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Finish

Timestamp:: 06/22/13 01:41:06 (11 years ago)
Author:: divyashri.bhat@gmail.com
Comment:: --

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GEC17Agenda/GettingStartedWithGENI_III_GIMI/Procedure/Finish

-                      v8
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 = Finish =
 == E. Push to iRODS ==
 === E.1 Overview ===
+== D. Push to iRODS ==
+=== D.1 Overview ===
 In 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).
 …
 ----
 === E.2 Storing data on iRODS ===
+=== D.2 Storing data on iRODS ===
 * 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.
 === E.2.1 iRODS command line tools in the user work space ===
+=== D.2.1 iRODS command line tools in the user work space ===
   * The GENI [http://groups.geni.net/geni/wiki/GECTutorialVMInstructions User Workspace] comes already with the iRODS command line tools installed.
   * 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.
 …
     (<unit> is not required.)
 === E.2.2 iRODS web interface ===
+=== D.2.2 iRODS web interface ===
 iRODS also provides a nice and easy to use [https://www.irods.org/web/index.php web interface], which we will explore in the following.
   * Point the browser in your user workspace to the following link: https://www.irods.org/web/index.php
 …
 ----
 === E.3 IRODS and OML ===
+=== D.3 IRODS and OML ===
 In 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.
 ----
 === E.4 DISCLAIMER ===
+=== D.4 DISCLAIMER ===
 The 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.
 ----
+[[BR]]
+[[BR]]
+In Section F we went through the exercise of retrieving data from iRODS to a local computer. In this Section, we will introduce
+=== E.1 iRODS Environment Settings ===
+If you haven't already performed this step in A.1, you first have to configure the your local iRODS environment:
+* The iRODS client uses a configuration file (~/.irods/.irodsEnv) that sets certain parameter for the icommands. Here is and example:
+{{{
+# iRODS personal configuration file.
+#
+# This file was automatically created during iRODS installation.
+#   Created Thu Feb 16 14:06:27 2012
+#
+# iRODS server host name:
+irodsHost 'emmy9.casa.umass.edu'
+# iRODS server port number:
+irodsPort 1247
+# Default storage resource name:
+irodsDefResource 'iRODSUmass2'
+# Home directory in iRODS:
+irodsHome '/geniRenci/home/gimiXX'
+# Current directory in iRODS:
+irodsCwd '/geniRenci/home/gimiXX'
+# Account name:
+irodsUserName 'gimiXX'
+# Zone:
+irodsZone 'geniRenci'
+}}}
+  * First of all copy the iRODS configuration file to .irodsEnv with the following command (replace gimiXX with your username):
+{{{
+$ cp ~/Tutorials/GIMI/gimiXX/gimiXXIrodsEnv ~/.irods/.irodsEnv
+}}}
+ * Register with iRODS server by issuing the following command (more details on iRODS will be given shortly):
+{{{
+$ iinit
+}}}
+ * You will be prompted for a password. Please type in the password you were provided with on the paper handout!!
+----
+=== E.2 Retrieving Data from iRODS to Local System ===
+In the following we list the steps and commands that will allow you to retrieve data from the iRODS storage to your
+local storage:
+  * List content of your home directory
+{{{
+$ ils
+}}}
+  * To change to a different directory use
+{{{
+$ icd
+}}}
+  * Retrieve file from your iRODS home directory into user workspace.
+{{{
+$ iget <file_name>
+}}}
+  Assuming you wanted to retrieve a file called gimitesting.sq3 the command would look as follows:
+{{{
+$ iget gimitesting.sq3
+}}}
+  * A complete overview on the iRODS commands can be found [https://www.irods.org/index.php/icommands here].
+=== E.3 Searching the Catalogue for Data ===
+{{{
+$ imeta qu -d SliceName like gimi28
+}}}
+[[BR]]
+[[BR]]
+In Section E we went through the exercise of retrieving data from iRODS to a local computer. In this Section, we will introduce
 two different methods that can be used to analyze the measurement data. Analysis of measurement data obtained with OMF/OML is not
 limited to these two methods, we simply use them for demonstration purposes.
 …
 ----
 === G.1 R Scripts ===
+=== F.1 R Scripts ===
 One potential way to visualize the data is making use of [http://www.r-project.org/ R], which provides a visualization language.
 …
 The benefit of using R scripts is that they can produce graphs that can be used in documents!
+The results can then be stored into iRODS using the itools presented in Section E.2.
+----
+=== G.2 omf_web ===
+The second alternative we use in the tutorial is omf_web, which already has been presented in Section D.
+----
+The results can then be stored into iRODS using the itools presented in Section D.2.
 [[BR]]
 [[BR]]
+=== F.1 iRODS Environment Settings ===
+If you haven't already performed this step in A.1, you first have to configure the your local iRODS environment:
+* The iRODS client uses a configuration file (~/.irods/.irodsEnv) that sets certain parameter for the icommands. Here is and example:
+{{{
+# iRODS personal configuration file.
+#
+# This file was automatically created during iRODS installation.
+#   Created Thu Feb 16 14:06:27 2012
+#
+# iRODS server host name:
+irodsHost 'emmy9.casa.umass.edu'
+# iRODS server port number:
+irodsPort 1247
+# Default storage resource name:
+irodsDefResource 'iRODSUmass2'
+# Home directory in iRODS:
+irodsHome '/geniRenci/home/gimiXX'
+# Current directory in iRODS:
+irodsCwd '/geniRenci/home/gimiXX'
+# Account name:
+irodsUserName 'gimiXX'
+# Zone:
+irodsZone 'geniRenci'
+}}}
+  * First of all copy the iRODS configuration file to .irodsEnv with the following command (replace gimiXX with your username):
+{{{
+$ cp ~/Tutorials/GIMI/gimiXX/gimiXXIrodsEnv ~/.irods/.irodsEnv
+}}}
+ * Register with iRODS server by issuing the following command (more details on iRODS will be given shortly):
+{{{
+$ iinit
+}}}
+ * You will be prompted for a password. Please type in the password you were provided with on the paper handout!!
+----
+=== F.2 Retrieving Data from iRODS to Local System ===
+In the following we list the steps and commands that will allow you to retrieve data from the iRODS storage to your
+local storage:
+  * List content of your home directory
+{{{
+$ ils
+}}}
+  * To change to a different directory use
+{{{
+$ icd
+}}}
+  * Retrieve file from your iRODS home directory into user workspace.
+{{{
+$ iget <file_name>
+}}}
+  Assuming you wanted to retrieve a file called gimitesting.sq3 the command would look as follows:
+{{{
+$ iget gimitesting.sq3
+}}}
+  * A complete overview on the iRODS commands can be found [https://www.irods.org/index.php/icommands here].
+=== F.3 Searching the Catalogue for Data ===
+{{{
+$ imeta qu -d SliceName like gimi28
+}}}
+----
+=== H.1 Delete Slice ===
+In Flukes select the ''Manifest View'' tab enter your slice name (gimiXX) and select ''Delete slice''.
+----
+[[BR]]
+[[BR]]
+=== G.1 Delete Slice ===
+In Flack, click on the 'Delete' button and select 'Delete at used Managers' as shown below: [[BR]]
+[[Image Flack4.png]]
+----
+[[BR]]
+[[BR]]