1.Environment configuration

This session will cover following topics

1.1. 1. Connection to the Gateway

In order to use Gateway, you have to meet following requirements:

• You have to have Gateway account (in case you don't have one, you have to request it) - refer to this link
• You have to install NX client

1.2. 2. Kepler installation

1.2.1. 2.1 Back up

Before you begin, make sure to backup all the Kepler related data in your $HOME directory

shell> cd $HOME
shell> mv kepler kepler_03.2018
shell> mv .kepler .kepler_03.2018
shell> mv KeplerData KeplerData_03.2018

After you have backed up your data, install Kepler

1.2.2. 2.2. Kepler installation

In order to install most recent release of Kepler you should execute following commands:

• Set-up KEPLER_DIR system variable

  shell> mkdir -p $ITMWORK/mykeplers
  shell> setenv KEPLER_DIR $ITMWORK/mykeplers

• List all available Kepler releases

  shell> list_keplers.sh -all
  List of available Kepler installations
  Local installations
  - local (default)
  Version based on Kepler 2.4
  - 2.4/R3_RC/local
  - 2.4/R3.13/local
  - 2.4/R3.12/local
  - 2.4/R3.11/local
  - 2.4/ETS_4.10b.10_v5.0/local
  - 2.4/ETS_4.10b.10_v5.0.3/local
  - 2.4/ETS_4.10b.10_v5.0.2/local
  - 2.4/ETS_4.10b.10_v5.0.1/local
  - 2.4/ETS_4.10b.10_v4/local
  - 2.4/ETS_4.10b.10_v4.1/local
  - 2.4/ETS_4.10b.10_v3/local
  Version based on Kepler 2.5
  - 2.5/R4_RC/local
  - 2.5/R4.0.13/local
  - 2.5/R4.0.12/local
  - 2.5/R3_RC/local
  Version based on Kepler - trunk
  - trunk/R5_RC/local
  - trunk/R5.0.13/local
  - trunk/R4_trunk/local
  - trunk/ETS_4.10b.10_v5.0/local
  - trunk/ETS_4.10b.10_v5.0.3/local
  Central installations
  - central (default)
  - rc
  Version based on Kepler 2.4
  - 2.4/R3_RC_ETS/central
  - 2.4/R3_RC_ETS2/central
  - 2.4/R3_RC/central
  - 2.4/R3.13/central
  - 2.4/R3.12/central
  - 2.4/R3.11/central
  - 2.4/ETS_4.10b.10_v5.0/central
  - 2.4/ETS_4.10b.10_v5.0.3/central
  - 2.4/ETS_4.10b.10_v5.0.2/central
  - 2.4/ETS_4.10b.10_v5.0.1/central
  - 2.4/ETS_4.10b.10_v4/central
  - 2.4/ETS_4.10b.10_v4.1/central
  - 2.4/ETS_4.10b.10_v3/central
  Version based on Kepler 2.5
  - 2.5/R4_RC/central
  - 2.5/R4.0.13/central
  - 2.5/R4.0.12/central
  - 2.5/R3_RC/central
  Version based on Kepler - trunk
  - trunk/R5_RC/central
  - trunk/R5.0.13/central
  - trunk/R4_trunk/central
  - trunk/ETS_4.10b.10_v5.0/central
  - trunk/ETS_4.10b.10_v5.0.3/central

• Install chosen version of Kepler

  shell> install_kepler.sh kepler_central central 'tutorial Kepler installation'
  Using location at: /pfs/work/g2dfigat/my_keplers/
  Linking common ...
  /pfs/work/g2dfigat/my_keplers/kepler_central/kepler ~
  ~
  Linking gui ...
  /pfs/work/g2dfigat/my_keplers/kepler_central/kepler ~
  ~
  Linking kepler-tasks ...
  Linking build-area ...
  Linking build-area/target ...
  Copying kepler.sh ...
  Creating itm subdirectory structure ...
  Linking directories ...
    build-area
    settings
    target
    itm
    resources
    kar
    src
    cpp
    itm
    eu
    itm
    target
    classes
    eu
    itm
    lib64
    python
    kepler-tasks-2.4
    lib
    jar
    common-2.4
    configs
    ptolemy
    configs
    kepler
    ontologies
    gui-2.4
    resources
    configurations
  Creating info file
  Creating Kepler related directories
  Kepler was installed inside /pfs/work/g2dfigat/my_keplers//kepler_central

  install_kepler.sh

  shell> install_kepler.sh [target dir] [source Kepler] [description]
   * target dir      : chosen directory inside KEPLER_DIR
   * source Kepler   : name of Kepler release (list available through 'list_kepler.sh -all')
                       - local        : default Kepler (local)
                       - central      : default Kepler (central)
                       - rc           : release candidate Kepler (central)
                       - R#.#/local   : tagged Kepler version R#.# (local)
                       - R#.#/central : tagged Kepler version R#.# (central)
   * description     : chosen description (e.g. 'this is my test kepler')

• Switch to chosen Kepler

  bash> switch_to_kepler.sh kepler_central
  Using location at: /pfs/work/g2dfigat/my_keplers/
  Removing old links                                                    [ OK ]
  Linking new kepler: kepler_central                                    [ OK ]

• List all your Kepler installations

  shell> list_my_keplers.sh
  Using location at: /pfs/work/g2dfigat/my_keplers/
  Following kepler installations are ready for use
  selected   type          name - 'description'
   [ ]     [Local ]        2.5-R3_RC-local - 'kepler 2.5 R3_RC local'
   [x]     [Central ]      kepler_central - 'tutorial Kepler installation'
   [ ]     [Local ]        local-default - 'local Kepler instalation'

1.3. 3. Setting up tutorial environment

In order to work with MDSPlus database you have to create and initialize MDSPlus database structure (details can be found here). This can be done by issuing following command:

$ITMSCRIPTDIR/create_user_itm_dir.sh test 4.10b
 
Usage: create_user_itm_dir.sh <tokamak name> <Data Structure version>'

After this command is executed, you will be able to locate MDSPlus files under following location: $HOME/public/itmdb/. This location is a link to your $ITMWORK file system, where actual data can be found.

At this point you have created your database structure inside $ITMWORK file system. This is required for further parts of the tutorial.

You should execute an ITM initialization script:

source $ITMSCRIPTDIR/ITMv2 test kepler > /dev/null
 
Usage: source ITMv2 <TokamakName> [<local_kepler_folder>]
      <TokamakName>: identifies the Tokamak entry in itmdb
      <local_kepler_folder>: [optional] name of Kepler folder or link to Kepler folder in $HOME
                             [if not specified, "kepler" link will be used]

echo "\n" >> ~/.login
echo "source $ITMSCRIPTDIR/ITMv2 test kepler > /dev/null" >> ~/.login

After this script is executed you will have an access to following tools:

• FC2K
• HPC2K
• Kepler
• jTraverser
• ISE

These tools will be discussed later in the tutorial.

1.4. 4. Getting tutorial sources and input data

1.4.1. 4.1. Copying examples

Copy tutorial examples. You can install them by issuing following command from Terminal.

shell> mkdir $ITMWORK/tutorials
shell> cp -r $SWITMDIR/resources/tutorials/2016-09-Ljubljana $ITMWORK/tutorials

1.4.2. 4.1. Copying input data

Copy data files used throughout the tutorial:

# copy data files 
shell> cp $SWITMDIR/resources/tutorials/2016-09-Ljubljana/pulsefiles/* $MDSPLUS_TREE_BASE_0

1.4.3. 4.1. Set TUTORIAL_DIR variable

Copy tutorial examples. You can install them by issuing following command from Terminal.

shell> setenv TUTORIAL_DIR $ITMWORK/tutorials/2018-03-ITER

1.4.4. 5. Varia

JVMJ9VM003W JIT compiler "/afs/rzg/@sys/soft/java/jdk6/bin/javac" not found. Will use interpreter. 

You are now ready to follow tutorial sessions!