Changes between Version 8 and Version 9 of GEC17Agenda/GettingStartedWithGENI_III_GIMI/Procedure/Finish


Ignore:
Timestamp:
06/22/13 01:41:06 (6 years ago)
Author:
divyashri.bhat@gmail.com
Comment:

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  • GEC17Agenda/GettingStartedWithGENI_III_GIMI/Procedure/Finish

    v8 v9  
    11= Finish =
    22
    3 == E. Push to iRODS ==
    4 
    5 === E.1 Overview ===
     3== D. Push to iRODS ==
     4
     5=== D.1 Overview ===
    66
    77In 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).
     
    99----
    1010
    11 === E.2 Storing data on iRODS ===
     11=== D.2 Storing data on iRODS ===
    1212
    1313* 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.
    1414 
    15 === E.2.1 iRODS command line tools in the user work space ===
     15=== D.2.1 iRODS command line tools in the user work space ===
    1616  * The GENI [http://groups.geni.net/geni/wiki/GECTutorialVMInstructions User Workspace] comes already with the iRODS command line tools installed.
    1717  * 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.
     
    6969    (<unit> is not required.)
    7070
    71 === E.2.2 iRODS web interface ===
     71=== D.2.2 iRODS web interface ===
    7272iRODS also provides a nice and easy to use [https://www.irods.org/web/index.php web interface], which we will explore in the following.
    7373  * Point the browser in your user workspace to the following link: https://www.irods.org/web/index.php
     
    8383----
    8484
    85 === E.3 IRODS and OML ===
     85=== D.3 IRODS and OML ===
    8686In 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.
    8787
    8888----
    8989
    90 === E.4 DISCLAIMER ===
     90=== D.4 DISCLAIMER ===
    9191The 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.
    9292
    9393----
    9494
    95 
    96 [[BR]]
    97 [[BR]]
    98 
    99 In Section F we went through the exercise of retrieving data from iRODS to a local computer. In this Section, we will introduce
     95=== E.1 iRODS Environment Settings ===
     96If you haven't already performed this step in A.1, you first have to configure the your local iRODS environment:
     97
     98* The iRODS client uses a configuration file (~/.irods/.irodsEnv) that sets certain parameter for the icommands. Here is and example:
     99{{{
     100# iRODS personal configuration file.
     101#
     102# This file was automatically created during iRODS installation.
     103#   Created Thu Feb 16 14:06:27 2012
     104#
     105# iRODS server host name:
     106irodsHost 'emmy9.casa.umass.edu'
     107# iRODS server port number:
     108irodsPort 1247
     109
     110# Default storage resource name:
     111irodsDefResource 'iRODSUmass2'
     112# Home directory in iRODS:
     113irodsHome '/geniRenci/home/gimiXX'
     114# Current directory in iRODS:
     115irodsCwd '/geniRenci/home/gimiXX'
     116# Account name:
     117irodsUserName 'gimiXX'
     118# Zone:
     119irodsZone 'geniRenci'
     120}}}
     121 
     122  * First of all copy the iRODS configuration file to .irodsEnv with the following command (replace gimiXX with your username):
     123{{{
     124$ cp ~/Tutorials/GIMI/gimiXX/gimiXXIrodsEnv ~/.irods/.irodsEnv
     125}}}
     126 * Register with iRODS server by issuing the following command (more details on iRODS will be given shortly):
     127{{{
     128$ iinit
     129}}}
     130 
     131 * You will be prompted for a password. Please type in the password you were provided with on the paper handout!!
     132
     133----
     134
     135=== E.2 Retrieving Data from iRODS to Local System ===
     136In the following we list the steps and commands that will allow you to retrieve data from the iRODS storage to your
     137local storage:
     138
     139  * List content of your home directory
     140{{{
     141$ ils
     142}}}
     143  * To change to a different directory use
     144{{{
     145$ icd
     146}}}
     147  * Retrieve file from your iRODS home directory into user workspace.
     148{{{
     149$ iget <file_name>
     150}}}
     151
     152  Assuming you wanted to retrieve a file called gimitesting.sq3 the command would look as follows:
     153{{{
     154$ iget gimitesting.sq3
     155}}}
     156  * A complete overview on the iRODS commands can be found [https://www.irods.org/index.php/icommands here].
     157
     158=== E.3 Searching the Catalogue for Data ===
     159{{{
     160$ imeta qu -d SliceName like gimi28
     161}}}
     162
     163
     164
     165[[BR]]
     166[[BR]]
     167
     168In Section E we went through the exercise of retrieving data from iRODS to a local computer. In this Section, we will introduce
    100169two different methods that can be used to analyze the measurement data. Analysis of measurement data obtained with OMF/OML is not
    101170limited to these two methods, we simply use them for demonstration purposes.
     
    103172----
    104173
    105 === G.1 R Scripts ===
     174=== F.1 R Scripts ===
    106175
    107176One potential way to visualize the data is making use of [http://www.r-project.org/ R], which provides a visualization language.
     
    265334The benefit of using R scripts is that they can produce graphs that can be used in documents!
    266335
    267 The results can then be stored into iRODS using the itools presented in Section E.2.
    268 
    269 
    270 ----
    271 
    272 === G.2 omf_web ===
    273 
    274 The second alternative we use in the tutorial is omf_web, which already has been presented in Section D.
    275 
    276 ----
     336The results can then be stored into iRODS using the itools presented in Section D.2.
     337
     338
     339
    277340 
    278341[[BR]]
    279342[[BR]]
    280343
    281 === F.1 iRODS Environment Settings ===
    282 If you haven't already performed this step in A.1, you first have to configure the your local iRODS environment:
    283 
    284 * The iRODS client uses a configuration file (~/.irods/.irodsEnv) that sets certain parameter for the icommands. Here is and example:
    285 {{{
    286 # iRODS personal configuration file.
    287 #
    288 # This file was automatically created during iRODS installation.
    289 #   Created Thu Feb 16 14:06:27 2012
    290 #
    291 # iRODS server host name:
    292 irodsHost 'emmy9.casa.umass.edu'
    293 # iRODS server port number:
    294 irodsPort 1247
    295 
    296 # Default storage resource name:
    297 irodsDefResource 'iRODSUmass2'
    298 # Home directory in iRODS:
    299 irodsHome '/geniRenci/home/gimiXX'
    300 # Current directory in iRODS:
    301 irodsCwd '/geniRenci/home/gimiXX'
    302 # Account name:
    303 irodsUserName 'gimiXX'
    304 # Zone:
    305 irodsZone 'geniRenci'
    306 }}}
    307  
    308   * First of all copy the iRODS configuration file to .irodsEnv with the following command (replace gimiXX with your username):
    309 {{{
    310 $ cp ~/Tutorials/GIMI/gimiXX/gimiXXIrodsEnv ~/.irods/.irodsEnv
    311 }}}
    312  * Register with iRODS server by issuing the following command (more details on iRODS will be given shortly):
    313 {{{
    314 $ iinit
    315 }}}
    316  
    317  * You will be prompted for a password. Please type in the password you were provided with on the paper handout!!
    318 
    319 ----
    320 
    321 === F.2 Retrieving Data from iRODS to Local System ===
    322 In the following we list the steps and commands that will allow you to retrieve data from the iRODS storage to your
    323 local storage:
    324 
    325   * List content of your home directory
    326 {{{
    327 $ ils
    328 }}}
    329   * To change to a different directory use
    330 {{{
    331 $ icd
    332 }}}
    333   * Retrieve file from your iRODS home directory into user workspace.
    334 {{{
    335 $ iget <file_name>
    336 }}}
    337 
    338   Assuming you wanted to retrieve a file called gimitesting.sq3 the command would look as follows:
    339 {{{
    340 $ iget gimitesting.sq3
    341 }}}
    342   * A complete overview on the iRODS commands can be found [https://www.irods.org/index.php/icommands here].
    343 
    344 === F.3 Searching the Catalogue for Data ===
    345 {{{
    346 $ imeta qu -d SliceName like gimi28
    347 }}}
    348 
    349 
    350 ----
    351 === H.1 Delete Slice ===
    352 
    353 In Flukes select the ''Manifest View'' tab enter your slice name (gimiXX) and select ''Delete slice''.
    354 
    355 ----
    356 
    357 [[BR]]
    358 [[BR]]
     344
     345=== G.1 Delete Slice ===
     346
     347In Flack, click on the 'Delete' button and select 'Delete at used Managers' as shown below: [[BR]]
     348
     349[[Image Flack4.png]]
     350
     351----
     352
     353[[BR]]
     354[[BR]]