Read the Docs build information
Build id: 1259214
Project: northeastern-university-rc-public-documentation
Version: latest
Commit: 9c0d60e7ddff2171ece6b05cd5925cdc27e06ae5
Date: 2023-01-18T17:41:13.039452Z
State: finished
Success: True


[rtd-command-info] start-time: 2023-01-18T17:41:15.252662Z, end-time: 2023-01-18T17:41:18.700651Z, duration: 3, 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: 2023-01-18T17:41:18.885728Z, end-time: 2023-01-18T17:41:19.586817Z, 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 9c0d60e Merge pull request #31 from northeastern-rc/conda-pytorch-update

[rtd-command-info] start-time: 2023-01-18T17:41:19.782708Z, end-time: 2023-01-18T17:41:19.855912Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2023-01-18T17:41:21.391153Z, end-time: 2023-01-18T17:41:26.284387Z, duration: 4, exit-code: 0
python3.7 -mvirtualenv 
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: 2023-01-18T17:41:26.467323Z, end-time: 2023-01-18T17:41:28.307416Z, duration: 1, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools<58.3.0
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/envs/latest/lib/python3.7/site-packages (22.3.1)
Collecting setuptools<58.3.0
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Installing collected packages: setuptools
  Attempting uninstall: setuptools
    Found existing installation: setuptools 66.0.0
    Uninstalling setuptools-66.0.0:
      Successfully uninstalled setuptools-66.0.0
Successfully installed setuptools-58.2.0

[rtd-command-info] start-time: 2023-01-18T17:41:28.490900Z, end-time: 2023-01-18T17:41:35.281888Z, duration: 6, 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
Collecting pillow
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  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
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Collecting packaging
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Collecting imagesize
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Collecting Pygments>=2.0
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Collecting snowballstemmer>=1.1
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Collecting pytz>=2015.7
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Collecting urllib3<1.27,>=1.21.1
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Collecting charset-normalizer<4,>=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=23772 sha256=70a30af0a9f749123653ec925824c9b531d15b2dc5b5afda5329c8c5a9694784
  Stored in directory: /tmp/pip-ephem-wheel-cache-qfhh095h/wheels/d1/33/8e/f9d24f00cc130866aacfe7c3bc15571217e2b22cc4c4e1b443
Successfully built mock
Installing collected packages: snowballstemmer, pytz, mock, commonmark, charset-normalizer, urllib3, sphinxcontrib-serializinghtml, six, Pygments, pillow, packaging, MarkupSafe, imagesize, idna, docutils, certifi, babel, alabaster, sphinxcontrib-websupport, requests, jinja2, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark
Successfully installed MarkupSafe-2.1.2 Pygments-2.14.0 alabaster-0.7.13 babel-2.11.0 certifi-2022.12.7 charset-normalizer-3.0.1 commonmark-0.9.1 docutils-0.17.1 idna-3.4 imagesize-1.4.1 jinja2-3.0.3 mock-1.0.1 packaging-23.0 pillow-9.4.0 pytz-2022.7.1 readthedocs-sphinx-ext-2.2.0 recommonmark-0.5.0 requests-2.28.2 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 urllib3-1.26.14

[rtd-command-info] start-time: 2023-01-18T17:41:35.471420Z, end-time: 2023-01-18T17:41:37.223090Z, duration: 1, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt
Collecting sphinx-markdown-tables==0.0.16
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Requirement already satisfied: sphinx>=1.6 in /home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/envs/latest/lib/python3.7/site-packages (from sphinx-rtd-theme==1.0.0->-r docs/requirements.txt (line 2)) (1.8.6)
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Collecting importlib-metadata>=4.4
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Requirement already satisfied: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/envs/latest/lib/python3.7/site-packages (from sphinx>=1.6->sphinx-rtd-theme==1.0.0->-r docs/requirements.txt (line 2)) (2.11.0)
Requirement already satisfied: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/envs/latest/lib/python3.7/site-packages (from sphinx>=1.6->sphinx-rtd-theme==1.0.0->-r docs/requirements.txt (line 2)) (1.16.0)
Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/envs/latest/lib/python3.7/site-packages (from sphinx>=1.6->sphinx-rtd-theme==1.0.0->-r docs/requirements.txt (line 2)) (1.4.1)
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Collecting zipp>=0.5
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Installing collected packages: zipp, typing-extensions, importlib-metadata, sphinx-rtd-theme, markdown, sphinx-markdown-tables
  Attempting uninstall: sphinx-rtd-theme
    Found existing installation: sphinx-rtd-theme 0.4.3
    Uninstalling sphinx-rtd-theme-0.4.3:
      Successfully uninstalled sphinx-rtd-theme-0.4.3
Successfully installed importlib-metadata-6.0.0 markdown-3.4.1 sphinx-markdown-tables-0.0.16 sphinx-rtd-theme-1.0.0 typing-extensions-4.4.0 zipp-3.11.0

[rtd-command-info] start-time: 2023-01-18T17:41:39.037255Z, end-time: 2023-01-18T17:41:39.111743Z, 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:
    theme = importlib.import_module('sphinx_rtd_theme')
    html_theme = 'sphinx_rtd_theme'
    html_style = None
    html_theme_options = {}
    if 'html_theme_path' in globals():
        html_theme_path.append(theme.get_html_theme_path())
    else:
        html_theme_path = [theme.get_html_theme_path()]

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': '9c0d60e7',
}

# 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/1259214/'

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: 2023-01-18T17:41:39.327846Z, end-time: 2023-01-18T17:41:42.227454Z, duration: 2, exit-code: 0
python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/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
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, 5 warnings.

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

[rtd-command-info] start-time: 2023-01-18T17:41:42.573505Z, end-time: 2023-01-18T17:41:44.852114Z, duration: 2, exit-code: 0
python -m sphinx -T -E -b readthedocssinglehtmllocalmedia -d _build/doctrees -D language=en . _build/localmedia
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
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, 5 warnings.

The HTML page is in _build/localmedia.
Updating searchtools for Read the Docs search...

[rtd-command-info] start-time: 2023-01-18T17:41:45.197179Z, end-time: 2023-01-18T17:41:45.275204Z, duration: 0, exit-code: 0
mktemp --directory
/tmp/tmp.6F1cGoWLfM

[rtd-command-info] start-time: 2023-01-18T17:41:45.453422Z, end-time: 2023-01-18T17:41:45.677206Z, duration: 0, exit-code: 0
mv /home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/checkouts/latest/docs/source/_build/localmedia /tmp/tmp.6F1cGoWLfM/northeastern-university-rc-public-documentation-latest


[rtd-command-info] start-time: 2023-01-18T17:41:45.918296Z, end-time: 2023-01-18T17:41:51.153501Z, duration: 5, exit-code: 0
zip --recurse-paths --symlinks /home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/artifacts/latest/sphinx_localmedia/northeastern-university-rc-public-documentation.zip northeastern-university-rc-public-documentation-latest
adding: northeastern-university-rc-public-documentation-latest/ (stored 0%)
  adding: northeastern-university-rc-public-documentation-latest/.buildinfo (deflated 25%)
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[rtd-command-info] start-time: 2023-01-18T17:41:51.333851Z, end-time: 2023-01-18T17:41:52.503238Z, duration: 1, exit-code: 0
python -m sphinx -b latex -D language=en -d _build/doctrees . _build/latex
Running Sphinx v1.8.6
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copying TeX support files...
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build succeeded.

The LaTeX files are in _build/latex.
Run 'make' in that directory to run these through (pdf)latex
(use `make latexpdf' here to do that automatically).
/home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/envs/latest/lib/python3.7/site-packages/sphinx/builders/latex/__init__.py:201: FutureWarning: 
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[rtd-command-info] start-time: 2023-01-18T17:41:55.594003Z, end-time: 2023-01-18T17:41:55.650823Z, 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: 2023-01-18T17:41:55.856076Z, end-time: 2023-01-18T17:42:13.464450Z, duration: 17, exit-code: 0
latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=northeastern-university-rc-public-documentation -interaction=nonstopmode
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Chapter 5.

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Chapter 6.

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Chapter 8.

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Chapter 9.

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Chapter 17.

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Chapter 24.

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Chapter 26.

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Chapter 1.
[1] [2 <./discovery.png>]
Chapter 2.
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Chapter 3.
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Chapter 4.
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name>@login.discovery.neu.
[8] [9] [10]
Chapter 5.
[11] [12]
Chapter 6.
[13] [14]
Chapter 7.
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[18]
Chapter 8.

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Chapter 9.

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Chapter 10.
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Chapter 11.

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Chapter 13.

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Chapter 14.
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Chapter 15.
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Chapter 16.

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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 23.
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Chapter 24.
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Chapter 25.
[71] [72 <./checkpointing.png>] [73] [74] [75] [76]
Chapter 26.
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Chapter 27.
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Chapter 28.
[81] [82 <./ood_apps_2021.jpg>] [83] [84]
Chapter 29.
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Chapter 30.
[89 <./cps-ood-menu.png>] [90 <./cps-ood-jupyterform.png> <./cps-ood-jupyterlab
-start-session.png>] [91 <./cps-ood-build-window.png> <./cps-ood-jupyterlab-fol
ders-view.png>] [92 <./cps-ood-jupyterlab-students-folder.png> <./cps-ood-jupyt
erlab-username-folder.png> <./cps-ood-jupyterlab-ipykernel-launcher.png>]
[93 <./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.
[7]
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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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Chapter 9.

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[21]
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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]
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[34] [35] [36]
Chapter 13.

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[37]
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[38]
Chapter 14.
[39] [40]
Chapter 15.
[41] [42]
Chapter 16.

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Chapter 17.

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[45]
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[46] [47] [48]
Chapter 18.
[49] [50] [51] [52]
Chapter 19.
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Chapter 20.

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Chapter 21.
[61] [62]
Chapter 22.
[63] [64] [65] [66]
Chapter 23.
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Chapter 24.
[69] [70]
Chapter 25.
[71] [72 <./checkpointing.png>] [73] [74] [75] [76]
Chapter 26.
[77] [78]
Chapter 27.
[79] [80]
Chapter 28.
[81] [82 <./ood_apps_2021.jpg>] [83] [84]
Chapter 29.
[85] [86] [87] [88]
Chapter 30.
[89 <./cps-ood-menu.png>] [90 <./cps-ood-jupyterform.png> <./cps-ood-jupyterlab
-start-session.png>] [91 <./cps-ood-build-window.png> <./cps-ood-jupyterlab-fol
ders-view.png>] [92 <./cps-ood-jupyterlab-students-folder.png> <./cps-ood-jupyt
erlab-username-folder.png> <./cps-ood-jupyterlab-ipykernel-launcher.png>]
[93 <./cps-ood-jupyterlab-ipykernel.png> <./cps-ood-jupyterlab-new-launcher.png
> <./cps-ood-jupyterlab-open-terminal.png>]
(./northeastern-university-rc-public-documentation.ind) [94 <./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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reading sources... [ 93%] using-ood/introduction
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/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: 
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WARNING: conf value "version" should not be empty for EPUB3
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build succeeded, 12 warnings.

The ePub file is in _build/epub.
Updating searchtools for Read the Docs search...

[rtd-command-info] start-time: 2023-01-18T17:42:17.306351Z, end-time: 2023-01-18T17:42:17.399831Z, duration: 0, exit-code: 0
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