Running Jupyter Notebook

Revision as of 23:42, 22 January 2020 by H.wolff (talk | contribs) (On Gadi)


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.


  • 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.


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

git clone

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 '')
    -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