From 88fea06b923d521f360dd28d3d09d455e9fe98b1 Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Wed, 12 Feb 2025 12:38:45 +0100 Subject: [PATCH] DOC: Update surf instructions with environment creation --- .../tutorials/surf_research_cloud_setup.ipynb | 40 +++++++++++++------ 1 file changed, 28 insertions(+), 12 deletions(-) diff --git a/docs/user-guide/tutorials/surf_research_cloud_setup.ipynb b/docs/user-guide/tutorials/surf_research_cloud_setup.ipynb index 330581eb..32e90fe9 100644 --- a/docs/user-guide/tutorials/surf_research_cloud_setup.ipynb +++ b/docs/user-guide/tutorials/surf_research_cloud_setup.ipynb @@ -11,28 +11,39 @@ "# SURF Resarch Cloud: Virtualship environment setup\n", "\n", "> Note: \n", - "> This guide is specific to students who are enrolled at UU in the {} course.\n", + "> This guide is specific to students who are enrolled at UU in the Dynamical Oceanography course.\n", "\n", "In the class, we use virtualship in the cloud (in this case, SURF Research Cloud - called SURF RC from here-on). This has several advantages:\n", "\n", "- You aren't limited to the power of your laptop\n", "- Input datasets are downloaded faster, as they're downloaded to the cloud instance (and not to your laptop)\n", - "- It's easier to collaborate with your peers\n", "\n", - "For each team, we have set up a Jupyter workspace (with virtualship installed)along with 100Gb of persistent storage. The storage and the workspace are named after a research vessel. **Only use the workspace associated with your research vessel.**\n", "\n", - "100Gb should be sufficient for the data that you need to download - just make sure to clear up space from prior runs if you run out.\n", + "## 1. Accepting SURF RC invite\n", "\n", - "> IMPORTANT: Make sure to pause the instance when you're not using it, and if you're done with a run, and resume it next time you log in.\n", + "In your student email you'll have an invite to join a project on SURF RC. Accept this invite.\n", "\n", + "## 2. Create the environment\n", "\n", - "## 1. Accepting SURF RC invite\n", + "Navigate to the [SURF Research Cloud Dashboard](https://portal.live.surfresearchcloud.nl/), and create the storage and compute resources you need.\n", "\n", - "In your student email you'll have an invite to join a project on SURF RC. Accept this invite.\n", + "Below we show create the storage.\n", + "\n", + "![Adding storage GIF](./assets/add-storage.gif)\n", + "\n", + "As shown: to create the storage go to the storage tab, click `+`, and add a SURF volume of 100Gb (naming it something unique and memorable). This will be your persistent storage for your workspace instance.\n", + "\n", + "Below we show create the workspace.\n", "\n", - "## 2. Navigate to the SURF Research Cloud Dashboard\n", + "![Adding workspace GIF](./assets/add-workspace.gif)\n", "\n", - "You'll arrive at a dashboard that looks like the following. Here you can click \"Resume\" to boot up your instance. Once started, an \"Access\" button will appear in the same spot. Clicking this will open the Jupyter workspace in a new tab.\n", + "\n", + "As shown: to create the workspace instance go to the workspace tab, click `+`, search for and select \"virtualship\", then choose the storage you just created.\n", + "\n", + "Once the workspace is created, you can click \"Access\" to open it in a new tab.\n", + "\n", + "\n", + "> IMPORTANT: Make sure to pause the instance when you’re not using it, and resume it next time you log in. Only the workspace creator can pause, resume, and delete the workspace - this is an unavoidable limitation of SURF RC.\n", "\n", "\n", "## 3. Jupyter workspace layout and additional config\n", @@ -45,11 +56,11 @@ "├── KERNEL-README.ipynb\n", "├── data\n", "│ └── datasets\n", - "| └── {your research vessel name} <--- Your persistent storage\n", + "| └── {your storage name} <--- Your persistent storage\n", "└── scratch\n", "```\n", "\n", - "The `data/{your research vessel name}` folder is your persistent storage. This is the primary place you should store your `virtualship` configs and content relevant to this unit.\n", + "The `data/{your storage name}` folder is your persistent storage. This is the primary place you should store your `virtualship` configs and content relevant to this unit.\n", "\n", "---\n", "\n", @@ -81,12 +92,17 @@ "virtualship /etc/miniconda/envs/virtualship`\n", "```\n", "\n", - "Here you can do `conda activate virtualship` to activate the environment called \"virtualship\". Now you have access to the `virtualship` command in your terminal, which can be confirmed by running `virtualship --help`. From here you can `cd` into `data/{your research vessel name}` and run `virtualship` commands as you would on your local machine.\n", + "Here you can do `conda activate virtualship` to activate the environment called \"virtualship\". Now you have access to the `virtualship` command in your terminal, which can be confirmed by running `virtualship --help`. From here you can `cd` into `data/{your storage name}` and run `virtualship` commands as you would on your local machine.\n", "\n", "---\n", "Finally, when you're working in Jupyter Notebooks, you are able to access the Conda environment with `virtualship` and related dependencies by switching the Kernel in the top right of the UI.\n", "\n" ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [] } ], "metadata": {