0. 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_09.2016
shell> mv .kepler .kepler_09.2016
shell> mv KeplerData KeplerData_09.2016

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 ITM_KEPLER_DIR system variable

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

• List all available Kepler releases

  shell> list_keplers.sh -all
  List of available Kepler installations
  Local installations
  - local (default)
  - R3.9/local
  - R3.10/local
  - ETS4JET-training/local
  Central installations
  - central (default)
  - rc (release candidate)
  - R3.9/central
  - R3.10/central
  - ETS4JET-training/central

• Install chosen version of Kepler

  shell> install_kepler.sh R3.10_central R3.10/central 'tutorial Kepler installation'

  install_kepler.sh

  shell> install_kepler.sh [target dir] [source Kepler] [description]
   * target dir      : chosen directory inside ITM_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')

• List all your Kepler installations

  shell> list_my_keplers.sh
  Using location at: /pfs/work/bpalak/my_keplers
  Following kepler installations are ready for use
  selected   type          name - 'description'
   [ ]     [Local ]        kepler_3.10_loc - 'r3.10 local'
   [ ]     [Central ]      kepler_ets - ''
   [ ]     [Central ]      R3.10_central - 'tutorial Kepler installation'
   [x]     [Central ]      R3_RC_ETS_central - ''

• Switch to chosen Kepler

  bash> switch_to_kepler.sh R3.10_central

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 test 4.10b

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/ITMv1 kepler test 4.10b > /dev/null

echo "\n" >> ~/.login
echo "source $ITMSCRIPTDIR/ITMv1 kepler test 4.10b > /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/2016-09-Ljubljana

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!

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