Changes between Version 3 and Version 4 of GEC17Agenda/GettingStartedWithGENI_III_GIMI/Procedure/Finish


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Timestamp:
06/21/13 23:40:13 (11 years ago)
Author:
divyashri.bhat@gmail.com
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  • GEC17Agenda/GettingStartedWithGENI_III_GIMI/Procedure/Finish

    v3 v4  
     1= Finish =
     2== E. Push to iRODS ==
     3{{{
     4#!html
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     26<!-- Image map text links - End - -->
    127
    2 == D.1 !LabWiki ==
     28</div>
     29}}}
    330
    4 Labwiki is a tool which provides a user-friendly interface to visualize your experiment. To know more about !LabWiki please visit [https://github.com/mytestbed/labwiki LabWiki] [[BR]]
    5 Labwiki can be used to Plan, Prepare and Run your Experiment.[[BR]]
     31=== E.1 Overview ===
    632
    7 === D.1.1 Plan ===
    8 Labwiki accounts have already been created for you for this tutorial. To use Labwiki, go to [http://emmy9.casa.umass.edu:3005/users/sign_in GIMI portal] and login with the username and password you have been given.[[BR]]
     33In 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).
    934
    10 [[Image(Labwiki_1.png)]]
     35----
    1136
    12 Figure (1)
     37=== E.2 Storing data on iRODS ===
    1338
    14 After you have successfully been signed in you will be able to see a screen like the one below. [[BR]]
     39* 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.
     40 
     41=== E.2.1 iRODS command line tools in the user work space ===
     42  * The GENI [http://groups.geni.net/geni/wiki/GECTutorialVMInstructions User Workspace] comes already with the iRODS command line tools installed.
     43  * 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.
     44{{{
     45$ iinit
     46}}}
     47    You will be prompted for a password. Please enter the one given on the paper handout.
     48
     49  * The iRODS client uses a configuration file (~/.irods/.irodsEnv) that sets certain parameter for the icommands. Here is and example:
     50{{{
     51# iRODS personal configuration file.
     52#
     53# This file was automatically created during iRODS installation.
     54#   Created Thu Feb 16 14:06:27 2012
     55#
     56# iRODS server host name:
     57irodsHost 'emmy9.casa.umass.edu'
     58# iRODS server port number:
     59irodsPort 1247
     60
     61# Default storage resource name:
     62irodsDefResource 'iRODSUmass2'
     63# Home directory in iRODS:
     64irodsHome '/geniRenci/home/gimiXX'
     65# Current directory in iRODS:
     66irodsCwd '/geniRenci/home/gimiXX'
     67# Account name:
     68irodsUserName 'gimiXX'
     69# Zone:
     70irodsZone 'geniRenci'
     71}}}
     72  * Retrieve file from your iRODS home directory into user workspace.
     73{{{
     74$ iget <file_name>
     75}}}
     76
     77    Assuming you wanted to retrieve a file called gimitesting.sq3 the command would look as follows:
     78{{{
     79$ iget gimitesting.sq3
     80}}}
     81
     82  * Store data from user workspace into your iRODS home directory.
     83{{{
     84$ iput <file_name>
     85}}}
     86
     87  * Add metadata information to stored file.
     88{{{
     89$ imeta add -d <file_name> <name> <value> <unit>
     90}}}
     91    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:
     92{{{
     93$ imeta add -d gimi01-ping_all.sq3 SliceName gimi01
     94}}}
     95    (<unit> is not required.)
     96
     97=== E.2.2 iRODS web interface ===
     98iRODS also provides a nice and easy to use [https://www.irods.org/web/index.php web interface], which we will explore in the following.
     99  * Point the browser in your user workspace to the following link: https://www.irods.org/web/index.php
     100  * Input the following information to sign in:
     101{{{
     102Host/IP: emmy9.casa.umass.edu
     103Port: 1247
     104Username: as given on printout
     105Password: as given on printout
     106}}}
     107  * The following screenshot shows an example for the web interface: [[Image(irods_screen.png)]]
     108
     109----
     110
     111=== E.3 IRODS and OML ===
     112In 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.
     113
     114----
     115
     116=== E.4 DISCLAIMER ===
     117The 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.
     118
     119----
    15120
    16121
    17 [[Image(Labwiki_2a.png)]]
    18 
    19 Figure (2)
    20 
    21 
    22 The left column could contain the steps to run the experiment or general information about the experiment.[[BR]]
    23 
    24 
    25 
    26 [[Image(Labwiki_2.png)]]
    27 
    28 Figure (3)
    29 
    30 === D.1.2 Prepare ===
    31 In the Prepare column, you can select the experiment that you want to execute. In this column you will also be able to edit your experiment script.[[BR]]
    32 
    33 [[Image(Labwiki_3.png)]]
    34 
    35 Figure (4)
    36 
    37 After editing, click on the save icon at the top of the column to save your script. [[BR]]
    38 Next, click and drag the icon at the top left corner over to the right column Execute.[[BR]]
    39 
    40 === D.1.3 Execute ===
    41 
    42 Here, you can start your experiment and Visualise it. In the name tab, type in the name you wish to give the experiment. There are no particular rules for this.[[BR]]
    43 
    44 Under slice name, type in the name of your slice as you have entered in the Flukes tool while setting up your slice. [[BR]]
    45 Then. scroll towards the bottom of this column and under the tab named Graph, type 'true'.This enables the graph view on your execute column.[[BR]]
    46 Once the experiment starts running you will be able to scroll down and view the graph.[[BR]]
    47 
    48 [[Image(Labwiki_4.png)]]
    49 
    50 Figure(5)
    51 
    52 Click on 'Start Experiment' at the bottom of the screen.
    53 
    54 [[Image(Labwiki_5.png)]]
    55 
    56 Figure(6)
    57 
    58 After a couple of seconds, you can see the graph at the bottom of the screen.[[BR]]
    59 
    60 [[Image(Labwiki_6.png)]]
    61 
    62 Figure (7)
    63 
    64 
    65 You can click and drag it to the Plan screen just above Figure 12. This will display the graph along with the experiment description. This graph is also dynamic.[[BR]]
    66 
    67 [[Image(Labwiki_7.png)]]
    68 
    69 Figure (8)
    70 
    71 You can click and drag the experiment description to the Prepare column. This allows you to add any comments or details about the experiment results.[[BR]]
    72 Similarly, Experiments 2 and 3 can be run using the same procedure. Experiment 2 does not have a graph.[[BR]]
    73 
    74 [[Image(Labwiki_8.png)]]
    75 
    76 Figure(9)
    77 
    78 Once you have your slice up and running you can visualize any experiment using !LabWiki.
     122[[BR]]
     123[[BR]]