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This session will cover following topics
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1. Connecting to remote working space
1.1 Connecting to ITER cluster
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You will probably want to use an SSH client that supports remote X for graphical environment. The host hpc-login4.iter.org supports NX clients such as NoMachine whilst you can connect to hpc-app1.iter.org with X2go.
You can use your ITER username and password, which is the same for the collaborative websites
1.2 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
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Gateway |
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specific configuration of NX can be found here: here |
2.
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2.1 Back up
Before you begin, make sure to backup all the Kepler related data in your $HOME directory
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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
2.2. Kepler installation
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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 variableCode Block shell> mkdir -p $ITMWORK/mykeplers shell> setenv KEPLER_DIR $ITMWORK/mykeplers
List all available Kepler releases
Code Block 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
Code Block 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
Info title 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
Code Block 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
Code Block 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'
3. Setting up tutorial environment
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Make sure to initialize database structure. Simply follow the steps below. |
Setting IMAS
Loading all the IMAS modules. You will get access to libraries and most commonly used tools (FC2K, Kepler, Matlab interfaces, Python interfaces, etc.)
2.1. Setting IMAS @ ITER Cluster
The fastest way to setup the environment for Kepler, IMAS and all the other dependencies is to load kepler module
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module load fc2k kepler |
Please follow this >link< to get detailed instructions how to set-up IMAS environment on ITER cluster
2.2. Setting IMAS @ EUROfusion Gateway
You can switch to IMAS environment using:
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module load imasenv
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2.3. Setting IMAS @ JET (Freia)
You can switch to IMAS environment using:
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module load imas-modules # add all imas modules to module path
module load imas/3.17.1 # or other version of your choice; default is older
module swap mdsplus/7.7.11 # the default version 6.1 loaded by JAC module is too slow with IMAS
module load pyual |
The JET installation is maintained by Jonathan Hollocombe.
3. Database initialization
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:
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$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:
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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] |
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In order to make sure that source script is always started when you log in, add it to ~/.login echo "\n" >> ~/.login
echo "source $ITMSCRIPTDIR/ITMv2 test kepler > /dev/null" >> ~/.login |
After this script is executed you will have an access to following tools:
- FC2K
- HPC2K
- Kepler
- jTraverser
- ISE
These tools will be discussed later in the tutorial.
imasdb <machine_name>
e.g.:
imasdb test |
4. Getting tutorial sources and input data
4.1. Copying examples
Copy tutorial examples. You can install them by issuing following command from Terminal.
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4.1.1 IMAS @ ITER
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4.1.2 IMAS @ EUROfusion Gateway
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2. Copying input data
Copy data files used throughout the tutorial:
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4.2.1 IMAS @ ITER
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4.2.2 IMAS @ EUROfusion Gateway
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3. Set TUTORIAL_DIR variable
Copy tutorial examples. You can install them by issuing following command from Terminal.
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4.3.1 IMAS @ ITER
shell>
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export TUTORIAL_DIR
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=$HOME/tutorials/2018-03-ITER
5. Varia
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title | x2go issue |
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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
2 IMAS @ EUROfusion Gateway
shell> setenv TUTORIAL_DIR $HOME/tutorials/2018-03-ITER
5. Java memory settings
Please do not forget to set JAVA memory settings:
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export _JAVA_OPTIONS="-Xss20m -Xms1g -Xmx4g" |
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Before you start tutorial itself, please get familiar with following locations:
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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