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| 11 | + "# SURF Resarch Cloud: Virtualship environment setup\n", |
| 12 | + "\n", |
| 13 | + "> Note: \n", |
| 14 | + "> This guide is specific to students who are enrolled at UU in the Dynamical Oceanography course.\n", |
| 15 | + "\n", |
| 16 | + "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", |
| 17 | + "\n", |
| 18 | + "- You aren't limited to the power of your laptop\n", |
| 19 | + "- Input datasets are downloaded faster, as they're downloaded to the cloud instance (and not to your laptop)\n", |
| 20 | + "\n", |
| 21 | + "\n", |
| 22 | + "## 1. Accepting SURF RC invite\n", |
| 23 | + "\n", |
| 24 | + "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.\n", |
| 25 | + "\n", |
| 26 | + "## 2. Create the environment\n", |
| 27 | + "\n", |
| 28 | + "Navigate to the [SURF Research Cloud Dashboard](https://portal.live.surfresearchcloud.nl/), and create the storage and compute resources you need.\n", |
| 29 | + "\n", |
| 30 | + "Below we show create the storage.\n", |
| 31 | + "\n", |
| 32 | + "\n", |
| 33 | + "\n", |
| 34 | + "As shown: to create the storage go to the storage tab, click `+`, and add a SURF HPC Cloud Volume of 100Gb (naming it something unique and memorable). This will be your persistent storage for your workspace instance.\n", |
| 35 | + "\n", |
| 36 | + "Below we show create the workspace.\n", |
| 37 | + "\n", |
| 38 | + "\n", |
| 39 | + "\n", |
| 40 | + "\n", |
| 41 | + "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, adjust the expiration date to some time after 14 march 2025, and change the name/hostname to something memorable.\n", |
| 42 | + "\n", |
| 43 | + "Once the workspace is created, you can click \"Access\" to open it in a new tab. This might take a while (up to 10 minutes) - make sure to occasionally refresh the page.\n", |
| 44 | + "\n", |
| 45 | + "\n", |
| 46 | + "> 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", |
| 47 | + "\n", |
| 48 | + "\n", |
| 49 | + "## 3. Jupyter workspace layout and additional config\n", |
| 50 | + "\n", |
| 51 | + "> Note: This only needs to be done once during setup.\n", |
| 52 | + "\n", |
| 53 | + "In the Jupyter workspace, you'll see the following in your file explorer:\n", |
| 54 | + "```\n", |
| 55 | + ".\n", |
| 56 | + "├── KERNEL-README.ipynb\n", |
| 57 | + "├── data\n", |
| 58 | + "│ └── datasets\n", |
| 59 | + "| └── {your storage name} <--- Your persistent storage\n", |
| 60 | + "└── scratch\n", |
| 61 | + "```\n", |
| 62 | + "\n", |
| 63 | + "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", |
| 64 | + "\n", |
| 65 | + "---\n", |
| 66 | + "\n", |
| 67 | + "To be able to run virtualship from the terminal, we need to take some additional steps which are detailed in the `KERNEL-README.ipynb` contains important information for configuring your environment. Namely, for our uses, the \"Initialize conda\" section. Do the following.\n", |
| 68 | + "\n", |
| 69 | + "> #### Initialize conda\n", |
| 70 | + "> \n", |
| 71 | + "> To make the already installed conda-tool available for yourself, you have to initialize your terminal shell.\n", |
| 72 | + "> \n", |
| 73 | + "> Start a \"Terminal\" tab in the Jupyter Lab launcher and type:\n", |
| 74 | + "> ```\n", |
| 75 | + "> /etc/miniconda/bin/conda init\n", |
| 76 | + "> ```\n", |
| 77 | + "> Close the terminal tab and start a new one.\n", |
| 78 | + "> You will see that the terminal prompt has changed to something like\n", |
| 79 | + "> ```\n", |
| 80 | + "> (base) metheuser@mywsp:\n", |
| 81 | + "> ```\n", |
| 82 | + "> This is conda telling you that you are currently in the \"base\" environment.\n", |
| 83 | + "\n", |
| 84 | + "From here, you already have another environment set up for you. Running `conda env list` in the terminal, you should see:\n", |
| 85 | + "\n", |
| 86 | + "```bash\n", |
| 87 | + "(base) $ conda env list\n", |
| 88 | + "\n", |
| 89 | + "# conda environments:\n", |
| 90 | + "#\n", |
| 91 | + "base * /etc/miniconda\n", |
| 92 | + "virtualship /etc/miniconda/envs/virtualship`\n", |
| 93 | + "```\n", |
| 94 | + "\n", |
| 95 | + "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", |
| 96 | + "\n", |
| 97 | + "---\n", |
| 98 | + "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", |
| 99 | + "\n" |
| 100 | + ] |
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