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| <h1>How to Run PBS Jobs in PTP</h1> |
| <h2> |
| <a name="Introduction"></a>Introduction |
| </h2> |
| <p> |
| The PBS Eclipse plug-in, part of the <a |
| href="PLUGINS_ROOT/org.eclipse.ptp.doc.user/html/toc.html"> |
| Parallel Tools Platform</a> (PTP), allows you to launch and monitor |
| applications on local or remote PBS (Portable Batch System) |
| Distributed Resource Managers.<br> |
| </p> |
| <p> |
| The PBS Resource Managers use the new configurable (JAXB) framework. |
| (An in-detail explanation of the <a |
| href="PLUGINS_ROOT/org.eclipse.ptp.rm.jaxb.help/html/toc.html">JAXB |
| Model</a> can be found in the PTP Developer Guide.) What follows here is |
| a guide to the PBS-specific launch tabs. There are no special |
| requirements to run the PBS Resource Managers; consult <a |
| href="PLUGINS_ROOT/org.eclipse.ptp.doc.user/html/02resMgrSetup.html">Configuring |
| Resource Managers</a> for general information on resource-manager |
| requirements and set-up. |
| </p> |
| <h2 style="text-align: left;"> |
| <a name="Preferences"></a>Preferences |
| </h2> |
| <p>There is currently only one preference option. Since the PBS |
| Resource Manager is configured from an XML definition file, the file |
| can be cached the first time you add the resource manager (this is the |
| default behavior), or you can set it to reread the file every time you |
| start the Resource Manager. This is useful if you are doing |
| customization (see below) and are configuring from a special XML file |
| you have imported into your workspace. This way, if you make changes, |
| they will automatically be picked up without having to reboot the |
| application or recreate the Resource Manager. |
| <p> |
| <br> <br> |
| <div style="margin-left: 40px;"> |
| <img alt="Preferences" src="images/00Preferences.png"><br> |
| </div> |
| <br> |
| <br> |
| <ol> |
| <li>From the "Eclipse" menu, select "Preferences"</li> |
| <li>Open Parallel Tools / Resource Managers / Configurable |
| Resource Manager (JAXB)</li> |
| <li>Select "Always reload XML from URL" and click "Apply", then |
| "OK".</li> |
| </ol> |
| <h2 style="text-align: left;"> |
| <a name="ProvidedTypes"></a>Preconfigured PBS Resource Manager Types |
| </h2> |
| <p> |
| PTP provides two generic PBS Resource Managers, one which is |
| configured for batch submissions to the scheduler (<i>PBS-Generic-Batch</i>), |
| and one for interactive PBS submissions using a pseudo-terminal (i.e., |
| "qsub -I"; <i>PBS-Generic-Interactive</i>). The settings in these |
| configurations should work on most Torque systems and many PBS Pro |
| setups, though there may be differences in some of the attributes for |
| job submission which may have to be adjusted for depending on your |
| local system. |
| </p> |
| <br> |
| <br> |
| <div style="margin-left: 40px;"> |
| <img alt="PrefiguredTypes" src="images/01PrefiguredTypes.png"><br> |
| </div> |
| <br> |
| <br> |
| <p> |
| <b><i>For how to add, remove, start, stop and edit resource |
| managers, please refer to <a |
| href="PLUGINS_ROOT/org.eclipse.ptp.doc.user/html/02resMgrSetup.html">Configuring |
| Resource Managers</a> </i> </b> |
| </p> |
| <h2 style="text-align: left;"> |
| <a name="BatchSubmission"></a>Submission Using the PBS Batch Resource |
| Manager |
| </h2> |
| <p> |
| When you select the <i>PBS-Generic-Batch</i> manager, the Run |
| Configuration will have a Resources Tab with three sub-tabs available |
| for use. |
| <p> |
| <ul> |
| <li><b>Basic PBS Settings</b> |
| </li> |
| <li><b>Advanced PBS Settings</b> |
| </li> |
| <li><b>Import PBS Script</b> |
| </li> |
| </ul> |
| <p> |
| Each of these is an "independent" environment in the sense that the |
| specific variables set on one are not necessarily included in the |
| others, even though their underlying values are shared across all |
| three tabs; <b><i>the tab from which you select "Run" is the |
| environment that applies to the job</i> </b>. |
| </p> |
| <p>Thus if you use the Advanced Tab and set Job_Name to "pbs1", |
| then switch to the Basic tab, you will see Job_Name set to "pbs1" |
| there as well; however, if you launch from Basic, only the variables |
| seen on the Basic tab will be included in the configuration and script |
| for the job; any of the variables on the Advanced Tab not on the Basic |
| Tab will revert to an undefined or default value.</p> |
| |
| <h3 style="text-align: left;"> |
| <a name="BasicTab"></a>Basic Settings |
| </h3> |
| <p>Below is a view of the Basic tab. Job_Name and Wallclock Time |
| are validated fields, meaning that values with a specific syntax must |
| be provided (there are defaults); an error message on the top left of |
| the screen will appear in red in case these are incorrect. Hovering |
| over the Name label will display a tooltip, if there is one for that |
| attribute.</p> |
| <br> |
| <br> |
| <div style="margin-left: 40px;"> |
| <img alt="BasicTab" src="images/02Basic.png"><br> |
| </div> |
| <br> |
| <br> |
| <p>At the left bottom of the tab there are three buttons, "View |
| Script", "View Configuration" and "Restore Defaults". The first allows |
| you to inspect what the batch script that is generated from the |
| filled-in values will look like:</p> |
| <br> |
| <div style="margin-left: 40px;"> |
| <img alt="Configuration" src="images/04Script.png"><br> |
| </div> |
| <br> |
| <br> |
| <p>Similarly, the second button can be used to see the full |
| configuration underlying this particular tab setting (this is the |
| "environment" for the resource manager, and is useful to check to make |
| sure the values you have set on the tab will be correctly reported to |
| the resource manager):</p> |
| <br> |
| <br> |
| <div style="margin-left: 40px;"> |
| <img alt="Configuration" src="images/03Configuration.png"><br> |
| </div> |
| <br> |
| <br> |
| <p>"Restore Defaults" sets the values of the variables visible in |
| this tab back to their defaults, if they have any. This is different |
| from the "Revert" button on the lower right, which reverts to the |
| previously saved changes. All changes should be saved using the |
| "Apply" button next to it.</p> |
| <h3 style="text-align: left;"> |
| <a name="AdvancedTab"></a>Advanced Settings |
| </h3> |
| <p>The Advanced Tab exposes for configuration all the attributes |
| for job submission as defined in the XML. The viewer allows you to |
| select the ones that are applicable (only these will appear in the |
| configuration). The text box above the table/tree containing the |
| attribute list also displays a string of name=value defintions from |
| the table (here for viewing convenience only). The table has typed |
| values; it provides an appropriate editor (drop-down list, |
| numerical spinner, checkbox, etc.) to fill in the value according to |
| the value's type; doing "tab" after filling in the value effects the change. |
| The check box at the top left "Show Only Checked Items" allows you to |
| filter out unchecked items from the table list.</p> |
| <br> |
| <br> |
| <div style="margin-left: 40px;"> |
| <img alt="AdvancedTab" src="images/05AdvancedSettings.png"><br> |
| </div> |
| <br> |
| <br> |
| <h3 style="text-align: left;"> |
| <a name="ImportTab"></a>Importing a Predefined Batch Script |
| </h3> |
| <p>If you wish to use a custom script that does more than just |
| launch the application selected from you local or remote workspace, |
| this tab is where you do it. The "Browse Workspace" button at the top |
| right takes you first to your current workspace, in case you have |
| imported a batch script there from either your local machine or a |
| remote host; however, you can usually navigate from there to other |
| directories in your local file system to search for a script.</p> |
| <p>The path of the selected script is displayed in the textbox to |
| the left of the browse button, and the contents of the script in the |
| large (scrolling) text area below. The script is not editable there; |
| to edit, you will need to import it like any other file into your |
| workspace. The selection can be cleared or cancelled using the "Clear |
| Script" button.</p> |
| <br> |
| <br> |
| <div style="margin-left: 40px;"> |
| <img alt="Imported" src="images/06Imported.png"><br> |
| </div> |
| <br> |
| <br> |
| <h4 style="text-align: left;"> |
| <a name="OutputFiles"></a>Reading remote output and error files |
| </h4> |
| |
| <p>The JAXB/PBS manager has the capability of allowing you to |
| stream in to the console the output and error files associated with a |
| batch job when the job has completed. This is done in XML definition |
| file for the Basic and Advanced tabs by creating a link from the PBS |
| batch attributes defining Output Path and Error Path to special |
| variables understood by the resource manager. If you set those |
| variables, the change will be conveyed through this linked variable. |
| If they are not set, the configuration provides a value corresponding |
| to the default location where PBS would put them.</p> |
| <p> |
| <b>NOTE: </b>If you are using the Import Script tab, the two paths |
| must be manually adjusted to correspond to whatever you have done |
| inside the script; the default definitions are provided, but these can |
| be adjusted as necessary. You can also turn off this feature for this |
| tab by unchecking the "Enable remote output file read" to the left of |
| the text box. |
| </p> |
| <p>If there are files associated with this job, and the job |
| completes, the "Get Job Error" and "Get Job Output" actions, activated |
| by clicking row for the job in the monitor job table, can be used to |
| issue a streaming command which will write the file contents to the |
| console. If the files do no exist, these actions will be disabled.</p> |
| <br> |
| <br> |
| <div style="margin-left: 40px;"> |
| <img alt="Actions" src="images/08Actions.png"><br> |
| </div> |
| <br> |
| <br> |
| <h2 style="text-align: left;"> |
| <a name="InteractiveSubmission"></a>Submission Using the PBS |
| Interactive Resource Manager |
| </h2> |
| <p>The Interactive Resource Manager allows you to submit jobs |
| through a pseudo-terminal. This is done by issuing "qsub -I" (plus any |
| resource limits defined in the tab) upon the first launch, and waiting |
| for the interactive job to start. When the job turns from SUBMITTED to |
| RUNNING (this can be seen both from the reported state in monitor job |
| table views, as well as by the disappearance of the progress bars for |
| the submission), the job will then be streamed to the qsub terminal's |
| standard input, just as you would submit from a shell command-line. |
| Subsequent submissions will also be streamed to the same interactive |
| terminal process, for as long as it is running. If the time limit |
| expires, the next submission will resubmit the terminal request (qsub |
| -I).</p> |
| <br> |
| <p>The Launch Tab for this kind of job closely resembles the Basic |
| batch tab.</p> |
| <br> |
| <br> |
| <div style="margin-left: 40px;"> |
| <img alt="Imported" src="images/07Interactive.png"><br> |
| </div> |
| <br> |
| <br> |
| <p>The job output will go to the console when the job starts to |
| run, as seen here.</p> |
| <br> |
| <br> |
| <div style="margin-left: 40px;"> |
| <img alt="Output" src="images/09Output.png"><br> |
| </div> |
| <br> |
| <br> |
| <h2 style="text-align: left;"> |
| <a name="Customizing"></a>Customizing the Configuration |
| </h2> |
| <br> |
| <br> |
| <p>The Resource Manager configuration for PBS can of course be |
| customized to suit the needs of the systems you habitually work with. |
| Of course, an understanding of the basic structure and content of the |
| XML definition is necessary for this, but often it may simply be a |
| question of changing a few of the provided attribute defaults or |
| definitions or a special command definition.</p> |
| <p>The way to provide a specialized XML configuration is by placing |
| it in a project named "resourceManagers" in your current workspace. |
| You can import a XML file into your workspace in three different ways:</p> |
| <br> |
| <ul> |
| <li><b>Using Import :: General :: File System</b> for files on |
| your local machine;<br> |
| </li> |
| <li><b>Using Import :: Remote Systems :: Remote file system</b> |
| for files on a remote machine;</li> |
| <li><b>Using Import :: Resource Managers :: Resource Manager |
| Definition from Plug-in</b> for the predefined definitions provided with |
| the PTP distribution.<br> |
| </li> |
| </ul> |
| <br> |
| |
| <p>In the first two cases, you must have created the |
| "resourceManagers" project first; the third wizard asks you if you |
| wish to create one if one does not already exist. The following |
| illustrates the last kind of import.</p> |
| <ul> |
| <li>Open up your Remote C/C++ perspective containing your |
| workspace</li> |
| <li>Right click in the Project Explorer and then select "Import |
| :: Import..."</li> |
| </ul> |
| <br> |
| <br> |
| <div style="margin-left: 40px;"> |
| <img alt="Output1" src="images/10Import.png"><br> |
| </div> |
| <br> |
| <br> |
| <ul> |
| <li>Choose Resource Managers :: Resource Manager Definition from |
| Plug-in</li> |
| </ul> |
| <br> |
| <br> |
| <div style="margin-left: 40px;"> |
| <img alt="Output2" src="images/11Import.png"><br> |
| </div> |
| <br> |
| <br> |
| <ul> |
| <li>Select one of the configurations from the drop-down list, and |
| click "Finish".</li> |
| </ul> |
| <br> |
| <br> |
| <div style="margin-left: 40px;"> |
| <img alt="Output3" src="images/12Import.png"><br> |
| </div> |
| <br> |
| <br> |
| <p>The XML file will now appear in an editor in your workspace. The |
| XML editor which has been included in the PTP all-in-one download |
| ("Eclipse IDE for Parallel Application Developers") does syntax |
| highlighting and also provides a design tree-view for examining its |
| structure.</p> |
| <br> |
| <br> |
| <div style="margin-left: 40px;"> |
| <img alt="Output4" src="images/13Import.png"><br> |
| </div> |
| <br> |
| <br> |
| <hr> |
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