About Educloud OnDemand
OnDemand is a web portal that allows you to run software interactively on the Fox HPC cluster.
It does this by submitting a Slurm job, and will automatically connect the applications interface to your web browser. This allows you to use Fox HPC resources very easily, without writing job scripts or using the command line at all.
Note that your job will still have to wait in line if there is a queue.
To start using it, simply go to https://ondemand.educloud.no and log in with your Educloud credentials.
Within you can find a number of applications, a file browser, a terminal application and an overview of slurm jobs.
Installed software
Rclone
Ondemand automatically integrates with rclone. All you need to do is configure rclone from the command line, and once it is correctly set up your storage resource will automatically appear under the "Files" menu.
This can be used to easily integrate external storage, like for example object and cloud storage (Amazon S3, Google Drive, Dropbox, etc) so you can copy files back and forth.
For help setting up different types of storage, see the official rclone documentation.
Jupyter
We provide Jupyter Lab and Notebook.
See the Jupyter Ondemand documentation for more information.
RStudio Server
We currently have two different implementations of RStudio Server. One uses an Apptainer, while the other uses a software module.
The containerized installation includes a number of pre-installed libraries and packages. The container is made using Apptainer (previously known as Singularity) and transparently mounts home directories, project areas, scratch and other required paths.
This allows you to build your own ecosystem from scratch, which can be useful if the system-installed R modules are not suitable for your application.
The module based installation uses EasyBuild and LMod so that you can reliably load components from the appropriate toolchain. See the "Installing software on Fox" section for more details.
Building your own custom RStudio container
For your convenience, there is an option to run your own custom container image. You can load containers both from your home directory and from project directories, which for example can be used to avoid repeated time-consuming installing of packages.
See the Apptainer documentation for details on how to work with apptainer and definition files.
Note: You should only modify the %post section of the definition file - the other sections are required to maintain compatibility with Educloud OnDemand.
Quick start:
## Log in to Fox via ssh, or use the OnDemand shell access
## Clone the Fox RStudio container git repo
$ git clone https://github.com/unioslo/fox-rstudio-container
## Edit the definition file to add your libraries and packages
$ vim fox-rstudio.def
## Build a new apptainer
$ apptainer build my-custom-rstudio-container.sif fox-rstudio.def
## Copy the file to a suitable location and make note of the path
$ cp my-custom-rstudio-container.sif /fp/projects01/ec01/ec01-rstudio.sif
You can now use /fp/projects01/ec01/ec01-rstudio.sif as a custom RStudio container in OnDemand. Other users who have read access to the file can also use it.
Fox Desktop
A containerized desktop environment that lets you use normal GUI applications. This container is also used to run specific applications such as Matlab, 3D Slicer and ImageJ.
You can use Fox Desktop to run software you install yourself, or use the installed software modules.
Matlab
If you are a UiO employee you can run the desktop version of Matlab. We do not currently provide Matlab licenses for non-UiO users or projects.
Troubleshooting
If you are having problems with an application, you can find a log file for each job in your home directory under the path ondemand/data/sys/dashboard/batch_connect/sys/<application>/output/<session>/output.log
The "session" field is the same as is shown in the Ondemand user interface.
Hint: run ls -ltr to quickly find the latest session directory.
Note that these session directories are automatically deleted after 30 days. It is safe to delete them (or the entire "ondemand" directory) should you wish.