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Reproduction of the computations on the article "Amazon Forest Green-Up During 2005 Drought"

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amazonGreenUp2005

Reproduction of the computations on the article "Amazon Forest Green-Up During 2005 Drought"

Pre-requisites:

  • Docker.io
  • SSH
  • Internet access

Files:

  • LICENSE - License file.
  • README.md - This file.
  • <li>Docker-related files
    <ul>
    	<li><code>setup.sh</code> - (host) Script for generating a docker image.</li>
    	<li><code>Dockerfile</code> - (host) Docker file for building a Docker Image.</li>
    </ul>
    </li>
    <li>SciDB-related files:
    <ul>
    	<li><code>conf</code> - SHIM configuration file. SHIM is SciDB's web service</li>
    	<li><code>scidb_docker_XX.ini</code> - SciDB's configuration files. Here you can control things such as the number of instances (see table below).</li>
    	<li><code>iquery.conf</code> - IQuery configuration file. IQuery is SciDB's native client able to process AQL and AFL queries.</li>
    	<li><code>startScidb.sh</code> - Script for starting SciDB.</li>
    	<li><code>stopScidb.sh</code> - Script for stopping SciDB.</li>
    	<li><code>containerSetup.sh</code> - Commands for setting up SciDB inside a container. It also creates some test data.</li>
    	<li><code>anomalyComputation.afl</code> - Array Functional Language instructions to calculate EVI2 anomalies.</li>		
    </ul>
        </li>
        <li>R scripts
    <ul>
                <li><code>anomalyHistogram.R</code> - Script for retrieving and ploting the resulting EVI2 anomaly histogram.</li>
                <li><code>exploreResults.R</code> - Script with general functions for retrieving and ploting the resulting EVI2 anomalies.</li>
                <li><code>installPackages.R</code> - R script for installing R packages.</li>
        </ul>
        </li>
    <li>Other files
    <ul>
    	<li><code>installBoost_1570.shh</code> - Install Boost libraries.</li>
    	<li><code>installGribModis2SciDB.sh</code> - Install a tool for exporting HDFs to SciDB's binary.</li>
                <li><code>installParallel.sh</code> - Script for installing parallel.Parallel allows to execute scripts at the same time.</li>
    	<li><code>install_pyhdf.sh</code> - DEPRECATED - Install an interface for enabling python to handle HDFs.</li>
    	<li><code>downloadData.R</code> - DEPRECATED - R script for downloading MODIS data from NASA website.</li>
    	<li><code>downloadData.sh</code> - DEPRECATED - Script for downloading MODIS in parallel. It is a wrapper of <code>downloadData.R</code></li>
    	<li><code>hdf2bin.sh</code> - DEPRECATED - Script for exporting HDFs to binary files. It is a wrapper of the python scripts available at <a href="http://github.com/albhasan/modis2scidb" target="_blank">modis2scidb</a>.</li>
    </ul>
    </li>
    

Instructions:

  1. Clone this project git clone https://github.com/albhasan/amazonGreenUp2005.git
  2. Setup SciDB on Docker and other required stuff:
    • Build a docker image ./setup.sh. This script will build the Docker image scidb_amazon_img and it will start the Docker container scidb_amazon1.
    • Login the SciDB Docker container scidb_amazon1 by using ssh -p 49911 root@localhost. The default password is xxxx.xxxx.xxxx
  3. Run the container script using one of the SciDB configuration file names as a parameter, for example: /home/root/./containerSetup.sh scidb_docker_2a.ini.
  4. The array with the results is MODIS_AMZ_EVI2_ANOM
  5. You can use exploreResults.R to get the computation results in R, either form the container or the host.
SciDB setup configurations files:
Name Instances per server
Max concurrent connections
CPU cores per server
GB per server
scidb_docker_1.ini 1
2 2 2
scidb_docker_2.ini 2 2 4 4
scidb_docker_2a.ini 2 2 4 8
scidb_docker_2b.ini 2 2 4 16
scidb_docker_4.ini 4 4 4 16
scidb_docker_8.ini 8 16 24 160

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