{"type":"doc","content":[{"type":"paragraph","content":[{"text":"Goal","type":"text","marks":[{"type":"strong"}]},{"text":": When using Jupyter how are python packages managed?","type":"text"}]},{"type":"rule"},{"type":"extension","attrs":{"layout":"default","extensionType":"com.atlassian.confluence.macro.core","extensionKey":"toc","parameters":{"macroParams":{"minLevel":{"value":"1"},"maxLevel":{"value":"1"},"outline":{"value":"false"},"style":{"value":"none"},"type":{"value":"list"},"printable":{"value":"true"}},"macroMetadata":{"macroId":{"value":"66b7f25a-daf8-4eb5-99ad-cdd71c373ca2"},"schemaVersion":{"value":"1"},"title":"Table of Contents"}},"localId":"5512dfa8-e27c-4725-8613-d1feb2634ef4"}},{"type":"rule"},{"type":"heading","attrs":{"level":1},"content":[{"text":"Where are Python Packages Installed During a Jupyter Session?","type":"text"}]},{"type":"panel","attrs":{"panelType":"info"},"content":[{"type":"paragraph","content":[{"text":"You can use ","type":"text"},{"text":"pip list -v","type":"text","marks":[{"type":"code"}]},{"text":" and ","type":"text"},{"text":"conda list","type":"text","marks":[{"type":"code"}]},{"text":" to inspect what is in your environment.","type":"text"}]}]},{"type":"panel","attrs":{"panelType":"info"},"content":[{"type":"paragraph","content":[{"text":"Example using the ","type":"text"},{"text":"default","type":"text","marks":[{"type":"em"}]},{"text":" Python kernel:","type":"text"}]}]},{"type":"codeBlock","content":[{"text":"# Cell\nimport sys\nprint(sys.version)","type":"text"}]},{"type":"codeBlock","content":[{"text":"3.12.3 | packaged by Anaconda, Inc. | (main, May 6 2024, 19:46:43) [GCC 11.2.0]","type":"text"}]},{"type":"expand","attrs":{"title":"pip list -v"},"content":[{"type":"codeBlock","content":[{"text":"Package Version Location Installer\n------------------------- ----------- ---------------------------------------------------------- ---------\nanyio 4.2.0 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nargon2-cffi 21.3.0 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nargon2-cffi-bindings 21.2.0 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nasttokens 2.0.5 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nasync-lru 2.0.4 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nattrs 23.1.0 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nBabel 2.11.0 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nbeautifulsoup4 4.12.2 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nbleach 4.1.0 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nBrotli 1.0.9 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\ncertifi 2024.2.2 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\ncffi 1.16.0 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\ncharset-normalizer 2.0.4 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\ncomm 0.2.1 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\ndebugpy 1.6.7 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\ndecorator 5.1.1 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\ndefusedxml 0.7.1 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nexecuting 0.8.3 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nfastjsonschema 2.16.2 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nidna 3.7 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nipykernel 6.28.0 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nipython 8.20.0 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nipywidgets 8.1.2 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\njedi 0.18.1 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nJinja2 3.1.3 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\njson5 0.9.6 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\njsonschema 4.19.2 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\njsonschema-specifications 2023.7.1 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\njupyter 1.0.0 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\njupyter_client 8.6.0 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\njupyter-console 6.6.3 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\njupyter_core 5.5.0 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\njupyter-events 0.8.0 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\njupyter-lsp 2.2.0 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\njupyter_server 2.10.0 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\njupyter_server_terminals 0.4.4 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\njupyterlab 4.0.11 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\njupyterlab-pygments 0.1.2 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\njupyterlab_server 2.25.1 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\njupyterlab-widgets 3.0.10 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nMarkupSafe 2.1.3 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nmatplotlib-inline 0.1.6 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nmistune 2.0.4 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nnbclient 0.8.0 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nnbconvert 7.10.0 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nnbformat 5.9.2 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nnest-asyncio 1.6.0 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nnotebook 7.0.8 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nnotebook_shim 0.2.3 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nnumpy 2.0.0 /home//.local/lib/python3.12/site-packages pip\noverrides 7.4.0 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\npackaging 23.2 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\npandocfilters 1.5.0 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nparso 0.8.3 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\npexpect 4.8.0 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\npip 24.0 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages\nplatformdirs 3.10.0 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nply 3.11 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nprometheus-client 0.14.1 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nprompt-toolkit 3.0.43 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\npsutil 5.9.0 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nptyprocess 0.7.0 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\npure-eval 0.2.2 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\npycparser 2.21 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nPygments 2.15.1 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nPyQt5 5.15.10 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nPyQt5-sip 12.13.0 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nPySocks 1.7.1 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\npython-dateutil 2.9.0.post0 /home//.local/lib/python3.12/site-packages pip\npython-json-logger 2.0.7 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\npytz 2024.1 /home//.local/lib/python3.12/site-packages pip\nPyYAML 6.0.1 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\npyzmq 25.1.2 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nqtconsole 5.5.1 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nQtPy 2.4.1 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nreferencing 0.30.2 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nrequests 2.31.0 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nrfc3339-validator 0.1.4 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nrfc3986-validator 0.1.1 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nrpds-py 0.10.6 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nSend2Trash 1.8.2 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nsetuptools 69.5.1 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages\nsip 6.7.12 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nsix 1.16.0 /home//.local/lib/python3.12/site-packages pip\nsniffio 1.3.0 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nsoupsieve 2.5 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nstack-data 0.2.0 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nterminado 0.17.1 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\ntinycss2 1.2.1 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\ntornado 6.3.3 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\ntraitlets 5.7.1 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\ntyping_extensions 4.11.0 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\ntzdata 2024.1 /home//.local/lib/python3.12/site-packages pip\nurllib3 2.2.1 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nwcwidth 0.2.5 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nwebencodings 0.5.1 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nwebsocket-client 0.58.0 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nwheel 0.43.0 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages\nwidgetsnbextension 4.0.10 /apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages conda\nNote: you may need to restart the kernel to use updated packages.","type":"text"}]}]},{"type":"panel","attrs":{"panelType":"info"},"content":[{"type":"paragraph","content":[{"text":"Notice there are two paths:","type":"text"}]},{"type":"orderedList","attrs":{"order":1},"content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"The library path of the conda environment that this default kernel is running from: ","type":"text"},{"text":"/apps/s/jupyterlab/miniconda3/lib/python3.12/site-packages","type":"text","marks":[{"type":"code"}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Your local home library path related to the version of Python within this kernel: ","type":"text"},{"text":"/home//.local/lib/python3.12/site-packages","type":"text","marks":[{"type":"code"}]}]}]}]}]},{"type":"rule"},{"type":"heading","attrs":{"level":1},"content":[{"text":"Can I ","type":"text"},{"text":"pip install","type":"text","marks":[{"type":"code"}]},{"text":"?","type":"text"}]},{"type":"panel","attrs":{"panelType":"info"},"content":[{"type":"paragraph","content":[{"text":"Yes. And this will installed into your local home under the appropriate library/version folder.","type":"text"}]}]},{"type":"codeBlock","content":[{"text":"# Before pip install:\n[~]$ ls .local/lib/python3.12/site-packages/\ndateutil numpy-2.0.0.dist-info __pycache__ pytz six-1.16.0.dist-info tzdata\nnumpy numpy.libs python_dateutil-2.9.0.post0.dist-info pytz-2024.1.dist-info six.py tzdata-2024.1.dist-info","type":"text"}]},{"type":"codeBlock","content":[{"text":"# Within Cell:\npip install nltk","type":"text"}]},{"type":"expand","attrs":{"title":"Cell Result"},"content":[{"type":"codeBlock","content":[{"text":"Defaulting to user installation because normal site-packages is not writeable\nCollecting nltk\n Using cached nltk-3.8.1-py3-none-any.whl.metadata (2.8 kB)\nCollecting click (from nltk)\n Using cached click-8.1.7-py3-none-any.whl.metadata (3.0 kB)\nCollecting joblib (from nltk)\n Using cached joblib-1.4.2-py3-none-any.whl.metadata (5.4 kB)\nCollecting regex>=2021.8.3 (from nltk)\n Using cached regex-2024.7.24-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (40 kB)\nCollecting tqdm (from nltk)\n Downloading tqdm-4.66.5-py3-none-any.whl.metadata (57 kB)\n ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 57.6/57.6 kB 1.5 MB/s eta 0:00:00\nUsing cached nltk-3.8.1-py3-none-any.whl (1.5 MB)\nUsing cached regex-2024.7.24-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (790 kB)\nUsing cached click-8.1.7-py3-none-any.whl (97 kB)\nUsing cached joblib-1.4.2-py3-none-any.whl (301 kB)\nDownloading tqdm-4.66.5-py3-none-any.whl (78 kB)\n ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 78.4/78.4 kB 2.9 MB/s eta 0:00:00\nInstalling collected packages: tqdm, regex, joblib, click, nltk\nSuccessfully installed click-8.1.7 joblib-1.4.2 nltk-3.8.1 regex-2024.7.24 tqdm-4.66.5\nNote: you may need to restart the kernel to use updated packages.","type":"text"}]}]},{"type":"codeBlock","content":[{"text":"# After Installation:\n# Notice the new packages installed.\n[~]$ ls .local/lib/python3.12/site-packages/\nclick joblib-1.4.2.dist-info numpy-2.0.0.dist-info pytz six-1.16.0.dist-info tzdata\nclick-8.1.7.dist-info nltk numpy.libs pytz-2024.1.dist-info six.py tzdata-2024.1.dist-info\ndateutil nltk-3.8.1.dist-info __pycache__ regex tqdm\njoblib numpy python_dateutil-2.9.0.post0.dist-info regex-2024.7.24.dist-info tqdm-4.66.5.dist-info","type":"text"}]},{"type":"panel","attrs":{"panelType":"warning"},"content":[{"type":"paragraph","content":[{"text":"Remember","type":"text","marks":[{"type":"strong"}]},{"text":": Any previously install Python packages under this location will be available to your notebook.","type":"text"}]},{"type":"paragraph","content":[{"text":"Any installs/updates within the notebook will thus also affect any other Python environments you have that use this location and packages.","type":"text"}]},{"type":"paragraph","content":[{"text":"This could cause issues with dependencies and versions.","type":"text"}]}]},{"type":"rule"},{"type":"heading","attrs":{"level":1},"content":[{"text":"Can I Use Conda Within My Notebook?","type":"text"}]},{"type":"panel","attrs":{"panelType":"info"},"content":[{"type":"paragraph","content":[{"text":"Yes and no…","type":"text"}]}]},{"type":"expand","attrs":{"title":"conda list"},"content":[{"type":"codeBlock","content":[{"text":"# packages in environment at /apps/s/jupyterlab/miniconda3:\n#\n# Name Version Build Channel\n_libgcc_mutex 0.1 main \n_openmp_mutex 5.1 1_gnu \nanyio 4.2.0 py312h06a4308_0 \n... \nzlib 1.2.13 h5eee18b_1 \nzstd 1.5.5 hc292b87_2 \nNote: you may need to restart the kernel to use updated packages.","type":"text"}]}]},{"type":"expand","attrs":{"title":"conda search nltk"},"content":[{"type":"codeBlock","content":[{"text":"Loading channels: done\n# Name Version Build Channel \nnltk 3.2.1 py27_0 conda-forge \nnltk 3.2.1 py34_0 conda-forge \n... \nnltk 3.8.1 py39h06a4308_0 pkgs/main \nnltk 3.8.1 pyhd8ed1ab_0 conda-forge \nNote: you may need to restart the kernel to use updated packages.","type":"text"}]}]},{"type":"expand","attrs":{"title":"conda install nltk"},"content":[{"type":"codeBlock","content":[{"text":"Retrieving notices: ...working... done\nChannels:\n - conda-forge\n - defaults\nPlatform: linux-64\nCollecting package metadata (repodata.json): done\nSolving environment: done\n\n## Package Plan ##\n environment location: /apps/s/jupyterlab/miniconda3\n added / updated specs:\n - nltk\n\nThe following packages will be downloaded:\n package | build\n ---------------------------|-----------------\n certifi-2024.7.4 | pyhd8ed1ab_0 156 KB conda-forge\n nltk-3.8.1 | pyhd8ed1ab_0 1.0 MB conda-forge\n regex-2023.10.3 | py312h5eee18b_0 386 KB\n tqdm-4.66.5 | pyhd8ed1ab_0 87 KB conda-forge\n ------------------------------------------------------------\n Total: 1.6 MB\n\nThe following NEW packages will be INSTALLED:\n click conda-forge/noarch::click-8.1.7-unix_pyh707e725_0 \n colorama conda-forge/noarch::colorama-0.4.6-pyhd8ed1ab_0 \n joblib conda-forge/noarch::joblib-1.4.2-pyhd8ed1ab_0 \n nltk conda-forge/noarch::nltk-3.8.1-pyhd8ed1ab_0 \n regex pkgs/main/linux-64::regex-2023.10.3-py312h5eee18b_0 \n tqdm conda-forge/noarch::tqdm-4.66.5-pyhd8ed1ab_0 \n\nThe following packages will be UPDATED:\n ca-certificates pkgs/main::ca-certificates-2024.3.11-~ --> conda-forge::ca-certificates-2024.7.4-hbcca054_0 \n certifi pkgs/main/linux-64::certifi-2024.2.2-~ --> conda-forge/noarch::certifi-2024.7.4-pyhd8ed1ab_0 \n libgcc-ng pkgs/main::libgcc-ng-11.2.0-h1234567_1 --> conda-forge::libgcc-ng-14.1.0-h77fa898_0 \n libgomp pkgs/main::libgomp-11.2.0-h1234567_1 --> conda-forge::libgomp-14.1.0-h77fa898_0 \n openssl pkgs/main::openssl-3.0.13-h7f8727e_1 --> conda-forge::openssl-3.3.1-h4bc722e_2 \n\nThe following packages will be SUPERSEDED by a higher-priority channel:\n _libgcc_mutex pkgs/main::_libgcc_mutex-0.1-main --> conda-forge::_libgcc_mutex-0.1-conda_forge \n _openmp_mutex pkgs/main::_openmp_mutex-5.1-1_gnu --> conda-forge::_openmp_mutex-4.5-2_gnu \n... \nPreparing transaction: done\nVerifying transaction: failed\n\nEnvironmentNotWritableError: The current user does not have write permissions to the target environment.\n environment location: /apps/s/jupyterlab/miniconda3\n uid: 10275911\n gid: 10275911\n\nNote: you may need to restart the kernel to use updated packages.","type":"text"}]}]},{"type":"panel","attrs":{"panelType":"warning"},"content":[{"type":"paragraph","content":[{"text":"You can use ","type":"text"},{"text":"conda","type":"text","marks":[{"type":"code"}]},{"text":" commands within cells to inspect and search.","type":"text"}]},{"type":"paragraph","content":[{"text":"You will not have permissions to ","type":"text"},{"text":"conda install","type":"text","marks":[{"type":"code"}]},{"text":" under this ","type":"text"},{"text":"default Python kernel","type":"text","marks":[{"type":"em"}]},{"text":" since you do not own this folder, so do not have permissions to install/update anything within it.","type":"text"}]}]},{"type":"panel","attrs":{"panelType":"info"},"content":[{"type":"paragraph","content":[{"text":" But, you should be able to if ","type":"text"},{"text":"you","type":"text","marks":[{"type":"strong"},{"type":"em"}]},{"text":" have created the kernel, own it, and thus have permissions.","type":"text"}]}]},{"type":"rule"},{"type":"heading","attrs":{"level":1},"content":[{"text":"Jupyter Sessions","type":"text"}]},{"type":"panel","attrs":{"panelType":"info"},"content":[{"type":"paragraph","content":[{"text":"When you start a Jupyter session via OnDemand, you get a ","type":"text"},{"text":"Session ID","type":"text","marks":[{"type":"strong"}]},{"text":", which also creates a corresponding folder within your home:","type":"text"}]}]},{"type":"mediaSingle","attrs":{"layout":"center","width":844,"widthType":"pixel"},"content":[{"type":"media","attrs":{"width":844,"alt":"image-20240806-144730.png","id":"c4a4d3b1-627b-4206-9f70-cc7eaffb2d37","collection":"contentId-2250113039","type":"file","height":291}}]},{"type":"panel","attrs":{"panelType":"info"},"content":[{"type":"paragraph","content":[{"text":"Clicking on the Session ID link will open up a new tab of the form:","type":"text"}]}]},{"type":"mediaSingle","attrs":{"layout":"center","width":1000,"widthType":"pixel"},"content":[{"type":"media","attrs":{"width":529,"alt":"image-20240821-152226.png","id":"8c91b6e2-8be1-4f2b-b6db-514399d9ec67","collection":"contentId-2250113039","type":"file","height":26}}]},{"type":"panel","attrs":{"panelType":"info"},"content":[{"type":"paragraph","content":[{"text":"Or, you can navigate to it via the command-line:","type":"text"}]}]},{"type":"codeBlock","content":[{"text":"[]$ ls ~/ondemand/data/sys/dashboard/batch_connect/sys/jupyter/form/output/8c0766ae-b302-47d7-8f40-007460cc3ad1/\nafter.sh before.sh config.py connection.yml job_script_content.sh job_script_options.json output.log script.sh user_defined_context.json","type":"text"}]},{"type":"panel","attrs":{"panelType":"info"},"content":[{"type":"paragraph","content":[{"text":"You can view the ","type":"text"},{"text":"output.log","type":"text","marks":[{"type":"code"}]},{"text":" file under this folder to track the session.","type":"text"}]}]},{"type":"rule"},{"type":"heading","attrs":{"level":1},"content":[{"text":"Issue: Jupyter Doesn’t Start?","type":"text"}]},{"type":"panel","attrs":{"panelType":"warning"},"content":[{"type":"paragraph","content":[{"text":"Sometimes when you try and start a Jupyter session it immediately fails to open.","type":"text"}]},{"type":"paragraph","content":[{"text":"This is typically caused by something that you have done/run/installed that has installed a python package under the library/version folder that is causing a dependency issue with a Python package installed under the kernel..","type":"text"}]}]},{"type":"panel","attrs":{"panelType":"info"},"content":[{"type":"paragraph","content":[{"text":"If you do not have the Session ID, then list the child session folders, in date order, under ","type":"text"},{"text":"~/ondemand/data/sys/dashboard/batch_connect/sys/jupyter/form/output/","type":"text","marks":[{"type":"code"}]},{"text":" and look at the ","type":"text"},{"text":"output.log","type":"text","marks":[{"type":"code"}]},{"text":" file under the last child folder created:","type":"text"}]}]},{"type":"codeBlock","content":[{"text":"[]$ ls -altr ~/ondemand/data/sys/dashboard/batch_connect/sys/jupyter/form/output/\n...\ndrwxr-xr-x 2 4096 Aug 6 08:07 8c0766ae-b302-47d7-8f40-007460cc3ad1","type":"text"}]},{"type":"rule"},{"type":"heading","attrs":{"level":1},"content":[{"text":"Issue: Jupyter Doesn’t Start: Example","type":"text"}]},{"type":"panel","attrs":{"panelType":"info"},"content":[{"type":"paragraph","content":[{"text":"This example is from an older cluster/version of OnDemand, but the principle still applies.","type":"text"}]}]},{"type":"panel","attrs":{"panelType":"info"},"content":[{"type":"paragraph","content":[{"text":"The ","type":"text"},{"text":"fakeusername","type":"text","marks":[{"type":"code"}]},{"text":" user had the following error:","type":"text"}]}]},{"type":"expand","attrs":{"title":"Full Trace:"},"content":[{"type":"codeBlock","content":[{"text":"[fakeusername@blog2 d248fc5c-162c-42c6-b96d-e2ea46cbf3c1]$ cat output.log\n...\nTIMING - Starting jupyter at: Fri Jul 26 13:20:12 MDT 2024\nTraceback (most recent call last):\n File \"/apps/s/jupyterlab/miniconda3/bin/jupyter-lab\", line 6, in \n from jupyterlab.labapp import main\n File \"/apps/s/jupyterlab/miniconda3/lib/python3.9/site-packages/jupyterlab/__init__.py\", line 7, in \n from .labapp import LabApp\n File \"/apps/s/jupyterlab/miniconda3/lib/python3.9/site-packages/jupyterlab/labapp.py\", line 18, in \n from jupyterlab_server import WORKSPACE_EXTENSION, LabServerApp, slugify\n File \"/apps/s/jupyterlab/miniconda3/lib/python3.9/site-packages/jupyterlab_server/__init__.py\", line 4, in \n from .app import LabServerApp\n File \"/apps/s/jupyterlab/miniconda3/lib/python3.9/site-packages/jupyterlab_server/app.py\", line 11, in \n from .handlers import LabConfig, add_handlers\n File \"/apps/s/jupyterlab/miniconda3/lib/python3.9/site-packages/jupyterlab_server/handlers.py\", line 19, in \n from .translations_handler import TranslationsHandler\n File \"/apps/s/jupyterlab/miniconda3/lib/python3.9/site-packages/jupyterlab_server/translations_handler.py\", line 16, in \n from .translation_utils import get_language_pack, get_language_packs, is_valid_locale, translator\n File \"/apps/s/jupyterlab/miniconda3/lib/python3.9/site-packages/jupyterlab_server/translation_utils.py\", line 15, in \n import pkg_resources\n File \"/home/fakeusername/.local/lib/python3.9/site-packages/pkg_resources/__init__.py\", line 96, in \n from jaraco.text import (\n File \"/home/fakeusername/.local/lib/python3.9/site-packages/setuptools/_vendor/jaraco/text/__init__.py\", line 12, in \n from jaraco.context import ExceptionTrap\n File \"/home/fakeusername/.local/lib/python3.9/site-packages/setuptools/_vendor/jaraco/context.py\", line 17, in \n from backports import tarfile\nImportError: cannot import name 'tarfile' from 'backports' (/apps/s/jupyterlab/miniconda3/lib/python3.9/site-packages/backports/__init__.py)\nTimed out waiting for Jupyter Notebook server to open port 40276!\nTIMING - Wait ended at: Fri Jul 26 13:21:19 MDT 2024\nCleaning up...","type":"text"}]}]},{"type":"panel","attrs":{"panelType":"warning"},"content":[{"type":"paragraph","content":[{"text":"Two things to notice.","type":"text"}]},{"type":"orderedList","attrs":{"order":1},"content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"The ","type":"text"},{"text":"ImportError","type":"text","marks":[{"type":"code"}]},{"text":" caused by a dependency issue: ","type":"text"},{"text":"ImportError: cannot import name 'tarfile' from 'backports'","type":"text","marks":[{"type":"code"}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"The location of the package, that has been installed, where this is originating from: ","type":"text"},{"text":"/home/fakeusername/.local/lib/python3.9/site-packages/pkg_resources","type":"text","marks":[{"type":"code"}]}]}]}]}]},{"type":"panel","attrs":{"panelType":"info"},"content":[{"type":"paragraph","content":[{"text":"Unfortunately","type":"text","marks":[{"type":"em"}]},{"text":", the simplest way to resolve is to remove this folder.","type":"text"}]},{"type":"paragraph","content":[{"text":"How this effects your environment/pipeline you will have to figure out.","type":"text"}]},{"type":"paragraph","content":[{"text":"Unfortunately","type":"text","marks":[{"type":"em"}]},{"text":", the more complicated you try and make a single environment, the more likely this is too occur.","type":"text"}]},{"type":"paragraph","content":[{"text":"Suggestion","type":"text","marks":[{"type":"strong"}]},{"text":": Maybe consider creating a separate Conda environment/kernel.","type":"text"}]}]},{"type":"rule"},{"type":"table","attrs":{"layout":"default","width":1011.0,"localId":"75c65d22-e93b-4bfb-b634-6d4eeea8a9f3"},"content":[{"type":"tableRow","content":[{"type":"tableCell","attrs":{"colspan":1,"rowspan":1,"colwidth":[333.0]},"content":[{"type":"paragraph","content":[{"text":"Prev","type":"text","marks":[{"type":"strong"}]}]},{"type":"paragraph","content":[{"text":"Extend Conda Environment to Jupyter Kernel","type":"text","marks":[{"type":"link","attrs":{"href":"https://arccwiki.atlassian.net/wiki/spaces/DOCUMENTAT/pages/2237988917"}}]}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1,"colwidth":[326.0]},"content":[{"type":"paragraph","marks":[{"type":"alignment","attrs":{"align":"center"}}],"content":[{"text":"Workshop Home","type":"text","marks":[{"type":"strong"}]}]},{"type":"paragraph","marks":[{"type":"alignment","attrs":{"align":"center"}}],"content":[{"text":"Using Python, Conda and Pip on the Cluster","type":"text","marks":[{"type":"link","attrs":{"href":"https://arccwiki.atlassian.net/wiki/spaces/DOCUMENTAT/pages/2136342529"}}]}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1,"colwidth":[349.0]},"content":[{"type":"paragraph","marks":[{"type":"alignment","attrs":{"align":"end"}}],"content":[{"text":"Next","type":"text","marks":[{"type":"strong"}]}]},{"type":"paragraph","marks":[{"type":"alignment","attrs":{"align":"end"}}],"content":[{"text":"Conda and Pip Environments and Reproducibility","type":"text","marks":[{"type":"link","attrs":{"href":"https://arccwiki.atlassian.net/wiki/spaces/DOCUMENTAT/pages/2236809260"}}]}]}]}]}]},{"type":"paragraph","content":[{"text":" ","type":"text"}]}],"version":1}

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