Read the Docs build information
Build id: 1488017
Project: northeastern-university-rc-public-documentation
Version: latest
Commit: 6e6730a753f0d3c8cb99b5810ba7d1efda0a4da7
Date: 2023-05-22T19:09:44.813274Z
State: finished
Success: True


[rtd-command-info] start-time: 2023-05-22T19:09:46.986083Z, end-time: 2023-05-22T19:09:52.438750Z, 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: 2023-05-22T19:09:52.675796Z, end-time: 2023-05-22T19:09:53.382858Z, 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 6e6730a Merge pull request #48 from northeastern-rc/passwordlessssh

[rtd-command-info] start-time: 2023-05-22T19:09:53.629973Z, end-time: 2023-05-22T19:09:53.712126Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2023-05-22T19:09:55.023387Z, end-time: 2023-05-22T19:09:59.792366Z, 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.

[rtd-command-info] start-time: 2023-05-22T19:10:00.032060Z, end-time: 2023-05-22T19:10:01.219850Z, 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: 2023-05-22T19:10:01.547193Z, end-time: 2023-05-22T19:10:08.706382Z, 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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  Preparing metadata (setup.py): started
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Collecting snowballstemmer>=1.1 (from sphinx<2)
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Collecting babel!=2.0,>=1.3 (from sphinx<2)
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Collecting pytz>=2015.7 (from babel!=2.0,>=1.3->sphinx<2)
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Collecting charset-normalizer<4,>=2 (from requests>=2.0.0->sphinx<2)
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Collecting urllib3<3,>=1.21.1 (from requests>=2.0.0->sphinx<2)
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Collecting certifi>=2017.4.17 (from requests>=2.0.0->sphinx<2)
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Building wheels for collected packages: mock
  Building wheel for mock (setup.py): started
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  Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23753 sha256=94a156412d8798a352f969fdc36bf6eeb12343640128ac27e037a19e8b60fe6d
  Stored in directory: /tmp/pip-ephem-wheel-cache-8yksjbda/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-2.1.2 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

[rtd-command-info] start-time: 2023-05-22T19:10:08.920292Z, end-time: 2023-05-22T19:10:10.869819Z, duration: 1, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt
Collecting urllib3<2.0 (from -r docs/requirements.txt (line 1))
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Collecting importlib-metadata>=4.4 (from markdown>=3.0.1->sphinx-markdown-tables==0.0.16->-r docs/requirements.txt (line 2))
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Installing collected packages: zipp, urllib3, typing-extensions, importlib-metadata, markdown, sphinx-rtd-theme, sphinx-markdown-tables
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    Uninstalling sphinx-rtd-theme-0.4.3:
      Successfully uninstalled sphinx-rtd-theme-0.4.3
Successfully installed importlib-metadata-6.6.0 markdown-3.4.3 sphinx-markdown-tables-0.0.16 sphinx-rtd-theme-1.0.0 typing-extensions-4.5.0 urllib3-1.26.15 zipp-3.15.0

[rtd-command-info] start-time: 2023-05-22T19:10:12.365205Z, end-time: 2023-05-22T19:10:12.427824Z, 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 = 'Northeastern University Research Computing'
copyright = '2019-2021, Northeastern University Research Computing'
author = 'Northeastern University Research Computing'

# 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 = ['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 = []


# -- 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_rtd_theme'

#add logo to the upper left in the help system
html_logo = 'images/NU_logo_small.png'
html_theme_options = {'logo_only': 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']




###########################################################################
#          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': '6e6730a7',
}

# 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/1488017/'

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: 2023-05-22T19:10:12.622941Z, end-time: 2023-05-22T19:10:15.638987Z, duration: 3, exit-code: 0
python -m sphinx -T -E -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html
Running Sphinx v1.8.6
loading translations [en]... done
making output directory...
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: 32 added, 0 changed, 0 removed
reading sources... [  3%] best-practices/checkpointing
reading sources... [  6%] classroom/class_use
reading sources... [  9%] classroom/cps_ood
reading sources... [ 12%] first_steps/bashrc
reading sources... [ 15%] first_steps/connect_mac
reading sources... [ 18%] first_steps/connect_ood
reading sources... [ 21%] first_steps/connect_windows
reading sources... [ 25%] first_steps/cps_ood
reading sources... [ 28%] first_steps/get_access
reading sources... [ 31%] hardware/hardware_overview
reading sources... [ 34%] hardware/partitions
reading sources... [ 37%] index
reading sources... [ 40%] software/conda
reading sources... [ 43%] software/matlab
reading sources... [ 46%] software/modules
reading sources... [ 50%] software/mpi
reading sources... [ 53%] software/r
reading sources... [ 56%] software/softwareoverview
reading sources... [ 59%] software/spack
reading sources... [ 62%] storage/discovery_storage
reading sources... [ 65%] storage/general_storage
reading sources... [ 68%] using-discovery/globus
reading sources... [ 71%] using-discovery/sbatch
reading sources... [ 75%] using-discovery/srun
reading sources... [ 78%] using-discovery/transferringdata
reading sources... [ 81%] using-discovery/usingslurm
reading sources... [ 84%] using-discovery/workingwithgpu
reading sources... [ 87%] using-ood/fileexplore
reading sources... [ 90%] using-ood/interactiveapps
reading sources... [ 93%] using-ood/introduction
reading sources... [ 96%] welcome/gettinghelp
reading sources... [100%] welcome/welcome

/home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/envs/latest/lib/python3.7/site-packages/sphinx/util/nodes.py:94: FutureWarning: 
   The iterable returned by Node.traverse()
   will become an iterator instead of a list in Docutils > 0.16.
  for classifier in reversed(node.parent.traverse(nodes.classifier)):
/home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/checkouts/latest/docs/source/best-practices/checkpointing.rst:3: WARNING: Duplicate explicit target name: "gromacs".
/home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/checkouts/latest/docs/source/best-practices/checkpointing.rst:3: WARNING: Duplicate explicit target name: "here".
/home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/checkouts/latest/docs/source/best-practices/checkpointing.rst:3: WARNING: Duplicate explicit target name: "here".
/home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/checkouts/latest/docs/source/first_steps/cps_ood.rst:5: WARNING: duplicate label cps_ood, other instance in /home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/checkouts/latest/docs/source/classroom/cps_ood.rst
/home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/checkouts/latest/docs/source/using-discovery/workingwithgpu.rst:5: WARNING: Duplicate explicit target name: "ampere".
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/checkouts/latest/docs/source/first_steps/cps_ood.rst: WARNING: document isn't included in any toctree
done
preparing documents... done
writing output... [  3%] best-practices/checkpointing
writing output... [  6%] classroom/class_use
writing output... [  9%] classroom/cps_ood
writing output... [ 12%] first_steps/bashrc
writing output... [ 15%] first_steps/connect_mac
writing output... [ 18%] first_steps/connect_ood
writing output... [ 21%] first_steps/connect_windows
writing output... [ 25%] first_steps/cps_ood
writing output... [ 28%] first_steps/get_access
writing output... [ 31%] hardware/hardware_overview
writing output... [ 34%] hardware/partitions
writing output... [ 37%] index
writing output... [ 40%] software/conda
writing output... [ 43%] software/matlab
writing output... [ 46%] software/modules
writing output... [ 50%] software/mpi
writing output... [ 53%] software/r
writing output... [ 56%] software/softwareoverview
writing output... [ 59%] software/spack
writing output... [ 62%] storage/discovery_storage
writing output... [ 65%] storage/general_storage
writing output... [ 68%] using-discovery/globus
writing output... [ 71%] using-discovery/sbatch
writing output... [ 75%] using-discovery/srun
writing output... [ 78%] using-discovery/transferringdata
writing output... [ 81%] using-discovery/usingslurm
writing output... [ 84%] using-discovery/workingwithgpu
writing output... [ 87%] using-ood/fileexplore
writing output... [ 90%] using-ood/interactiveapps
writing output... [ 93%] using-ood/introduction
writing output... [ 96%] welcome/gettinghelp
writing output... [100%] welcome/welcome

generating indices... genindex
writing additional pages... search
copying images... [  4%] images/checkpointing.png
copying images... [  9%] images/cps-ood-menu.png
copying images... [ 14%] images/cps-ood-jupyterform.png
copying images... [ 19%] images/cps-ood-jupyterlab-start-session.png
copying images... [ 23%] images/cps-ood-build-window.png
copying images... [ 28%] images/cps-ood-jupyterlab-folders-view.png
copying images... [ 33%] images/cps-ood-jupyterlab-students-folder.png
copying images... [ 38%] images/cps-ood-jupyterlab-username-folder.png
copying images... [ 42%] images/cps-ood-jupyterlab-ipykernel-launcher.png
copying images... [ 47%] images/cps-ood-jupyterlab-ipykernel.png
copying images... [ 52%] images/cps-ood-jupyterlab-new-launcher.png
copying images... [ 57%] images/cps-ood-jupyterlab-open-terminal.png
copying images... [ 61%] images/cps-ood-commandline.png
copying images... [ 66%] images/catbashrc.jpg
copying images... [ 71%] images/minicondabashrc.jpg
copying images... [ 76%] images/nanobashrc.png
copying images... [ 80%] images/moduleshow.jpg
copying images... [ 85%] images/moduleload.jpg
copying images... [ 90%] images/srun_example.jpg
copying images... [ 95%] images/ood_apps_2021.jpg
copying images... [100%] images/discovery.png

copying static files... done
copying extra files... done
dumping search index in English (code: en) ... done
dumping object inventory... done
build succeeded, 6 warnings.

The HTML pages are in ../../_readthedocs/html.
Updating searchtools for Read the Docs search...

[rtd-command-info] start-time: 2023-05-22T19:10:15.897023Z, end-time: 2023-05-22T19:10:18.235772Z, duration: 2, exit-code: 0
python -m sphinx -T -E -b readthedocssinglehtmllocalmedia -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/htmlzip
Running Sphinx v1.8.6
loading translations [en]... done
making output directory...
building [mo]: targets for 0 po files that are out of date
building [readthedocssinglehtmllocalmedia]: all documents
updating environment: 32 added, 0 changed, 0 removed
reading sources... [  3%] best-practices/checkpointing
reading sources... [  6%] classroom/class_use
reading sources... [  9%] classroom/cps_ood
reading sources... [ 12%] first_steps/bashrc
reading sources... [ 15%] first_steps/connect_mac
reading sources... [ 18%] first_steps/connect_ood
reading sources... [ 21%] first_steps/connect_windows
reading sources... [ 25%] first_steps/cps_ood
reading sources... [ 28%] first_steps/get_access
reading sources... [ 31%] hardware/hardware_overview
reading sources... [ 34%] hardware/partitions
reading sources... [ 37%] index
reading sources... [ 40%] software/conda
reading sources... [ 43%] software/matlab
reading sources... [ 46%] software/modules
reading sources... [ 50%] software/mpi
reading sources... [ 53%] software/r
reading sources... [ 56%] software/softwareoverview
reading sources... [ 59%] software/spack
reading sources... [ 62%] storage/discovery_storage
reading sources... [ 65%] storage/general_storage
reading sources... [ 68%] using-discovery/globus
reading sources... [ 71%] using-discovery/sbatch
reading sources... [ 75%] using-discovery/srun
reading sources... [ 78%] using-discovery/transferringdata
reading sources... [ 81%] using-discovery/usingslurm
reading sources... [ 84%] using-discovery/workingwithgpu
reading sources... [ 87%] using-ood/fileexplore
reading sources... [ 90%] using-ood/interactiveapps
reading sources... [ 93%] using-ood/introduction
reading sources... [ 96%] welcome/gettinghelp
reading sources... [100%] welcome/welcome

/home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/envs/latest/lib/python3.7/site-packages/sphinx/util/nodes.py:94: FutureWarning: 
   The iterable returned by Node.traverse()
   will become an iterator instead of a list in Docutils > 0.16.
  for classifier in reversed(node.parent.traverse(nodes.classifier)):
/home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/checkouts/latest/docs/source/best-practices/checkpointing.rst:3: WARNING: Duplicate explicit target name: "gromacs".
/home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/checkouts/latest/docs/source/best-practices/checkpointing.rst:3: WARNING: Duplicate explicit target name: "here".
/home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/checkouts/latest/docs/source/best-practices/checkpointing.rst:3: WARNING: Duplicate explicit target name: "here".
/home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/checkouts/latest/docs/source/first_steps/cps_ood.rst:5: WARNING: duplicate label cps_ood, other instance in /home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/checkouts/latest/docs/source/classroom/cps_ood.rst
/home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/checkouts/latest/docs/source/using-discovery/workingwithgpu.rst:5: WARNING: Duplicate explicit target name: "ampere".
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/checkouts/latest/docs/source/first_steps/cps_ood.rst: WARNING: document isn't included in any toctree
done
preparing documents... done
assembling single document... welcome/welcome welcome/gettinghelp first_steps/get_access first_steps/connect_mac first_steps/connect_windows first_steps/connect_ood first_steps/bashrc hardware/hardware_overview hardware/partitions software/softwareoverview software/modules software/matlab software/conda software/spack software/r software/mpi using-discovery/usingslurm using-discovery/sbatch using-discovery/srun using-discovery/workingwithgpu using-discovery/transferringdata using-discovery/globus storage/discovery_storage storage/general_storage best-practices/checkpointing using-ood/introduction using-ood/fileexplore using-ood/interactiveapps classroom/class_use classroom/cps_ood 
writing... done
writing additional files...
copying images... [  4%] images/discovery.png
copying images... [  9%] images/catbashrc.jpg
copying images... [ 14%] images/minicondabashrc.jpg
copying images... [ 19%] images/nanobashrc.png
copying images... [ 23%] images/moduleshow.jpg
copying images... [ 28%] images/moduleload.jpg
copying images... [ 33%] images/srun_example.jpg
copying images... [ 38%] images/checkpointing.png
copying images... [ 42%] images/ood_apps_2021.jpg
copying images... [ 47%] images/cps-ood-menu.png
copying images... [ 52%] images/cps-ood-jupyterform.png
copying images... [ 57%] images/cps-ood-jupyterlab-start-session.png
copying images... [ 61%] images/cps-ood-build-window.png
copying images... [ 66%] images/cps-ood-jupyterlab-folders-view.png
copying images... [ 71%] images/cps-ood-jupyterlab-students-folder.png
copying images... [ 76%] images/cps-ood-jupyterlab-username-folder.png
copying images... [ 80%] images/cps-ood-jupyterlab-ipykernel-launcher.png
copying images... [ 85%] images/cps-ood-jupyterlab-ipykernel.png
copying images... [ 90%] images/cps-ood-jupyterlab-new-launcher.png
copying images... [ 95%] images/cps-ood-jupyterlab-open-terminal.png
copying images... [100%] images/cps-ood-commandline.png

copying static files... done
copying extra files... done
dumping object inventory... done
build succeeded, 6 warnings.

The HTML page is in ../../_readthedocs/htmlzip.
Updating searchtools for Read the Docs search...

[rtd-command-info] start-time: 2023-05-22T19:10:24.057640Z, end-time: 2023-05-22T19:10:26.241189Z, duration: 2, exit-code: 0
python -m sphinx -T -E -b latex -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/pdf
Running Sphinx v1.8.6
loading translations [en]... done
making output directory...
building [mo]: targets for 0 po files that are out of date
building [latex]: all documents
updating environment: 32 added, 0 changed, 0 removed
reading sources... [  3%] best-practices/checkpointing
reading sources... [  6%] classroom/class_use
reading sources... [  9%] classroom/cps_ood
reading sources... [ 12%] first_steps/bashrc
reading sources... [ 15%] first_steps/connect_mac
reading sources... [ 18%] first_steps/connect_ood
reading sources... [ 21%] first_steps/connect_windows
reading sources... [ 25%] first_steps/cps_ood
reading sources... [ 28%] first_steps/get_access
reading sources... [ 31%] hardware/hardware_overview
reading sources... [ 34%] hardware/partitions
reading sources... [ 37%] index
reading sources... [ 40%] software/conda
reading sources... [ 43%] software/matlab
reading sources... [ 46%] software/modules
reading sources... [ 50%] software/mpi
reading sources... [ 53%] software/r
reading sources... [ 56%] software/softwareoverview
reading sources... [ 59%] software/spack
reading sources... [ 62%] storage/discovery_storage
reading sources... [ 65%] storage/general_storage
reading sources... [ 68%] using-discovery/globus
reading sources... [ 71%] using-discovery/sbatch
reading sources... [ 75%] using-discovery/srun
reading sources... [ 78%] using-discovery/transferringdata
reading sources... [ 81%] using-discovery/usingslurm
reading sources... [ 84%] using-discovery/workingwithgpu
reading sources... [ 87%] using-ood/fileexplore
reading sources... [ 90%] using-ood/interactiveapps
reading sources... [ 93%] using-ood/introduction
reading sources... [ 96%] welcome/gettinghelp
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Chapter 5.

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Chapter 6.

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Chapter 1.
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Chapter 5.
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Chapter 6.
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Chapter 11.

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[34] [35] [36]
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Chapter 14.
[39] [40]
Chapter 15.
[41] [42] [43] [44]
Chapter 16.

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[45] [46]
Chapter 17.

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[48] [49] [50]
Chapter 18.
[51] [52] [53] [54]
Chapter 19.
[55 <./srun_example.jpg>] [56]
Chapter 20.

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[58] [59] [60] [61] [62]
Chapter 21.
[63] [64]
Chapter 22.
[65] [66] [67] [68]
Chapter 23.
[69] [70]
Chapter 24.
[71] [72]
Chapter 25.
[73] [74 <./checkpointing.png>] [75] [76] [77] [78]
Chapter 26.
[79] [80]
Chapter 27.
[81] [82]
Chapter 28.
[83] [84 <./ood_apps_2021.jpg>] [85] [86]
Chapter 29.
[87] [88] [89] [90]
Chapter 30.
[91 <./cps-ood-menu.png>] [92 <./cps-ood-jupyterform.png> <./cps-ood-jupyterlab
-start-session.png>] [93 <./cps-ood-build-window.png> <./cps-ood-jupyterlab-fol
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erlab-username-folder.png> <./cps-ood-jupyterlab-ipykernel-launcher.png>]
[95 <./cps-ood-jupyterlab-ipykernel.png> <./cps-ood-jupyterlab-new-launcher.png
> <./cps-ood-jupyterlab-open-terminal.png>]
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Chapter 1.
[1] [2 <./discovery.png>]
Chapter 2.
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Chapter 3.
[5] [6]
Chapter 4.
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[]\T1/ptm/m/n/10 Type \T1/pcr/m/n/10 ssh-copy-id -i ~/.ssh/id_rsa.pub <youruser
name>@login.discovery.neu.
[8] [9] [10]
Chapter 5.
[11] [12]
Chapter 6.
[13] [14]
Chapter 7.
[15] [16 <./catbashrc.jpg> <./minicondabashrc.jpg>] [17 <./nanobashrc.png>]
[18]
Chapter 8.

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[20]
Chapter 9.

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[22] [23] [24]
Chapter 10.
[25] [26]
Chapter 11.

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[27] [28] [29 <./moduleshow.jpg> <./moduleload.jpg>] [30]
Chapter 12.
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[34] [35] [36]
Chapter 13.

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[37]
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iconda/
[38]
Chapter 14.
[39] [40]
Chapter 15.
[41] [42] [43] [44]
Chapter 16.

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0.5-skylake-gcc10.1 openmpi/4.0.3-cuda
[45] [46]
Chapter 17.

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[47]
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[48] [49] [50]
Chapter 18.
[51] [52] [53] [54]
Chapter 19.
[55 <./srun_example.jpg>] [56]
Chapter 20.

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[57]
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[58] [59] [60] [61] [62]
Chapter 21.
[63] [64]
Chapter 22.
[65] [66] [67] [68]
Chapter 23.
[69] [70]
Chapter 24.
[71] [72]
Chapter 25.
[73] [74 <./checkpointing.png>] [75] [76] [77] [78]
Chapter 26.
[79] [80]
Chapter 27.
[81] [82]
Chapter 28.
[83] [84 <./ood_apps_2021.jpg>] [85] [86]
Chapter 29.
[87] [88] [89] [90]
Chapter 30.
[91 <./cps-ood-menu.png>] [92 <./cps-ood-jupyterform.png> <./cps-ood-jupyterlab
-start-session.png>] [93 <./cps-ood-build-window.png> <./cps-ood-jupyterlab-fol
ders-view.png>] [94 <./cps-ood-jupyterlab-students-folder.png> <./cps-ood-jupyt
erlab-username-folder.png> <./cps-ood-jupyterlab-ipykernel-launcher.png>]
[95 <./cps-ood-jupyterlab-ipykernel.png> <./cps-ood-jupyterlab-new-launcher.png
> <./cps-ood-jupyterlab-open-terminal.png>]
(./northeastern-university-rc-public-documentation.ind) [96 <./cps-ood-commandl
ine.png>] (./northeastern-university-rc-public-documentation.aux) )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
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