SURF Resarch Cloud: Collaborative Workspace Setup Guide#
Note: This guide is specific to students who are enrolled at Utrecht University.
In the class, we will use VirtualShip in the cloud (in this case, SURF Research Cloud - called SURF RC from here-on). This has several advantages:
You aren’t limited to the power of your laptop.
Everyone can work in the same collaborative environment.
The environment is pre-configured with all necessary software and dependencies.
1. Accepting SURF RC invite#
In your student email you’ll have an invite from SURF Research Access Management (SRAM) to join a project on SURF RC. Accept this invite.
2. Open the workspace#
Navigate to the SURF Research Cloud Dashboard, and click “access” on the shared workspace.
3. Open Terminal session#
In the Jupyter launcher, you should see an option to open Terminal session. Click this to open Terminal.
4. Launch VirtualShip environment#
❗️ Before proceeding any further, you should type the following command in the Terminal and then hit Enter: bash ❗️
This will ensure that you are in a bash shell for the rest of the setup.
You will see that the Terminal prompt has changed to something like:
(base) metheuser@mywsp:
This is conda telling you that you are currently in the “base” environment.
From here, you already have another environment set up for you. Running conda env list in the Terminal, you should see:
conda env list
# conda environments:
#
base * /etc/miniconda3
virtualship /etc/miniconda3/envs/virtualship
Next, to launch the VirtualShip environment, type the following command in the Terminal and hit Enter: conda activate virtualship
This will activate the VirtualShip conda environment, which has all the necessary dependencies installed. You can confirm that you are in the correct environment by checking that your Terminal prompt now looks something like:
(virtualship) metheuser@mywsp:
With the virtualship environment, you now have access to the virtualship command in your Terminal.
This can be confirmed by typing the following command in the Terminal and hitting Enter: virtualship --help.
You should see something like:
virtualship --help
Usage: virtualship [OPTIONS] COMMAND [ARGS]...
Options:
--version Show the version and exit.
--help Show this message and exit.
Commands:
fetch Download input data for an expedition.
init Initialize a directory for a new expedition, with an example...
plan Launch UI to help build schedule and ship config files.
run Run the expedition.
If you close the Terminal window at any point, you may need to re-open it and re-run the bash and conda activate virtualship commands to ensure you are in a bash shell and the correct conda environment.