{"type":"doc","content":[{"type":"paragraph","attrs":{"localId":"9c722473-d9ab-461c-95f8-dec9a1901ae4"},"content":[{"text":"Installing your own python distribution is straightforward. Follow these steps:","type":"text"}]},{"type":"panel","attrs":{"panelType":"warning","localId":"aead1647-fd3a-4fe5-8248-317d9e23d10b"},"content":[{"type":"paragraph","attrs":{"localId":"1c34a4f0-04cf-4efd-8246-5e376d6d3759"},"content":[{"text":"Warning! If you choose to install and use your own Python distribution, please ensure that your ","type":"text"},{"text":"~/.bashrc","type":"text","marks":[{"type":"code"}]},{"text":" is free from references to any other old/existing ","type":"text"},{"text":"conda","type":"text","marks":[{"type":"code"}]},{"text":"-like installation. E.g., you should first remove lines from your ","type":"text"},{"text":"~/.bashrc","type":"text","marks":[{"type":"code"}]},{"text":" like:","type":"text"}]},{"type":"codeBlock","attrs":{"localId":"0d55fb9f-0f81-4c00-9369-2ae07b0448f7"},"content":[{"text":"...\n...\n# >>> conda initialize >>>\n# !! Contents within this block are managed by 'conda init' !!\n__conda_setup=\"$('/home/YOUR_USERNAME/miniconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)\"\nif [ $? -eq 0 ]; then\n eval \"$__conda_setup\"\nelse\n if [ -f \"/home/YOUR_USERNAME/miniconda3/etc/profile.d/conda.sh\" ]; then\n . \"/home/YOUR_USERNAME/miniconda3/etc/profile.d/conda.sh\"\n else\n export PATH=\"/home/YOUR_USERNAME/miniconda3/bin:$PATH\"\n fi\nfi\nunset __conda_setup\n# <<< conda initialize <<<\n...\n...","type":"text"}]},{"type":"paragraph","attrs":{"localId":"33a2e94f-f546-47bd-b407-12ee774f9bd0"},"content":[{"text":"Once removed, the MiniForge installation that results from following the steps below will overwrite your ","type":"text"},{"text":"~/.bashrc","type":"text","marks":[{"type":"code"}]},{"text":" with the new initialisation.","type":"text"}]}]},{"type":"heading","attrs":{"level":1,"localId":"198afa2c-84ec-431b-a612-902330083961"},"content":[{"text":"Installing MiniForge","type":"text"}]},{"type":"orderedList","attrs":{"localId":"add42b36-b689-4a33-917f-effcee82a3f5","order":1},"content":[{"type":"listItem","attrs":{"localId":"e73dbe33-558b-4944-8c51-f71294daa9d5"},"content":[{"type":"paragraph","attrs":{"localId":"04923bf8-0a6a-447e-ae7d-5e94a1cae46f"},"content":[{"text":"Visit ","type":"text"},{"type":"inlineCard","attrs":{"localId":"36d3fd48-2c64-4b82-a0a7-5c285196cbba","url":"https://github.com/conda-forge/miniforge"}},{"text":" ","type":"text"}]}]},{"type":"listItem","attrs":{"localId":"3cc8ded7-2030-49fa-8469-4b83e7be268d"},"content":[{"type":"paragraph","attrs":{"localId":"a723e915-cb41-4b8b-b633-89e7d0cbf2dd"},"content":[{"text":"Navigate to the latest release","type":"text"}]}]},{"type":"listItem","attrs":{"localId":"14d01aab-57d9-4df8-8c73-e962421bab04"},"content":[{"type":"paragraph","attrs":{"localId":"4dfd5c91-6d12-4e7a-a0cd-ec1a18eafa9b"},"content":[{"text":"Copy the link address of the latest ","type":"text"},{"text":"x86","type":"text","marks":[{"type":"code"}]},{"text":" installation script (e.g., ","type":"text"},{"text":"https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh","type":"text","marks":[{"type":"link","attrs":{"href":"https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh"}}]},{"text":" )","type":"text"}]}]},{"type":"listItem","attrs":{"localId":"b6c79647-d19a-45af-9e5f-168473209bce"},"content":[{"type":"paragraph","attrs":{"localId":"f9f87d84-2e0f-4b42-aaad-9a4c6dce57db"},"content":[{"text":"SSH to a login node using your NHR@ZIB user account","type":"text"}]}]},{"type":"listItem","attrs":{"localId":"eb2db06e-e6d2-40e3-8c4c-02b827281ce1"},"content":[{"type":"paragraph","attrs":{"localId":"77736999-3336-4094-ac74-a2ae4de655be"},"content":[{"text":"Download the installation script: ","type":"text"},{"text":"wget YOUR_PASTED_LINK_FROM_STEP_3","type":"text","marks":[{"type":"code"}]}]}]},{"type":"listItem","attrs":{"localId":"fee76ba6-87b8-45bb-a139-8241d36021dd"},"content":[{"type":"paragraph","attrs":{"localId":"e49a73e5-ad3b-4642-abf6-ae0575ec978d"},"content":[{"text":"Run the script: ","type":"text"},{"text":"bash YOUR_DOWNLOADED_INSTALL_SCRIPT_FROM_STEP_5","type":"text","marks":[{"type":"code"}]}]}]},{"type":"listItem","attrs":{"localId":"89828523-2d3b-4e8d-b209-79fe75ac76ad"},"content":[{"type":"paragraph","attrs":{"localId":"f5b8c067-90bd-45d3-ba29-28ffbbbb56d5"},"content":[{"text":"Follow the installation instructions, choosing where you would like the MiniForge python distribution to be installed (it is recommended to install your own distributions in ","type":"text"},{"text":"SCRATCH","type":"text","marks":[{"type":"code"}]},{"text":" - e.g., ","type":"text"},{"text":"/scratch/usr/$(whoami)/miniforge3","type":"text","marks":[{"type":"code"}]},{"text":"- as the ","type":"text"},{"text":"HOME","type":"text","marks":[{"type":"code"}]},{"text":" directory can easily fill up do to package storage)","type":"text"}]}]},{"type":"listItem","attrs":{"localId":"336e7c4d-dd3a-439e-95ba-c8ffd85e151b"},"content":[{"type":"paragraph","attrs":{"localId":"28f1b65c-a643-45ee-9e63-47395428c8a2"},"content":[{"text":"You will be prompted about automatic initialisation: ","type":"text"}]},{"type":"codeBlock","attrs":{"localId":"31a83ff1-4e6b-400e-ae6a-be56671ee22b"},"content":[{"text":"Do you wish to update your shell profile to automatically initialize conda?\nThis will activate conda on startup and change the command prompt when activated.\nIf you'd prefer that conda's base environment not be activated on startup,\n run the following command when conda is activated:\n\nconda config --set auto_activate_base false\n\nNote: You can undo this later by running `conda init --reverse $SHELL`\n\nProceed with initialization? [yes|no]\n[no„] >>> ","type":"text"}]}]}]},{"type":"paragraph","attrs":{"localId":"b973ff97-02d0-4c4e-a22d-6bf4f37541e4"},"marks":[{"type":"indentation","attrs":{"level":1}}],"content":[{"text":"If you select yes, an initialisation block will be appended to your ","type":"text"},{"text":"~/.bashrc","type":"text","marks":[{"type":"code"}]},{"text":", such that every time you open a new shell, the shell will be aware of this new MiniForge installation. If your ","type":"text"},{"text":"~/.bashrc","type":"text","marks":[{"type":"code"}]},{"text":" is free of any old ","type":"text"},{"text":"conda","type":"text","marks":[{"type":"code"}]},{"text":"-like initialisation blocks, go ahead and enter ","type":"text"},{"text":"yes","type":"text","marks":[{"type":"code"}]},{"text":". Otherwise, you may wish to enter ","type":"text"},{"text":"no","type":"text","marks":[{"type":"code"}]},{"text":"and manage multiple Python installations manually to avoid clashes. If you decide for","type":"text"},{"text":"no","type":"text","marks":[{"type":"code"}]},{"text":" you need to manually ","type":"text"},{"text":"source /etc/profile.d/conda.sh","type":"text","marks":[{"type":"code"}]},{"text":"and ","type":"text"},{"text":"source /etc/profile.d/mamba.sh","type":"text","marks":[{"type":"code"}]},{"text":"each time. To automate this, you might want to add","type":"text"}]},{"type":"codeBlock","attrs":{"localId":"a97589a7-944d-4939-99e1-ad519866527f"},"marks":[{"type":"breakout","attrs":{"mode":"wide","width":760}}],"content":[{"text":"__miniforge_conda_setup=\"$(/bin/conda shell.bash hook 2> /dev/null)\"\n__miniforge_mamba_setup=\"$(/bin/mamba shell hook --shell bash --root-prefix 2> /dev/null)\"\nalias use_miniforge='eval \"$__miniforge_conda_setup\" && eval \"$__miniforge_mamba_setup\"'","type":"text"}]},{"type":"paragraph","attrs":{"localId":"493a0e52-38b1-42f3-96ee-b77b7e36bd73"},"marks":[{"type":"indentation","attrs":{"level":1}}],"content":[{"text":"to your ","type":"text"},{"text":".bashrc","type":"text","marks":[{"type":"code"}]},{"text":". So, next time, you only need to call ","type":"text"},{"text":"use_miniforge","type":"text","marks":[{"type":"code"}]}]},{"type":"orderedList","attrs":{"localId":"a7c07755-0f48-4a45-8458-173454057fd3","order":9},"content":[{"type":"listItem","attrs":{"localId":"a7f308cc-0a98-4ab9-a2b8-fbec8ef60e86"},"content":[{"type":"paragraph","attrs":{"localId":"dc424c66-679b-4530-90b5-e187e8f913d0"},"content":[{"text":"If you selected ","type":"text"},{"text":"yes","type":"text","marks":[{"type":"code"}]},{"text":", simply run","type":"text"},{"text":"source ~/.bashrc","type":"text","marks":[{"type":"code"}]},{"text":" to finish the initialisation. The next time you log in, your ","type":"text"},{"text":".bashrc","type":"text","marks":[{"type":"code"}]},{"text":"will be loaded automatically.","type":"text"}]}]}]},{"type":"heading","attrs":{"level":1,"localId":"a99de5c4-4476-4362-8f7b-2aceb899c5ef"},"content":[{"text":"Creating a new Environment","type":"text"}]},{"type":"orderedList","attrs":{"localId":"b98be811-dafb-4db9-a155-de672a2a3567","order":1},"content":[{"type":"listItem","attrs":{"localId":"bdfa9cb3-2979-4f8c-9f39-7f5641711e97"},"content":[{"type":"paragraph","attrs":{"localId":"cded5d01-d40f-445c-a77b-90f1ac99609f"},"content":[{"text":"Create a new (e.g., python 3.12) environment using ","type":"text"},{"text":"mamba create -n “my_environment” python=3.12","type":"text","marks":[{"type":"code"}]}]}]},{"type":"listItem","attrs":{"localId":"acec23f5-86cf-4393-b766-3e52e0306930"},"content":[{"type":"paragraph","attrs":{"localId":"8f2b7d36-37da-45ab-8436-126abf3bbb3a"},"content":[{"text":"Activate that environment using ","type":"text"},{"text":"mamba activate my_environment","type":"text","marks":[{"type":"code"}]}]}]}]},{"type":"paragraph","attrs":{"localId":"be14af2f-1b29-4a58-8f7a-a92a8bef532d"}},{"type":"paragraph","attrs":{"localId":"70565967-4e23-4030-9497-006042866128"},"content":[{"text":"From here, you can install python packages to that environment using ","type":"text"},{"text":"mamba","type":"text","marks":[{"type":"code"}]},{"text":" and/or run Python programs. ","type":"text"},{"text":"Recommendation","type":"text","marks":[{"type":"strong"}]},{"text":": preferably install packages using mamba only instead of conda (slower) or pip (slower, potential dependency conflicts). ","type":"text"},{"text":"Avoid","type":"text","marks":[{"type":"strong"}]},{"text":": mixing different package managers.","type":"text"}]},{"type":"paragraph","attrs":{"localId":"316e2557-5b7c-4e3a-bccb-af96cff861b7"}}],"version":1}