Baskerville Portal

Baskerville Portal provides web-based access to a range of Baskerville services and some GUI applications, such as JupyterLab. Access is granted automatically with your Baskerville account. Baskerville Portal uses Open OnDemand.

Check out our video tutorial below:

Connecting to the Baskerville Portal

To connect to Baskerville Portal, please navigate to https://portal.baskerville.ac.uk and sign-in using your Baskerville account.

Portal apps and paths outside the home directory

In order to navigate to a project’s directory on Baskerville you must know its path. However, this is incompatible with some GUI applications’ built-in file managers that will only allow you to graphically traverse a directory tree. In this case you should create a symlink to the required path from inside your home directory using the ln -s command. For example:

ln -s /bask/projects/_initial_/_projectname_ ~/_projectname_

Where _initial_ is the first letter of the project name

Once this has been created you’ll be able to use this symlink to enter the project directory via your home directory.

Moving your default portal output folder

By default, jobs running on Baskerville Portal store their output in a folder called ~/ondemand/. Due to the limited quotas on users’ home directories, you may instead wish to move this directory to a Baskerville project directory (e.g. /bask/projects/_initial_/_projectname_).

1. Login to Baskerville Admin:

   1. Follow the View my info link.
   2. Under Projects, select the project where you wish to store your Portal data and copy its path from the “Storage path” field on the subsequent page.

2. Open a shell by connecting to Baskerville directly or via Baskerville Portal at: Cluster -> Baskerville Tier 2 HPC Shell Access.

3. Make sure you don’t have any existing Baskerville Portal jobs running (you can do this by clicking on My Interactive Sessions). Then type these commands:

   SRC=~/ondemand
   DST=_storagepath_
   rsync --stats --archive "${SRC}/" "${DST}/ondemand-${USER}"
   

   Where _storagepath_ is the path you copied from step 1.

   This will make a copy of your ondemand folder in the project directory. If you have a lot of small files in your ondemand folder the last command may take a minute or two.

4. Now you can move the old folder out the way and link the new folder in its place, with these 2 commands:

   mv "${SRC}" "${SRC}.old"
   ln -s -T "${DST}/ondemand-${USER}" "${SRC}"
   

5. Run a test job to ensure your data is now available in your project folder.

Troubleshooting

If, when attempting to start an Interactive App, you get an Internal Server Error message, please try the following fixes sequentially:

1. Navigate to the Help dropdown towards the top-right of the page and select “Restart Web Server”.

2. Rename / move the ~/ondemand/data directory using one of the following methods:

   • Via the Portal’s built-in file manager:
     1. Open the file manager by clicking on “Files” (towards the top-left of the page) and then selecting “Home Directory”.
     2. Navigate to the ondemand directory and then click the three dots icon on the right of the data directory and select “Rename”. Enter a new name for the data directory, e.g. data.old.

   • Via your preferred terminal client (also applies to the Portal’s built-in terminal, which can be accessed via the “Clusters” link at the top of the page):

     mv "~/ondemand/data" "~/ondemand/data.old.$(date +%s)"
     

     This will rename the ~/ondemand/data directory, adding a suffix comprising “.old” and a unix timestamp representing when the copy was made.

   • If you performed the rename using one of the Portal-based methods, please now logout.

   • The next time you connect to Baskerville Portal a fresh ~/ondemand/data will be created.

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Last update: August 1, 2023