Michael Papka

Publications

• viewSq, a Visual Molecular Dynamics (VMD) module for calculating, analyzing, and visualizing X-ray and neutron structure factors from atomistic simulations
• Adapting the serial Alpgen parton-interaction generator to simulate LHC collisions on millions of parallel threads
• A Data Driven Scheduling Approach for Power Management on HPC Systems
• Streaming ultra high resolution images to large tiled display at nearly interactive frame rate with vl3
• Coupling LAMMPS and the vl3 framework for co-visualization of atomistic simulations
• Large-scale co-visualization for LAMMPS using vl3
• Early investigations into using a remote RAM pool with the vl3 visualization framework
• Optimal Execution of Co-analysis for Large-Scale Molecular Dynamics Simulations
• Modeling and evaluating user behavior in exploratory visual analysis
• Augmenting views on large format displays with tablets
• Expanding the Scope of High-Performance Computing Facilities
• Improving Data Movement Performance for Sparse Data Patterns on the Blue Gene/Q Supercomputer
• Visualizing multiphysics, fluid-structure interaction phenomena in intracranial aneurysms
• An Edge Service for Managing HPC Workflows
• Application power profiling on IBM Blue Gene/Q
• Waggle: An open sensor platform for edge computing
• Improving Communication Throughput by Multipath Load Balancing on Blue Gene/Q
• Exploring Features for Predicting Policy Citations
• In situ exploration of particle simulations with CPU ray tracing
• Automated dynamic data redistribution
• Multipath load balancing for M × N communication patterns on the blue gene/Q supercomputer interconnection network
• Big Data: Next-Generation Machines for Big Science
• Towards optimizing large-scale data transfers with end-to-end integrity verification
• Trade-Off between Prediction Accuracy and Underestimation Rate in Job Runtime Estimates
• Achieving production-level use of HEP software at the argonne leadership computing facility
• Advances in leadership computing [Guest editors' introduction]
• Genre cycling: The infrastructural function of an operational assessment review and reporting process at a federal scientific supercomputing user facility
• Improving models of document cycling: Accounting for the less visible writing activities of an annual reporting process at a supercomputing facility
• Parallel distributed, GPU-Accelerated, advanced lighting calculations for large-scale volume visualization
• Interactive multi-modal display spaces for visual analysis
• Operational metrics reporting processes at scientific user facilities: Comparing a high-energy x-ray synchrotron facility to a supercomputing facility
• Exploring void search for fault detection on extreme scale systems
• Tell me what do you see: Detecting perceptually-separable visual patterns via clustering of image-space features in visualizations
• Comparison of vendor supplied environmental data collection mechanisms
• Morse-smale analysis of ion diffusion in ab initio battery materials simulations
• Optimal scheduling of in-situ analysis for large-scale scientific simulations
• Evaluating user behavior and strategy during visual exploration
• Improving sparse data movement performance using multiple paths on the Blue Gene/Q supercomputer
• Scalable pCT Image Reconstruction Delivered as a Cloud Service
• A distributed graph approach for pre-processing linked RDF data using supercomputers
• Interstitial and Interlayer Ion Diffusion Geometry Extraction in Graphitic Nanosphere Battery Materials
• Predicting research that will be cited in policy documents
• CPU ray tracing large particle data with balanced P-k-d trees
• Quantitative modeling of power performance tradeoffs on extreme scale systems
• Effects of display size and resolution on user behavior and insight acquisition in visual exploration
• Hands-On Computer Science: The Array of Things Experimental Urban Instrument
• DIRAQ: scalable in situ data- and resource-aware indexing for optimized query performance
• DRAS: Deep Reinforcement Learning for Cluster Scheduling in High Performance Computing
• Simulation of LHC events on a millions threads
• Parallel streaming between heterogeneous HPC resources for real-time analysis
• Scalable parallel I/O on a blue Gene/Q supercomputer using compression, topology-aware data aggregation, and subfiling
• Examples of in transit visualization
• Experiences using Smaash to manage data-intensive simulations
• Using dynamic accounts to enable access to advanced resources through science gateways
• Distributed and hardware accelerated computing for clinical medical imaging using proton computed tomography (pCT)
• Early experience on the Blue Gene/Q supercomputing system
• Integrating dynamic pricing of electricity into energy aware scheduling for HPC systems
• Modeling resource-coupled computations
• Characterization and modeling of PIDX parallel I/O for performance optimization
• Measuring power consumption on IBM Blue Gene/Q
• A new computational paradigm in multiscale simulations: Application to brain blood flow
• Characterization and understanding machine-specific interconnects
• Interactive large data exploration over the wide area
• Visualization of multiscale simulation data: Brain blood flow
• Accelerating science gateway development with web 2.0 and swift
• ALCF MPI benchmarks: Understanding machine-specific communication behavior
• Visualizing large-scale atomistic simulations in ultra-resolution immersive environments
• Efficient parallel volume rendering of large-scale adaptive mesh refinement data
• Volume rendering with multidimensional peak finding
• Data-intensive management and analysis for scientific simulations
• Efficient data restructuring and aggregation for I/O acceleration in PIDX
• High-performance multiple-CPU/GPU proton computed tomography
• Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics): Preface
• Molecular dynamics simulation of amorphous SiO2fracture
• Enabling scientific teamwork
• Full-resolution interactive CPU volume rendering with coherent BVH traversal
• Accelerating I/O forwarding in IBM Blue Gene/P systems
• Scalable in situ scientific data encoding for analytical query processing
• New frontiers in leadership computing [guest editorial]
• A generic high-performance method for deinterleaving scientific data
• An Analysis of a distributed gpu implementation of proton computed tomographic (pct) reconstruction
• Abstract: Evaluating communication performance in BlueGene/Q and Cray XE6 supercomputers
• Ray tracing and volume rendering large molecular data on multi-core and many-core architectures
• Toward simulation-time data analysis and I/O acceleration on leadership-class systems
• Exploring large data over wide area networks
• Towards parallel access of multi-dimensional, multi-resolution scientific data
• Modeling early galaxies using radiation hydrodynamics
• Visualizing multiscale, multiphysics simulation data: Brain blood flow
• Web 2.0-based social informatics data grid
• A simultaneous 2D/3D autostereo workstation
• RBF volume ray casting on multicore and manycore CPUs
• Visualizing large, heterogeneous data in hybrid-reality environments
• Tightly coupled atomistic-continuum simulations of brain blood flow on Petaflop supercomputers
• A web 2.0-based scientific application framework
• The international exascale software project roadmap
• Collaboration as a second thought
• A solution looking for lots of problems: Generic portals for science infrastructure
• Electronic poster: Visualizing multiscale simulation data
• Topology-aware data movement and staging for I/O acceleration on Blue Gene/P supercomputing systems
• Proceedings of the 2009 Workshop on Ultrascale Visualization, UltraVis '09: Preface
• Real time change detection and alerts from highway traffic data
• High-resolution remote rendering of large datasets in a collaborative environment
• CupHolder: A multi-person interactive high-resolution workstation
• An infrastructure of network services for seamless integration in advanced collaborative computing environments
• Building the US National Fusion Grid: Results from the National Fusion Collaboratory Project
• Performance metrics of IP multicast sessions
• Large-scale data visualization using parallel data streaming
• Streaming visualization for collaborative environments
• Extending multicast communications by hybrid overlay network
• Simulation of neocortical epileptiform activity using parallel computing
• Terascale turbulence computation using the FLASH3 application framework on the IBM Blue Gene/L system
• Simulating and visualizing the human arterial system on the TeraGrid
• Toward an OpenSocial Life Science Gateway
• Immersive virtual anatomy course using a cluster of volume visualization machines and passive stereo
• Developing a distributed collaborative radiological visualization application
• Distributed collaborative radiological visualization using Access Grid
• Overview of the I-way: Wide-area visual supercomputing
• Genetic programming application in virtual reality
• UbiWorld: an environment integrating virtual reality, supercomputing and design
• Genetic programming application in virtual reality
• TeraGrid: Analysis of organization, system architecture, and middleware enabling new types of applications
• Tools for distributed collaborative environments: a research agenda
• Capability matching of data streams with network services
• Multi-parallel open technology to enable collaborative volume visualization: How to create global immersive virtual anatomy classrooms
• FLASH. Applications and future
• SIDGrid: A framework for distributed, integrated multimodal annotation, archiving, and analysis
• Developments in remote collaboration and computation
• Designing the Future of Collaborative Science: Argonne’s Futures Laboratory
• Interactive virtual reality in simulations: Exploring lag time
• Workshop on ultra-scale visualization
• Prototyping the workspaces of the future
• The data analysis computing hierarchy
• Grid support for collaborative control room in fusion science
• Numerical simulation and immersive visualization of hairpin vortices
• Grids for experimental science: The virtual control room
• Runtime visualization of the human arterial tree
• GridMapper: A tool for visualizing the behavior of large-scale distributed systems
• Enabling community access to TeraGrid visualization resources
• UbiWorld: An environment integrating virtual reality, supercomputing, and design
• Leveraging national laboratories to increase Black representation in STEM: recommendations within the Department of Energy
• ChemoGraph: Interactive Visual Exploration of the Chemical Space
• The State of the Art in Visualizing Dynamic Multivariate Networks
• An Edge Map based Ensemble Solution to Detect Water Level in Stream
• Hybrid workload scheduling on HPC systems
• BFTrainer: Low-cost training of neural networks on unfillable supercomputer nodes
• Toward real-time analysis of experimental science workloads on geographically distributed supercomputers
• Deep reinforcement agent for scheduling in HPC
• Direct Ordering: A Direct Manipulation Based Ordering Technique
• Scheduling beyond CPUs for HPC
• Balsam: Automated scheduling and execution of dynamic, data-intensive HPC workflows
• PxStream: Remote Visualization for Distributed Rendering Frameworks
• In situ visualization of performance metrics in multiple domains
• Corrigendum to “viewSq, a Visual Molecular Dynamics (VMD) module for calculating, analyzing, and visualizing X-ray and neutron structure factors from atomistic simulations” [Comput. Phys. Commun. 264 (2021) 107881] (Computer Physics Communications (2021) 264, (S0010465521000345), (10.1016/j.cpc.2021.107881))
• Balsam: Near real-time experimental data analysis on supercomputers
• Supercomputing Improves Predictions of Fluid Flow in Rock
• Massive Data Visualization Techniques for use in Virtual Reality Devices
• Petrel: A programmatically accessible research data service
• Hybrid Workload Scheduling on HPC Systems
• Encoding for Reinforcement Learning Driven Scheduling
• A Comprehensive Evaluation of Novel AI Accelerators for Deep Learning Workloads
• Measuring cities with software-defined sensors
• Characterization and identification of HPC applications at leadership computing facility
• GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics
• Distributed Neural Representation for Reactive in situ Visualization
• Cinema Transfer: A Containerized Visualization Workflow
• Evaluating Gradient Perception in Color-Coded Scalar Fields
• Toward Bi-directional In Situ Visualization and Analysis of Blood Flow Simulations With Dynamic Deforming Walls
• Spack meets singularity: Creating movable in-situ analysis stacks with EASE
• Toward an In-Depth Analysis of Multifidelity High Performance Computing Systems
• MRSch: Multi-Resource Scheduling for HPC
• Linking scientific instruments and computation: Patterns, technologies, and experiences
• Resource-Aware Optimal Scheduling of In Situ Analysis
• The U.S. High-Performance Computing Consortium in the Fight against COVID-19
• Color Nameability Predicts Inference Accuracy in Spatial Visualizations
• Instrumenting Multiphysics Blood Flow Simulation Codes for In Situ Visualization and Analysis
• GPU-based Image Compression for Efficient Compositing in Distributed Rendering Applications
• Accelerating Scientific Applications with SambaNova Reconfigurable Dataflow Architecture
• Interactive Virtual Reality Exploration of Large-Scale Datasets Using Omnidirectional Stereo Images
• Writing, Running, and Analyzing Large-scale Scientific Simulations with Jupyter Notebooks
• Topology-aware space-shared co-analysis of large-scale molecular dynamics simulations
• Deep reinforcement agent for scheduling in HPC
• Scheduling beyond CPUs for HPC
• Real-Time Omnidirectional Stereo Rendering: Generating 360° Surround-View Panoramic Images for Comfortable Immersive Viewing
• Predicting the Risk of Cancer with Computational Electrodynamics
• Linking Scientific Instruments and HPC: Patterns, Technologies, Experiences
• MELA: A visual analytics tool for studying multifidelity HPC system logs
• Molecular dynamics simulation of amorphous SiO2 fracture
• Exploring features for predicting policy citations
• Blue gene/q: Sequoia and mira
• Exploring Visualization Techniques with HACC Simulation Data
• System-wide trade-off modeling of performance, power, and resilience on petascale systems
• Automatic between-pulse analysis of DIII-D experimental data performed remotely on a supercomputer at argonne leadership computing facility
• Scalable in situ analysis of molecular dynamics simulations
• Virtual reality tools for the correction of automated volume segmentation errors using dense surface reconstructions
• Scientists in wonderland: A report on visualization applications in the CAVE virtual reality environment
• Libis: A lightweight library for flexible in transit visualization
• A Visual Analytics System for Optimizing Communications in Massively Parallel Applications
• RAM as a network managed resource
• Transferring data from high-performance simulations to extreme scale analysis applications in real-time
• In Situ Visualization and Analysis to Design Large Scale Experiments in Computational Fluid Dynamics
• Mixed precision: A strategy for new science opportunities
• Active Research Data Management with the Django Globus Portal Framework
• Scaling Computational Fluid Dynamics: In Situ Visualization of NekRS using SENSEI
• MalleTrain: Deep Neural Networks Training on Unfillable Supercomputer Nodes
• Color Maker: a Mixed-Initiative Approach to Creating Accessible Color Maps
• Image Synthesis from a Collection of Depth Enhanced Panoramas: Creating Interactive Extended Reality Experiences from Static Images
• DEMAC: A Platform for Education in High-performance Computing, Bridging the Gap Between Users and Hardware
• Distributed Neural Representation for Reactive In Situ Visualization
• 2023 IEEE Scientific Visualization Contest Winner: VisAnywhere: Developing Multi-platform Scientific Visualization Applications
• Trust Your Gut: Comparing Human and Machine Inference from Noisy Visualizations