Changes between Initial Version and Version 1 of GIMI-GEC16-Tutorials/GIMI-GEC16-TutorialB/Toirods


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Timestamp:
03/14/13 13:39:30 (11 years ago)
Author:
divyashri.bhat@gmail.com
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  • GIMI-GEC16-Tutorials/GIMI-GEC16-TutorialB/Toirods

    v1 v1  
     1== E. Push to iRODS ==
     2{{{
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     28}}}
     29
     30=== E.1 Overview ===
     31
     32In GIMI, [https://www.irods.org/ iRODS] is used as the repository for measurement data. At the moment our iRODS data system consist of three servers (RENCI, NICTA, and UMass) and a metadata catalog (located at RENCI).
     33
     34----
     35
     36=== E.2 Storing data on iRODS ===
     37
     38* After successful completion of an experiment the measurement data from the experiment have been stored in iRODS. We will now look into two options on how this data can be handled.
     39 
     40=== E.2.1 iRODS command line tools in the user work space ===
     41  * The GENI [http://groups.geni.net/geni/wiki/GECTutorialVMInstructions User Workspace] comes already with the iRODS command line tools installed.
     42  * If you have not done so far use [https://www.irods.org/index.php/iinit iinit] to create a file that contains your iRODS password in a scrambled form. This will then be used automatically by the [https://www.irods.org/index.php/icommands icommands] for authentication with the server.
     43{{{
     44$ iinit
     45}}}
     46    You will be prompted for a password. Please enter the one given on the paper handout.
     47
     48  * The iRODS client uses a configuration file (~/.irods/.irodsEnv) that sets certain parameter for the icommands. Here is and example:
     49{{{
     50# iRODS personal configuration file.
     51#
     52# This file was automatically created during iRODS installation.
     53#   Created Thu Feb 16 14:06:27 2012
     54#
     55# iRODS server host name:
     56irodsHost 'emmy9.casa.umass.edu'
     57# iRODS server port number:
     58irodsPort 1247
     59
     60# Default storage resource name:
     61irodsDefResource 'iRODSUmass2'
     62# Home directory in iRODS:
     63irodsHome '/geniRenci/home/gimiXX'
     64# Current directory in iRODS:
     65irodsCwd '/geniRenci/home/gimiXX'
     66# Account name:
     67irodsUserName 'gimiXX'
     68# Zone:
     69irodsZone 'geniRenci'
     70}}}
     71  * Retrieve file from your iRODS home directory into user workspace.
     72{{{
     73$ iget <file_name>
     74}}}
     75
     76    Assuming you wanted to retrieve a file called gimitesting.sq3 the command would look as follows:
     77{{{
     78$ iget gimitesting.sq3
     79}}}
     80
     81  * Store data from user workspace into your iRODS home directory.
     82{{{
     83$ iput <file_name>
     84}}}
     85
     86  * Add metadata information to stored file.
     87{{{
     88$ imeta add -d <file_name> <name> <value> <unit>
     89}}}
     90    For example if you wanted to add the slice name of the experiment as metadata for file gimi01-ping_all.sq3, the command would look as follows:
     91{{{
     92$ imeta add -d gimi01-ping_all.sq3 SliceName gimi01
     93}}}
     94    (<unit> is not required.)
     95
     96=== E.2.2 iRODS web interface ===
     97iRODS also provides a nice and easy to use [https://www.irods.org/web/index.php web interface], which we will explore in the following.
     98  * Point the browser in your user workspace to the following link: https://www.irods.org/web/index.php
     99  * Input the following information to sign in:
     100{{{
     101Host/IP: emmy9.casa.umass.edu
     102Port: 1247
     103Username: as given on printout
     104Password: as given on printout
     105}}}
     106  * The following screenshot shows an example for the web interface: [[Image(wiki:GIMIv1.0Tutorial:irods_screen.png)]]
     107
     108----
     109
     110=== E.3 IRODS and OML ===
     111In GIMI we have enabled an option in OML2.8 that allows the execution of script. We use this functionality to automatically save measurement results in IRODS after a measurement has successfully completed.
     112
     113----
     114
     115=== E.4 DISCLAIMER ===
     116The iRODS service we are offering within the scope of GIMI does NOT guarantee 100% reliable data storage (i.e., we do NOT back up the data). If you are performing your own experiments and want to use iRODS you are absolutely welcome but be aware that we do NOT guarantee recovery from data loss.
     117
     118----
     119
     120
     121[[BR]]
     122[[BR]]
     123
     124
     125[[http://groups.geni.net/geni/wiki/GIMIv1.1Tutorial/Observe Back to previous step]]
     126
     127[[http://groups.geni.net/geni/wiki/GIMIv1.1Tutorial/Analyze Forward to next step]]
     128
     129[[http://groups.geni.net/geni/wiki/GIMIv1.1Tutorial/ Back to tutorial main page]]