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README.md

README.md

#ADI

ARM Data Integrator, ADI, is an open source framework that automates the process of retrieving and preparing data for analysis, simplifies the design and creation of output data products produced by the analysis, and provides a modular, flexible software development architecture for implementing algorithms. These capabilities are supported through the use of a workflow for data integration, a source code generator that produces C, IDL and Python templates, and a graphical interface through which users can efficiently define their data input, preprocessing, and output characteristics.

ADI is used by the Atmospheric Radiation Measurement (ARM) Climate Research Facility to process raw data collected from ARM instruments, and to implement scientific algorithms that process one or more of ARM's existing data products to produce new, higher value, data products.

To Install ADI:

  • Install the requisite perl moduels. Run the following commands in a terminal. Accept all defaults to configure cpan. If you have to configure cspan you may need to repeat the install of JSON::XS
    • sudo cpan JSON::XS
    • sudo cpan CGI::Session
  • Install Homebrew if it's not already installed (http://brew.sh). Note it is good to do this within a bash terminal.
  • If you have installed a previous version execute the following
    • brew uninstall adi
    • brew untap arm-doe/adi
    • brew tap arm-doe/adi
    • brew tap homebrew/science
    • brew fetch --force adi
    • brew install adi
  • Otherwise for a first installation
    • if installing on El Capitan (OSX 10.11.x) install openssl brew install git --with-brewed-openssl
    • brew tap homebrew/science
    • brew tap arm-doe/adi
    • brew install adi
  • For Python programmers:
    • First, ensure your default version of Python is python 2.7, and has numpy and Cython installed. The easiest way to do this for new users is to install Anaconda.

    • If you have just installed Anaconda, be sure to restart your bash terminal session so that the new python version has been added to your path. Running python --version should show something like

      Python 2.7.10 :: Anaconda 2.3.0 (x86_64).

    • Download the adi python package from here

    • untar the file, and from inside it, run:

    • python setup.py install

    • This should install the ADI libraries for whichever is your default version of python.

  • For IDL programmers:
    • Requires ENVI/IDL which requies Java 6 and XQauartz. Note that on OS 10.11 El Capitan you need to install the Apple supports version of Java 6 from https://support.apple.com/kb/DL1572?locale=en_US
    • down the idl ADI libs from here.
    • unzip, untar, then move all the files downloaded into /usr/local/lib

Set Up an Environment for ADI

  • Download adi_home. This tarfile contains a directory structure to get you started running ADI quickly. Note that you can also configure the directory structure however you like on your own.

    A bit of explanation here: ADI's VAPs expect certain directories and environment variables to be present, so to run VAPs, you must re-create these directories and environment variables. adi_home gets this started for you; it contains all the directories needed to run vaps, and provides the required environment variables in the file env_vars. You can use the example1 vap to verify the ADI installation worked properly.

  • untar the file and copy the resulting adi_home directory to somewhere you want to work from, say, ~/Documents or your home directory in /Users, i.e. ~. These instructions will assume you copied it into ~.

  • A core database named dsdb has been provided in /usr/local/share. Create the directory path:

    • mkdir -p ~/adi_home/data/db/sqlite
  • Copy the core dsdb into it

    • cp /usr/local/share/dsdb/*core.sqlite ~/adi_home/data/db/sqlite/dsdb.sqlite
  • Enter your home directory and create a new file named .db_connect with the following entries

    • dsdb_data sqlite <your_home_directory>/adi_home/data/db/sqlite/dsdb.sqlite
    • dsdb_read sqlite <your_home_directory>/adi_home/data/db/sqlite/dsdb.sqlite
  • Enter the untarred adi_home directory

  • To set the required environment variables for running from ~/adi_home, cat ~/adi_home/env_vars_bash, and copy all the commands into your bash terminal. Later you may want to add these environment variables to your .bash_profile, as THESE WILL HAVE TO BE SET EACH TIME YOU ENTER A NEW TERMINAL. You will probably want to update ~/adi_home/env_vars_bash to set the locations explicitly so you can run your process from any location rather than from ~/adi_home.

  • Setup the example vap process:

    • go into /adi_home/dev/vap/src/adi_example1/process_dod_defs
    • import the process by running db_import_process -a dsdb_data -fmt json adi_example1.json
    • import the output data definitions by running db_load_dod -a dsdb_data cpc.json and db_load_dod -a dsdb_data met.json
  • Run C version of example1

    • Each time you open a new bash terminal you will need to setup the environment variables
      • source ~/adi_home/env_vars_bash
    • go to the ~/adi_home/dev/vap/src/adi_example1 directory
    • run make clean; make. If successful the binary ~/adi_home/dev/vap/bin/adi_example1_vap will be created.
    • run adi_example1_vap -s sbs -f S2 -b 20110401 -e 20110402 -D 2 -R this should complete successfully with an exit status of zero.
    • The output data created are: ~/adi_home/data/datastream/sbs/sbsadicpcexample1S2.a1/sbsadicpcexample1S2.a1.20110401.000000.cdf ~/adi_home/data/datastream/sbs/sbsadimetexample1S2.a1/sbsadimetexample1S2.a1.20110401.000000.cdf
  • Run Python version of example1

    • Each time you open a new bash terminal you will need to setup the environment variables
      • source ~/adi_home/env_vars_bash
    • go to the ~/adi_home/dev/vap/src/adi_example1_py directory
    • run `python adi_example1_vap.py -s sbs -f S2 -b 20110401 -e 20110402 -D 2 -R'
    • The output data created is the same as for the C run: ~/adi_home/data/datastream/sbs/sbsadicpcexample1S2.a1/sbsadicpcexample1S2.a1.20110401.000000.cdf ~/adi_home/data/datastream/sbs/sbsadimetexample1S2.a1/sbsadimetexample1S2.a1.20110401.000000.cdf
  • Run IDL version of example1

    • If its first time you running an ADI process, from an IDL prompt:
      • IDL> pref_set, 'idl_path','<IDL_DEFAULT>:/usr/local/lib',/commit
      • IDL> pref_set, 'idl_dlm_path','<IDL_DEFAULT>:/usr/local/lib',/commit
    • Each time you open a new terminal you will need to setup idl and the environment variables
      • source /Applications/exelis/idl84/bin/idl_setup.bash
      • source ~/adi_home/env_vars_bash
    • go to the ~/adi_home/dev/vap/src/adi_example1_idl directory
    • run $> idl -e "adi_example1_vap" -args -s sbs -f S2 -b 20110401 -e 20110402 -D 2
    • or to run in debug mode
      • $> idl -args -s sbs -f S2 -b 20110401 -e 20110402 -D 2 -R
      • $IDL> adi_example1_vap
    • The output data created is the same as for the C run: ~/adi_home/data/datastream/sbs/sbsadicpcexample1S2.a1/sbsadicpcexample1S2.a1.20110401.000000.cdf ~/adi_home/data/datastream/sbs/sbsadimetexample1S2.a1/sbsadimetexample1S2.a1.20110401.000000.cdf

To Add More Process Definitions to the DSDB:

The process definitions for adi_example1 have been included in your adi_home area. To run additional VAPs against your local database, you will need to import their process information.

  • Get the process definition from the PCM
    • Go to the Processing Configuration Manager and select the processes tab on the left hand side
    • Type the name of the process you want in the filter at the bottom, or find it by scrolling through the list
    • Double click the name of the process to bring it up on the right hand side
    • Click Text Export/Import in the lower right corner, and copy the text that appears to a file on your machine
  • Set your enviornment variables as specified in env_vars_bash from the last section
  • run db_import_process for the definition you retrieved
    • db_import_process -a dsdb_data -fmt json <process definition file name>
  • Load the DODs nessecary to run this process. The DODs used by a process are listed on that process's page in the PCM.
    • Load the DOD into the PCM datastream viewer.
    • Select the JSON format from the green export DOD icon at the top of the page to copy the DOD to your clipboard. Copy this into a file on your local machine
    • Load the dods into the local database
      • db_load_dod -a dsdb_data <dod file>

Important Links

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