Read the Docs build information Build id: 1656078 Project: northeastern-university-rc-public-documentation Version: latest Commit: af15c60b5195a6d85ace80d5783a1ae60f26a96d Date: 2023-08-11T15:56:19.708731Z State: finished Success: True [rtd-command-info] start-time: 2023-08-11T15:56:25.448329Z, end-time: 2023-08-11T15:56:30.123385Z, duration: 4, 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: 2023-08-11T15:56:30.423569Z, end-time: 2023-08-11T15:56:30.901246Z, duration: 0, exit-code: 0 git checkout --force origin/master Note: switching to 'origin/master'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by switching back to a branch. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example: git switch -c Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at af15c60 Revert "updated the text based on Serena's suggestions." [rtd-command-info] start-time: 2023-08-11T15:56:31.236956Z, end-time: 2023-08-11T15:56:31.315063Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2023-08-11T15:56:33.700299Z, end-time: 2023-08-11T15:56:46.462863Z, duration: 12, 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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(setup.py): finished with status 'done' Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23753 sha256=5b25fcdb9492ce4529919df8b5c44ee92ccd7a1d094eaaafdca5e436550fd91e Stored in directory: /tmp/pip-ephem-wheel-cache-_fe22ve8/wheels/7a/94/b1/0fdc5339a5bd487a5cc15421ec200d9ba3e2aa7190e4a727f1 Successfully built mock Installing collected packages: snowballstemmer, pytz, mock, commonmark, urllib3, sphinxcontrib-serializinghtml, six, Pygments, pillow, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, sphinxcontrib-websupport, requests, jinja2, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark Successfully installed MarkupSafe-2.1.3 Pygments-2.16.1 alabaster-0.7.13 babel-2.12.1 certifi-2023.7.22 charset-normalizer-3.2.0 commonmark-0.9.1 docutils-0.17.1 idna-3.4 imagesize-1.4.1 jinja2-3.0.3 mock-1.0.1 packaging-23.1 pillow-9.5.0 pytz-2023.3 readthedocs-sphinx-ext-2.2.2 recommonmark-0.5.0 requests-2.31.0 six-1.16.0 snowballstemmer-2.2.0 sphinx-1.8.6 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.5 sphinxcontrib-websupport-1.2.4 urllib3-2.0.4 [rtd-command-info] start-time: 2023-08-11T15:56:56.413003Z, end-time: 2023-08-11T15:57:12.812431Z, duration: 16, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt Collecting jupyterlab-myst (from -r docs/requirements.txt (line 1)) Obtaining dependency information for jupyterlab-myst from https://files.pythonhosted.org/packages/a1/79/e035ffc287c99524fb6e35ffa7463b8c5c15810ae32d61a8094582371555/jupyterlab_myst-1.2.0-py3-none-any.whl.metadata Downloading jupyterlab_myst-1.2.0-py3-none-any.whl.metadata (9.7 kB) Collecting myst-nb (from -r docs/requirements.txt (line 2)) Downloading myst_nb-0.17.2-py3-none-any.whl (78 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 78.6/78.6 kB 9.7 MB/s eta 0:00:00 Collecting myst-parser (from -r docs/requirements.txt (line 3)) Downloading myst_parser-1.0.0-py3-none-any.whl (77 kB) 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Downloading fastjsonschema-2.18.0-py3-none-any.whl (23 kB) Installing collected packages: wcwidth, ptyprocess, pickleshare, fastjsonschema, backcall, zipp, typing-extensions, traitlets, tornado, tabulate, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, soupsieve, pyzmq, pyyaml, 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-8.1.6 debugpy-1.6.7.post1 decorator-5.1.1 docutils-0.18.1 entrypoints-0.4 fastjsonschema-2.18.0 greenlet-2.0.2 importlib-resources-5.12.0 importlib_metadata-6.7.0 ipykernel-6.16.2 ipython-7.34.0 jedi-0.19.0 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-1.5.7 parso-0.8.3 pexpect-4.8.0 pickleshare-0.7.5 pkgutil-resolve-name-1.3.10 prompt-toolkit-3.0.39 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-6.0.1 pyzmq-25.1.1 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-1.4.49 tabulate-0.9.0 tornado-6.2 traitlets-5.9.0 typing-extensions-4.7.1 wcwidth-0.2.6 zipp-3.15.0 [rtd-command-info] start-time: 2023-08-11T15:57:16.629295Z, end-time: 2023-08-11T15:57:16.707171Z, 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", 'sphinx.ext.autosectionlabel', ] # Prefix document path to section labels, to use: # `path/to/file:heading` instead of just `heading` autosectionlabel_prefix_document = True intersphinx_mapping = {"python": ("https://docs.python.org/3", None)} myst_enable_extensions = [ "colon_fence", "deflist", "dollarmath", ] # 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 = ["using-ood/cps_ood.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/"), ("2.0.0", "/en/2.0.0/"), ("1.2.0", "/en/1.2.0/"), ("v1.1.0", "/en/v1.1.0/"), ], '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': 'af15c60b', } # 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/1656078/' 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: 2023-08-11T15:57:17.021757Z, end-time: 2023-08-11T15:57:31.277637Z, duration: 14, 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', 'dollarmath'], 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 62 source files that are out of date updating environment: [new config] 62 added, 0 changed, 0 removed reading sources... 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[rtd-command-info] start-time: 2023-08-11T15:57:31.536290Z, end-time: 2023-08-11T15:57:37.994920Z, duration: 6, 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', 'dollarmath'], 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] 62 added, 0 changed, 0 removed reading sources... 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' %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: 2023-08-11T15:57:54.653869Z, end-time: 2023-08-11T15:58:27.453135Z, duration: 32, 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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[27] [28] Chapter 11. [29] [30] Chapter 12. [31 <./catbashrc.jpg>] LaTeX Warning: Hyper reference `software/conda:mini-conda' on page 32 undefined on input line 1672. [32 <./minicondabashrc.jpg>] [33 <./nanobashrc.png>] LaTeX Warning: Hyper reference `slurmguide/introductiontoslurm:using-sbatch' on page 34 undefined on input line 1751. [34] Chapter 13. [35 <./bash-logo.png> <./terminal-view.png>] ! Package inputenc Error: Unicode char ⌘ (U+2318) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1828 Press Command(⌘ ) + Space on your Mac keyboard (alternatively, press... [36] (/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd) [37] Underfull \vbox (badness 10000) detected at line 2053 Underfull \vbox (badness 10000) detected at line 2053 [38] Underfull \vbox (badness 10000) detected at line 2053 Underfull \vbox (badness 10000) detected at line 2053 [39] Underfull \vbox (badness 10000) detected at line 2053 Underfull \vbox (badness 10000) detected at line 2053 [40] [41] [42] [43] [44] [45] LaTeX Warning: Hyper reference `datamanagement/transferringdata:transferring-da ta' on page 46 undefined on input line 2469. [46] [47] [48] [49] [50] [51] [52] [53] [54] Chapter 14. LaTeX Warning: Hyper reference `first_steps/get_access::doc' on page 55 undefin ed on input line 3317. LaTeX Warning: Hyper reference `using-ood/interactiveapps::doc' on page 55 unde fined on input line 3328. LaTeX Warning: Hyper reference `using-ood/fileexplore::doc' on page 55 undefine d on input line 3332. [55] [56] Chapter 15. 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[107] [108] Chapter 28. [109] [110] Chapter 29. LaTeX Warning: Hyper reference `software/modules:using-module' on page 111 unde fined on input line 5689. LaTeX Warning: Hyper reference `software/modules:using-module' on page 111 unde fined on input line 5715. LaTeX Warning: Hyper reference `using-ood/interactiveapps:accessing-ood' on pag e 111 undefined on input line 5736. LaTeX Warning: Hyper reference `software/spack:using-spack' on page 111 undefin ed on input line 5757. LaTeX Warning: Hyper reference `software/conda:using-conda' on page 111 undefin ed on input line 5785. [111] [112] Chapter 30. Underfull \hbox (badness 10000) in paragraph at lines 5969--5969 []\T1/txtt/m/n/10 module show <./moduleload.jpg>] Chapter 31. [115] [116] [117] [118] Overfull \vbox (1.27959pt too high) detected at line 6305 [119] [120] [121] [122] Chapter 32. [123] [124] Chapter 33. LaTeX Warning: Hyper reference `gettingsoftware/packagemanagers:conda' on page 125 undefined on input line 6479. 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[221] LaTeX Warning: Hyper reference `_developers/primer:links-references' on page 22 2 undefined on input line 10318. ! Package inputenc Error: Unicode char ❌ (U+274C) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.10339 ❌ Do Not ! Package inputenc Error: Unicode char ✅ (U+2705) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.10342 ✅ Do [222] No file northeastern-university-rc-public-documentation.ind. [223] (./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-ec.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.enc}< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi10.pfb> Output written on northeastern-university-rc-public-documentation.pdf (227 page s, 27509202 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' Latexmk: applying rule 'makeindex northeastern-university-rc-public-documentation.idx'... 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' ------------ ------------ 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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[29] [30] Chapter 12. [31 <./catbashrc.jpg>] [32 <./minicondabashrc.jpg>] [33 <./nanobashrc.png>] [34] Chapter 13. [35 <./bash-logo.png> <./terminal-view.png>] ! Package inputenc Error: Unicode char ⌘ (U+2318) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1828 Press Command(⌘ ) + Space on your Mac keyboard (alternatively, press... [36] (/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd) [37] Underfull \vbox (badness 10000) detected at line 2053 Underfull \vbox (badness 10000) detected at line 2053 [38] Underfull \vbox (badness 10000) detected at line 2053 Underfull \vbox (badness 10000) detected at line 2053 [39] Underfull \vbox (badness 10000) detected at line 2053 Underfull \vbox (badness 10000) detected at line 2053 [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] Chapter 14. [55] [56] Chapter 15. [57] [58] Chapter 16. [59] [60] Chapter 17. [61 <./ood_apps_2023_06.png>] [62] [63] [64] Chapter 18. [65] [66] Chapter 19. [67] [68] Chapter 20. [69] [70] Chapter 21. 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[77] [78] [79] [80] Chapter 23. [81] [82] Chapter 24. [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] [94] [95] [96] [97] [98] [99] [100] [101] [102] Chapter 25. [103] [104] Chapter 26. [105] [106] Chapter 27. [107] [108] Chapter 28. [109] [110] Chapter 29. [111] [112] Chapter 30. Underfull \hbox (badness 10000) in paragraph at lines 5969--5969 []\T1/txtt/m/n/10 module show <./moduleload.jpg>] Chapter 31. [115] [116] [117] [118] Overfull \vbox (1.27959pt too high) detected at line 6305 [119] [120] [121] [122] Chapter 32. [123] [124] Chapter 33. [125] [126] [127] [128] [129] [130] Chapter 34. [131] [132] Chapter 35. [133] [134] [135] [136] Chapter 36. [137 <./checkpointing.png>] [138] [139] [140] [141] [142] [143] [144] [145] [146] Chapter 37. [147] [148] Chapter 38. [149] [150] Chapter 39. [151] Underfull \hbox (badness 6477) in paragraph at lines 7663--7665 []\T1/qtm/m/n/10 To re-quest ac-cess to \T1/txtt/m/n/10 /work\T1/qtm/m/n/10 , s tu-dents can ei-ther cre-ate a [][]Ser-vi-ceNow ticket with RC[][] or email [152] Chapter 40. [153] [154] [155] [156] Chapter 41. [157] [158] [159] [160] Chapter 42. [161] [162] Chapter 43. [163] [164] Chapter 44. [165] [166] [167] [168] Chapter 45. [169 <./cps-ood-menu.png>] [170 <./cps-ood-jupyterform.png>] [171 <./cps-ood-ju pyterlab-start-session.png> <./cps-ood-build-window.png>] [172 <./cps-ood-jupyt erlab-folders-view.png> <./cps-ood-jupyterlab-students-folder.png>] [173 <./cps -ood-jupyterlab-username-folder.png> <./cps-ood-jupyterlab-ipykernel-launcher.p ng>] [174 <./cps-ood-jupyterlab-ipykernel.png> <./cps-ood-jupyterlab-new-launch er.png>] [175 <./cps-ood-jupyterlab-open-terminal.png>] [176] Chapter 46. [177] [178] Chapter 47. [179] [180] Chapter 48. [181] [182] Chapter 49. [183] [184] Chapter 50. [185] [186] Chapter 51. 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Type H for immediate help. ... l.10342 ✅ Do [222] (./northeastern-university-rc-public-documentation.ind) [223] (./northeastern-university-rc-public-documentation.aux) ) (see the transcript file for additional information){/usr/share/texmf/fonts/enc /dvips/tex-gyre/q-ec.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.enc}< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi10.pfb> Output written on northeastern-university-rc-public-documentation.pdf (231 page s, 27549524 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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1544--1547 \T1/qtm/m/n/10 re-quire more [26] [27] [28] Chapter 11. [29] [30] Chapter 12. [31 <./catbashrc.jpg>] [32 <./minicondabashrc.jpg>] [33 <./nanobashrc.png>] [34] Chapter 13. [35 <./bash-logo.png> <./terminal-view.png>] ! Package inputenc Error: Unicode char ⌘ (U+2318) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.1828 Press Command(⌘ ) + Space on your Mac keyboard (alternatively, press... [36] (/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd) [37] Underfull \vbox (badness 10000) detected at line 2053 Underfull \vbox (badness 10000) detected at line 2053 [38] Underfull \vbox (badness 10000) detected at line 2053 Underfull \vbox (badness 10000) detected at line 2053 [39] Underfull \vbox (badness 10000) detected at line 2053 Underfull \vbox (badness 10000) detected at line 2053 [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] Chapter 14. [55] [56] Chapter 15. [57] [58] Chapter 16. [59] [60] Chapter 17. [61 <./ood_apps_2023_06.png>] [62] [63] [64] Chapter 18. [65] [66] Chapter 19. [67] [68] Chapter 20. [69] [70] Chapter 21. 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[77] [78] [79] [80] Chapter 23. [81] [82] Chapter 24. [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] [94] [95] [96] [97] [98] [99] [100] [101] [102] Chapter 25. [103] [104] Chapter 26. [105] [106] Chapter 27. [107] [108] Chapter 28. [109] [110] Chapter 29. [111] [112] Chapter 30. Underfull \hbox (badness 10000) in paragraph at lines 5969--5969 []\T1/txtt/m/n/10 module show <./moduleload.jpg>] Chapter 31. [115] [116] [117] [118] Overfull \vbox (1.27959pt too high) detected at line 6305 [119] [120] [121] [122] Chapter 32. [123] [124] Chapter 33. [125] [126] [127] [128] [129] [130] Chapter 34. [131] [132] Chapter 35. [133] [134] [135] [136] Chapter 36. [137 <./checkpointing.png>] [138] [139] [140] [141] [142] [143] [144] [145] [146] Chapter 37. [147] [148] Chapter 38. [149] [150] Chapter 39. [151] Underfull \hbox (badness 6477) in paragraph at lines 7663--7665 []\T1/qtm/m/n/10 To re-quest ac-cess to \T1/txtt/m/n/10 /work\T1/qtm/m/n/10 , s tu-dents can ei-ther cre-ate a [][]Ser-vi-ceNow ticket with RC[][] or email [152] Chapter 40. [153] [154] [155] [156] Chapter 41. [157] [158] [159] [160] Chapter 42. [161] [162] Chapter 43. [163] [164] Chapter 44. [165] [166] [167] [168] Chapter 45. [169 <./cps-ood-menu.png>] [170 <./cps-ood-jupyterform.png>] [171 <./cps-ood-ju pyterlab-start-session.png> <./cps-ood-build-window.png>] [172 <./cps-ood-jupyt erlab-folders-view.png> <./cps-ood-jupyterlab-students-folder.png>] [173 <./cps -ood-jupyterlab-username-folder.png> <./cps-ood-jupyterlab-ipykernel-launcher.p ng>] [174 <./cps-ood-jupyterlab-ipykernel.png> <./cps-ood-jupyterlab-new-launch er.png>] [175 <./cps-ood-jupyterlab-open-terminal.png>] [176] Chapter 46. [177] [178] Chapter 47. [179] [180] Chapter 48. [181] [182] Chapter 49. [183] [184] Chapter 50. [185] [186] Chapter 51. [187] [188] Chapter 52. [189] [190] Chapter 53. [191] [192] Chapter 54. [193] [194] Chapter 55. [195] Underfull \hbox (badness 10000) in paragraph at lines 8655--8657 []\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 [196] [197] [198] Chapter 56. [199] [200] Chapter 57. [201] [202] Underfull \hbox (badness 7133) in paragraph at lines 9026--9028 []\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: [203] [204] Chapter 58. [205] [206] [207] [208] Chapter 59. [209] [210] [211] [212] Chapter 60. [213] [214] [215] [216] Chapter 61. [217] ! Package inputenc Error: Unicode char ❌ (U+274C) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.9846 ❌ Do Not ! Package inputenc Error: Unicode char ✅ (U+2705) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.9849 ✅ Do ! Package inputenc Error: Unicode char ❌ (U+274C) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.9875 ❌ Do Not ! Package inputenc Error: Unicode char ✅ (U+2705) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.9878 ✅ Do ! Package inputenc Error: Unicode char ❌ (U+274C) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.9904 ❌ Do Not ! Package inputenc Error: Unicode char ✅ (U+2705) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.9907 ✅ Do ! Package inputenc Error: Unicode char ❌ (U+274C) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.9933 ❌ Do Not ! Package inputenc Error: Unicode char ✅ (U+2705) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.9936 ✅ Do [218] [219] [220] [221] ! Package inputenc Error: Unicode char ❌ (U+274C) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.10339 ❌ Do Not ! Package inputenc Error: Unicode char ✅ (U+2705) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ... l.10342 ✅ Do [222] (./northeastern-university-rc-public-documentation.ind) [223] (./northeastern-university-rc-public-documentation.aux) ) (see the transcript file for additional information){/usr/share/texmf/fonts/enc /dvips/tex-gyre/q-ec.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.enc}< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi10.pfb> Output written on northeastern-university-rc-public-documentation.pdf (231 page s, 27549524 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: 2023-08-11T15:58:28.272083Z, end-time: 2023-08-11T15:58:34.622500Z, duration: 6, 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', 'dollarmath'], 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 62 source files that are out of date updating environment: [new config] 62 added, 0 changed, 0 removed reading sources... 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