell (VPIC) memory usage optimizations on cutting-edge computer architectures
• A Roadmap to Robust Science for High-throughput Applications: The Scientists’ Perspective
• Assessing Resource Provisioning and Allocation of Ensembles of In Situ Workflows
• AI4IO: A suite of AI-based tools for IO-aware scheduling
• A lightweight method for evaluating in situ workflow efficiency
• Building a Vision for Reproducibility in the Cyberinfrastructure Ecosystem: Leveraging Community Efforts
• SOMOSPIE: A Modular SOil MOisture SPatial Inference Engine Based on Data-Driven Decisions
• Initial Thoughts on Cybersecurity And Reproducibility
• Characterizing In Situ and In Transit Analytics of Molecular Dynamics Simulations for Next-Generation Supercomputers
• Applicability Study of the PRIMAD Model to LIGO Gravitational Wave Search Workflows
• Record-and-Replay Techniques for HPC Systems: A Survey
• Graphic Encoding of Macromolecules for Efficient High-Throughput Analysis
• High frequency accuracy and loss data of random neural networks trained on image datasets
• Foreword from the general chair and technical program chair/vice chair
• Building a vision for reproducibility in the cyberinfrastructure ecosystem: Leveraging community efforts
• Flux: Overcoming Scheduling Challenges for Exascale Workflows
• Flux: Overcoming scheduling challenges for exascale workflows
• Reproducibility of the First Image of a Black Hole in the Galaxy M87 From the Event Horizon Telescope Collaboration
• KeyBin2: Distributed Clustering for Scalable and In-Situ Analysis
• Spatial Gap-Filling of ESA CCI Satellite-Derived Soil Moisture Based on Geostatistical Techniques and Multiple Regression
• Runtime Steering of Molecular Dynamics Simulations Through In Situ Analysis and Annotation of Collective Variables
• Development of Large-Scale Scientific Cyberinfrastructure and the Growing Opportunity to Democratize Access to Platforms and Data
• VPIC 2.0: Next Generation Particle-in-Cell Simulations
• A Roadmap to Robust Science for High-throughput Applications: The Developers’ Perspective
• A Case Study in Scientific Reproducibility from the Event Horizon Telescope (EHT)
• Usability and Performance Improvements in Hatchet
• Optimize Memory Usage in Vector Particle-In-Cell (VPIC) to Break the 10 Trillion Particle Barrier in Plasma Simulations
• Identifying Degree and Sources of Non-Determinism in MPI Applications Via Graph Kernels
• Reproducing GW150914: The First Observation of Gravitational Waves From a Binary Black Hole Merger
• A Graphic Encoding Method for Quantitative Classification of Protein Structure and Representation of Conformational Changes
• A Novel Metric to Evaluate In Situ Workflows
• Memory-Efficient and Skew-Tolerant MapReduce Over MPI for Supercomputing Systems
• CanarIO: Sounding the Alarm on IO-Related Performance Degradation
• Creating a portable, high-level graph analytics paradigm for compute and data-intensive applications
• A three-phase workflow for general and expressive representations of nondeterminism in HPC applications
• Characterization of Power Usage and Performance in Data-Intensive Applications Using MapReduce over MPI
• The future of scientific workflows
• Leveraging In Situ Data Analysis to Enable Computational Steering of Brain's Neocortex Simulations with GENESIS
• On the Power of Combiner Optimizations in MapReduce Over MPI Workflows
• Building Trust in Earth Science Findings through Data Traceability and Results Explainability
• A Survey of Graph Comparison Methods with Applications to Nondeterminism in High-Performance Computing
• Orchestration of materials science workflows for heterogeneous resources at large scale
• Studying Latency and Throughput Constraints for Geo-Distributed Data in the National Science Data Fabric
• GEOtiled: A Scalable Workflow for Generating Large Datasets of High-Resolution Terrain Parameters
• Composable Workflow for Accelerating Neural Architecture Search Using In Situ Analytics for Protein Classification
• Scalable Incremental Checkpointing using GPU-Accelerated De-Duplication
• Toward a Compatible Reproducibility Taxonomy for Computational and Computing Sciences.
• SC18 selects the next reproducibility challenge paper
• A survey of algorithms for transforming molecular dynamics data into metadata for in situ analytics based on machine learning methods
• Mimir: Memory-Efficient and Scalable MapReduce for Large Supercomputing Systems
• Machine Learning Predictions of Runtime and IO Traffic on High-End Clusters
• High Performance Computing
• Gender and volunteer computing: A survey study
• Development of a Scalable Method for Creating Food Groups Using the NHANES Dataset and MapReduce
• Record and replay techniques for HPC systems: A survey
• Preface
• Data movement in data-intensive high performance computing
• HPDC15 Chairs' welcome
• Message from BDCloud Chairs
• Scheduling DAG-based workflows on single cloud instances: High-performance and cost effectiveness with a static scheduler
• Message from the General Chair
• From HPC performance to climate modeling: Transforming methods for HPC predictions into models of extreme climate conditions
• Study of the network impact on earthquake early warning in the Quake-Catcher Network project
• A testing engine for high-performance and cost-effective workflow execution in the cloud
• Bandwidth Modeling in Large Distributed Systems for Big Data Applications
• Resource management for running HPC applications in container clouds
• A genetic programming approach to design resource allocation policies for heterogeneous workflows in the cloud
• Enhancing reproducibility for computational methods
• CLUSTER 2015 general co-chairs welcome message
• Performance tuning of MapReduce jobs using surrogate-based modeling
• Benchmarking the Performance of Scientific Applications with Irregular I/O at the Extreme Scale
• Rapid earthquake characterization using MEMS accelerometers and volunteer hosts following the M 7.2 Darfield, New Zealand, earthquake
• Pursuing coordinated trajectory progression and efficient resource utilization of GPU-enabled molecular dynamics simulations
• In situ data analytics and indexing of protein trajectories
• PRIONN: Predicting Runtime and IO using Neural Networks
• Message from the General Chair
• Performance characterization of irregular I/O at the extreme scale
• Special Issue on Cluster Computing
• Network Quality of Service in Docker Containers
• Modeling the Next-Generation High Performance Schedulers
• AsHES'15 Keynote Speaker - The numerical reproducibility fair trade: Facing the concurrency challenges at the extreme scale
• Dynamic CPU Resource Allocation in Containerized Cloud Environments
• A Two-Tiered Approach to I/O Quality of Service in Docker Containers
• Who is Afraid of I/O?
• HiCOMB 2015 Keynote and Invited Talks
• On the Need for Reproducible Numerical Accuracy through Intelligent Runtime Selection of Reduction Algorithms at the Extreme Scale
• Accurate Scoring of Drug Conformations at the Extreme Scale
• Data analytics for modeling soil moisture patterns across united states ecoclimatic domains
• Scheduling Matters: Area-Oriented Heuristic for Resource Management
• Scalable I/O-Aware Job Scheduling for Burst Buffer Enabled HPC Clusters
• Using surrogate-based modeling to predict optimal I/O parameters of applications at the extreme scale
• HYPPO: A Hybrid, Piecewise Polynomial Modeling Technique for Non-Smooth Surfaces
• Applying frequency analysis techniques to dag-based workflows to benchmark and predict resource behavior on non-dedicated clusters
• Enabling In-Situ Data Analysis for Large Protein-Folding Trajectory Datasets
• Bloomfish: A Highly Scalable Distributed K-mer Counting Framework
• Study of Neocortex Simulations with GENESIS on High Performance Computing Resources
• High Performance Computing
• Free energetics of carbon nanotube association in aqueous inorganic NaI salt solutions: Temperature effects using all-atom molecular dynamics simulations
• Enabling scalable and accurate clustering of distributed ligand geometries on supercomputers
• Providing Quality of Science in Volunteer Computing
• Rolling partial prefix-sums to speedup evaluation of uniform and affine recurrence equations
• FENZI: GPU-Enabled Molecular Dynamics Simulations of Large Membrane Regions Based on the CHARMM Force Field and PME
• Challenges in designing scheduling policies in volunteer computing
• A dynamic programming algorithm for finding the optimal segmentation of an RNA sequence in secondary structure predictions
• Performance impact of I/O on QMCPack simulations at the petascale and beyond
• Workshop on desktop grids and volunteer computing systems - PCGrid
• 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
• Performance prediction and analysis of BOINC projects: An empirical study with EmBOINC
• MNEMONIC: A network environment for automatic optimization and tuning of data movement over advanced networks
• Enhancement of accuracy and efficiency for RNA secondary structure prediction by sequence segmentation and MapReduce
• A scalable and accurate method for classifying protein-ligand binding geometries using a MapReduce approach
• Hierarchical fractional-step approximations and parallel kinetic Monte Carlo algorithms
• ExSciTecH: Expanding volunteer computing to explore science, technology, and health
• Message from the workshop chairs
• A modularized MapReduce framework to support RNA secondary structure prediction and analysis workflows
• On the powerful use of simulations in the Quake-Catcher Network to efficiently position low-cost earthquake sensors
• Towards large-scale molecular dynamics simulations on graphics processors
• Balancing scientist needs and volunteer preferences in volunteer computing using constraint optimization
• PseudoBase++: An extension of PseudoBase for easy searching, formatting and visualization of pseudoknots
• Molecular dynamics simulations of aqueous ions at the liquid-vapor interface accelerated using graphics processors
• On the powerful use of simulations in the quake-catcher network to efficiently position low-cost earthquake sensors
• Special issue of computer communications on information and future communication security
• IPDPS 2009 - Proceedings of the 2009 IEEE International Parallel and Distributed Processing Symposium: Message from the workshop chairs
• On the effectiveness of application-aware self-management for scientific discovery in volunteer computing systems
• Computational multiscale modeling in protein - Ligand docking
• Structural, dynamic, and electrostatic properties of fully hydrated DMPC bilayers from molecular dynamics simulations accelerated with graphical processing units (GPUs)
• A 3′ terminal stem-loop structure in Nodamura virus RNA2 forms an essential cis-acting signal for RNA replication
• Simulating application resilience at exascale
• On the cost of a general GPU framework: The strange case of CUDA 4.0 vs. CUDA 5.0
• Performance impact of dynamic parallelism on different clustering algorithms
• Computer-Aided Design of Drugs on Emerging Hybrid High Performance Computers
• GPU-Enabled Macromolecular Simulation: Challenges and Opportunities
• Modeling Job Lifespan Delays in Volunteer Computing Projects
• EmBOINC: An emulator for performance analysis of BOINC projects
• Improving numerical reproducibility and stability in large-scale numerical simulations on GPUs
• Parallelization of tau-leap coarse-grained Monte Carlo simulations on GPUs
• On the Effectiveness of Rebuilding RNA Secondary Structures from Sequence Chunks
• Performance Dissection of a Molecular Dynamics Code across CUDA and GPU Generations
• A distributed evolutionary method to design scheduling policies for volunteer computing
• Efficient SDS Simulations on Multi-GPU Nodes of XSEDE High-End Clusters
• Benchmarking Gender Differences in Volunteer Computing Projects
• Automatic selection of near-native protein-ligand conformations using a hierarchical clustering and volunteer computing
• Accelerating HMMER on GPUs by implementing hybrid data and task parallelism
• Dealing with performance/portability and performance/accuracy trade-offs in heterogeneous computing systems: a case study with matrix multiplication modulo primes
• Reengineering High-throughput Molecular Datasets for Scalable Clustering Using MapReduce
• Secondary structure predictions for long RNA sequences based on inversion excursions
• Secondary Structure Predictions for Long RNA Sequences Based on Inversion Excursions and MapReduce
• Poster
• On Efficiently Capturing Scientific Properties in Distributed Big Data without Moving the Data: A Case Study in Distributed Structural Biology Using MapReduce
• Topaz: Extending Firefox to Accommodate the GridFTP Protocol
• SimBA: A Discrete Event Simulator for Performance Prediction of Volunteer Computing Projects
• Characterizing and evaluating desktop grids: an empirical study
• Implementation and characterization of protein folding on a desktop computational grid. Is CHARMM a suitable candidate for the United Devices MetaProcessor?
• DGMonitor: A performance monitoring tool for sandbox-based desktop grid platforms
• Study of a highly accurate and fast protein-ligand docking algorithm based on molecular dynamics
• Characterizing and evaluating desktop grids: An empirical study
• Evaluation of IEEE 754 floating-point arithmetic compliance across a wide range of heterogeneous computers
• Scalability and resource usage of an OLAP benchmark on clusters of PCs
• PredictorΗome: A "protein structure prediction supercomputer" based on global computing
• compPknots: A framework for parallel prediction and comparison of RNA secondary structures with pseudoknots
• Metrics for effective resource management in global computing environments
• Moving volunteer computing towards knowledge-constructed, dynamically-adaptive modeling and scheduling
• DGMonitor: A performance monitoring tool for sandbox-based desktop grid platforms
• Study of a highly accurate and fast protein-ligand docking method based on molecular dynamics
• Combining task- and data parallelism to speed up protein folding on a desktop grid platform
• On the migration of the scientific code Dyana from SMPs to clusters of PCs and on to the grid
• The computational chemistry prototyping environment
• Accurate Performance Evaluation, Modelling and Prediction of a Message Passing Simulation Code based on Middleware
• Molecular dynamics simulations on Cray clusters using the SCIDDLE-PVM environment
• Molecular Dynamics Simulations on Cray Clusters using the SCIDDLE-PVM environment
• Study of a highly accurate and fast protein-ligand docking algorithm based on molecular dynamics
• Poster reception---SimBA
• Towards Optimal Scheduling for Global Computing under Probabilistic, Interval, and Fuzzy Uncertainty, with Potential Applications to Bioinformatics
• A performance monitor based on virtual global time for clusters of PCs
• DGMonitor: a performance monitoring tool for sandbox-based desktop grid platforms
• Performance characterization of a molecular dynamics code on PC clusters: is there any easy parallelism in CHARMM?
• A systematic multi-step methodology for performance analysis of communication traces of distributed applications based on hierarchical clustering
• RNAVLab: A unified environment for computational RNA structure analysis based on grid computing technology
• Homogeneous Redundancy: a Technique to Ensure Integrity of Molecular Simulation Results Using Public Computing
• Predictor@Home: A "Protein Structure Prediction Supercomputer" Based on Public-Resource Computing
• The Effectiveness of Threshold-Based Scheduling Policies in BOINC Projects
• Design Concerns for Integrated Scripting and Interactive Visualization in Notebook Environments
• NSDF-Services: Integrating Networking, Storage, and Computing Services into a Testbed for Democratization of Data Delivery
• Enhancing Scientific Research with FAIR Digital Objects in the National Science Data Fabric
• HPC and Cloud Convergence Beyond Technical Boundaries: Strategies for Economic Sustainability, Standardization, and Data Accessibility
• Reproducing the Results for Neutron Star Interior Composition Explorer Observation of PSR J0030 + 0451
• Mirror, Mirror on the Wall, What is the Best Topology of Them All?
• Towards Affordable Reproducibility Using Scalable Capture and Comparison of Intermediate Multi-Run Results
• Increasing the Efficiency of Ensemble Molecular Dynamics Simulations with Termination of Unproductive Trajectories Identified at Runtime