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High Performance & Scientific Computing

Open OnDemand on Secure Enclave



Introduction

OpenOnDemand is a web-based portal/interface that provides access to the cluster’s HPC resources. You can manage files, jobs, and access graphical interfaces all through Open OnDemand. This document describes how to access and use Open OnDemand and its related services in the Secure Enclave. 

Access and Login

Please follow the below steps to successfully log in to web based graphical interface of ISAAC Secure Enclave cluster.

Figure 7.1: Initial login interface of Citrix
  • After clicking Log on button, below window will appear. Authenticate with DUO push or request a passcode.
Figure 7.2: Two step verification window to login to Secure Enclave
  • Once logged in, click on the APPS menu and Open Chrome Secure Enclave.
Figure 7.3: Different applications in Citrix environment
  • Once the Chrome web browser is opened, type sip-login1-se.utk.tennessee.edu  in the address bar. You will be prompted to enter the username and password as shown in Figure 7.4. below.
Figure 7.4: Open OnDemand login screen
  • Enter the same username and password as you used to login to Citrix. Press Enter or click on Sign in button.

Upon successful authentication, you will see the Open OnDemand dashboard. The top dark gray ribbon of the dashboard contains several menus that grant access to files, jobs, and your current interactive sessions as shown in Figure 7.5.

Figure 7.5: Open OnDemand Dashboard

File Explorer

The “Files” menu in the top-left of the Open OnDemand dashboard gives you access to your files on the ISAAC Secure Enclave HPSC cluster from within a browser. Initially, the File Explorer shows your home directory and all its contents. Figure 4.6 shows the File Explorer interface.

Figure 7.6: file explorer interface

File Explorer Navigation

To navigate through directories, double click on the directory you wish to enter. To return to your former directory, double click on the directory highlighted with a red box. If you are unsure where you are located within the directory tree, look above the directory listing pane (above the red box marked in Figure 7.6). You will see several names and letters separated by forward slashes (/). This indicates the absolute pathname of your current location. In Figure 7.6, the current directory of the user is his/her home directory located at /nics/b/home/<netID>.

In the left most pane of the File Explorer, you see the button for your home directory. If at any time you wish to return to the top-level of your home directory, click on Home Directory. You may also navigate to directories within your home directory using central pane.

To quickly navigate to a specific directory, click on the Go To.. button highlighted with red box as shown in Figure 7.7. A new window similar to below will appear.

Figure 7.7: Entry widget to change to any directory

Enter the absolute path of the directory to which you wish to change and click OK. For example, to navigate to your Lustre directory, type /lustre/sip/proj/<project-name>/<netID> where <netID> is your University NetID. The file explorer will then place you in the specified directory and display its contents as shown in Figure 7.8.

Figure 7.8: Change directory option in file explorer to change to any directory and current location (project name and netID are redacted)

Open OnDemand’s file explorer can show permissions, ownership, and hidden files. In the top-right of the explorer window, check the boxes for “Show Dotfiles” and “Show Owner/Mode” to enable these views. Figure 7.9 shows the directory listing pane with the Show Owner/Mode option enabled. Permissions and ownership cannot be modified from within this interface. Hidden files are prefaced with a dot (.) and are usually user configuration files.

Figure 7.9: File explorer options to view access permissions

To view a specific file, select the file in the directory listing pane. Double Click on the file or select the file and click on the View button highlighted with red box on the left as shown in Figure 7.10, the plaintext contents of the file will appear in a new window. To edit the file select Edit option next to View.

Figure 7.10: Editing and viewing a file.

Editing files

To create a new file in the File Explorer, select the option labelled New File as shown in Figure 7.10 on the top right above the central pane. Its icon is a sheet of paper with a plus (+) symbol. When you click on the option, the File Explorer will prompt you to name the file. After you name the file and confirm its creation, it will be placed within your current directory.

Figure 7.11: File Editor in Open OnDemand

To modify the file, select the file in the directory listing pane, then select the option labelled Edit as discussed above Figure 7.10. The OpenOnDemand editor will open. You can then type the information you wish to put in the file. The editor features several customization options, such as the editor’s theme and text mode. When you finish editing the file, click “Save” in the top-left of the editor. When you return to the File Explorer and view the file, you can view the changes you made.

The File Explorer also allows you to rename existing files and directories. To rename a file or directory, select the item you wish to rename in the directory listing pane. Next to Edit button, there is a Rename/Move button, click it. The File Explorer will prompt you for the new name, and once you confirm it, your changes will take immediate effect.

Files and directories can be copied and pasted within the File Explorer. To copy a file or directory, select the item in the directory listing pane, then select the option labelled Copy next to Download button highlighted blue (Figure 7.10). Once the item has been copied to your clipboard, navigate to the location to which you intend to copy the file, then select the option labelled “Paste.” next to Copy button. The copied item will then appear in your current directory.

If you wish to delete a file or directory, select the item in the directory listing pane, then click the Delete button (red) on the right hand side of the explorer window. You will be prompted to confirm the deletion. Once confirmed, the item will be permanently deleted.

Downloading and Uploading Files

We do not recommend downloading files using Open OnDemand File Explorer. The web interface of ISAAC Secure Enclave cluster is accessed via Google Chrome browser which is installed in a Virtual machine inside the Secure Enclave, therefore, when you will click download, the browser will try to save the file onto the VM. However, no such permissions are granted to the users to write on the VM hosting the Secure Enclave applications. Due to these restrictions, users will also not be able to upload the files directly to cluster.

We recommend the users to refer to the Secure Enclave Data Transfer page to see the possible options to transfer data to/from Secure Enclave HPSC cluster.

Job Management

Under the Jobs drop-down menu next to Files menu in the OOD dashboard (Figure 7.5), you have two options: Active Jobs and Job Composer. Both options provide advanced job management from within a web browser.

Job Monitoring

In the Active Jobs section, you will see an organized list of your queued and running batch jobs on the cluster. Figure 4.9 shows the Active Jobs interface. You can filter through jobs to see particular entries, in addition to sorting by the attributes of your choice. To do this, click on the arrows next to the attributes until the list is sorted as you desire.

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Figure 7.12: Active jobs interface

When a job is queued or running on the cluster, you can view detailed information on the job from within the Active Jobs interface. Figure 4.2 shows the information you will see on queued and running jobs.

To access this view on a queued or running job, click the right-facing arrow on the far-left of the job’s row. You will then see statistics and information about the selected job. Of note is the Output Location of the job, which Figure 4.10 highlights. Each job you create and start through OpenOnDemand is placed within your /home/ondemand directory, so when you wish to retrieve the job’s data, remember to navigate to your ondemand directory. You can specify another output location when you create the job through OpenOnDemand or edit the job script to supply another location.

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Figure 7.13: Detailed view of a running job

Job Creation

In the Job Composer section, you can create new batch jobs to run on the cluster based upon several criteria. Figure 4.11 shows the Job Composer interface. When you initially open the Job Composer, the system will briefly explain each option available to you. Once you click through these prompts, you may then click “New Job,” then select the template, path, or job you wish to add. Note that if you close the initial information menu, you will not need to click through each prompt.

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Figure 7.14: Job composer interface

When you add a new job from the default template, the Job Composer will create a Simple Sequential Job. In addition to the job, it will create a job script and a job directory. Figure 4.11 shows the Job Composer interface when a job is created with the default template. To modify the job’s options, select Job Options. You can specify the job’s name, cluster, script, and account. To edit the job script, highlight the job and select the Edit Files option in the Job Composer interface. Select the job script, then select Edit. You may also rename the job script if necessary. Additional files can also be uploaded or created in the job’s directory from the File Explorer.

Jobs may also be created with other templates. These can be the default templates or templates that you build within the Job Composer and can be found under the dropdown menu +New Job as shown in Figure 4.11.

In addition to template-based job creation, you may also create jobs based upon a specified path or an existing job. With a specified path, you create a job based upon a directory that already exists. The path will either be to your home or project directory. Once you specify the path, you then modify the typical attributes of the job. With a job created based upon an existing one, select an existing job in the queue, navigate to New Job, then select “From Selected Job.”

Beyond job creation, the Job Composer allows you to submit, stop, and delete your existing jobs. Like the Active Jobs menu, you can filter and sort the available jobs.

noVNC

noVNC allows users to interact with the cluster in a graphical desktop environment from within a web browser. noVNC is particularly useful when you require a graphical X11 application.

To launch a noVNC session, log in to OpenOnDemand. In the dashboard, select “Interactive Apps” from the top-left of the window. In the dropdown menu, select “SIP Desktop.” This will open the session submission form depicted in Figures 7.15.

Figure 7.15: SIP Desktop session submission form

In this form, specify the resources your application(s) require. All the available options map to sbatch options for interactive jobs. To learn the meaning behind these options, please review the Interactive Jobs section of the Running Jobs document. For most situations, a single node with one core is sufficient. If your application requires GPUs, please specify campus-gpu as the partition. Please be aware that the number of cores per node you request directly influences the memory your job receives. Therefore, make sure to request enough cores for your job so that your job does not runs out of memory leading to the termination of the job.

It is also important to note that you can request node-exclusivity for your session. With node-exclusivity, no other session will run on the node your session receives. In cases where the application you will use in the session is resource-intensive, setting this option to “Yes” may be beneficial. Otherwise, leave this option as “No.”

Submit the noVNC session to the scheduler by clicking on the Launch button in Figure 7.15. For most single-node, single-core jobs, the session should begin within five minutes; however, this is dependent on the current resource utilization of the cluster. If you requested multiple nodes, it could take longer for the session to start. When the session is ready, access it by clicking the Launch SIP Desktop in New Tab button. Figure 4.13 highlights this button.

Figure 7.16: Active noVNC interactive session

When you access the session, you will see a standard Linux XFCE desktop environment. In the top-left of the GUI, the Applications menu contains links to several useful packages. In the bottom-middle of the GUI, you can open your home directory with the file cabinet icon. The black icon with a greater-than (>) symbol in it opens a terminal. From this terminal you can perform any task you would from a standard terminal such as accessing files, loading modules, and running applications.

If you wish to manually terminate the noVNC session, click on your username in the top-right of the GUI and select “Log Out.” Then, delete the session in OpenOnDemand. You will receive an email confirmation of the job’s deletion.

Jupyter Notebook

Launching Jupyter Notebook

Jupyter Notebook is a web-based application that enables you to intuitively create and manipulate data on the cluster. It features a fully-functional Python 3 IDE (integrated development environment), a text editor, and a file manager. The sections below outline how to access and set up Jupyter Notebooks on the cluster.

To access Jupyter Notebook, navigate to Interactive Apps on the OpenOnDemand dashboard. Select Jupyter Notebook from the dropdown menu. The Jupyter Notebook session submission form will appear as it does in Figure 7.17.

Figure 7.17: Jupyter notebook session submission form

The Jupyter notebook in Open OnDemand is configured with Anacond3. We have provided two different version of Anaconda. In this form, specify one of Anaconda versions to use the associated Jupyter Notebook, the account under which the job should run, the partition, the number of hours the job will run, and the number of cores your job requires. If you require the use of GPUs in your Jupyter Notebook session, select the campus-gpu partition. Please review the Running Jobs document for more information on these fields.

When you specify the necessary options in the form and select Launch. It will not take for the system long to deploy the Jupyter Notebook session, but this is dependent on the resources you requested. When the session is ready, you will see the similar interface that appears in Figure 7.18. The “Connect to” option will open a new Jupyter Notebook tab in your browser. Figure 7.18 highlights this option.

Figure 7.18: Jupyter notebook session ready to launch