0. Environment configuration

This session will cover following topics

Topics of the tutorial

installation and configuration of NX client
configuration of the environment at Gateway
installation of Kepler

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

NX connection to the Gateway

This tutorial assumes that Gateway accounts will be used for starting up Kepler application.
If you are not familiar with NX setup for the Gateway, take a look at following location NX setup where you can find how to download NXPlayer.

Gateway specific configuration of NX can be found here: here

x2go issue

There is a bug related to $PATH variable if you use x2g >= 4.0.3.0. You should use release 4.0.2.0 instead .

If you see message similar to this one:

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

It might be that you use broken release of x2go

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_10.2015
shell> mv .kepler .kepler_10.2015
shell> mv KeplerData KeplerData_10.2015

After you have backed up your data, install Kepler

1.2.2. 2.2. Kepler installation

Kepler can be installed by copying its files to user directory, however we recommend "central installation". In this type of installation, most of the Kepler sources remain on the public directory and a script will add a mirror in your local directory. The real advantage of such approach, beside sparring some disk space in your account, is that patches and bug fixes (especially for ualactors) are distributed automatically to all mirrors without changing anything to your installation. Of course FC2K actors you are creating or installing yourself will remain in the local part of the mirror.
In order to install most recent release of Kepler you should execute following commands:

shell>  create_personal_kepler.sh $SWITMDIR/kepler/central $ITMHOME/kepler_central

This command will create kepler_central directory inside $HOME. If you want to, you can always link it to "kepler":

shell> cd ~ 
shell> ln -s kepler_central kepler

1.3. 3. Setting up tutorial environment

Warning
Make sure to initialize database structure. Simply follow the steps below.

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

Adding source script into .login
In order to make sure that source script is always started when you log in, add it to ~/.login

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/2015-10-FC2K $ITMWORK/tutorials

1.4.2. 4.1. Copying input data

Copy data files used throughout the tutorial:

# copy data files (pay attention to *_dot_* at the end of command line!)
cp ~michalo/public/itmdb/itm_trees/test/4.10b/mdsplus/0/euitm_120002.* .
cp ~michalo/public/itmdb/itm_trees/test/4.10b/mdsplus/0/euitm_130003.* .

shell> cp $SWITMDIR/resources/tutorials/2015-10-FC2K/pulsefiles/* $MDSPLUS_TREE_BASE_0

1.4.3. 4.1. Set TUTORIAL_DIR variable