This session will cover following topics
 | Topics of the tutorial
|
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. |
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
Kepler: local vs. central installation
Kepler can be installed by copying its files to user directory, however we recommend "central" (lightweight) 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:
Set-up
KEPLER_DIRsystem variableshell> 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) - 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 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 - ''
sss
bash> switch_to_kepler.sh R3.10_central
- ddd
- ddd
1.3. 3. Setting up tutorial environment
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 shell> cp $SWITMDIR/resources/tutorials/2015-10-FC2K/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/2015-10-FC2K
1.4.4. 5. Varia
 | 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 |
You are now ready to follow tutorial sessions!
| Useful Links Before you start tutorial itself, please get familiar with following locations:
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