Read the Docs build information
Build id: 1513082
Project: northeastern-university-rc-public-documentation
Version: latest
Commit: a6f1ca4ef3620283571fefc257671df00f4b8544
Date: 2023-06-02T18:32:23.043518Z
State: finished
Success: True


[rtd-command-info] start-time: 2023-06-02T18:32:24.905234Z, end-time: 2023-06-02T18:32:30.030309Z, duration: 5, 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: 2023-06-02T18:32:30.300285Z, end-time: 2023-06-02T18:32:30.532676Z, 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 <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at a6f1ca4 Merge pull request #51 from northeastern-rc/joe/rtd2.0

[rtd-command-info] start-time: 2023-06-02T18:32:30.874259Z, end-time: 2023-06-02T18:32:30.940807Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2023-06-02T18:32:32.363326Z, end-time: 2023-06-02T18:32:45.026644Z, 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.

[rtd-command-info] start-time: 2023-06-02T18:32:45.302771Z, end-time: 2023-06-02T18:32:46.835794Z, duration: 1, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/envs/latest/lib/python3.7/site-packages (23.1.2)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/envs/latest/lib/python3.7/site-packages (67.8.0)

[rtd-command-info] start-time: 2023-06-02T18:32:47.092895Z, end-time: 2023-06-02T18:32:54.662983Z, duration: 7, exit-code: 0
python -m pip install --upgrade --no-cache-dir pillow mock==1.0.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.9.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.3 jinja2<3.1.0
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Building wheels for collected packages: mock
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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-2.1.2 Pygments-2.15.1 alabaster-0.7.13 babel-2.12.1 certifi-2023.5.7 charset-normalizer-3.1.0 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-2.2.0 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 urllib3-2.0.2

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python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt
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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-8.1.3 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-6.6.0 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: 2023-06-02T18:33:13.534919Z, end-time: 2023-06-02T18:33:13.618766Z, 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 = ["02_first_steps/cps_ood.md"]


# -- 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': 'https://rc-docs.northeastern.edu/en/latest/',
    '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': 'a6f1ca4e',
}

# 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():
    
    html_context.update(context)
    
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/1513082/'

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: 2023-06-02T18:33:13.805887Z, end-time: 2023-06-02T18:33:21.936870Z, duration: 8, 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 32 source files that are out of date
updating environment: [new config] 32 added, 0 changed, 0 removed
reading sources... [  3%] 01_welcome/01_welcome
reading sources... [  6%] 01_welcome/02_gettinghelp
reading sources... [  9%] 02_first_steps/01_get_access
reading sources... [ 12%] 02_first_steps/02_connect_mac
reading sources... [ 15%] 02_first_steps/03_connect_windows
reading sources... [ 18%] 02_first_steps/04_connect_ood
reading sources... [ 21%] 02_first_steps/05_bashrc
reading sources... [ 25%] 03_hardware/01_hardware_overview
reading sources... [ 28%] 03_hardware/02_partitions
reading sources... [ 31%] 04_software/01_softwareoverview
reading sources... [ 34%] 04_software/02_modules
reading sources... [ 37%] 04_software/03_matlab
reading sources... [ 40%] 04_software/04_conda
reading sources... [ 43%] 04_software/05_spack
reading sources... [ 46%] 04_software/06_r
reading sources... [ 50%] 04_software/07_mpi
reading sources... [ 53%] 05_using-discovery/01_usingslurm
reading sources... [ 56%] 05_using-discovery/02_sbatch
reading sources... [ 59%] 05_using-discovery/03_srun
reading sources... [ 62%] 05_using-discovery/04_workingwithgpu
reading sources... [ 65%] 05_using-discovery/05_transferringdata
reading sources... [ 68%] 05_using-discovery/06_globus
reading sources... [ 71%] 06_storage/01_discovery_storage
reading sources... [ 75%] 06_storage/02_general_storage
reading sources... [ 78%] 07_best-practices/01_checkpointing
reading sources... [ 81%] 08_using-ood/01_introduction
reading sources... [ 84%] 08_using-ood/02_fileexplore
reading sources... [ 87%] 08_using-ood/03_interactiveapps
reading sources... [ 90%] 09_classroom/01_class_use
reading sources... [ 93%] 09_classroom/02_cps_ood
reading sources... [ 96%] _snippets/next-steps
reading sources... [100%] index

looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [  3%] 01_welcome/01_welcome
writing output... [  6%] 01_welcome/02_gettinghelp
writing output... [  9%] 02_first_steps/01_get_access
writing output... [ 12%] 02_first_steps/02_connect_mac
writing output... [ 15%] 02_first_steps/03_connect_windows
writing output... [ 18%] 02_first_steps/04_connect_ood
writing output... [ 21%] 02_first_steps/05_bashrc
writing output... [ 25%] 03_hardware/01_hardware_overview
writing output... [ 28%] 03_hardware/02_partitions
writing output... [ 31%] 04_software/01_softwareoverview
writing output... [ 34%] 04_software/02_modules
writing output... [ 37%] 04_software/03_matlab
writing output... [ 40%] 04_software/04_conda
writing output... [ 43%] 04_software/05_spack
writing output... [ 46%] 04_software/06_r
writing output... [ 50%] 04_software/07_mpi
writing output... [ 53%] 05_using-discovery/01_usingslurm
writing output... [ 56%] 05_using-discovery/02_sbatch
writing output... [ 59%] 05_using-discovery/03_srun
writing output... [ 62%] 05_using-discovery/04_workingwithgpu
writing output... [ 65%] 05_using-discovery/05_transferringdata
writing output... [ 68%] 05_using-discovery/06_globus
writing output... [ 71%] 06_storage/01_discovery_storage
writing output... [ 75%] 06_storage/02_general_storage
writing output... [ 78%] 07_best-practices/01_checkpointing
writing output... [ 81%] 08_using-ood/01_introduction
writing output... [ 84%] 08_using-ood/02_fileexplore
writing output... [ 87%] 08_using-ood/03_interactiveapps
writing output... [ 90%] 09_classroom/01_class_use
writing output... [ 93%] 09_classroom/02_cps_ood
writing output... [ 96%] _snippets/next-steps
writing output... [100%] index

generating indices... genindex done
writing additional pages... search done
copying images... [  5%] images/discovery.png
copying images... [ 10%] images/catbashrc.jpg
copying images... [ 15%] images/minicondabashrc.jpg
copying images... [ 20%] images/nanobashrc.png
copying images... [ 25%] images/moduleshow.jpg
copying images... [ 30%] images/moduleload.jpg
copying images... [ 35%] images/srun_example.jpg
copying images... [ 40%] images/checkpointing.png
copying images... [ 45%] images/ood_apps_2021.jpg
copying images... [ 50%] images/cps-ood-menu.png
copying images... [ 55%] images/cps-ood-jupyterform.png
copying images... [ 60%] images/cps-ood-jupyterlab-start-session.png
copying images... [ 65%] images/cps-ood-build-window.png
copying images... [ 70%] images/cps-ood-jupyterlab-folders-view.png
copying images... [ 75%] images/cps-ood-jupyterlab-students-folder.png
copying images... [ 80%] images/cps-ood-jupyterlab-username-folder.png
copying images... [ 85%] images/cps-ood-jupyterlab-ipykernel-launcher.png
copying images... [ 90%] images/cps-ood-jupyterlab-ipykernel.png
copying images... [ 95%] images/cps-ood-jupyterlab-new-launcher.png
copying images... [100%] images/cps-ood-jupyterlab-open-terminal.png

copying static files... done
copying extra files... done
dumping search index in English (code: en)... done
dumping object inventory... done
Updating searchtools for Read the Docs search... build succeeded.

The HTML pages are in ../../_readthedocs/html.

[rtd-command-info] start-time: 2023-06-02T18:33:22.199770Z, end-time: 2023-06-02T18:33:26.922950Z, 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] 32 added, 0 changed, 0 removed
reading sources... [  3%] 01_welcome/01_welcome
reading sources... [  6%] 01_welcome/02_gettinghelp
reading sources... [  9%] 02_first_steps/01_get_access
reading sources... [ 12%] 02_first_steps/02_connect_mac
reading sources... [ 15%] 02_first_steps/03_connect_windows
reading sources... [ 18%] 02_first_steps/04_connect_ood
reading sources... [ 21%] 02_first_steps/05_bashrc
reading sources... [ 25%] 03_hardware/01_hardware_overview
reading sources... [ 28%] 03_hardware/02_partitions
reading sources... [ 31%] 04_software/01_softwareoverview
reading sources... [ 34%] 04_software/02_modules
reading sources... [ 37%] 04_software/03_matlab
reading sources... [ 40%] 04_software/04_conda
reading sources... [ 43%] 04_software/05_spack
reading sources... [ 46%] 04_software/06_r
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[rtd-command-info] start-time: 2023-06-02T18:33:33.096164Z, end-time: 2023-06-02T18:33:37.304801Z, duration: 4, exit-code: 0
python -m sphinx -T -E -b latex -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/pdf
Running Sphinx v5.3.0
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[rtd-command-info] start-time: 2023-06-02T18:33:40.783614Z, end-time: 2023-06-02T18:33:40.854158Z, 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: 2023-06-02T18:33:41.081459Z, end-time: 2023-06-02T18:34:05.486539Z, duration: 24, 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, <GEN1> chunk 1.
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Latexmk: This is Latexmk, John Collins, 1 January 2015, version: 4.41.
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Chapter 5.

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Chapter 10.

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Chapter 11.

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[34]
Chapter 13.

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Chapter 14.

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Chapter 15.

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Chapter 17.

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Chapter 18.

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Chapter 19.

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Chapter 20.

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Chapter 21.

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Chapter 22.

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Chapter 24.

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Chapter 26.

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              {Welcome}
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              {Welcome}
[2]
Chapter 1.
[3] [4 <./discovery.png>]
Chapter 2.
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Chapter 3.
[7] [8]
Chapter 4.
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Chapter 5.
[13] [14]
Chapter 6.
[15] [16]
Chapter 7.
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Chapter 8.
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Chapter 9.
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[24] [25] [26]
Chapter 10.
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Chapter 11.

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[34]
Chapter 13.

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[36]
Chapter 14.

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Chapter 15.
[39] [40]
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[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.

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[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.
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Chapter 29.
[83] [84] [85] [86]
Chapter 30.
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              {Welcome}
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              {Welcome}
[2]
Chapter 1.
[3] [4 <./discovery.png>]
Chapter 2.
[5] [6]
Chapter 3.
[7] [8]
Chapter 4.
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Chapter 5.
[13] [14]
Chapter 6.
[15] [16]
Chapter 7.
[17 <./catbashrc.jpg>] [18 <./minicondabashrc.jpg>] [19 <./nanobashrc.png>]
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Chapter 8.
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Chapter 9.
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[24] [25] [26]
Chapter 10.
[27] [28]
Chapter 11.

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[29] [30 <./moduleshow.jpg> <./moduleload.jpg>]
Chapter 12.
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[34]
Chapter 13.

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[36]
Chapter 14.

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Chapter 15.
[39] [40]
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[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.

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[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
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