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Title: Efficient LiDAR point cloud data encoding for scalable data management within the Hadoop eco-system
This paper introduces a novel LiDAR point cloud data encoding solution that is compact, flexible, and fully supports distributed data storage within the Hadoop distributed computing environment. The proposed data encoding solution is developed based on Sequence File and Google Protocol Buffers. Sequence File is a generic splittable binary file format built in the Hadoop framework for storage of arbitrary binary data. The key challenge in adopting the Sequence File format for LiDAR data is in the strategy for effectively encoding the LiDAR data as binary sequences in a way that the data can be represented compactly, while allowing necessary mutation. For that purpose, a data encoding solution, based on Google Protocol Buffers (a language-neutral, cross-platform, extensible data serialisation framework) was developed and evaluated. Since neither of the underlying technologies is sufficient to completely and efficiently represent all necessary point formats for distributed computing, an innovative fusion of them was required to provide a viable data storage solution. This paper presents the details of such a data encoding implementation and rigorously evaluates the efficiency of the proposed data encoding solution. Benchmarking was done against a straightforward, naive text encoding implementation using a high-density aerial LiDAR scan of a portion of Dublin, Ireland. The results demonstrated a 6-times reduction in data volume, a 4-times reduction in database ingestion time, and up to a 5 times reduction in querying time.  more » « less
Award ID(s):
1826134
NSF-PAR ID:
10205029
Author(s) / Creator(s):
; ; ; ; ; ; ;
Date Published:
Journal Name:
2019 IEEE International Conference on Big Data
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
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    Version: 2.0

    Changes versus version 1.0 are the addition of the free energy of folding, adsorption, and pairing calculations (Sim_Figure-7) and shifting of the figure numbers to accommodate this addition.


    Conventions Used in These Files
    ===============================

    Structure Files
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    - graph_*.psf or sol_*.psf (original NAMD (XPLOR?) format psf file including atom details (type, charge, mass), as well as definitions of bonds, angles, dihedrals, and impropers for each dipeptide.)

    - graph_*.pdb or sol_*.pdb (initial coordinates before equilibration)
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    Force Field Parameters
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    CHARMM format parameter files:
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    - toppar_water_ions_prot_cgenff.str (CHARMM water and ions with NBFIX parameters needed for protein and CGenFF included and others commented out)

    Template NAMD Configuration Files
    ---------------------------------
    These contain the most commonly used simulation parameters. They are called by the other NAMD configuration files (which are in the namd/ subdirectory):
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    - template_abf.namd (for adaptive biasing force)

    Minimization
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    - namd/min_*.0.namd

    Equilibration
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    - namd/eq_*.0.namd

    Adaptive biasing force calculations
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    - namd/eabfZRest7_graph_chp1404.0.namd
    - namd/eabfZRest7_graph_chp1404.1.namd (continuation of eabfZRest7_graph_chp1404.0.namd)

    Log Files
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    For each NAMD configuration file given in the last two sections, there is a log file with the same prefix, which gives the text output of NAMD. For instance, the output of namd/eabfZRest7_graph_chp1404.0.namd is eabfZRest7_graph_chp1404.0.log.

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    CONTENTS
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    Sim_Figure-4: Simulation of four peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) at the graphite–water interface at 370 K.

    Sim_Figure-5: Simulation of four peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) at the graphite–water interface at 295 K.

    Sim_Figure-5_replica: Temperature replica exchange molecular dynamics simulations for the peptide cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) with 20 replicas for temperatures from 295 to 454 K.

    Sim_Figure-6: Simulation of the peptide molecule cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) in free solution (no graphite).

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    Sim_Figure-9: Two replicates of a simulation of nine peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) at the graphite–water interface at 370 K.

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    Sim_Figure-10: Adaptive biasing for calculation of the free energy of the folded peptide as a function of the angle between its long axis and the zigzag directions of the underlying graphene sheet.

     

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