06.1. IMAS- accessing IDS data from commandline(POZ'19Oct)

Quote of the day:
I love the smell of broken configuration in the morning ...
- Anonymous tutorial lecturer

In this tutorial

installation and configuration of MDSPlus databases

Table of Contents

Warning

Stop here for a moment. Make sure you have followed the configuration setup before proceeding any further!

Configuration related tutorial is here -> Click me! <-

1.1. 2.1. Introduction

For the future versions of UAL physical implementation of back-ends will be fully transparent,

however current version of UAL is coupled only with MDSPlus engine used for storing/ reading data locally.

This part of tutorial provides you some tricks useful in everyday work.

1.2. 2.2. MDSPlus database

MDSplus is a set of software tools for data acquisition and storage and a methodology for management of complex scientific data (source).

In order to benefit from UAL layer, scientific data must be stored in MDSPlus database. Before you will be able to use it, you have to create database's structure. This is fairly simple. All you have to do is to execute following commands:

imasdb <machine_name>

At this point, you can check your public directory and browse through the database structure.

cd $HOME/public/imasdb/

Explanation of the tree structure:

location	description
$HOME/public/itmdb/<machine_name>/<data_version>/<MDSPlus_tree_number>/ids_<shot><run>.* example: ~/public/imasdb/test/3/0/ids_120001.*
<machine_name> example: test	defines the equipment used for acquiring the results; "test" - is most commonly used for artificial, test data
<data_version> example: 3	Major Data Dictionary version
*<MDSPlus_tree_number>* example: 0	Contains all the *shot* and *runs* for given data tree
Shot number	Shot number is represented by first digits in database file ids_SSSSRRRR.*; there is no limit for number of digits used
Run number	Run number is represented by last four digits in database file ids_SSSSRRRR.*
ids_####.datafile, ids_####.tree, ids_####.characteristics	Contains data for given shot/run

1.3. 2.3. Accessing MDSPlus database data

1.3.1.1. 2.3.1 Listing pulse files

itmdbs command

Usage: imasdbs [OPTIONS] [COMMAND]

This program lists existing databases.

Possible commands are:

list <shot number>- list existing databases

slices <shot number> <run number> - list existing databases, including number of timeslices and time range for time-dependent IDSes

times <shot number> <run number> - list existing databases, including number of timeslices their time points for time-dependent IDSes

tokamak - list existing tokamaks (with data versions)

dataversion - list existing dataversions (with tokamaks)

If the optional arguments shot number and run number are given, only databases with these numbers will be shown.

If no command is given, the list command is performed.

To see databases stored in the public database, use 'public' as the user name.

Options:

-h, --help show this help message and exit

-u USER, --user=USER Show databases of specified user

-t TOKAMAK, --tokamak=TOKAMAK

Show only databases for specified tokamaks

-v VERSION, --version=VERSION

Show only databases for specified data version

--backend=BACKEND Show databases written with given backend(s). Comma-

separated list of backends (Currently supported:

mdsplus, hdf5). By default all backends are shown.

-c, --compact Compact/reduced output

shell> imasdbs -t test slices 10 40
Tokamak: test
   Data version: 3
      UAL Backend: mdsplus
         Shot    10
             Run:     40
                 core_profiles:   25 slices (345.0 - 345.48)
                  core_sources:   25 slices (345.0 - 345.48)
                core_transport:   25 slices (345.0 - 345.48)
                   equilibrium:   25 slices (345.0 - 345.48)
               transport_solver_numerics:   25 slices (345.0 - 345.48)
                          wall:   25 slices (345.0 - 345.48)

shell> imasdbs  -u palakb
Tokamak: test
   Data version: 3
      UAL Backend: mdsplus
         Shot     1 Runs:     1
         Shot     2 Runs:     3   666   777   999
         Shot    10 Runs:    30    40    42    60    61    64    65    66    80    81    99   123   666   999  1234
         Shot    12 Runs:     1     2    99
         Shot    13 Runs:     1

1.3.1.2. 2.3.2 Dumping pulse files

shell> idsdump
Usage: idsdump <USER> <TOKAMAK> <VERSION> <SHOT> <RUN> <IDS>
         or
       idsdump <SHOT> <RUN> <IDS>

[palakb@hpc-login4 ~]$ idsdump 13 1 equilibrium
class equilibrium
Attribute ids_properties
        class ids_properties
        Attribute comment:
        Attribute homogeneous_time: 1
        Attribute source:
        Attribute provider:
        Attribute creation_date:
[.......]
Attribute code
        class code
        Attribute name:
        Attribute commit:
        Attribute version:
        Attribute repository:
        Attribute parameters:
        Attribute output_flag
        []
Attribute time
[ 0.  1.  2.]

1.3.1.3. 2.3.3 Copying database files directly

In case you know user name, machine name, shot number and run number, you can import users' database files copying them directly from the users' public directories. Database files are located inside:

~$USERNAME/public/imasdb/$TOKAMAKNAME/$DATAVERSION/0/ids_SSSSRRRR.*

Take a look at the example below. We will copy data from user michalo, machine test, shot: 12 and run: 2

# change directory in your $HOME
cd $HOME/public/imasdb/test/3/0/

# copy data files (pay attention to *_dot_* at the end of command line!)
cp ~michalo/public/imasdb/test/3/0/ids_120002.* .
cp ~michalo/public/imasdb/test/3/0/ids_130003.* .

Currently UAL uses only MDSPlus engine for storing/ reading data locally.

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