Web Access to MedicineBow: Featuring OnDemand

Owned by Lisa Stafford
Last updated: Aug 29, 2024
6 min read

this page is being reviewed for content (completeness, accuracy, usability, etc)

Overview

MedicineBow OnDemand (formerly named Southpass on Beartooth) is ARCC’s latest implementation of OnDemand. It is a publicly accessible site for access to ARCC’s newest High Performance Computing resource, MedicineBow.

Requirements

Requirements Specific to MedicineBow

 

How to Log In

MBOnDemand is available on and off campus from the https://medicinebow.arcc.uwyo.edu website and will require UWYO 2 Factor Authentication be set up for all UWYO accounts.

When browsing to the site, you will be presented with UW’s ARCC’s Login Screen. As a good cybersecurity practice, make sure the website reflects an arcc.uwyo.edu website address before putting in your uwyo username and password. ARCC’s MedicineBow Login Screen should display the following login screen:

All UW Users will need authenticate to UWYO using 2 factor authentication. If you do not receive any 2 factor prompt, log into: https://wyosecure.uwyo.edu and check your default 2 factor settings to make sure you’re not locked out of 2 factor, and that your default 2 factor method is accurate.

You will hit the <enter> or <return> key, after you enter your username and password, unless you are using a yubikey.
**If you are using a yubikey, see the section below on authenticating with a yubikey.

Otherwise, you may authenticate with 2 factor as you would normally. If you don’t know what your default 2 factor method is, this is set for your account in your https://wyosecure.uwyo.edu settings. (Usually default is to receive a push on your default duo device. If you have never set up duo on any device, you may receive a phone call on your default phone number). Specific login instructions for each 2 factor method may be found here.

If you have not set up a default method for 2 factor authentication, you may be provided with a list of options to 2-factor authenticate, similar to the following screenshot:

If provided with an option select one now, to authenticate. Otherwise, you should have received your default method for 2 factor authentication.

Once you have authenticated through a two factor mechanism, you should see the MBOnDemand dashboard.

If using a yubikey for 2 factor authentication: you will enter your uwyo username in the username field, and your UWYO account password in the password field, followed by a comma (,) then touch your yubikey to authenticate.
Note: After you’ve entered your password and the comma, do NOT hit enter. Instead, your login prompt should look like this:

then without hitting enter, touch the yubikey to provide 2 factor authentication.

This will log you in.

Using OnDemand

Once you are logged into MedicineBow OnDemand you will be presented with a web interface that looks similar to the following:

 

 

The MedicineBow OnDemand interface is broken into different areas:

  • The gold menu bar across the top of the page, which contains tabs for:

    • Apps - All Applications

    • Files - Allows you to work with files from different authorized file systems

    • Jobs - Job management tools

    • Clusters - Access to and status of different clusters

    • Interactive Applications - Allow you to run specific tasks or software

    • SSH - To manage ssh keys for access to the cluster.

    • My Interactive Sessions - A link to all current OnDemand sessions you are running on MedicineBow

  • Pinned Apps, the area on the bottom left of the web page, contains quick access tiles to different applications supported on MedicineBow OnDemand.

  • Message of the day, located in the bottom right corner of the web page, providing HPC users with important, up-to-date information.

 

Accessing Your Files

Note: The current max file size is limit is set to 10GB.

After connecting, click on the home directory from your MedicineBow OnDemand dashboard or click on files in the drop down menu:

You should then see your home directory on MedicineBow, but may also access your project or gscratch space:

File and directory modification options are available along the top of this window:

“show owner/mode”: Show who owns the file/directory (often helpful in shared Project folders).

“show DotFiles”: Show hidden files.

The Files drop down allows you to see your different storage space that you have access to. After selecting a storage space, you will be shown the files in that area. You can then:

  • Create a new directory

  • Create a new file

  • Download/Upload files to the current directory

  • Copy and Move files to a new location

  • Rename Files

  • Delete Files

  • Edit Files

 

Jobs Dropdown

From the Jobs drop down, you can either view your jobs or all jobs currently running on the MedicineBow Cluster. From the Job Composer subpage, you can manage all aspects of running jobs on the MedicineBow Cluster:

  • Create New jobs from templates to run on the cluster.

  • Create personnel job templates to support your work

  • Submit jobs to the cluster

  • Delete jobs that have been submitted to the cluster.

  • Edit job files

  • Set job options for a job

  • Delete Job files that are not longer needed

Note: Job composer script is limited in size and defaults to approximately 65kb. If your job script is larger than 65kb it will not be accepted.

Clusters Dropdown

This provides a link to obtain shell access to the MedicineBow cluster login nodes. This is the same as using SSH in a command line interface (CLI) to connect to the cluster’s login nodes where you can launch an interactive salloc session, or submit jobs via sbatch. Note that:

  • since we’re on the login nodes, do not run intensive jobs/tasks directly here.

  • there is also MedicineBow Shell Access tile in the Pinned Apps area.

  • finally, be aware that if you have a custom shell prompt, some browsers may not display it properly.

The Clusters Dropdown and the Pinned Apps area also have a MedicineBow System Status link/tile which provides a high level summary of the current cluster usage.

Interactive Apps

The Interactive Apps drop down contains items to launch certain GUI environments on MedicineBow compute nodes (this has limited node support). You will get a complete Linux desktop when you submit the job and connect to the environment. ARCC currently supports the Xfce desktop GUI environment within MBOnDemand. Once you have submitted the job, your job will be queued and when resources are available you will be provided a “Launch MedicineBow XX Desktop” button. Clicking this button will open a new browser tab and the GUI will be displayed.

You should properly close out the Desktop when you no longer need it. This can be down by using the GUI logout feature or using the Delete button on the job page. This releases all requested resources back to the the system. You should also occasionally delete any old jobs as they are left in your home directory. Not doing so may lead to your home directory quota being consumed.

Servers (Applications)

The interactive server part of the Apps drop down contains items to launch certain GUI applications interactively on different MedicineBow cluster compute resources. One then gets a fully functioning application on the requested compute resources. Some of the currently supported applications include:

  • Jupyter Lab and Notebook