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Using the OnDemand Web Portal on the UMD HPC clusters

This page provides some instructions on the use of the Open OnDemand Portal (OOD) for interacting with the UMD HPC clusters. This is a good place to start reading for new users to the cluster, especially those who are not very familiar with using the Linux/Unix command line, as it has features that can increase the usability of the cluster in such cases. However, even advanced users might find various features, in particular Interactive Applications, Batch Jobs and Shell Access useful, especially when on the road.

NOTE: the OnDemand Portal only provides access to the Deepthought2 and Juggernaut clusters at this time. Access to Bluecrab is NOT supported.

WARNING
If you ever use the OnDemand portal from a public/shared system, ALWAYS BE SURE to COMPLETELY EXIT THE BROWSER when you are finished. Otherwise your login credentials could be stored in session cookies and the next person to use the machine might be able to access your accounts on the HPC clusters.
  1. Connecting to OnDemand
  2. Using the OnDemand File Manager
    1. Overview of File Manager screen
    2. Navigating directories
    3. Manipulating files
    4. Miscellaneous items
  3. Interactive Apps
    1. Interactive Desktop Session
    2. Interactive Matlab Session
    3. Interactive Jupyter Session
  4. Batch Jobs
    1. The Job Composer
    2. The Job Templates
  5. Monitoring your jobs, etc
  6. Shell access
  7. Developer documentation

Connecting to the OnDemand Portal

Connecting to the OnDemand Portal is easy. Just open a web browser on your desktop/workstation/etc, and go to the URL for the HPC cluster you are using:

HPC Cluster URL for OnDemand Portal
Zaratan https://portal.zaratan.umd.edu
Juggernaut https://portal.juggernaut.umd.edu
MARCC/Bluecrab No OnDemand Portal at this time
WARNING
You must completely exit your web browser in order to fully log out from the OnDemand portal. If you ever use OnDemand from a public/shared system, ALWAYS BE SURE to COMPLETELY EXIT THE BROWSER when you are finished. Otherwise your login credentials could be stored in session cookies and the next person to use the machine might be able to access your accounts on the HPC clusters.

You will be prompted for your username and password, use the same credentials you use to access the login node for the cluster. Once logged in, you will see the Dashboard home page, the main feature of which is the red navigation menu bar across the top, as shown below: Various sections of the OnDemand Dashboard screen

The navigation menu bar is what you will use to access much of the portal functionality. A similar navigation bar occurs on most of the other pages, although a different color and fewer and different menu options. Note the following features of the dashboard navigation bar, going from left to right:

  1. All the way at the left (marked A) is a label with the name of the cluster the OnDemand portal is for. Although not particularly needed on the dashboard screen (since the cluster is clearly indicated in the large logo beneath the navigation bar), this occurs on most of the child screens for portal, where it might be more useful, and you can click on it to get back to the dashboard.
  2. Next is the Files dropdown menu (labeled B in the screenshot). The dropdown will give a list of directories, including your home and lustre directories, and selecting one of the will open the OnDemand File Manager in that directory.
  3. The next menu item is the Jobs menu (indicated by the C), which provides access to utilities for dealing with batch jobs. In particular, there is a link to monitoring your batch jobs and a link to the
  4. The Job Composer utility.
  5. The Clusters dropdown menu (labeled D) comes next. Currently we have separate portals for each cluster, so this will only have a single item, which provides shell access to one of the login nodes for the specified cluster. You will need to use the Linux/Unix command line to make use of that, but it is handy if you need to access the cluster from a machine without an ssh client installed.
  6. The next two menu items deal with interactive applications and sessions. The Interactive Apps drop down menu (marked E) returns a list of interactive applications supported by the portal. These will launch interactive jobs running the specified application and supporting a graphical interface through the web client. The jobs go through the scheduler and run on compute nodes, so there might be significant waits before resources are available if the cluster is busy. But it does allow graphical displays without needing to install X on your workstation. The My Interactive Sessions entry (indicated by the F) will allow you to review, connect to disconnected sessions, and/or terminate interactive sessions.
  7. Some users may see a Develop menu (G in the screenshot). This is for more advanced users who are working with DIT to develop job templates, etc. to assist less advanced users in their field. This is discussed more in the section on Developer documentation Contact systems staff if you are interested in developing job templates.
  8. The Help drop down menu (marked H) contains links to URLs to submit help tickets, access the HPC documentation, change your password, etc.
  9. The final bits of the navigation menu (marked I in the screenshot) list the username with which you are logged into the system. That could be helpful for people with a normal account and say a temporary class account. There is also a Log Out button; do NOT use this. In order to provide it's functionality, OnDemand uses cookies, cached passwords, etc., and you need to fully exit your web browser to really log out. The Log Out button will not really log you out.

Note: to fully log out, you should exit the web browser, as otherwise some credentials might still be cached, enabling the browser to login automatically (without your entering a password) if the site is revisited within a day or so. ALWAYS FULLY EXIT the web browser, especially on shared machines. You might also want to consider using private browsing sessions if your web browser supports it.

WARNING
If you ever use the OnDemand portal from a public/shared system, ALWAYS BE SURE to COMPLETELY EXIT THE BROWSER when you are finished. Otherwise your login credentials could be stored in session cookies and the next person to use the machine might be able to access your accounts on the HPC clusters.

Using the OnDemand File Manager

The first bit of functionality we will discuss is the OOD File Manager app, which is accessed via the leftmost Files drop down menu on the navigation menu bar at the top of the Dashboard. When clicked, you get a choice of where you want the File Manager to start (where USERNAME is your username below):

NOTE: you will only see the options currently available to you, so you might see only one of the two lustre options.

Click on the directory you wish to explore, and click on it, and the explorer window will open, based in the selected directory.

Overview of File Manager screen

The File Manager page has a lot going on in it, and here we provide a brief overview to the various components it presents.

Various sections of the File Manager screen

Navigating directories

This section gives a brief tutorial on how to navigate to the desired directory in the OOD File Manager. In general, there are several ways to accomplish this.

Probably the easiest way to navigate to directories under the base directory with which the File Manager was launched is to double click on the directory name in the file list frame (E). This will cause the current directory to descend to the selected directory. To move up the directory tree, you can double click on the special .. directory at the type of the directory list (in Unix, .. stands for the parent directory).

Alternatively, you can double click on a directory in the directory tree view (A). With the ability to expand and collapse branches, this offers an easy way to jump between directories.

Finally, you can also click on the Go To... button in the main menu bar (B). This will open a dialog in which you can enter the path to the directory you wish to navigate to.

Whichever choice you use, when you change directories the path listed in the current directory field (C) will be updated to reflect the new path, and the contents of the file list frame (E) will show the new directory. Also, the directory tree view (A) will highlight the appropriate directory, in most cases. If the directory is not visible in the tree view because the branch it is in has been collapsed, the closest parent of the branch that is visible will be highlighted. And if you leave the root branch with which the File Manager opened (either by using the Go To ... button or navigating to the parent of the root directory, the Directory Tree view will just highlight the root directory).

Manipulating files

This section gives a quick overview of how to use File Manager to manipulate files. In general, the first step is to navigate to the directory containing the file you wish to manipulate in the main file list frame (E), and select the file you wish to manipulate. (For creating a new file/directory, or uploading a file, just navigate to and open the directory in which the new file/directory should go.)

To see the contents of a file, just select the file and click on the View button in the file manipulation menu bar (D). NOTE: the viewer in the File Manager is limited in terms of what type of files it can view. Text files are OK, and it handles most common graphical image files (html, pdf, png, jpg, etc). Using it on other binary files (including ps, zip, tar, various Office formats, etc) is likely to produce unsatisfactory results. The exact list of what formats work and which do not is likely dependent on your browser and its addons/settings.

To create a new empty file or directory, navigate to and open the desired parent directory, and then click on New File or New Dir in the main menu bar (B) for a new file or directory, respectively. This will open a dialog allowing you to enter the name for the new file or directory.

To upload a file from your workstation to the cluster, navigate to and open the desired parent directory, then click the Upload button in the main menu bar (B). This will open a dialog with a Browse button, click on the browse button and a file dialog will open. Select the file on your workstation which you wish to upload, and it will be uploaded to the currently open directory.

To download a file from the cluster to your workstation, navigate to the directory containing the file and select the file. Then download the file as you would any other web content (e.g. on Firefox, right click on the file and select Save Link as).

To edit the file, you can simple navigate to the containing directory, select the file, and then click on the Edit button in the file manipulation menu bar (D). This will open a simple WYSIWYG editor inside OOD. Make your eidts, and when you are done, click on the blue Save button in the upper left. To abandon your edits, simply abandon the page without saving (i.e. close the browser window).

To delete a file or directory, navigate to the parent directory and select the file/directory you wish to delete. Then click on the red Delete button on the right of the file manipulation menu bar (D). This will open a dialog confirming that you wish to delete the object. NOTE: Once you delete something, it is GONE, it cannot be recovered. NOTE: The Delete button will allow you to delete a directory with files and/or subdirectories without any additional warnings (other than the aforementioned basic confirmation). USE THE DELETE BUTTON WITH CARE.

The Rename/Move allows you to rename or move a file. Just navigate to the parent directory and select the file to be renamed/moved, and then click the Rename/Move button. This will open a dialog allowing you to type the new file name (defaulting to the current name). You can then type a new name. If you do not include a directory path separator ("/"), it will rename the file in the same directory. If you include a path separator, it will move (and possibly rename as well if you changed the base name) to the new directory. Note: the new directory must already exist.

To copy one or more files to a new directory, it is you can use the copy and paste method. Navigate to the containing directory and select the file(s) you wish to copy (to select multiple files, first select one, then hold the control key down when selecting subsequent files. Or you can hold the shift key to select a range of files), and then click on the Copy button in the file manipulation menu bar (D). Then navigate to the new directory, and click the Paste button to copy the files to the new location.

To make a copy of a file in the same directory with a different name is not well supported. I think the best option is to copy and paste the file to a different directory (creating a temp subdirectory if needed), then rename the file in that directory and then move back to the original directory.

Miscellaneous items

Normally, the main file list frame (E) only shows file/directory name, size, and modification date. If you click the check box Show Owner/Mode in the main menu bar (B), it will also show the file/directory owner and the mode/permission bits (the latter will be in the standard Unix format).

Also, by default, files and directories whose name start with a '.' (period) character are omitted in the list --- this is in accord with the standard Unix custom to treat files with such names as hidden files/directories. You can check the Show Dotfiles checkbox in the main menu bar (B) if you wish to see these "hidden" files.

The Open in Terminal button in the main menu bar (B) will open an ssh session on one of the login nodes for the cluster. Despite being in the File Manager section, it does not automatically change directory for you. This can be an alternative to installing an ssh client on a system.

Interactive Apps

One of the more interesting features of the OnDemand portal is that availability of "interactive applications". These allow you to launch an interactive session on one of the cluster compute nodes. What is especially nice is that these applications support graphics without the overhead of installing an X server on your workstation --- you get a full graphical interactive session over your web browser.

You can access the various interactive apps from the Interactive Apps drop down on the main, top menu bar from the OnDemand dashboard. They are also listed in the navigation frame on the left from the interactive app menu page, allowing you to quickly jump around between applications.

When an interactive app is launched, it waits in the queue for an available node just like any other job. Depending on how busy the cluster is, the wait time can be a couple of minutes to several hours. You can often reduce the wait time by using the debug partition, but in those cases your interactive job is limited to 15 minutes. Even in the non-debug partitions, various choices you make (such as number of cores/nodes, walltime, if you need GPUs or not) can affect your wait times.

WARNING
The VNC connection used for displaying the GUI is rather dependent on the browser being used. In particular, we have seen issues when connecting with Chrome browsers on Windows workstations. We recommend Firefox for Windows users.

The Division of IT is working to add more applications to the list of those supported in this section of the portal, so it might be worth checking back here periodically. Currently, the following interactive applications are supported:

  1. Interactive Desktop Session
  2. Interactive Matlab Session
  3. Interactive Jupyter Session

When you click on an interactive app in the drop-down list, you end up on the main setup page for that application. This starts with a line or two describing the application, and then has a form with a number of fields to fill out. At the bottom of the form is a blue Launch button; clicking this button will cause the interactive job to be submitted.

Although the form fields are application specific, a number of the fields crop up frequently and will be discussed here.

At the bottom is a blue Launch button, when all the form elements are set to the proper values you can click on that button to submit the interactive job. At this point you will be redirectored to an interactive session page, which show information about the job as seen below: Various sections of an Interactive Job screen

There is a heading bar at the top, with background colors representing various states of the job. On the left side of this bar are the name of the application (labeled A in the diagram, and showing Deepthought2 since this screenshot for the Deepthought2 desktop application) and the job number (labeled B or 3134478 in this example). On the right side of this menu bar are information about the size of the job (labeled C; this example requested 1 core on 1 node) and the state of the job (labeleed D, with a value of Running in this screenshot). The background color of the bar varies with job state (gray for pending, blue for starting, green for running). The session data will go away when the job completes.

When the job is running, there will be a field (labeled E in the diagram) showing on which node the job is running, this field is absent until the job starts. The session ID, the long string of letters and numbers ( labeled H in our screenshot), is how the portal identifies your job. That string represents a directory under the ondemand subfolder in your home directory where the portal saves various information related to your job. You can click on the link to open the directory in the File Manager (and see the full path, if desired). By default, the output and any error files will go hear, as well as copies of the actual batch script used, etc.

If you change your mind about the job, you can use the red Delete button (strong>F on the right just below the header bar to cancel/delete the job. If clicked on, a dialog will open asking you to confirm the action.

The blue button at the lower left (indicated by the I in the diagram) is probably the piece you are most interested in. It typically will be labeled with the a word like "Launch" or "Connect", e.g. Launch Deepthought2, Launch MATLAB, or Connect to Jupyter. If you click this button, your browser will open a new tab containing an interactive graphical session on the node your job is running. E.g., for the interactive Desktop application, you get an Unix X11 desktop; for the Matlab application, you get the GUI for the Matlab program; for Jupyter you get an interface to Jupyter. You can interact with the program basically just as you would if you were sitting at a workstation.

While all of the applications discussed in this section are referred to as "Interactive applications", and indeed are interactive in that they enable you to interact directly with the application, many also support a "detached" mode. I.e., it is possible to launch an interactive Matlab session, do some work, then start a calculation that will take a couple of hours, and disconnect from the session (and even possibly log out and/or shutdown your workstation/laptop). Assuming you allocated enough time to the interactive session, you could then reconnect later to check up on the progress of the calculation.

Note: When you are finished with an interactive session, you should use the Delete button in the My Interactive Sessions tab to terminate the interactive session. You can also use that tab to ensure that the interactive application is truly terminated and not just disconnected (when terminated, it will not appear as an active session in that page).

Note: your allocation will be charged for the entire duration of the interactive session, whether you are connected to the session or not.

While disconnecting from interactive sessions, like described above, is permissible, please be mindful of the fact that the HPC resources are valuable, and it is wasteful and inconsiderate to colleagues to leave an active session sitting idly. So, returning to our Matlab example, if you start a calculation in an interactive session that you expect will take about two hours to complete, it is reasonable to disconnect and reconnect an hour or two later. But if you disconnect and only reconnect four hours later, the Matlab process would likely have been sitting idle for about two hours, despite the resources it is running on being reserved for your use --- that would be wasteful and inconsiderate. Generally, it is best to use the Interactive Applications feature when you really will be interacting with the application, and submit batch jobs for longer calculations which do not require user interaction.

Most (but not all) of the interactive applications make use of the noVNC javascript implementation of the VNC protocol for handling the remote display. In these cases, there will be a noVNC menu bar on the left edge of the screen. It is normally minimized, looking only like a small tab with an arrow pointing to the right. Click on that to open the menu (you can click on the arrow again to minimize it). In particular, the bottom most icon (sort of a rectangle split at a 45 degree angle with a line through it) is the button for disconnecting the session. Clicking on that will disconnect you from the session, but still leave the job running. You can use the My Interactive Sessions on the main OnDemand top menu bar to reconnect to the session later. Note: Disconnecting from the session does NOT end the job --- use the Delete button (F) to terminate the job. Your allocation account will be charged until the job is terminated.

The View Only (Share-able Link) button (labeled J) behaves somewhat similarly, but only allows one to view the program. You are unable to use the mouse or keyboard to control the program or enter data. The intent is that you can email the URL for this link to a colleague, and then they can watch as you interact with the program, presumably so one of you can assist the other with the use of the program.

If you disconnect from an interactive job but leave it running, you can use the My Interactive Sessions item on the main top menubar for the OnDemand dashboard to see what active interactive sessions you have. This will list the sessions and provide a blue button to reconnect to the session. You can also use this to confirm that all interactive sessions have been completely terminated and not just disconnect --- Note: disconnected but not terminated interactive sessions are still charging your allocation account. Use the Delete button (labeled F in the previous figure) in the My Interactive Sessions screen to terminate the job when you are finished.

Interactive Desktop Session

This application will open an interactive GUI desktop on one of the compute nodes. When you select the blue button (I in diagram above, labeled something like Launch noVNS in New Tab or Launch Deepthought2 or Launch Juggernaut) you will get a fairly standard Unix graphical desktop. You can open applications from the Applications menu (typically in upper left unless you moved it), etc. just as if you were sitting at a workstation.

Interactive Matlab Session

This application will start the requested version of Matlab on one of the compute nodes. When you select the Launch noVNS in New Tab button (I in diagram above), you will get a fairly standard Unix desktop running the Matlab GUI. You can enter matlab commands, plot data, etc.

The menu for configuring the job will have a MATLAB version field allowing you to specify the version of Matlab you wish to run.

Interactive Jupyter Session

This interactive application will allow you to start a jupyter notebook server on one of the compute nodes. Once the job starts, there should be a blue Connect to Jupyter button. If you click on that, you will get a interactive Jupyter session in a new tab.
This tab will show on the Files panel your home directory from where you can navigate to existing notebooks (file extension: .ipynb) or you can choose from the New pulldown menue (top right) whether to create a notebook for Python3 or R code.

The Logout button in the upper right of the Jupyter session deserve some special attention. If you click the Logout button, it will disconnect your session with the Jupyter server, but the Jupyter server will continue to run. You can reconnect with the session later from the My Interactive Sessions menu in the main top menu bar of the OnDemand dashboard. Note: Your allocation account will be charged as long as the job is running. So make sure you use the Delete Quit if you wish to finish the job. You can verify if you still have any interactive sessions running from the My Interactive Sessions option on the main top menu bar in the OnDemand dashboard.

Batch Jobs

The support for Interactive Applications in OnDemand is nice, but most production work on HPC clusters is done via batch jobs. Typically, one sets up a calculation that will run for many hours, or even days, and submits it to the cluster to run when resources become available (which in itself might take hours), and then return to look at the results after the job is done. Indeed, researchers often submit many jobs that are very similar, differing maybe only in the input data, or due to a slight tweak in a parameter or adjustment to the code.

Traditionally, the setting up and submission of jobs in that sort of production use of the HPC is done from the Unix command line, and while the various Unix command line utilities still probably make that the most efficient route for experienced Unix users, this presents a steep learning curve to potential HPC users without much Unix/Linux experience.

The Job Composer applet in the OnDemand portal can simplify this somewhat. While it does not eliminate all of the complexity involved in submitting batch jobs to the cluster, it does simplify many of the aspects, especially when combined with job templates, whereby you can start with some standard "template" jobs (developed by system administrators and/or other users) and submit these after making the requisite modifications.

The OnDemand portal also provides an easy to use interface for monitoring and managing your batch jobs once they have been submitted.

Job Composer

The Job Composer applet simplifies the process of creating and submitting batch jobs to the cluster. It is accessible using the Job Composer item on the Jobs drop down on the navigation menu of the OnDemand dashboard (marked C on the screenshot of the dashboard). You should see a web page similar to the one shown below. Your first time visiting the page, you will likely see some popup "help" windows leading you through the steps needed to create a job; you can click the Next button in each popup to move on. If you wish to see that sequence again, you can just click on the Help button in the navigation bar (D in the screenshot below).

Various sections of the Job Composer screen

At the top of the screen is the Job Composer navigation bar. To the left (marked A) is the name of the cluster the portal is for, and clicking on it will return you to the OnDemand Dashboard. There are also buttons Jobs (labeled B) and Templates(labeled C) which indicates which section of the Job Composer you are in. We are currently in the "Jobs" section; the "Templates" portion will be discussed more in the next section. The final piece of the navigation menu is the Help button at the far right (marked D). Clicking on this will open a sequence of helpful popups leading you through the process of creating and submitting a job (I believe this sequence will also run whenever you start the Job Composer without any jobs listed in the section marked L).

Job Composer: Basic use and navigation

The Job Composer allows one to create, edit, submit, and manage jobs based on templates or previously submitted jobs. The composer overloads the meaning of the term job; when you create a "job" in the Job Composer, it creates a new directory under the ondemand folder in your home directory and copies the relevant files to that directory. You then have a chance to edit, add, and/or delete files in that directory (typically via the OnDemand file manager), and when you are satisfied, you can submit the job to the scheduler on the cluster, at which point it becomes a "job" in the traditional HPC sense (i.e. from the scheduler's perspective). The Job Composer allows you to easily watch the status of the job, and even cancel the job if desired. You can also examine the output files generated by the job, and if desired use the Job Composer to create new jobs based on that job.

The starting point for all of this is the New Job button, labeled E in the screenshot. When you click on that button, you get four options for creating a new job:

  1. From Default Template: this will create a job from the default template. The default template is typcially a fairly basic and generic sequential job, so this is probably not a great choice in production. But it is useful for learning to use the composer.
  2. From Template: This will switch you to the "Templates" section of the Job Composer and gives you a selection of templates to choose from. This will be discussed more in the next section.
  3. From Specified Path: this will allow you to create a Job Composer job from a job created outside of the Job Composer. You will need to specify the path to the directory containing the job, and some other parameters. The contents of the directory you specify will be copied into the newly created Job Composer job directory.
  4. From Selected Job: this will copy an existing Job Composer job to a new Job Composer job. Before you can use this, you must have jobs in your job list (the table marked L in the screenshot) and have selected one of those jobs.

In production, you most likely will mainly be using the From Template and From Selected Job options, but for now select the From Default Template When you do this, a Job Composer job will be created and appear in the job listing (the section labeled L in the screenshot). The new job will look much like the third job in the screenshot (the Simple Sequential Job (default) from January 30, 2020 12:54 pm. Because you just created it, it will be "selected"; this is indicated by the blue highlighting (like the job with ID 2103 in the screenshot). A couple items to note:

The Job Details section (M in the screenshot) contains various details about the selected Job Composer job. They are fairly self-explanatory, but we point out several important ones below:

Script location
Earlier, we mentioned the the Job Composer basically creates a new directory for the Job Composer job and copies various files there. This is the path to the new directory for the job.
Script name
This is the name of the job submission script for the job, relative to the Script location directory above. This is the equivalent to the script you would pass to the sbatch command if running from the command line. When the job starts to run, this script is run on the first compute node assigned to the job and kicks off the calculations, etc.
Folder contents
This lists all of the files in the job directory. Each file name is a link; you can click on it and the file will open in the OnDemand editor (obviously, this is only useful for text files). For the default job, you should just see the submit script (submit.sh).
Submit script
This displays the contents of the submit script, as this script controls your job and so is rather important. You can review the script to make sure the job will do what you intend. If not, there are three buttons after the submit script you can use to make changes.
"Open Editor" button
This button will open the submit script in the OnDemand editor. You can use this to make changes to your script.
"Open Terminal" button
This will launch an ssh session to a login node and then cd to the Script location directory. This allows you easy access to the Job directory if you want to verify or make changes using the Unix shell/command line. Note that this does the same thing as the button Open Terminal labeled H in the screenshot.
"Open Dir" button
This will launch the OnDemand File Manager, looking at the Job directory. This is a good option if you need to make changes to multiple files, etc. This button does the same thing as the more readily accessible Edit Files button (labeled F in the screenshot).

The job defined by the default job template is quite simple. The submit script specifies some information to the scheduler (via the #SBATCH lines), telling it that it wants 1 CPU core and 1 GB (1024 MB) of RAM for at most 5 minutes on the debug partition, and that other jobs can run on the same node. It then does a module load to set up the environment for our hello-umd program, creates a temporary directory in the local node scratch space, and then outputs some basic information about the job. It then runs the hello-umd, saving the output to hello.out in the temporary directory, and then copies the hello.out back to the job submission directory. The hello-umd is just a simple Hello, World! program, i.e. it just prints out some identification and a welcome message. (The hello-umd code has both sequential and MPI variants, so it normally identified which of potentially numerous processes the greeting comes from. This "default" job just runs the sequential variant, so it should always be "process 0 of 1", but other job templates use the MPI variant which will print a greeting from each MPI task.)

Although this job, and indeed most of the job templates, are very simple examples, we tried to write the templates so as to follow good practices even when such are a bit of overkill for such simple cases. We have tried to generously comment the scripts to make it easier to follow what they are doing. We note the following features and practices in this job script and those of most of the other job templates:

Normally, you would make various changes to the submit script or other files in the job directory. If you started with a standard job template, you would likely want to change things so the job performs the calculation you are interested in. If you started with a previously submitted job of yours that failed, you would edit the submit script, etc. in an attempt to fix the problem. If you started with a job than ran successfully, you would edit things to perform a new (probably similar) calculation.

For now, however, we will just run the job as is. As previously mentioned, once you have a job (and it is selected), a number of buttons above the job listing table become active. The button Edit Files(F in the screenshot) launches the OnDemand File Manager starting in the Job directory for the job, and the Open Terminal button launches shell session to a login node and changes to the job directory, just like the Open Dir and Open Terminal buttons beneath the submit script in the Job Detail section (M in screenshot). The Job Options button (G in the screenshot) will allow you to change a few options for the job (job name, allocation account charged, and for advanced users job array options).

But the button we are first concerned with is the Submit button (marked as I in the screenshot). If you click this button, the Job Composer will submit the job to the scheduler. At this point, the job becomes both a Job Composer job and a scheduler (Slurm) job. The Status for the job should change to Queued, indicating that the job was successfully submitted to the scheduler and is waiting for the scheduler to assign it resources. Jobs from the default Job template get submitted to the debug partition, and so should start up quickly (usually less than 15 minutes, often within a minute or two). When the job starts, the Status will change to Running, and then to Completed when the job finishes. (Because the debug partition tends to have fast turn around, and the job is very quick to run, you might or might not see all of the intermediate states, depending on the timing of the job and the refresh of the OnDemand screen. But you should see the final Completed state.)

Once the job has completed, you should find that two additional files are present in the job directory, namely the files myscript.out and a file named something like slurm-XXXX.out where the X-es should be replaced with the job ID. (From earlier parts of this section, you can see the files using the Edit Files button (F in screenshot) or Open Dir button at the bottom of the Job Details section (M), or from the Folder contents list in the Job Details section (M)). The hello.out file contains the results of running the hello-umd command, because the output of that command was redirected to that file in the submit script. The slurm*.out file contains all the output from the submit script; basically the identifying information and time stamps. Although this job should not have produced errors, if errors occurred they could end up in either file.

Now that you have a job in the job listing section (L in the screenshot), you can select a job (with one job it is likely already selected) and click on the New Job button (E) and this time select From Selected Job. This will create a new job directory for the new Job Composer job, and copy the contents of the selected job's job directory into it. Note that the new job directory includes the hello.out and slurm*.out files from the previous job --- the Job Composer is not smart enough to omit those from its cloning process. I would suggest opening the OnDemand File Manager (e.g. use the Edit Files (F) or Open Dir (at bottom of M) buttons) and delete those two files --- they still exist in the original job directory, but you generally don't need or want copies of them. You can edit the job submit script for the new job if desired, or the myscript.sh if desired, and submit the new job.

Finishing off are discussion of the various components on the Job Composer screen are three more buttons: