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Oloso, Amidu

Publications and source records attributed to Oloso, Amidu.

Implementing Connected Component Labeling as a User Defined Operator for SciDB

We have implemented a flexible User Defined Operator (UDO) for labeling connected components of a binary mask expressed as an array in SciDB, a parallel distributed database management system based on the array data model. This UDO is able to process very large multidimensional arrays by exploiting SciDB's memory management mechanism that efficiently manipulates arrays whose memory requirements far exceed available physical memory. The UDO takes as primary inputs a binary mask array and a binary stencil array that specifies the connectivity of a given cell to its neighbors. The UDO returns an array of the same shape as the input mask array with each foreground cell containing the label of the component it belongs to. By default, dimensions are treated as non-periodic, but the UDO also accepts optional input parameters to specify periodicity in any of the array dimensions. The UDO requires four stages to completely label connected components. In the first stage, labels are computed for each subarray or chunk of the mask array in parallel across SciDB instances using the weighted quick union (WQU) with half-path compression algorithm. In the second stage, labels around chunk boundaries from the first stage are stored in a temporary SciDB array that is then replicated across all SciDB instances. Equivalences are resolved by again applying the WQU algorithm to these boundary labels. In the third stage, relabeling is done for each chunk using the resolved equivalences. In the fourth stage, the resolved labels, which so far are "flattened" coordinates of the original binary mask array, are renamed with sequential integers for legibility. The UDO is demonstrated on a 3-D mask of O(1011) elements, with O(108) foreground cells and O(106) connected components. The operator completes in 19 minutes using 84 SciDB instances.

UDO

Addressing the Big-Earth-Data Variety Challenge with the Hierarchical Triangular Mesh

We have implemented an updated Hierarchical Triangular Mesh (HTM) as the basis for a unified data model and an indexing scheme for geoscience data to address the variety challenge of Big Earth Data. We observe that, in the absence of variety, the volume challenge of Big Data is relatively easily addressable with parallel processing. The more important challenge in achieving optimal value with a Big Data solution for Earth Science (ES) data analysis, however, is being able to achieve good scalability with variety. With HTM unifying at least the three popular data models, i.e. Grid, Swath, and Point, used by current ES data products, data preparation time for integrative analysis of diverse datasets can be drastically reduced and better variety scaling can be achieved. In addition, since HTM is also an indexing scheme, when it is used to index all ES datasets, data placement alignment (or co-location) on the shared nothing architecture, which most Big Data systems are based on, is guaranteed and better performance is ensured. Moreover, our updated HTM encoding turns most geospatial set operations into integer interval operations, gaining further performance advantages.

SciDB

Evaluating the Impact of Data Placement to Spark and SciDB with an Earth Science Use Case

We investigate the impact of data placement for two Big Data technologies, Spark and SciDB, with a use case from Earth Science where data arrays are multidimensional. Simultaneously, this investigation provides an opportunity to evaluate the performance of the technologies involved. Two datastores, HDFS and Cassandra, are used with Spark for our comparison. It is found that Spark with Cassandra performs better than with HDFS, but SciDB performs better yet than Spark with either datastore. The investigation also underscores the value of having data aligned for the most common analysis scenarios in advance on a shared nothing architecture. Otherwise, repartitioning needs to be carried out on the fly, degrading overall performance.

Spark

ldentifying Episodes of Earth Science Phenomena Using a Big-Data Technology

A significant portion of Earth Science investigations is phenomenon- (or event-) based, such as the studies of Rossby waves, volcano eruptions, tsunamis, mesoscale convective systems, and tropical cyclones. However, except for a few high-impact phenomena, e.g. tropical cyclones, comprehensive records are absent for the occurrences or events of these phenomena. Phenomenon-based studies therefore often focus on a few prominent cases while the lesser ones are overlooked. Without an automated means to gather the events, comprehensive investigation of a phenomenon is at least time-consuming if not impossible. We have constructed a prototype Automated Event Service (AES) system that is used to methodically mine custom-defined events in the reanalysis data sets of atmospheric general circulation models. Our AES will enable researchers to specify their custom, numeric event criteria using a user-friendly web interface to search the reanalysis data sets. Moreover, we have included a social component to enable dynamic formation of collaboration groups for researchers to cooperate on event definitions of common interest and for the analysis of these events. An Earth Science event (ES event) is defined here as an episode of an Earth Science phenomenon (ES phenomenon). A cumulus cloud, a thunderstorm shower, a rogue wave, a tornado, an earthquake, a tsunami, a hurricane, or an El Nino, is each an episode of a named ES phenomenon, and, from the small and insignificant to the large and potent, all are examples of ES events. An ES event has a duration (often finite) and an associated geo-location as a function of time; it's therefore an entity embedded in four-dimensional (4D) spatiotemporal space. Earth Science phenomena with the potential to cause massive economic disruption or loss of life often rivet the attention of researchers. But, broader scientific curiosity also drives the study of phenomena that pose no immediate danger, such as land/sea breezes. Due to Earth System's intricate dynamics, we are continuously discovering novel ES phenomena. We generally gain understanding of a given phenomenon by observing and studying individual events. This process usually begins by identifying the occurrences of these events. Once representative events are identified or found, we must locate associated observed or simulated data prior to commencing analysis and concerted studies of the phenomenon. Knowledge concerning the phenomenon can accumulate only after analysis has started. However, as mentioned previously, comprehensive records only exist for a very limited set of high-impact phenomena; aside from these, finding events and locating associated data currently may take a prohibitive amount of time and effort on the part of an individual investigator. The reason for the lack of comprehensive records for most of the ES phenomena is mainly due to the perception that they do not pose immediate and/or severe threat to life and property. Thus they are not consistently tracked, monitored, and catalogued. Many phenomena even lack precise and/or commonly accepted criteria for definitions. Moreover, various Earth Science observations and data have accumulated to a previously unfathomable volume; NASA Earth Observing System Data Information System (EOSDIS) alone archives several petabytes (PB) of satellite remote sensing data, which are steadily increasing. All of these factors contribute to the difficulty of methodically identifying events corresponding to a given phenomenon and significantly impede systematic investigations. We have not only envisioned AES as an environment for identifying customdefined events but also aspired for it to be an interactive environment with quick turnaround time for revisions of query criteria and results, as well as a collaborative environment where geographically distributed experts may work together on the same phenomena. A Big Data technology is thus required for the realization of such a system. In the following, we first introduce the technology selected for AES in the next section. We then demonstrate the utility of AES using a use case, Blizzard, before we conclude.

Kuo, Kwo-Sen