ArrayBridge: Interweaving declarative array processing with high-performance computing

Scientists are increasingly turning to datacenter-scale computers to produce and analyze massive arrays. Despite decades of database research that extols the virtues of declarative query processing, scientists still write, debug and parallelize imperative HPC kernels even for the most mundane queries. This impedance mismatch has been partly attributed to the cumbersome data loading process; in response, the database community has proposed in situ mechanisms to access data in scientific file formats. Scientists, however, desire more than a passive access method that reads arrays from files. This paper describes ArrayBridge, a bi-directional array view mechanism for scientific file formats, that aims to make declarative array manipulations interoperable with imperative file-centric analyses. Our prototype implementation of ArrayBridge uses HDF5 as the underlying array storage library and seamlessly integrates into the SciDB open-source array database system. In addition to fast querying over external array objects, ArrayBridge produces arrays in the HDF5 file format just as easily as it can read from it. ArrayBridge also supports time travel queries from imperative kernels through the unmodified HDF5 API, and automatically deduplicates between array versions for space efficiency. Our extensive performance evaluation in NERSC, a large-scale scientific computing facility, shows that ArrayBridge exhibits statistically indistinguishable performance and I/O scalability to the native SciDB storage engine.Comment: 12 pages, 13 figure

Novel gene rearrangement pattern in mitochondrial genome of Ooencyrtus plautus Huang & Noyes, 1994: new gene order in Encyrtidae (Hymenoptera, Chalcidoidea)

Studies of mitochondrial genomes have a wide range of applications in phylogeny, population genetics, and evolutionary biology. In this study, we sequenced and analyzed the mitochondrial genome of Ooencyrtus plautus Huang & Noyes, 1994 (Hymenoptera, Encyrtidae). The nearly complete mitogenome of O. plautus was 15,730 bp in size, including 13 PCGs (protein-coding genes), 22 tRNAs, 2 rRNAs, and a nearly complete control region. The nucleotide composition was significantly biased toward adenine and thymine, with an A + T content of 84.6%. We used the reference sequence of Chouioia cunea and calculated the Ka/Ks ratio for each set of PCGs. The highest value of the Ka/Ks ratio within 13 PCGs was found in nad2 with 1.1, suggesting that they were subjected to positive selection. This phenomenon was first discovered in Encyrtidae. Compared with other encyrtid mitogenomes, a translocation of trnW was found in O. plautus, which was the first of its kind to be reported in Encyrtidae. Comparing with ancestral arrangement pattern, wasps reflect extensive gene rearrangements. Although these insects have a high frequency of gene rearrangement, species from the same family and genus tend to have similar gene sequences. As the number of sequenced mitochondrial genomes in Chalcidoidea increases, we summarize some of the rules of gene rearrangement in Chalcidoidea, that is four gene clusters with frequent gene rearrangements. Ten mitogenomes were included to reconstruct the phylogenetic trees of Encyrtidae based on both 13 PCGs (nucleotides of protein coding genes) and AA matrix (amino acids of protein coding genes) using the maximum likelihood and Bayesian inference methods. The phylogenetic tree reconstructed by Bayesian inference based on AA data set showed that Aenasius arizonensis and Metaphycus eriococci formed a clade representing Tetracneminae. The remaining six species formed a monophyletic clade representing Encyrtinae. In Encyrtinae, Encyrtus forms a monophyletic clade as a sister group to the clade formed by O. plautus and Diaphorencyrtus aligarhensis. Encyrtus sasakii and Encyrtus rhodooccisiae were most closely related species in this monophyletic clade. In addition, gene rearrangements can provide a valuable information for molecular phylogenetic reconstruction. These results enhance our understanding of phylogenetic relationships among Encyrtidae

Data and Code.zip

The data and code of the paper titled "A prototype-based sampling method for spatial data sampling and its application in landslide susceptibility mapping".</p

ArrayBridge: Interweaving declarative array processing with high-performance computing

Scientists are increasingly turning to datacenter-scale computers to produce and analyze massive arrays. Despite decades of database research that extols the virtues of declarative query processing, scientists still write, debug and parallelize imperative HPC kernels even for the most mundane queries. This impedance mismatch has been partly attributed to the cumbersome data loading process; in response, the database community has proposed in situ mechanisms to access data in scientific file formats. Scientists, however, desire more than a passive access method that reads arrays from files. This paper describes ArrayBridge, a bi-directional array view mechanism for scientific file formats, that aims to make declarative array manipulations interoperable with imperative file-centric analyses. Our prototype implementation of ArrayBridge uses HDF5 as the underlying array storage library and seamlessly integrates into the SciDB open-source array database system. In addition to fast querying over external array objects, ArrayBridge produces arrays in the HDF5 file format just as easily as it can read from it. ArrayBridge also supports time travel queries from imperative kernels through the unmodified HDF5 API, and automatically deduplicates between array versions for space efficiency. Our extensive performance evaluation in NERSC, a large-scale scientific computing facility, shows that ArrayBridge exhibits statistically indistinguishable performance and I/O scalability to the native SciDB storage engine

Landslide susceptibility assessment in the Anfu County, China: comparing different statistical and probabilistic models considering the new topo-hydrological factor (HAND)

The present study is aimed at producing landslide susceptibility map of a landslide-prone area (Anfu County, China) by using evidential belief function (EBF), frequency ratio (FR) and Mahalanobis distance (MD) models. To this aim, 302 landslides were mapped based on earlier reports and aerial photographs, as well as, carrying out several field surveys. The landslide inventory was randomly split into a training dataset (70%; 212landslides) for training the models and the remaining (30%; 90 landslides) was cast off for validation purpose. A total of sixteen geo-environmental conditioning factors were considered as inputs to the models: slope degree, slope aspect, plan curvature, profile curvature, the new topo-hydrological factor termed height above the nearest drainage (HAND), average annual rainfall, altitude, distance from rivers, distance from roads, distance from faults, lithology, normalized difference vegetation index (NDVI), sediment transport index (STI), stream power index (SPI), soil texture, and land use/cover. The validation of susceptibility maps was evaluated using the area under the receiver operating characteristic curve (AUROC). As a results, the FR outperformed other models with an AUROC of 84.98%, followed by EBF (78.63%) and MD (78.50%) models. The percentage of susceptibility classes for each model revealed that MD model managed to build a compendious map focused at highly susceptible areas (high and very high classes) with an overall area of approximately 17%, followed by FR (22.76%) and EBF (31%). The premier model (FR) attested that the five factors mostly influenced the landslide occurrence in the area: NDVI, soil texture, slope degree, altitude, and HAND. Interestingly, HAND could manifest clearer pattern with regard to landslide occurrence compared to other topo-hydrological factors such as SPI, STI, and distance to rivers. Lastly, it can be conceived that the susceptibility of the area to landsliding is more subjected to a complex environmental set of factors rather than anthropological ones (residential areas and distance to roads). This upshot can make a platform for further pragmatic measures regarding hazard-planning actions

Progressive failure simulation of notched tensile specimen for triaxially-braided composites

The mechanical characterization of textile composites is a challenging task, due to their nonuniform deformation and complicated failure phenomena. This article introduces a three-dimensional mesoscale finite element model to investigate the progressive damage behavior of a notched single-layer triaxially-braided composite subjected to axial tension. The damage initiation and propagation in fiber bundles are simulated using three-dimensional failure criteria and damage evolution law. A traction-separation law has been applied to predict the interfacial damage of fiber bundles. The proposed model is correlated and validated by the experimentally measured full field strain distributions and effective strength of the notched specimen. The progressive damage behavior of the fiber bundles is studied by examining the damage and stress contours at different loading stages. Parametric numerical studies are conducted to explore the role of modeling parameters and geometric characteristics on the internal damage behavior and global measured properties of the notched specimen. Moreover, the correlations of damage behavior, global stress-strain response, and the efficiency of the notched specimen are discussed in detail. The results of this paper deliver a throughout understanding of the damage behavior of braided composites and can help the specimen design of textile composites.Structural Integrity & Composite