Read the Docs build information Build id: 1552702 Project: northeastern-university-rc-public-documentation Version: latest Commit: 0cb3a91d6399c01beae45afb043bfb2404b7a6e1 Date: 2023-06-21T17:18:03.613903Z State: finished Success: True [rtd-command-info] start-time: 2023-06-21T17:18:05.706068Z, end-time: 2023-06-21T17:18:13.762684Z, duration: 8, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/northeastern-rc/rc-public-documentation . Cloning into '.'... [rtd-command-info] start-time: 2023-06-21T17:18:15.006000Z, end-time: 2023-06-21T17:18:19.846410Z, duration: 4, exit-code: 0 python3.7 -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH Using base prefix '/home/docs/.pyenv/versions/3.7.9' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/envs/latest/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/envs/latest/bin/python Installing setuptools, pip, wheel... done. 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python-dateutil, pyrsistent, psutil, prompt-toolkit, pkgutil-resolve-name, pexpect, parso, nest-asyncio, mdurl, latexcodec, jupyterlab-myst, greenlet, entrypoints, docutils, decorator, debugpy, accessible-pygments, pybtex, matplotlib-inline, markdown-it-py, jupyter-core, jedi, importlib-resources, importlib_metadata, beautifulsoup4, sqlalchemy, sphinx, pybtex-docutils, mdit-py-plugins, jupyter-client, ipython, click, attrs, sphinxcontrib-bibtex, sphinx-togglebutton, sphinx-tabs, sphinx_design, sphinx-copybutton, pydata-sphinx-theme, myst-parser, jsonschema, ipykernel, sphinx-book-theme, nbformat, nbclient, jupyter-cache, myst-nb Attempting uninstall: docutils Found existing installation: docutils 0.17.1 Uninstalling docutils-0.17.1: Successfully uninstalled docutils-0.17.1 Attempting uninstall: sphinx Found existing installation: Sphinx 1.8.6 Uninstalling Sphinx-1.8.6: Successfully uninstalled Sphinx-1.8.6 Successfully installed accessible-pygments-0.0.4 attrs-23.1.0 backcall-0.2.0 beautifulsoup4-4.12.2 click-8.1.3 debugpy-1.6.7 decorator-5.1.1 docutils-0.18.1 entrypoints-0.4 fastjsonschema-2.17.1 greenlet-2.0.2 importlib-resources-5.12.0 importlib_metadata-6.7.0 ipykernel-6.16.2 ipython-7.34.0 jedi-0.18.2 jsonschema-4.17.3 jupyter-cache-0.5.0 jupyter-client-7.4.9 jupyter-core-4.12.0 jupyterlab-myst-1.2.0 latexcodec-2.0.1 markdown-it-py-2.2.0 matplotlib-inline-0.1.6 mdit-py-plugins-0.3.5 mdurl-0.1.2 myst-nb-0.17.2 myst-parser-0.18.1 nbclient-0.5.13 nbformat-5.8.0 nest-asyncio-1.5.6 parso-0.8.3 pexpect-4.8.0 pickleshare-0.7.5 pkgutil-resolve-name-1.3.10 prompt-toolkit-3.0.38 psutil-5.9.5 ptyprocess-0.7.0 pybtex-0.24.0 pybtex-docutils-1.0.2 pydata-sphinx-theme-0.13.3 pyrsistent-0.19.3 python-dateutil-2.8.2 pyyaml-6.0 pyzmq-25.1.0 soupsieve-2.4.1 sphinx-5.3.0 sphinx-book-theme-1.0.1 sphinx-copybutton-0.5.2 sphinx-tabs-3.4.1 sphinx-togglebutton-0.3.2 sphinx_design-0.4.1 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-bibtex-2.5.0 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sqlalchemy-1.4.48 tabulate-0.9.0 tornado-6.2 traitlets-5.9.0 typing-extensions-4.6.3 wcwidth-0.2.6 zipp-3.15.0 [rtd-command-info] start-time: 2023-06-21T17:18:47.442988Z, end-time: 2023-06-21T17:18:47.506330Z, duration: 0, exit-code: 0 cat docs/source/conf.py # Configuration file for the Sphinx documentation builder. # # This file only contains a selection of the most common options. For a full # list see the documentation: # http://www.sphinx-doc.org/en/master/config # -- Path setup -------------------------------------------------------------- # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. # # import os # import sys # sys.path.insert(0, os.path.abspath('.')) # -- Project information ----------------------------------------------------- project = "HPC Documentation" logo = "_static/logo-square.png" copyright = "2023" author = "Research Computing, Northeastern University" # The full version, including alpha/beta/rc tags release = "2.0.0" # -- General configuration --------------------------------------------------- # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ "myst_nb", "sphinx.ext.autodoc", "sphinx.ext.autosectionlabel", "sphinx.ext.intersphinx", "sphinx.ext.viewcode", "sphinx_copybutton", "sphinx_design", # https://pypi.org/project/sphinx_design/ "sphinx_tabs.tabs", "sphinx_togglebutton", # https://sphinx-togglebutton.readthedocs.io/en/latest/use.html # "sphinxcontrib.bibtex", # "sphinxext.opengraph", # For the kitchen sink "sphinx.ext.todo", ] intersphinx_mapping = {"python": ("https://docs.python.org/3", None)} myst_enable_extensions = [ "colon_fence", "deflist", ] # extensions = ['sphinx_markdown_tables',] # Add any paths that contain templates here, relative to this directory. templates_path = ["_templates"] # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. # This pattern also affects html_static_path and html_extra_path. exclude_patterns = ["first_steps/cps_ood.md", "using-discovery/bash.md", "_snippets/*"] # -- Options for HTML output ------------------------------------------------- # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. # html_theme = "sphinx_book_theme" # add logo to the upper left in the help system html_logo = "_static/logo-square.png" html_theme_options = { "show_toc_level": 2, "repository_url": "https://github.com/northeastern-rc/rc-public-documentation", "use_repository_button": True, "use_edit_page_button": False, "use_issues_button": True, } # custom css file html_css_files = ["../css/custom.css"] # If true, “(C) Copyright …” is shown in the HTML footer. Default is True. html_show_copyright = True # If true, “Created using Sphinx” is shown in the HTML footer. Default is True. html_show_sphinx = False # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ["_static", "_static/video"] master_doc = "index" source_suffix = [".rst", ".md"] ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/main/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # # Note: this file shouldn't rely on extra dependencies. import importlib import sys import os.path # Borrowed from six. PY3 = sys.version_info[0] == 3 string_types = str if PY3 else basestring from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix elif isinstance(source_suffix, (list, tuple)): # Sphinx >= 1.3 supports list/tuple to define multiple suffixes SUFFIX = source_suffix[0] elif isinstance(source_suffix, dict): # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility else: # default to .rst SUFFIX = '.rst' else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = ( ( 'html_theme' in globals() and html_theme in ['default'] and # Allow people to bail with a hack of having an html_style 'html_style' not in globals() ) or 'html_theme' not in globals() ) if using_rtd_theme: html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} # This following legacy behavior will gradually be sliced out until its deprecated and removed. # Skipped for Sphinx 6+ # Skipped by internal Feature flag SKIP_SPHINX_HTML_THEME_PATH # Skipped by all new projects since SKIP_SPHINX_HTML_THEME_PATH's introduction (jan 2023) if ( using_rtd_theme and version_info < (6,0) and not False ): theme = importlib.import_module('sphinx_rtd_theme') if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] # Define websupport2_base_url and websupport2_static_url if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.com/websupport' websupport2_static_url = 'https://assets.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'proxied_static_path': "/_/static/", 'versions': [ ("latest", "/en/latest/"), ], 'downloads': [ ("pdf", "//rc-docs.northeastern.edu/_/downloads/en/latest/pdf/"), ("html", "//rc-docs.northeastern.edu/_/downloads/en/latest/htmlzip/"), ("epub", "//rc-docs.northeastern.edu/_/downloads/en/latest/epub/"), ], 'subprojects': [ ], 'slug': 'northeastern-university-rc-public-documentation', 'name': u'rc-public-documentation', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': '', 'analytics_code': 'UA-53190950-13', 'single_version': False, 'conf_py_path': '/docs/source/', 'api_host': 'https://readthedocs.com', 'github_user': 'northeastern-rc', 'proxied_api_host': '/_', 'github_repo': 'rc-public-documentation', 'github_version': 'master', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'master', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'docsearch_disabled': False, 'user_analytics_code': 'UA-53190950-13', 'global_analytics_code': 'UA-17997319-2', 'commit': '0cb3a91d', } # For sphinx >=1.8 we can use html_baseurl to set the canonical URL. # https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl if version_info >= (1, 8): if not globals().get('html_baseurl'): html_baseurl = context['canonical_url'] context['canonical_url'] = None if 'html_context' in globals(): for key in context: if key not in html_context: html_context[key] = context[key] else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'branch' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") readthedocs_vcs_url = 'None' readthedocs_build_url = 'https://readthedocs.com/projects/northeastern-university-rc-public-documentation/builds/1552702/' project_language = 'en' # User's Sphinx configurations language_user = globals().get('language', None) latex_engine_user = globals().get('latex_engine', None) latex_elements_user = globals().get('latex_elements', None) # Remove this once xindy gets installed in Docker image and XINDYOPS # env variable is supported # https://github.com/rtfd/readthedocs-docker-images/pull/98 latex_use_xindy = False chinese = any([ language_user in ('zh_CN', 'zh_TW'), project_language in ('zh_CN', 'zh_TW'), ]) japanese = any([ language_user == 'ja', project_language == 'ja', ]) if chinese: latex_engine = latex_engine_user or 'xelatex' latex_elements_rtd = { 'preamble': '\\usepackage[UTF8]{ctex}\n', } latex_elements = latex_elements_user or latex_elements_rtd elif japanese: latex_engine = latex_engine_user or 'platex' # Make sure our build directory is always excluded exclude_patterns = globals().get('exclude_patterns', []) exclude_patterns.extend(['_build']) [rtd-command-info] start-time: 2023-06-21T17:18:47.877058Z, end-time: 2023-06-21T17:18:55.567033Z, duration: 7, exit-code: 0 python -m sphinx -T -E -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html Running Sphinx v5.3.0 making output directory... done myst v0.18.1: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=['colon_fence', 'deflist'], disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, highlight_code_blocks=True, number_code_blocks=[], title_to_header=False, heading_anchors=None, heading_slug_func=None, footnote_transition=True, words_per_minute=200, sub_delimiters=('{', '}'), linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area') myst-nb v0.17.2: NbParserConfig(custom_formats={}, metadata_key='mystnb', cell_metadata_key='mystnb', kernel_rgx_aliases={}, execution_mode='auto', execution_cache_path='', execution_excludepatterns=(), execution_timeout=30, execution_in_temp=False, execution_allow_errors=False, execution_raise_on_error=False, execution_show_tb=False, merge_streams=False, render_plugin='default', remove_code_source=False, remove_code_outputs=False, code_prompt_show='Show code cell {type}', code_prompt_hide='Hide code cell {type}', number_source_lines=False, output_stderr='show', render_text_lexer='myst-ansi', render_error_lexer='ipythontb', render_image_options={}, render_figure_options={}, render_markdown_format='commonmark', output_folder='build', append_css=True, metadata_to_fm=False) Using jupyter-cache at: /home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/checkouts/latest/_readthedocs/.jupyter_cache loading intersphinx inventory from https://docs.python.org/3/objects.inv... building [mo]: targets for 0 po files that are out of date building [html]: targets for 31 source files that are out of date updating environment: [new config] 31 added, 0 changed, 0 removed reading sources... 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[ 93%] using-ood/introduction writing output... [ 96%] welcome/gettinghelp writing output... [100%] welcome/welcome generating indices... genindex done writing additional pages... search done copying images... [ 5%] images/checkpointing.png copying images... [ 10%] images/cps-ood-menu.png copying images... [ 15%] images/cps-ood-jupyterform.png copying images... [ 20%] images/cps-ood-jupyterlab-start-session.png copying images... [ 25%] images/cps-ood-build-window.png copying images... [ 30%] images/cps-ood-jupyterlab-folders-view.png copying images... [ 35%] images/cps-ood-jupyterlab-students-folder.png copying images... [ 40%] images/cps-ood-jupyterlab-username-folder.png copying images... [ 45%] images/cps-ood-jupyterlab-ipykernel-launcher.png copying images... [ 50%] images/cps-ood-jupyterlab-ipykernel.png copying images... [ 55%] images/cps-ood-jupyterlab-new-launcher.png copying images... [ 60%] images/cps-ood-jupyterlab-open-terminal.png copying images... 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[rtd-command-info] start-time: 2023-06-21T17:18:55.811715Z, end-time: 2023-06-21T17:19:00.324601Z, duration: 4, exit-code: 0 python -m sphinx -T -E -b readthedocssinglehtmllocalmedia -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/htmlzip Running Sphinx v5.3.0 making output directory... done myst v0.18.1: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=['colon_fence', 'deflist'], disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, highlight_code_blocks=True, number_code_blocks=[], title_to_header=False, heading_anchors=None, heading_slug_func=None, footnote_transition=True, words_per_minute=200, sub_delimiters=('{', '}'), linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area') myst-nb v0.17.2: NbParserConfig(custom_formats={}, metadata_key='mystnb', cell_metadata_key='mystnb', kernel_rgx_aliases={}, execution_mode='auto', execution_cache_path='', execution_excludepatterns=(), execution_timeout=30, execution_in_temp=False, execution_allow_errors=False, execution_raise_on_error=False, execution_show_tb=False, merge_streams=False, render_plugin='default', remove_code_source=False, remove_code_outputs=False, code_prompt_show='Show code cell {type}', code_prompt_hide='Hide code cell {type}', number_source_lines=False, output_stderr='show', render_text_lexer='myst-ansi', render_error_lexer='ipythontb', render_image_options={}, render_figure_options={}, render_markdown_format='commonmark', output_folder='build', append_css=True, metadata_to_fm=False) Using jupyter-cache at: /home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/checkouts/latest/_readthedocs/.jupyter_cache loading intersphinx inventory from https://docs.python.org/3/objects.inv... building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: [new config] 31 added, 0 changed, 0 removed reading sources... 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[rtd-command-info] start-time: 2023-06-21T17:19:06.231120Z, end-time: 2023-06-21T17:19:09.975969Z, duration: 3, exit-code: 0 python -m sphinx -T -E -b latex -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/pdf Running Sphinx v5.3.0 making output directory... done myst v0.18.1: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=['colon_fence', 'deflist'], disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, highlight_code_blocks=True, number_code_blocks=[], title_to_header=False, heading_anchors=None, heading_slug_func=None, footnote_transition=True, words_per_minute=200, sub_delimiters=('{', '}'), linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area') myst-nb v0.17.2: NbParserConfig(custom_formats={}, metadata_key='mystnb', cell_metadata_key='mystnb', kernel_rgx_aliases={}, execution_mode='auto', execution_cache_path='', execution_excludepatterns=(), execution_timeout=30, execution_in_temp=False, execution_allow_errors=False, execution_raise_on_error=False, execution_show_tb=False, merge_streams=False, render_plugin='default', remove_code_source=False, remove_code_outputs=False, code_prompt_show='Show code cell {type}', code_prompt_hide='Hide code cell {type}', number_source_lines=False, output_stderr='show', render_text_lexer='myst-ansi', render_error_lexer='ipythontb', render_image_options={}, render_figure_options={}, render_markdown_format='commonmark', output_folder='build', append_css=True, metadata_to_fm=False) Using jupyter-cache at: /home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/checkouts/latest/_readthedocs/.jupyter_cache loading intersphinx inventory from https://docs.python.org/3/objects.inv... building [mo]: targets for 0 po files that are out of date building [latex]: all documents updating environment: [new config] 31 added, 0 changed, 0 removed reading sources... 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[100%] images/cps-ood-jupyterlab-open-terminal.png copying TeX support files... copying TeX support files... done WARNING: Missing searchtools: /home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/checkouts/latest/_readthedocs/pdf/_static/searchtools.js build succeeded, 1 warning. The LaTeX files are in ../../_readthedocs/pdf. Run 'make' in that directory to run these through (pdf)latex (use `make latexpdf' here to do that automatically). [rtd-command-info] start-time: 2023-06-21T17:19:12.817897Z, end-time: 2023-06-21T17:19:12.885173Z, duration: 0, exit-code: 0 cat latexmkrc $latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $pdflatex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $lualatex = 'lualatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $xelatex = 'xelatex --no-pdf ' . $ENV{'LATEXOPTS'} . ' %O %S'; $makeindex = 'makeindex -s python.ist %O -o %D %S'; add_cus_dep( "glo", "gls", 0, "makeglo" ); sub makeglo { return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" ); } [rtd-command-info] start-time: 2023-06-21T17:19:13.109446Z, end-time: 2023-06-21T17:19:29.442894Z, duration: 16, exit-code: 0 latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=northeastern-university-rc-public-documentation -interaction=nonstopmode Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 1, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 2, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 3, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 4, chunk 1. Subroutine makeglo redefined at (eval 11) line 7, chunk 1. 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Rule 'pdflatex': Rules & subrules not known to be previously run: pdflatex Rule 'pdflatex': The following rules & subrules became out-of-date: 'pdflatex' ------------ Run number 1 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="northeastern-university-rc-public-documentation" "hpc.tex"' ------------ Latexmk: applying rule 'pdflatex'... This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./hpc.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. 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LaTeX Warning: Hyper reference `storage/general_storage:general-storage' on pag e 65 undefined on input line 4054. [65] [66] Chapter 24. LaTeX Warning: Hyper reference `storage/discovery_storage::doc' on page 67 unde fined on input line 4074. LaTeX Warning: Hyper reference `storage/general_storage:connecting-to-research' on page 67 undefined on input line 4084. [67] [68] Chapter 25. [69] [70 <./checkpointing.png>] [71] [72] [73] [74] Chapter 26. LaTeX Warning: Hyper reference `first_steps/get_access::doc' on page 75 undefin ed on input line 4458. LaTeX Warning: Hyper reference `using-ood/interactiveapps::doc' on page 75 unde fined on input line 4474. LaTeX Warning: Hyper reference `using-ood/fileexplore::doc' on page 75 undefine d on input line 4478. [75] [76] Chapter 27. LaTeX Warning: Hyper reference `using-ood/interactiveapps::doc' on page 77 unde fined on input line 4534. [77] [78] Chapter 28. 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[87 <./cps-ood-menu.png>] [88 <./cps-ood-jupyterform.png>] [89 <./cps-ood-jupyt erlab-start-session.png> <./cps-ood-build-window.png>] [90 <./cps-ood-jupyterla b-folders-view.png> <./cps-ood-jupyterlab-students-folder.png>] [91 <./cps-ood- jupyterlab-username-folder.png> <./cps-ood-jupyterlab-ipykernel-launcher.png>] [92 <./cps-ood-jupyterlab-ipykernel.png> <./cps-ood-jupyterlab-new-launcher.png >] No file northeastern-university-rc-public-documentation.ind. [93 <./cps-ood-jupyterlab-open-terminal.png>] (./northeastern-university-rc-public-documentation.aux) Package rerunfilecheck Warning: File `northeastern-university-rc-public-documen tation.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information){/usr/share/texmf/fonts/enc /dvips/tex-gyre/q-ts1.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ec.enc}< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi5.pfb> Output written on northeastern-university-rc-public-documentation.pdf (97 pages , 27550873 bytes). Transcript written on northeastern-university-rc-public-documentation.log. Latexmk: Index file 'northeastern-university-rc-public-documentation.idx' was written Latexmk: Missing input file: 'northeastern-university-rc-public-documentation.ind' from line 'No file northeastern-university-rc-public-documentation.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'northeastern-university-rc-public-documentation.pdf' Latexmk: Log file says output to 'northeastern-university-rc-public-documentation.pdf' Rule 'makeindex northeastern-university-rc-public-documentation.idx': File changes, etc: Non-existent destination files: 'northeastern-university-rc-public-documentation.ind' ------------ Run number 1 of rule 'makeindex northeastern-university-rc-public-documentation.idx' ------------ Latexmk: applying rule 'makeindex northeastern-university-rc-public-documentation.idx'... ------------ Running 'makeindex -s python.ist -o "northeastern-university-rc-public-documentation.ind" "northeastern-university-rc-public-documentation.idx"' ------------ This is makeindex, version 2.15 [TeX Live 2017] (kpathsea + Thai support). Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored). Scanning input file northeastern-university-rc-public-documentation.idx...done (0 entries accepted, 0 rejected). 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PACKAGE INPUTENC ERROR: UNICODE CHAR П�� (U+1F44B) (INPUTENC) NOT SET UP FOR USE WITH LATEX. SEE THE INPUTENC PACKAGE DOCUMENTATION FOR EXPLANATION. Type H for immediate help. ... l.81 \sphinxtableofcontents (./northeastern-university-rc-public-documentation.toc (/usr/share/texlive/texmf-dist/tex/latex/txfonts/t1txtt.fd) [1] [2]) [3] [4] ! PACKAGE INPUTENC ERROR: UNICODE CHAR П�� (U+1F44B) (INPUTENC) NOT SET UP FOR USE WITH LATEX. SEE THE INPUTENC PACKAGE DOCUMENTATION FOR EXPLANATION. Type H for immediate help. ... l.286 \chapter {Welcome} [1] ! PACKAGE INPUTENC ERROR: UNICODE CHAR П�� (U+1F44B) (INPUTENC) NOT SET UP FOR USE WITH LATEX. SEE THE INPUTENC PACKAGE DOCUMENTATION FOR EXPLANATION. Type H for immediate help. ... l.286 \chapter {Welcome} [2] Chapter 1. [3] [4 <./discovery.png>] Chapter 2. [5] [6] Chapter 3. [7] [8] Chapter 4. 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[27] [28] Chapter 11. Underfull \hbox (badness 10000) in paragraph at lines 1765--1765 []\T1/txtt/m/n/10 module show <./moduleload.jpg>] Chapter 12. (/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd) [31] [32] [33] [34] Chapter 13. Underfull \hbox (badness 10000) in paragraph at lines 2168--2170 []\T1/qtm/m/n/10 To delete a Conda en-vi-ron-ment and all of its re-lated pack- ages, type \T1/txtt/m/n/10 conda remove []n [35] Underfull \hbox (badness 10000) in paragraph at lines 2216--2218 []\T1/qtm/m/n/10 Af-ter com-plet-ing steps 1 through 6 in the pre-vi-ous pro-ce -dure, type \T1/txtt/m/n/10 conda create [][]name [36] Chapter 14. Underfull \hbox (badness 10000) in paragraph at lines 2276--2278 []\T1/qtm/m/n/10 From the ter-mi-nal, type \T1/txtt/m/n/10 git clone []c featur e.manyFiles=true https://github.com/spack/ [37] [38] Chapter 15. 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[59] [60] Chapter 22. [61] [62] [63] [64] Chapter 23. [65] [66] Chapter 24. [67] [68] Chapter 25. [69] [70 <./checkpointing.png>] [71] [72] [73] [74] Chapter 26. [75] [76] Chapter 27. [77] [78] Chapter 28. [79 <./ood_apps_2021.jpg>] [80] [81] [82] Chapter 29. [83] [84] [85] [86] Chapter 30. [87 <./cps-ood-menu.png>] [88 <./cps-ood-jupyterform.png>] [89 <./cps-ood-jupyt erlab-start-session.png> <./cps-ood-build-window.png>] [90 <./cps-ood-jupyterla b-folders-view.png> <./cps-ood-jupyterlab-students-folder.png>] [91 <./cps-ood- jupyterlab-username-folder.png> <./cps-ood-jupyterlab-ipykernel-launcher.png>] [92 <./cps-ood-jupyterlab-ipykernel.png> <./cps-ood-jupyterlab-new-launcher.png >] (./northeastern-university-rc-public-documentation.ind) [93 <./cps-ood-jupyt erlab-open-terminal.png>] (./northeastern-university-rc-public-documentation.aux) ) (see the transcript file for additional information){/usr/share/texmf/fonts/enc /dvips/tex-gyre/q-ts1.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ec.enc}< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi5.pfb> Output written on northeastern-university-rc-public-documentation.pdf (99 pages , 27569295 bytes). Transcript written on northeastern-university-rc-public-documentation.log. Latexmk: Index file 'northeastern-university-rc-public-documentation.idx' was written Latexmk: Log file says output to 'northeastern-university-rc-public-documentation.pdf' Latexmk: Log file says output to 'northeastern-university-rc-public-documentation.pdf' Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'northeastern-university-rc-public-documentation.out' 'northeastern-university-rc-public-documentation.toc' ------------ Run number 3 of rule 'pdflatex' ------------ Latexmk: applying rule 'pdflatex'... ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="northeastern-university-rc-public-documentation" "hpc.tex"' ------------ This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./hpc.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. 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(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty) (./sphinxmessages.sty) Writing index file northeastern-university-rc-public-documentation.idx (./northeastern-university-rc-public-documentation.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) 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PACKAGE INPUTENC ERROR: UNICODE CHAR П�� (U+1F44B) (INPUTENC) NOT SET UP FOR USE WITH LATEX. SEE THE INPUTENC PACKAGE DOCUMENTATION FOR EXPLANATION. Type H for immediate help. ... l.81 \sphinxtableofcontents (./northeastern-university-rc-public-documentation.toc (/usr/share/texlive/texmf-dist/tex/latex/txfonts/t1txtt.fd) [1] [2]) [3] [4] ! PACKAGE INPUTENC ERROR: UNICODE CHAR П�� (U+1F44B) (INPUTENC) NOT SET UP FOR USE WITH LATEX. SEE THE INPUTENC PACKAGE DOCUMENTATION FOR EXPLANATION. Type H for immediate help. ... l.286 \chapter {Welcome} [1] ! PACKAGE INPUTENC ERROR: UNICODE CHAR П�� (U+1F44B) (INPUTENC) NOT SET UP FOR USE WITH LATEX. SEE THE INPUTENC PACKAGE DOCUMENTATION FOR EXPLANATION. Type H for immediate help. ... l.286 \chapter {Welcome} [2] Chapter 1. [3] [4 <./discovery.png>] Chapter 2. [5] [6] Chapter 3. [7] [8] Chapter 4. [9] Underfull \hbox (badness 10000) in paragraph at lines 721--723 []\T1/qtm/m/n/10 Type \T1/txtt/m/n/10 ssh[]copy[]id []i ~/.ssh/id_rsa.pub @login.discovery.neu.edu \T1/qtm/m/n/10 to copy [10] [11] [12] Chapter 5. [13] [14] Chapter 6. [15] [16] Chapter 7. [17 <./catbashrc.jpg>] [18 <./minicondabashrc.jpg>] [19 <./nanobashrc.png>] [20] Chapter 8. [21] [22] Chapter 9. (/usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd) Overfull \hbox (11.62366pt too wide) in paragraph at lines 1424--1424 []\T1/qhv/m/n/10 Name| Underfull \hbox (badness 10000) in paragraph at lines 1424--1424 []\T1/qhv/m/n/10 Re- Overfull \hbox (0.50366pt too wide) in paragraph at lines 1424--1424 \T1/qhv/m/n/10 quires Underfull \hbox (badness 10000) in paragraph at lines 1424--1424 \T1/qhv/m/n/10 ap- Overfull \hbox (5.66368pt too wide) in paragraph at lines 1424--1424 \T1/qhv/m/n/10 proval?| Underfull \hbox (badness 10000) in paragraph at lines 1424--1424 []\T1/qhv/m/n/10 Time Underfull \hbox (badness 10000) in paragraph at lines 1424--1424 \T1/qhv/m/n/10 limit Underfull \hbox (badness 10000) in paragraph at lines 1424--1424 \T1/qhv/m/n/10 (de- Overfull \hbox (11.63968pt too wide) in paragraph at lines 1424--1424 \T1/qhv/m/n/10 fault/max)| Overfull \hbox (3.51933pt too wide) in paragraph at lines 1424--1424 []\T1/qhv/m/n/10 Run- Overfull \hbox (0.84933pt too wide) in paragraph at lines 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256GB| Underfull \hbox (badness 10000) in paragraph at lines 1424--1424 []\T1/qtm/m/n/10 ex- Overfull \hbox (5.55367pt too wide) in paragraph at lines 1424--1424 \T1/qtm/m/n/10 press| Underfull \hbox (badness 10000) in paragraph at lines 1424--1424 \T1/qtm/m/n/10 utes/60 Overfull \hbox (9.72934pt too wide) in paragraph at lines 1424--1424 []\T1/qtm/m/n/10 50/250| Overfull \hbox (7.78366pt too wide) in paragraph at lines 1424--1424 []\T1/qtm/m/n/10 25TB| Overfull \hbox (5.25365pt too wide) in paragraph at lines 1424--1424 []\T1/qtm/m/n/10 short| Underfull \hbox (badness 10000) in paragraph at lines 1424--1424 []\T1/qtm/m/n/10 4 Overfull \hbox (2.83969pt too wide) in paragraph at lines 1424--1424 \T1/qtm/m/n/10 hours/24 Overfull \hbox (9.72934pt too wide) in paragraph at lines 1424--1424 []\T1/qtm/m/n/10 50/500| Overfull \hbox (7.78366pt too wide) in paragraph at lines 1424--1424 []\T1/qtm/m/n/10 25TB| Overfull \hbox (2.78366pt too wide) in paragraph at lines 1424--1424 []\T1/qtm/m/n/10 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[23] Underfull \hbox (badness 10000) in paragraph at lines 1442--1444 []|\T1/qhv/m/n/10 Re- Underfull \hbox (badness 10000) in paragraph at lines 1442--1444 \T1/qhv/m/n/10 quires Underfull \hbox (badness 10000) in paragraph at lines 1442--1444 \T1/qhv/m/n/10 ap- Underfull \hbox (badness 10000) in paragraph at lines 1445--1447 []|\T1/qhv/m/n/10 Time Overfull \hbox (4.04942pt too wide) in paragraph at lines 1445--1447 \T1/qhv/m/n/10 fault/max)| Underfull \hbox (badness 10000) in paragraph at lines 1448--1450 []|\T1/qhv/m/n/10 Run-ning Underfull \hbox (badness 10000) in paragraph at lines 1454--1456 []|\T1/qhv/m/n/10 GPU Underfull \hbox (badness 10000) in paragraph at lines 1457--1459 []|\T1/qhv/m/n/10 GPU Underfull \hbox (badness 10000) in paragraph at lines 1496--1498 []|\T1/qtm/m/n/10 4 Underfull \hbox (badness 10000) in paragraph at lines 1496--1498 \T1/qtm/m/n/10 hours/24 Underfull \hbox (badness 10000) in paragraph at lines 1511--1514 []|\T1/qtm/m/n/10 For jobs that Underfull \hbox (badness 10000) in paragraph at lines 1511--1514 \T1/qtm/m/n/10 re-quire more [24] [25] [26] Chapter 10. [27] [28] Chapter 11. Underfull \hbox (badness 10000) in paragraph at lines 1765--1765 []\T1/txtt/m/n/10 module show <./moduleload.jpg>] Chapter 12. (/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd) [31] [32] [33] [34] Chapter 13. Underfull \hbox (badness 10000) in paragraph at lines 2168--2170 []\T1/qtm/m/n/10 To delete a Conda en-vi-ron-ment and all of its re-lated pack- ages, type \T1/txtt/m/n/10 conda remove []n [35] Underfull \hbox (badness 10000) in paragraph at lines 2216--2218 []\T1/qtm/m/n/10 Af-ter com-plet-ing steps 1 through 6 in the pre-vi-ous pro-ce -dure, type \T1/txtt/m/n/10 conda create [][]name [36] Chapter 14. Underfull \hbox (badness 10000) in paragraph at lines 2276--2278 []\T1/qtm/m/n/10 From the ter-mi-nal, type \T1/txtt/m/n/10 git clone []c featur e.manyFiles=true https://github.com/spack/ [37] [38] Chapter 15. [39] [40] Underfull \hbox (badness 7133) in paragraph at lines 2584--2586 []\T1/qtm/m/n/10 To dis-con-nect pack-rat and al-low for pack-age in-stal-la-ti on out-side of your pack-rat project folder: [41] [42] Chapter 16. [43] [44] Chapter 17. [45] [46] Chapter 18. [47] [48] [49] [50] Chapter 19. [51 <./srun_example.jpg>] [52] Chapter 20. Underfull \hbox (badness 10000) in paragraph at lines 3288--3288 []\T1/qhv/m/n/10 GPU Underfull \hbox (badness 10000) in paragraph at lines 3288--3288 []\T1/qhv/m/n/10 Ten-sor Underfull \hbox (badness 10000) in paragraph at lines 3288--3288 []\T1/qhv/m/n/10 CUDA Underfull \hbox (badness 10000) in paragraph at lines 3288--3288 []\T1/qtm/m/n/10 quadro ([][]Quadro Underfull \hbox (badness 10000) in paragraph at lines 3288--3288 []\T1/qtm/m/n/10 41 & Underfull \hbox (badness 10000) in paragraph at lines 3288--3288 []\T1/qtm/m/n/10 a5000 ([][]Am-pere Underfull \hbox (badness 10000) in paragraph at lines 3288--3288 []\T1/qtm/m/n/10 a6000 ([][]Am-pere Underfull \hbox (badness 10000) in paragraph at lines 3371--3371 []\T1/qhv/m/n/10 Re-quires Ap- Underfull \hbox (badness 10000) in paragraph at lines 3371--3371 []\T1/qhv/m/n/10 Time limit (De- Underfull \hbox (badness 10000) in paragraph at lines 3371--3371 []\T1/qhv/m/n/10 Sub-mit-ted Underfull \hbox (badness 10000) in paragraph at lines 3371--3371 []\T1/qtm/m/n/10 multi- [53] [54] [55] [56] [57] [58] Chapter 21. [59] [60] Chapter 22. [61] [62] [63] [64] Chapter 23. [65] [66] Chapter 24. [67] [68] Chapter 25. [69] [70 <./checkpointing.png>] [71] [72] [73] [74] Chapter 26. [75] [76] Chapter 27. [77] [78] Chapter 28. [79 <./ood_apps_2021.jpg>] [80] [81] [82] Chapter 29. [83] [84] [85] [86] Chapter 30. [87 <./cps-ood-menu.png>] [88 <./cps-ood-jupyterform.png>] [89 <./cps-ood-jupyt erlab-start-session.png> <./cps-ood-build-window.png>] [90 <./cps-ood-jupyterla b-folders-view.png> <./cps-ood-jupyterlab-students-folder.png>] [91 <./cps-ood- jupyterlab-username-folder.png> <./cps-ood-jupyterlab-ipykernel-launcher.png>] [92 <./cps-ood-jupyterlab-ipykernel.png> <./cps-ood-jupyterlab-new-launcher.png >] (./northeastern-university-rc-public-documentation.ind) [93 <./cps-ood-jupyt erlab-open-terminal.png>] (./northeastern-university-rc-public-documentation.aux) ) (see the transcript file for additional information){/usr/share/texmf/fonts/enc /dvips/tex-gyre/q-ts1.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ec.enc}< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi5.pfb> Output written on northeastern-university-rc-public-documentation.pdf (99 pages , 27569295 bytes). Transcript written on northeastern-university-rc-public-documentation.log. Latexmk: Index file 'northeastern-university-rc-public-documentation.idx' was written Latexmk: Log file says output to 'northeastern-university-rc-public-documentation.pdf' Latexmk: Log file says output to 'northeastern-university-rc-public-documentation.pdf' Latexmk: Errors, in force_mode: so I tried finishing targets Collected error summary (may duplicate other messages): pdflatex: Command for 'pdflatex' gave return code 256 [rtd-command-info] start-time: 2023-06-21T17:19:30.063523Z, end-time: 2023-06-21T17:19:34.732021Z, duration: 4, exit-code: 0 python -m sphinx -T -E -b epub -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/epub Running Sphinx v5.3.0 making output directory... done WARNING: conf value "version" should not be empty for EPUB3 myst v0.18.1: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=['colon_fence', 'deflist'], disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, highlight_code_blocks=True, number_code_blocks=[], title_to_header=False, heading_anchors=None, heading_slug_func=None, footnote_transition=True, words_per_minute=200, sub_delimiters=('{', '}'), linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area') myst-nb v0.17.2: NbParserConfig(custom_formats={}, metadata_key='mystnb', cell_metadata_key='mystnb', kernel_rgx_aliases={}, execution_mode='auto', execution_cache_path='', execution_excludepatterns=(), execution_timeout=30, execution_in_temp=False, execution_allow_errors=False, execution_raise_on_error=False, execution_show_tb=False, merge_streams=False, render_plugin='default', remove_code_source=False, remove_code_outputs=False, code_prompt_show='Show code cell {type}', code_prompt_hide='Hide code cell {type}', number_source_lines=False, output_stderr='show', render_text_lexer='myst-ansi', render_error_lexer='ipythontb', render_image_options={}, render_figure_options={}, render_markdown_format='commonmark', output_folder='build', append_css=True, metadata_to_fm=False) Using jupyter-cache at: /home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/checkouts/latest/_readthedocs/.jupyter_cache loading intersphinx inventory from https://docs.python.org/3/objects.inv... building [mo]: targets for 0 po files that are out of date building [epub]: targets for 31 source files that are out of date updating environment: [new config] 31 added, 0 changed, 0 removed reading sources... 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[ 93%] using-ood/introduction writing output... [ 96%] welcome/gettinghelp writing output... [100%] welcome/welcome generating indices... genindex done writing additional pages... done copying images... [ 5%] images/checkpointing.png copying images... [ 10%] images/cps-ood-menu.png copying images... [ 15%] images/cps-ood-jupyterform.png copying images... [ 20%] images/cps-ood-jupyterlab-start-session.png copying images... [ 25%] images/cps-ood-build-window.png copying images... [ 30%] images/cps-ood-jupyterlab-folders-view.png copying images... [ 35%] images/cps-ood-jupyterlab-students-folder.png copying images... [ 40%] images/cps-ood-jupyterlab-username-folder.png copying images... [ 45%] images/cps-ood-jupyterlab-ipykernel-launcher.png copying images... [ 50%] images/cps-ood-jupyterlab-ipykernel.png copying images... [ 55%] images/cps-ood-jupyterlab-new-launcher.png copying images... [ 60%] images/cps-ood-jupyterlab-open-terminal.png copying images... 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