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Supplementary.1

S.1.1 : NeSI Mahuika Jupyter login

  1. Follow https://jupyter.nesi.org.nz/hub/login

  2. Enter NeSI username, HPC password and 6 digit second factor token
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  3. Choose server options as below

  • make sure to choose the correct project code nesi02659, number of CPUs CPUs=4, memory 8 GB prior to pressing image button.


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S.1.2 : Opening a Jupyter teminal, create a working directory, switch Jupyter file explorer to correct path and open sismonr Jupyter kernel (sismonr/R-4.1.0)

  1. Start a terminal session from the JupyterLab launcher
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    • When you connect to NeSI JupyterLab you always start in a new hidden directory. To make sure you can find your work next time, you should change to another location. Here we will create a working directory in project nesi02659 workspace for each attendee and then create a symlink from home (~) for easy access.

    cd ~
mkdir -p /nesi/project/nesi02659/sismonr_workshop/workingdir/$USER
ln -s  /nesi/project/nesi02659/sismonr_workshop/workingdir/$USER ~/sism

  2. Guide Jupyter file explorer (left panel) to above working directory
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  3. Open 'sismonr/R-4.1.0 kernel'
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S.1.3 : Restart Jupyter Server Session

Only in an instance where the current session was not started according to the instructions on S.1. (above) OR the current session is completely unresponsive


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S.1.4 : Local setup

The sismonr package depends on the programming language Julia. It is preferable to install Julia on your computer before installing sismonr.

Installing Julia

To install Julia, go to https://julialang.org/downloads/ and follow the instructions. The sismonr package currently works with version >= 1.0.

Please make sure to include the Julia executable in your environmental variable PATH. Linux users can use the following command in the terminal: 

sudo ln -s path_to_julia_folder/bin/julia /usr/local/bin/julia
to create a symbolic link to julia inside the /usr/local/bin folder.

Windows users can open the Control Panel and go to System > Advanced system settings > Environment variables. Select the PATH variable, click on Edit > New and copy-paste the path path_to_julia_folder/bin.

You may need to restart your computer.

Installing sismonr

sismonr is available on GitHub. You can install sismonr from R or Rstudio using the following commands:

library(devtools)
install_github("oliviaAB/sismonr")

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