Running Jupyter Notebook

On VDI

Currently, the easiest way to run IPython Notebook is on NCI's Virtual Desktop Infrastructure (VDI). For a guide to set up and use VDI, click here.

Within VDI, open a Linux terminal (Applications menu -> System Tools -> Terminal). Inside the Terminal, load the conda environment

module use /g/data/hh5/public/modules
module load conda

You should then be able to start the notebook with

jupyter notebook

On Gadi

You can also run a notebook from Gadi's compute nodes using the gadi_jupyter script.

Notes

• You need to download this script to your own computer and execute there. The script handles the connection.
• This job requires an implementation of bash. This is default on MacOS and Linux, but not Windows.
• This will cost SU depending on the queue and the resources requested (default: 1 cores, express queue)
• You also won't have access to the internet to, for example, download data.

Running

You can download the script from the link above directly, or by running

git clone https://github.com/coecms/nci_scripts.git

which will download the script into a directory called nci_scripts.

There are several options that you can use when running the script:

General Options:
    -h:         Print help
    -l:         NCI username
    -L:         NCI login node (default 'gadi.nci.org.au')
    -e:         Conda environment

Queue Options:
    -q QUEUE:   Queue name
    -n NCPU:    Use NCPU cpus
    -m MEM:     Memory allocation (default 4*NCPU GB)
    -t TIME:    Walltime limit (default 1 hour)
    -J JOBFS:   Jobfs allocation (default 100 GB)
    -P PROJ:    Submit job under project PROJ