Optimizing Lossy Compression Rate-Distortion from Automatic Online Selection between SZ and ZFP

With ever-increasing volumes of scientific data produced by HPC applications, significantly reducing data size is critical because of limited capacity of storage space and potential bottlenecks on I/O or networks in writing/reading or transferring data. SZ and ZFP are the two leading lossy compressors available to compress scientific data sets. However, their performance is not consistent across different data sets and across different fields of some data sets: for some fields SZ provides better compression performance, while other fields are better compressed with ZFP. This situation raises the need for an automatic online (during compression) selection between SZ and ZFP, with a minimal overhead. In this paper, the automatic selection optimizes the rate-distortion, an important statistical quality metric based on the signal-to-noise ratio. To optimize for rate-distortion, we investigate the principles of SZ and ZFP. We then propose an efficient online, low-overhead selection algorithm that predicts the compression quality accurately for two compressors in early processing stages and selects the best-fit compressor for each data field. We implement the selection algorithm into an open-source library, and we evaluate the effectiveness of our proposed solution against plain SZ and ZFP in a parallel environment with 1,024 cores. Evaluation results on three data sets representing about 100 fields show that our selection algorithm improves the compression ratio up to 70% with the same level of data distortion because of very accurate selection (around 99%) of the best-fit compressor, with little overhead (less than 7% in the experiments).Comment: 14 pages, 9 figures, first revisio

MGARD+: Optimizing Multilevel Methods for Error-Bounded Scientific Data Reduction

Nowadays, data reduction is becoming increasingly important in dealing with the large amounts of scientific data. Existing multilevel compression algorithms offer a promising way to manage scientific data at scale but may suffer from relatively low performance and reduction quality. In this paper, we propose MGARD+, a multilevel data reduction and refactoring framework drawing on previous multilevel methods, to achieve high-performance data decomposition and high-quality error-bounded lossy compression. Our contributions are four-fold: 1) We propose to leverage a level-wise coefficient quantization method, which uses different error tolerances to quantize the multilevel coefficients. 2) We propose an adaptive decomposition method which treats the multilevel decomposition as a preconditioner and terminates the decomposition process at an appropriate level. 3) We leverage a set of algorithmic optimization strategies to significantly improve the performance of multilevel decomposition/recompositing. 4) We evaluate our proposed method using four real-world scientific datasets and compare with several state-of-the-art lossy compressors. Experiments demonstrate that our optimizations improve the decomposition/recompositing performance of the existing multilevel method by up to $70 \times$70x, and the proposed compression method can improve compression ratio by up to $2 \times$2x compared with other state-of-the-art error-bounded lossy compressors under the same level of data distortion

Atomic electron tomography in three and four dimensions

Atomic electron tomography (AET) has become a powerful tool for atomic-scale structural characterization in three and four dimensions. It provides the ability to correlate structures and properties of materials at the single-atom level. With recent advances in data acquisition methods, iterative three-dimensional (3D) reconstruction algorithms, and post-processing methods, AET can now determine 3D atomic coordinates and chemical species with sub-Angstrom precision, and reveal their atomic-scale time evolution during dynamical processes. Here, we review the recent experimental and algorithmic developments of AET and highlight several groundbreaking experiments, which include pinpointing the 3D atom positions and chemical order/disorder in technologically relevant materials and capturing how atoms rearrange during early nucleation at four-dimensional atomic resolution

A Hybrid In Situ Approach for Cost Efficient Image Database Generation

The visualization of results while the simulation is running is increasingly common in extreme scale computing environments. We present a novel approach for in situ generation of image databases to achieve cost savings on supercomputers. Our approach, a hybrid between traditional inline and in transit techniques, dynamically distributes visualization tasks between simulation nodes and visualization nodes, using probing as a basis to estimate rendering cost. Our hybrid design differs from previous works in that it creates opportunities to minimize idle time from four fundamental types of inefficiency: variability, limited scalability, overhead, and rightsizing. We demonstrate our results by comparing our method against both inline and in transit methods for a variety of configurations, including two simulation codes and a scaling study that goes above 19K cores. Our findings show that our approach is superior in many configurations. As in situ visualization becomes increasingly ubiquitous, we believe our technique could lead to significant amounts of reclaimed cycles on supercomputers.</p

Integrating and Visualizing Tropical Cyclone Data Using the Real Time Mission Monitor

The Real Time Mission Monitor (RTMM) is a visualization and information system that fuses multiple Earth science data sources, to enable real time decision-making for airborne and ground validation experiments. Developed at the NASA Marshall Space Flight Center, RTMM is a situational awareness, decision-support system that integrates satellite imagery, radar, surface and airborne instrument data sets, model output parameters, lightning location observations, aircraft navigation data, soundings, and other applicable Earth science data sets. The integration and delivery of this information is made possible using data acquisition systems, network communication links, network server resources, and visualizations through the Google Earth virtual globe application. RTMM is extremely valuable for optimizing individual Earth science airborne field experiments. Flight planners, scientists, and managers appreciate the contributions that RTMM makes to their flight projects. A broad spectrum of interdisciplinary scientists used RTMM during field campaigns including the hurricane-focused 2006 NASA African Monsoon Multidisciplinary Analyses (NAMMA), 2007 NOAA-NASA Aerosonde Hurricane Noel flight, 2007 Tropical Composition, Cloud, and Climate Coupling (TC4), plus a soil moisture (SMAP-VEX) and two arctic research experiments (ARCTAS) in 2008. Improving and evolving RTMM is a continuous process. RTMM recently integrated the Waypoint Planning Tool, a Java-based application that enables aircraft mission scientists to easily develop a pre-mission flight plan through an interactive point-and-click interface. Individual flight legs are automatically calculated "on the fly". The resultant flight plan is then immediately posted to the Google Earth-based RTMM for interested scientists to view the planned flight track and subsequently compare it to the actual real time flight progress. We are planning additional capabilities to RTMM including collaborations with the Jet Propulsion Laboratory in the joint development of a Tropical Cyclone Integrated Data Exchange and Analysis System (TC IDEAS) which will serve as a web portal for access to tropical cyclone data, visualizations and model output

Improving accuracy of total knee component cementation: description of a simple technique

<p>Abstract</p> <p>Background</p> <p>Total knee arthroplasty represents a common orthopedic surgical procedure. Achieving proper alignment of its components with the predrilled patellar and tibial peg holes prior to polymerization of the bone cement can be challenging.</p> <p>Technique</p> <p>After establishing the femoral, patellar and tibial bone cuts, the cancellous bone around the tibial keel, as well as the peg holes for the patella and femoral components are marked with methylene blue using a cotton swab stick. If bone cement is then placed onto the cut and marked bone edges, the methylene blue leaches through the bone cement and clearly outlines the tibial keel and predrilled femoral and patellar peg holes. This allows excellent visualization of the bone preparations for each component, ensuring safe and prompt positioning of TKA components while minimizing intraoperative difficulties with component alignment while the cement hardens.</p> <p>Conclusion</p> <p>The presented technical note helps to improve the accuracy and ease of insertion when the components of total knee arthroplasty are impacted to their final position.</p

Artifact-Based Rendering: Harnessing Natural and Traditional Visual Media for More Expressive and Engaging 3D Visualizations

We introduce Artifact-Based Rendering (ABR), a framework of tools, algorithms, and processes that makes it possible to produce real, data-driven 3D scientific visualizations with a visual language derived entirely from colors, lines, textures, and forms created using traditional physical media or found in nature. A theory and process for ABR is presented to address three current needs: (i) designing better visualizations by making it possible for non-programmers to rapidly design and critique many alternative data-to-visual mappings; (ii) expanding the visual vocabulary used in scientific visualizations to depict increasingly complex multivariate data; (iii) bringing a more engaging, natural, and human-relatable handcrafted aesthetic to data visualization. New tools and algorithms to support ABR include front-end applets for constructing artifact-based colormaps, optimizing 3D scanned meshes for use in data visualization, and synthesizing textures from artifacts. These are complemented by an interactive rendering engine with custom algorithms and interfaces that demonstrate multiple new visual styles for depicting point, line, surface, and volume data. A within-the-research-team design study provides early evidence of the shift in visualization design processes that ABR is believed to enable when compared to traditional scientific visualization systems. Qualitative user feedback on applications to climate science and brain imaging support the utility of ABR for scientific discovery and public communication.Comment: Published in IEEE VIS 2019, 9 pages of content with 2 pages of references, 12 figure

You can't always sketch what you want: Understanding Sensemaking in Visual Query Systems

Visual query systems (VQSs) empower users to interactively search for line charts with desired visual patterns, typically specified using intuitive sketch-based interfaces. Despite decades of past work on VQSs, these efforts have not translated to adoption in practice, possibly because VQSs are largely evaluated in unrealistic lab-based settings. To remedy this gap in adoption, we collaborated with experts from three diverse domains---astronomy, genetics, and material science---via a year-long user-centered design process to develop a VQS that supports their workflow and analytical needs, and evaluate how VQSs can be used in practice. Our study results reveal that ad-hoc sketch-only querying is not as commonly used as prior work suggests, since analysts are often unable to precisely express their patterns of interest. In addition, we characterize three essential sensemaking processes supported by our enhanced VQS. We discover that participants employ all three processes, but in different proportions, depending on the analytical needs in each domain. Our findings suggest that all three sensemaking processes must be integrated in order to make future VQSs useful for a wide range of analytical inquiries.Comment: Accepted for presentation at IEEE VAST 2019, to be held October 20-25 in Vancouver, Canada. Paper will also be published in a special issue of IEEE Transactions on Visualization and Computer Graphics (TVCG) IEEE VIS (InfoVis/VAST/SciVis) 2019 ACM 2012 CCS - Human-centered computing, Visualization, Visualization design and evaluation method