2.1. Getting Started

This section describes setting the environment configuration required to run the IMASViz tool and how to run the application itself.

2.1.1. Running IMASViz as a module

The procedure below describes how to load and run IMASViz which is available as a module on the GateWay and ITER HPC cluster.

2.1.1.1. On the GateWay HPC

2.1.1.1.1. Setting the Environment

In a new terminal, execute the following command in order to load the required modules:

module load cineca
module load imasenv   # or any other specific imasenv module version
module load imas-viz/v2

# The next few modules should be loaded together with imasenv module
# Listing them all here in case of module related issues.
# module load itm-gcc/6.1.0
# module unload itm-python/2.7
# module load itm-python/3.6
# module load itm-qt/5.8.0

# Listing all available imas-viz modules can be done by running
module av imas-viz

# With the imas-viz module loaded (version 2.3.0 or never)
# the documentation can be accessed by running
biz-doc

Warning

IMPORTANT! IMAS databases (IDSs) were written using specific version of IMAS. In order to open these IDSs the same IMAS module version should be used due to possible IDS database structure changes through different versions. Any tools or utilities that work with IDSs, including IMASViz, cannot work properly if this “IMAS version mismatch” is too great (!).

2.1.1.1.2. Running IMASViz

With the environment set, run the IMASviz by simply typing the following command:

viz

The main GUI window of IMAS_VIZ should display, as shown in the figure below:

The description of the above input parameters is as follows:

GUI Fields	Description
User name	Creator/owner of the IMAS IDSs database
IMAS database name	IMAS database label, usually device/machine name of the IMAS IDS database (i. e. iter, aug, west…)
Shot number	Pulse shot number
Run number	Pulse run number

2.1.1.1.3. Available testing IMAS databases

On the GateWay HPC there are a few testing IMAS IDS cases available. These databases are the main source of data used for IMASViz testing purposes and were also included in writing the this documentation. Users can freely use them for examples and practice purposes.

Note

There IMAS IDS cases are confirmed to work with IMAS versions 3.23.2 - 3.24.0.

Available IMAS IDS Case Parameters
Parameters	Case 1	Case 2	Case 3
User name	g2penkod	g2penkod	g2penkod
IMAS database name	viztest	viztest	viztest
Shot number	52344	52682	53223
Run number	0	0	0

2.1.1.2. On ITER HPC

2.1.1.2.1. Setting the Environment

In a new terminal, execute the following command in order to load the required modules:

module load
module load IMAS   # or any other specific IMAS module version
module load Viz

# The next few modules should be loaded together with imasenv module
# Listing them all here in case of module related issues.
# Qt5/5.10.1-intel-2018a
# PyQt5/5.9.2-intel-2018a-Python-3.6.4
# PyQtGraph/0.10.0-intel-2018a-Python-3.6.4

# Listing all available Viz modules can be done by running
module av Viz

Warning

IMPORTANT! IMAS databases (IDSs) were written using specific version of IMAS. In order to open these IDSs the same IMAS module version should be used due to possible IDS database structure changes through different versions. Any tools or utilities that work with IDSs, including IMASViz, cannot work properly if this “IMAS version mismatch” is too great (!).

2.1.1.2.2. Running IMASViz

With the environment set, run the IMASViz by simply typing the following command:

viz

The main GUI window of IMAS_VIZ should display, as shown in the figure below:

The description of the above input parameters is as follows:

GUI Fields	Description
User name	Creator/owner of the IMAS IDSs database
IMAS database name	IMAS database label, usually device/machine name of the IMAS IDS database (i. e. iter, aug, west…)
Shot number	Pulse shot number
Run number	Pulse run number

2.1.1.2.3. Available testing IMAS databases

On the ITER HPC there are a few testing IMAS IDS cases available. These databases are the main source of data used for IMASViz testing purposes and were also included in writing the this documentation. Users can freely use them for examples and practice purposes.

Note

There IMAS IDS cases are confirmed to work with IMAS versions 3.23.2 - 3.24.0

Available IMAS IDS Case Parameters
Parameters	Case 1	Case 2
User name	penkod	penkod
IMAS database name	viztest	viztest
Shot number	52344	52682
Run number	0	0

2.1.2. Running IMASViz from source

The procedure below describes how to run IMASViz from source.

2.1.2.1. Requirements

The fundamental requirements in order to locally run IMASViz are:

• IMAS

• Python3 and Python libraries:

  • PyQt5

  • pyqtgraph

  • matplotlib

  • Sphinx (pip3 install sphinx)

  • Sphinx RTD theme (pip3 install sphinx_rtd_theme)

2.1.2.2. Obtaining the source code

To obtain the IMASViz code source the next two steps are required:

1. Clone repository from git.iter.org (permissions are required!).

   git clone ssh://git@git.iter.org/vis/viz.git
   

   Direct link to the IMASViz git.iter repository: IMASViz.

2. Switch to IMASViz2.0 branch (required if master branch is not updated yet)

   git fetch # optional
   git branch -r # optional
   git checkout develop
   

2.1.2.3. Setting the environment

To set the environment, go to viz directory and set VIZ_HOME and VIZ_PRODUCTION environment variables by running the next commands in the terminal:

cd viz
# bash
export VIZ_PRODUCTION=0
export VIZ_HOME=$PWD
# csh
setenv VIZ_PRODUCTION 0
setenv VIZ_HOME $PWD

Then proceed with the next instructions.

2.1.2.3.1. GateWay HPC

Load next modules:

module load cineca
module load imasenv
module load itm-gcc/6.1.0
module load itm-python/3.6
module load itm-qt/5.8.0

2.1.2.3.2. ITER HPC

Load next module:

module load IMAS/3.20.0-3.8.3

2.1.2.4. Running IMASViz

To run IMASViz, run the next commands in terminal:

python3 $VIZ_HOME/imasviz/VizGUI/QtVIZ_GUI.py

The main GUI window of IMAS_VIZ should display, as shown in the figure below:

The description of the above input parameters is as follows:

GUI Fields	Description
User name	Creator/owner of the IMAS IDSs database
IMAS database name	IMAS database label, usually device/machine name of the IMAS IDS database (i. e. iter, aug, west…)
Shot number	Pulse shot number
Run number	Pulse run number

2.1.3. Latest documentation and manual

The documentation provided on other sources (confluence pages etc.) than the project repository might not be up to date. To get the latest documentation, first obtain the IMASViz source code (see Obtaining the source code).

Then navigate to

cd $VIZ_HOME/doc

and run

# for PDF documentation
module load texlive
make pdflatex
firefox build/latex/IMASViz.pdf
# for HTML documentation
make html
firefox build/html/index.html

Note

Additional prerequisites for generating the documentation: Sphinx and Sphinx RTD theme (listed in Requirements)