This session will cover following topics
Tutorial topics
- Installation and configuration of NX client
- Configuration of the environment at Gateway
- Installation of Kepler
1.1. 0. Connection to the EUROfusion 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
NX connection to the Gateway
This tutorial assumes that Gateway accounts will be used for starting up Kepler application.
Gateway specific configuration of NX can be found here: here
1.2. 1.Setting IMAS
1.2.1. 1.1. Setting IMAS @ EUROfusion Gateway
You can switch to IMAS environment using:
module load imasenv imasdb <machine_name>
- This script will load all the modules in IMAS flavor. You will get access to most commonly used tools (FC2K, Kepler, Matlab interfaces, Python interfaces, etc.)
- You should be able to proceed with all the tools in a similar way as before
- You have to be aware of the fact that data access in IMAS and ITM is slightly different (similar, but still different)
1.2.2. 1.2. Setting IMAS @ ITER cluster
Please follow this >link< to get instructions how to set-up IMAS environment on ITER cluster
1.3. 2. Kepler installation
1.3.1. 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
1.3.2. 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_DIR
system 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) 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'
1.4. 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.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]
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/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.
1.5. 4. Getting tutorial sources and input data
1.5.1. 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
1.5.2. 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
1.5.3. 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
1.6. 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
IPP WIKI pages | https://itm.ipp.mpg.de/wiki/ITM |
Gateway TWIKI pages | https://portal.eufus.eu//itm/portal/auth/index.php?page=TWIKI |
Gateway CPT-ISIP pages | https://portal.eufus.eu//twiki/bin/view/Main/ISIP |
GForge Project list | http://gforge.eufus.eu/gf/project/ |
GForge Bug Tracker page | http://gforge.eufus.eu/gf/project/generalsupport/ |
Guidelines related to reporting bugs | https://portal.eufus.eu//twiki/bin/view/Main/HowToReportAnIssue |