From 78bf37b478d470d3d65b01c3f61c3ede804a42ac Mon Sep 17 00:00:00 2001
From: "github-actions[bot]" <github-actions[bot]@users.noreply.github.com>
Date: Fri, 10 May 2024 18:18:00 +0000
Subject: [PATCH] deploy: ba6f8c3a917a28d022baba6f9a2257ec9978297f

---
 versions/master/html/CIME_api/CIME.case.html  |   3 -
 versions/master/html/CIME_api/CIME.html       |   2 +-
 versions/master/html/CIME_api/CIME.tests.html |   3 +
 versions/master/html/CIME_api/modules.html    |   2 +-
 .../html/_sources/CIME_api/CIME.case.rst.txt  |   8 -
 .../html/_sources/CIME_api/CIME.tests.rst.txt |   8 +
 .../_sources/users_guide/components.rst.txt   |  62 +++++
 .../html/_sources/users_guide/index.rst.txt   |   1 +
 versions/master/html/build_cpl/index.html     |   4 +-
 versions/master/html/index.html               |  19 +-
 versions/master/html/objects.inv              | Bin 5304 -> 5316 bytes
 versions/master/html/searchindex.js           |   2 +-
 .../master/html/users_guide/cime-dir.html     |  29 +--
 .../html/users_guide/cime-internals.html      |  23 +-
 .../master/html/users_guide/components.html   | 233 ++++++++++++++++++
 .../master/html/users_guide/compsets.html     |  45 ++--
 versions/master/html/users_guide/grids.html   |  41 +--
 versions/master/html/users_guide/index.html   |  96 ++++----
 versions/master/html/users_guide/machine.html |  53 ++--
 .../html/users_guide/multi-instance.html      |  33 +--
 .../master/html/users_guide/pes-threads.html  |  49 ++--
 .../master/html/users_guide/porting-cime.html |  57 ++---
 .../master/html/users_guide/unit_testing.html | 101 ++++----
 .../master/html/users_guide/workflows.html    |  33 +--
 24 files changed, 610 insertions(+), 297 deletions(-)
 create mode 100644 versions/master/html/_sources/users_guide/components.rst.txt
 create mode 100644 versions/master/html/users_guide/components.html

diff --git a/versions/master/html/CIME_api/CIME.case.html b/versions/master/html/CIME_api/CIME.case.html
index d474da1df96..2cef9044d3b 100644
--- a/versions/master/html/CIME_api/CIME.case.html
+++ b/versions/master/html/CIME_api/CIME.case.html
@@ -170,9 +170,6 @@ <h2>CIME.case.case_test module<a class="headerlink" href="#cime-case-case-test-m
 <section id="cime-case-check-input-data-module">
 <h2>CIME.case.check_input_data module<a class="headerlink" href="#cime-case-check-input-data-module" title="Link to this heading"></a></h2>
 </section>
-<section id="cime-case-check-lockedfiles-module">
-<h2>CIME.case.check_lockedfiles module<a class="headerlink" href="#cime-case-check-lockedfiles-module" title="Link to this heading"></a></h2>
-</section>
 <section id="cime-case-preview-namelists-module">
 <h2>CIME.case.preview_namelists module<a class="headerlink" href="#cime-case-preview-namelists-module" title="Link to this heading"></a></h2>
 </section>
diff --git a/versions/master/html/CIME_api/CIME.html b/versions/master/html/CIME_api/CIME.html
index 0256f7fea15..7f9b26acb44 100644
--- a/versions/master/html/CIME_api/CIME.html
+++ b/versions/master/html/CIME_api/CIME.html
@@ -276,7 +276,6 @@ <h2>Subpackages<a class="headerlink" href="#subpackages" title="Link to this hea
 <li class="toctree-l2"><a class="reference internal" href="CIME.case.html#cime-case-case-submit-module">CIME.case.case_submit module</a></li>
 <li class="toctree-l2"><a class="reference internal" href="CIME.case.html#cime-case-case-test-module">CIME.case.case_test module</a></li>
 <li class="toctree-l2"><a class="reference internal" href="CIME.case.html#cime-case-check-input-data-module">CIME.case.check_input_data module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="CIME.case.html#cime-case-check-lockedfiles-module">CIME.case.check_lockedfiles module</a></li>
 <li class="toctree-l2"><a class="reference internal" href="CIME.case.html#cime-case-preview-namelists-module">CIME.case.preview_namelists module</a></li>
 <li class="toctree-l2"><a class="reference internal" href="CIME.case.html#module-contents">Module contents</a></li>
 </ul>
@@ -369,6 +368,7 @@ <h2>Subpackages<a class="headerlink" href="#subpackages" title="Link to this hea
 <li class="toctree-l2"><a class="reference internal" href="CIME.tests.html#cime-tests-test-unit-expected-fails-file-module">CIME.tests.test_unit_expected_fails_file module</a></li>
 <li class="toctree-l2"><a class="reference internal" href="CIME.tests.html#cime-tests-test-unit-grids-module">CIME.tests.test_unit_grids module</a></li>
 <li class="toctree-l2"><a class="reference internal" href="CIME.tests.html#cime-tests-test-unit-hist-utils-module">CIME.tests.test_unit_hist_utils module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="CIME.tests.html#cime-tests-test-unit-locked-files-module">CIME.tests.test_unit_locked_files module</a></li>
 <li class="toctree-l2"><a class="reference internal" href="CIME.tests.html#cime-tests-test-unit-nmlgen-module">CIME.tests.test_unit_nmlgen module</a></li>
 <li class="toctree-l2"><a class="reference internal" href="CIME.tests.html#module-CIME.tests.test_unit_paramgen">CIME.tests.test_unit_paramgen module</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="CIME.tests.html#CIME.tests.test_unit_paramgen.DummyCase"><code class="docutils literal notranslate"><span class="pre">DummyCase</span></code></a><ul>
diff --git a/versions/master/html/CIME_api/CIME.tests.html b/versions/master/html/CIME_api/CIME.tests.html
index cc44a78f57b..f4f741ab2b2 100644
--- a/versions/master/html/CIME_api/CIME.tests.html
+++ b/versions/master/html/CIME_api/CIME.tests.html
@@ -381,6 +381,9 @@ <h2>CIME.tests.test_unit_grids module<a class="headerlink" href="#cime-tests-tes
 <section id="cime-tests-test-unit-hist-utils-module">
 <h2>CIME.tests.test_unit_hist_utils module<a class="headerlink" href="#cime-tests-test-unit-hist-utils-module" title="Link to this heading"></a></h2>
 </section>
+<section id="cime-tests-test-unit-locked-files-module">
+<h2>CIME.tests.test_unit_locked_files module<a class="headerlink" href="#cime-tests-test-unit-locked-files-module" title="Link to this heading"></a></h2>
+</section>
 <section id="cime-tests-test-unit-nmlgen-module">
 <h2>CIME.tests.test_unit_nmlgen module<a class="headerlink" href="#cime-tests-test-unit-nmlgen-module" title="Link to this heading"></a></h2>
 </section>
diff --git a/versions/master/html/CIME_api/modules.html b/versions/master/html/CIME_api/modules.html
index 8c61dde2fa6..8d64182c06f 100644
--- a/versions/master/html/CIME_api/modules.html
+++ b/versions/master/html/CIME_api/modules.html
@@ -221,7 +221,6 @@ <h1>CIME<a class="headerlink" href="#cime" title="Link to this heading"></a><
 <li class="toctree-l4"><a class="reference internal" href="CIME.case.html#cime-case-case-submit-module">CIME.case.case_submit module</a></li>
 <li class="toctree-l4"><a class="reference internal" href="CIME.case.html#cime-case-case-test-module">CIME.case.case_test module</a></li>
 <li class="toctree-l4"><a class="reference internal" href="CIME.case.html#cime-case-check-input-data-module">CIME.case.check_input_data module</a></li>
-<li class="toctree-l4"><a class="reference internal" href="CIME.case.html#cime-case-check-lockedfiles-module">CIME.case.check_lockedfiles module</a></li>
 <li class="toctree-l4"><a class="reference internal" href="CIME.case.html#cime-case-preview-namelists-module">CIME.case.preview_namelists module</a></li>
 <li class="toctree-l4"><a class="reference internal" href="CIME.case.html#module-contents">Module contents</a></li>
 </ul>
@@ -280,6 +279,7 @@ <h1>CIME<a class="headerlink" href="#cime" title="Link to this heading"></a><
 <li class="toctree-l4"><a class="reference internal" href="CIME.tests.html#cime-tests-test-unit-expected-fails-file-module">CIME.tests.test_unit_expected_fails_file module</a></li>
 <li class="toctree-l4"><a class="reference internal" href="CIME.tests.html#cime-tests-test-unit-grids-module">CIME.tests.test_unit_grids module</a></li>
 <li class="toctree-l4"><a class="reference internal" href="CIME.tests.html#cime-tests-test-unit-hist-utils-module">CIME.tests.test_unit_hist_utils module</a></li>
+<li class="toctree-l4"><a class="reference internal" href="CIME.tests.html#cime-tests-test-unit-locked-files-module">CIME.tests.test_unit_locked_files module</a></li>
 <li class="toctree-l4"><a class="reference internal" href="CIME.tests.html#cime-tests-test-unit-nmlgen-module">CIME.tests.test_unit_nmlgen module</a></li>
 <li class="toctree-l4"><a class="reference internal" href="CIME.tests.html#module-CIME.tests.test_unit_paramgen">CIME.tests.test_unit_paramgen module</a></li>
 <li class="toctree-l4"><a class="reference internal" href="CIME.tests.html#cime-tests-test-unit-system-tests-module">CIME.tests.test_unit_system_tests module</a></li>
diff --git a/versions/master/html/_sources/CIME_api/CIME.case.rst.txt b/versions/master/html/_sources/CIME_api/CIME.case.rst.txt
index 68500a8c4ec..d61acdcc80f 100644
--- a/versions/master/html/_sources/CIME_api/CIME.case.rst.txt
+++ b/versions/master/html/_sources/CIME_api/CIME.case.rst.txt
@@ -76,14 +76,6 @@ CIME.case.check\_input\_data module
    :undoc-members:
    :show-inheritance:
 
-CIME.case.check\_lockedfiles module
------------------------------------
-
-.. automodule:: CIME.case.check_lockedfiles
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
 CIME.case.preview\_namelists module
 -----------------------------------
 
diff --git a/versions/master/html/_sources/CIME_api/CIME.tests.rst.txt b/versions/master/html/_sources/CIME_api/CIME.tests.rst.txt
index d0d44ecbaa6..5d5fc35d4c5 100644
--- a/versions/master/html/_sources/CIME_api/CIME.tests.rst.txt
+++ b/versions/master/html/_sources/CIME_api/CIME.tests.rst.txt
@@ -300,6 +300,14 @@ CIME.tests.test\_unit\_hist\_utils module
    :undoc-members:
    :show-inheritance:
 
+CIME.tests.test\_unit\_locked\_files module
+-------------------------------------------
+
+.. automodule:: CIME.tests.test_unit_locked_files
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 CIME.tests.test\_unit\_nmlgen module
 ------------------------------------
 
diff --git a/versions/master/html/_sources/users_guide/components.rst.txt b/versions/master/html/_sources/users_guide/components.rst.txt
new file mode 100644
index 00000000000..3b48da0c4cc
--- /dev/null
+++ b/versions/master/html/_sources/users_guide/components.rst.txt
@@ -0,0 +1,62 @@
+.. _components:
+
+==========
+Components
+==========
+
+A single component in the smallest unit within a model. Multiple components make up a component set.
+
+Configuration
+--------------
+
+The configuration for a component can be found under `cime_config` in the component directory.
+
+Example contents of a components `config_component.xml`.
+
+::
+
+   <?xml version="1.0"?>
+
+   <?xml-stylesheet type="text/xsl" href="entry_id.xsl" ?>
+
+   <entry_id version="3.0">
+     <description>
+       <desc atm="SATM">Stub atm component</desc>
+     </description>
+
+     <entry id="COMP_ATM">
+       <type>char</type>
+       <valid_values>satm</valid_values>
+       <default_value>satm</default_value>
+       <group>case_comp</group>
+       <file>env_case.xml</file>
+       <desc>Name of atmosphere component</desc>
+     </entry>
+
+
+     <help>
+       =========================================
+       SATM naming conventions in compset name
+       =========================================
+     </help>
+
+   </entry_id>
+
+Triggering a rebuild
+--------------------
+
+It's the responsibility of a component to define which settings will require a component to be rebuilt.
+
+These triggers can be defined as follows.
+
+::
+
+  <entry id="REBUILD_TRIGGER_ATM">
+    <type>char</type>
+    <default_value>NTASKS,NTHREADS,NINST</default_value>
+    <group>rebuild_triggers</group>
+    <file>env_build.xml</file>
+    <desc>Settings that will trigger a rebuild</desc>
+  </entry>
+
+If a user was to change `NTASKS`, `NTHREADS`, or `NINST` in a case using the component, then a rebuild would be required before the case could be submitted again.
diff --git a/versions/master/html/_sources/users_guide/index.rst.txt b/versions/master/html/_sources/users_guide/index.rst.txt
index c16896cdb28..376518783b4 100644
--- a/versions/master/html/_sources/users_guide/index.rst.txt
+++ b/versions/master/html/_sources/users_guide/index.rst.txt
@@ -36,6 +36,7 @@ Configuring the Case Control System
    :numbered:
 
    cime-internals.rst
+   components.rst
    compsets.rst
    grids.rst
    machine.rst
diff --git a/versions/master/html/build_cpl/index.html b/versions/master/html/build_cpl/index.html
index f9076689c66..5abb8a71bac 100644
--- a/versions/master/html/build_cpl/index.html
+++ b/versions/master/html/build_cpl/index.html
@@ -23,7 +23,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="1. Introduction" href="introduction.html" />
-    <link rel="prev" title="10. Directory content" href="../users_guide/cime-dir.html" /> 
+    <link rel="prev" title="11. Directory content" href="../users_guide/cime-dir.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -114,7 +114,7 @@ <h2>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Li
            </div>
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="../users_guide/cime-dir.html" class="btn btn-neutral float-left" title="10. Directory content" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+        <a href="../users_guide/cime-dir.html" class="btn btn-neutral float-left" title="11. Directory content" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
         <a href="introduction.html" class="btn btn-neutral float-right" title="1. Introduction" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
     </div>
 
diff --git a/versions/master/html/index.html b/versions/master/html/index.html
index 962be1ceaf1..0cf02a58cf1 100644
--- a/versions/master/html/index.html
+++ b/versions/master/html/index.html
@@ -117,15 +117,16 @@ <h2>Table of contents<a class="headerlink" href="#table-of-contents" title="Link
 </li>
 <li class="toctree-l1"><a class="reference internal" href="users_guide/index.html#configuring-the-case-control-system">Configuring the Case Control System</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="users_guide/cime-internals.html">1. Main Configuration File</a></li>
-<li class="toctree-l2"><a class="reference internal" href="users_guide/compsets.html">2. Component sets</a></li>
-<li class="toctree-l2"><a class="reference internal" href="users_guide/grids.html">3. Model grids</a></li>
-<li class="toctree-l2"><a class="reference internal" href="users_guide/machine.html">4. Defining the machine</a></li>
-<li class="toctree-l2"><a class="reference internal" href="users_guide/pes-threads.html">5. Controlling processors and threads</a></li>
-<li class="toctree-l2"><a class="reference internal" href="users_guide/porting-cime.html">6. Porting and validating CIME on a new platform</a></li>
-<li class="toctree-l2"><a class="reference internal" href="users_guide/unit_testing.html">7. Fortran Unit Testing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="users_guide/multi-instance.html">8. Multi-instance component functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="users_guide/workflows.html">9. Workflows</a></li>
-<li class="toctree-l2"><a class="reference internal" href="users_guide/cime-dir.html">10. Directory content</a></li>
+<li class="toctree-l2"><a class="reference internal" href="users_guide/components.html">2. Components</a></li>
+<li class="toctree-l2"><a class="reference internal" href="users_guide/compsets.html">3. Component sets</a></li>
+<li class="toctree-l2"><a class="reference internal" href="users_guide/grids.html">4. Model grids</a></li>
+<li class="toctree-l2"><a class="reference internal" href="users_guide/machine.html">5. Defining the machine</a></li>
+<li class="toctree-l2"><a class="reference internal" href="users_guide/pes-threads.html">6. Controlling processors and threads</a></li>
+<li class="toctree-l2"><a class="reference internal" href="users_guide/porting-cime.html">7. Porting and validating CIME on a new platform</a></li>
+<li class="toctree-l2"><a class="reference internal" href="users_guide/unit_testing.html">8. Fortran Unit Testing</a></li>
+<li class="toctree-l2"><a class="reference internal" href="users_guide/multi-instance.html">9. Multi-instance component functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="users_guide/workflows.html">10. Workflows</a></li>
+<li class="toctree-l2"><a class="reference internal" href="users_guide/cime-dir.html">11. Directory content</a></li>
 <li class="toctree-l2"><a class="reference internal" href="users_guide/index.html#indices-and-tables">Indices and tables</a></li>
 </ul>
 </li>
diff --git a/versions/master/html/objects.inv b/versions/master/html/objects.inv
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diff --git a/versions/master/html/searchindex.js b/versions/master/html/searchindex.js
index 9f83c042000..c7567215298 100644
--- a/versions/master/html/searchindex.js
+++ b/versions/master/html/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"alltitles": {"Adding a \u2013user-mods-dir argument to create_newcase": [[86, "adding-a-user-mods-dir-argument-to-create-newcase"]], "Adding components": [[69, "adding-components"]], "Adding grids": [[87, "adding-grids"]], "Adding to the appropriate cmake file": [[99, "adding-to-the-appropriate-cmake-file"]], "Advice on setting your wallclock time": [[97, "advice-on-setting-your-wallclock-time"]], "An MPI example": [[93, "an-mpi-example"]], "Appendices": [[74, "appendices"]], "Archiving model output data": [[94, "archiving-model-output-data"]], "Assertion methods": [[99, "assertion-methods"]], "Backing up to a previous restart": [[94, "backing-up-to-a-previous-restart"]], "Baselines and Baseline Testing": [[96, "baselines-and-baseline-testing"]], "Batch system definition": [[90, "batch-system-definition"]], "Building a Case": [[78, "building-a-case"]], "Building a Coupled Model with CIME": [[70, "building-a-coupled-model-with-cime"]], "Building pFUnit": [[99, "building-pfunit"]], "CAM": [[79, "cam"]], "CCS and your environment": [[89, "ccs-and-your-environment"]], "CESM Coupled Model XML Files": [[103, "cesm-coupled-model-xml-files"]], "CESM Linux and Mac Support": [[93, "cesm-linux-and-mac-support"]], "CESM-ECT (CESM Ensemble Consistency Test):": [[75, "cesm-ect-cesm-ensemble-consistency-test"]], "CICE": [[79, "cice"]], "CIME": [[15, "cime"]], "CIME Atmosphere Data and Stub XML Files": [[102, "cime-atmosphere-data-and-stub-xml-files"]], "CIME ESP Data and Stub XML Files": [[108, "cime-esp-data-and-stub-xml-files"]], "CIME Land Data and Stub XML Files": [[110, "cime-land-data-and-stub-xml-files"]], "CIME Land Ice Data and Stub XML Files": [[111, "cime-land-ice-data-and-stub-xml-files"]], "CIME Load Balancing Tool": [[77, "cime-load-balancing-tool"]], "CIME Ocean Data and Stub XML Files": [[112, "cime-ocean-data-and-stub-xml-files"]], "CIME River Runoff Data and Stub XML Files": [[113, "cime-river-runoff-data-and-stub-xml-files"]], "CIME Sea Ice Data and Stub XML Files": [[114, "cime-sea-ice-data-and-stub-xml-files"]], "CIME Wave Data and Stub XML Files": [[115, "cime-wave-data-and-stub-xml-files"]], "CIME config": [[81, "cime-config"]], "CIME config and hooks": [[81, "cime-config-and-hooks"]], "CIME directory content": [[82, "id2"]], "CIME directory in a climate model": [[82, "id1"]], "CIME documentation": [[74, "cime-documentation"]], "CIME hooks": [[81, "cime-hooks"]], "CIME package": [[0, "cime-package"]], "CIME user config directory": [[80, "cime-user-config-directory"]], "CIME.BuildTools package": [[1, "cime-buildtools-package"]], "CIME.BuildTools.configure module": [[1, "cime-buildtools-configure-module"]], "CIME.Servers package": [[2, "cime-servers-package"]], "CIME.Servers.ftp module": [[2, "cime-servers-ftp-module"]], "CIME.Servers.generic_server module": [[2, "cime-servers-generic-server-module"]], "CIME.Servers.gftp module": [[2, "cime-servers-gftp-module"]], "CIME.Servers.svn module": [[2, "cime-servers-svn-module"]], "CIME.Servers.wget module": [[2, "cime-servers-wget-module"]], "CIME.SystemTests package": [[3, "cime-systemtests-package"]], "CIME.SystemTests.dae module": [[3, "cime-systemtests-dae-module"]], "CIME.SystemTests.eri module": [[3, "cime-systemtests-eri-module"]], "CIME.SystemTests.erio module": [[3, "cime-systemtests-erio-module"]], "CIME.SystemTests.erp module": [[3, "cime-systemtests-erp-module"]], "CIME.SystemTests.err module": [[3, "cime-systemtests-err-module"]], "CIME.SystemTests.erri module": [[3, "cime-systemtests-erri-module"]], "CIME.SystemTests.ers module": [[3, "cime-systemtests-ers-module"]], "CIME.SystemTests.ers2 module": [[3, "cime-systemtests-ers2-module"]], "CIME.SystemTests.ert module": [[3, "cime-systemtests-ert-module"]], "CIME.SystemTests.funit module": [[3, "cime-systemtests-funit-module"]], "CIME.SystemTests.homme module": [[3, "cime-systemtests-homme-module"]], "CIME.SystemTests.hommebaseclass module": [[3, "cime-systemtests-hommebaseclass-module"]], "CIME.SystemTests.hommebfb module": [[3, "cime-systemtests-hommebfb-module"]], "CIME.SystemTests.icp module": [[3, "cime-systemtests-icp-module"]], "CIME.SystemTests.irt module": [[3, "cime-systemtests-irt-module"]], "CIME.SystemTests.ldsta module": [[3, "cime-systemtests-ldsta-module"]], "CIME.SystemTests.mcc module": [[3, "cime-systemtests-mcc-module"]], "CIME.SystemTests.mvk module": [[3, "cime-systemtests-mvk-module"]], "CIME.SystemTests.nck module": [[3, "cime-systemtests-nck-module"]], "CIME.SystemTests.ncr module": [[3, "cime-systemtests-ncr-module"]], "CIME.SystemTests.nodefail module": [[3, "cime-systemtests-nodefail-module"]], "CIME.SystemTests.pea module": [[3, "cime-systemtests-pea-module"]], "CIME.SystemTests.pem module": [[3, "cime-systemtests-pem-module"]], "CIME.SystemTests.pet module": [[3, "cime-systemtests-pet-module"]], "CIME.SystemTests.pfs module": [[3, "cime-systemtests-pfs-module"]], "CIME.SystemTests.pgn module": [[3, "cime-systemtests-pgn-module"]], "CIME.SystemTests.pre module": [[3, "cime-systemtests-pre-module"]], "CIME.SystemTests.rep module": [[3, "cime-systemtests-rep-module"]], "CIME.SystemTests.restart_tests module": [[3, "cime-systemtests-restart-tests-module"]], "CIME.SystemTests.reuseinitfiles module": [[3, "cime-systemtests-reuseinitfiles-module"]], "CIME.SystemTests.seq module": [[3, "cime-systemtests-seq-module"]], "CIME.SystemTests.sms module": [[3, "cime-systemtests-sms-module"]], "CIME.SystemTests.system_tests_common module": [[3, "cime-systemtests-system-tests-common-module"]], "CIME.SystemTests.system_tests_compare_n module": [[3, "cime-systemtests-system-tests-compare-n-module"]], "CIME.SystemTests.system_tests_compare_two module": [[3, "cime-systemtests-system-tests-compare-two-module"]], "CIME.SystemTests.test_utils package": [[4, "cime-systemtests-test-utils-package"]], "CIME.SystemTests.test_utils.user_nl_utils module": [[4, "module-CIME.SystemTests.test_utils.user_nl_utils"]], "CIME.SystemTests.tsc module": [[3, "cime-systemtests-tsc-module"]], "CIME.Tools package": [[5, "cime-tools-package"]], "CIME.Tools.generate_cylc_workflow module": [[5, "cime-tools-generate-cylc-workflow-module"]], "CIME.Tools.standard_script_setup module": [[5, "cime-tools-standard-script-setup-module"]], "CIME.Tools.testreporter module": [[5, "cime-tools-testreporter-module"]], "CIME.XML package": [[6, "cime-xml-package"]], "CIME.XML.archive module": [[6, "cime-xml-archive-module"]], "CIME.XML.archive_base module": [[6, "cime-xml-archive-base-module"]], "CIME.XML.batch module": [[6, "cime-xml-batch-module"]], "CIME.XML.component module": [[6, "cime-xml-component-module"]], "CIME.XML.compsets module": [[6, "cime-xml-compsets-module"]], "CIME.XML.entry_id module": [[6, "cime-xml-entry-id-module"]], "CIME.XML.env_archive module": [[6, "cime-xml-env-archive-module"]], "CIME.XML.env_base module": [[6, "cime-xml-env-base-module"]], "CIME.XML.env_batch module": [[6, "cime-xml-env-batch-module"]], "CIME.XML.env_build module": [[6, "cime-xml-env-build-module"]], "CIME.XML.env_case module": [[6, "cime-xml-env-case-module"]], "CIME.XML.env_mach_pes module": [[6, "cime-xml-env-mach-pes-module"]], "CIME.XML.env_mach_specific module": [[6, "cime-xml-env-mach-specific-module"]], "CIME.XML.env_run module": [[6, "cime-xml-env-run-module"]], "CIME.XML.env_test module": [[6, "cime-xml-env-test-module"]], "CIME.XML.env_workflow module": [[6, "cime-xml-env-workflow-module"]], "CIME.XML.expected_fails_file module": [[6, "cime-xml-expected-fails-file-module"]], "CIME.XML.files module": [[6, "cime-xml-files-module"]], "CIME.XML.generic_xml module": [[6, "cime-xml-generic-xml-module"]], "CIME.XML.grids module": [[6, "cime-xml-grids-module"]], "CIME.XML.headers module": [[6, "cime-xml-headers-module"]], "CIME.XML.inputdata module": [[6, "cime-xml-inputdata-module"]], "CIME.XML.machines module": [[6, "cime-xml-machines-module"]], "CIME.XML.namelist_definition module": [[6, "cime-xml-namelist-definition-module"]], "CIME.XML.pes module": [[6, "cime-xml-pes-module"]], "CIME.XML.pio module": [[6, "cime-xml-pio-module"]], "CIME.XML.standard_module_setup module": [[6, "cime-xml-standard-module-setup-module"]], "CIME.XML.stream module": [[6, "cime-xml-stream-module"]], "CIME.XML.test_reporter module": [[6, "cime-xml-test-reporter-module"]], "CIME.XML.testlist module": [[6, "cime-xml-testlist-module"]], "CIME.XML.tests module": [[6, "cime-xml-tests-module"]], "CIME.XML.testspec module": [[6, "cime-xml-testspec-module"]], "CIME.XML.workflow module": [[6, "cime-xml-workflow-module"]], "CIME.aprun module": [[0, "cime-aprun-module"]], "CIME.baselines package": [[7, "cime-baselines-package"]], "CIME.baselines.performance module": [[7, "cime-baselines-performance-module"]], "CIME.bless_test_results module": [[0, "cime-bless-test-results-module"]], "CIME.build module": [[0, "cime-build-module"]], "CIME.build_scripts package": [[8, "cime-build-scripts-package"]], "CIME.buildlib module": [[0, "cime-buildlib-module"]], "CIME.buildnml module": [[0, "cime-buildnml-module"]], "CIME.case package": [[9, "cime-case-package"]], "CIME.case.case module": [[9, "cime-case-case-module"]], "CIME.case.case_clone module": [[9, "cime-case-case-clone-module"]], "CIME.case.case_cmpgen_namelists module": [[9, "cime-case-case-cmpgen-namelists-module"]], "CIME.case.case_run module": [[9, "cime-case-case-run-module"]], "CIME.case.case_setup module": [[9, "cime-case-case-setup-module"]], "CIME.case.case_st_archive module": [[9, "cime-case-case-st-archive-module"]], "CIME.case.case_submit module": [[9, "cime-case-case-submit-module"]], "CIME.case.case_test module": [[9, "cime-case-case-test-module"]], "CIME.case.check_input_data module": [[9, "cime-case-check-input-data-module"]], "CIME.case.check_lockedfiles module": [[9, "cime-case-check-lockedfiles-module"]], "CIME.case.preview_namelists module": [[9, "cime-case-preview-namelists-module"]], "CIME.code_checker module": [[0, "cime-code-checker-module"]], "CIME.compare_namelists module": [[0, "cime-compare-namelists-module"]], "CIME.compare_test_results module": [[0, "cime-compare-test-results-module"]], "CIME.config module": [[0, "cime-config-module"]], "CIME.cs_status module": [[0, "cime-cs-status-module"]], "CIME.cs_status_creator module": [[0, "cime-cs-status-creator-module"]], "CIME.data package": [[10, "cime-data-package"]], "CIME.data.config package": [[11, "cime-data-config-package"]], "CIME.data.templates package": [[12, "cime-data-templates-package"]], "CIME.date module": [[0, "cime-date-module"]], "CIME.expected_fails module": [[0, "cime-expected-fails-module"]], "CIME.get_tests module": [[0, "cime-get-tests-module"]], "CIME.get_timing module": [[0, "cime-get-timing-module"]], "CIME.hist_utils module": [[0, "cime-hist-utils-module"]], "CIME.jenkins_generic_job module": [[0, "cime-jenkins-generic-job-module"]], "CIME.locked_files module": [[0, "cime-locked-files-module"]], "CIME.namelist module": [[0, "cime-namelist-module"]], "CIME.nmlgen module": [[0, "cime-nmlgen-module"]], "CIME.provenance module": [[0, "cime-provenance-module"]], "CIME.scripts package": [[13, "cime-scripts-package"]], "CIME.scripts.create_clone module": [[13, "cime-scripts-create-clone-module"]], "CIME.scripts.create_newcase module": [[13, "cime-scripts-create-newcase-module"]], "CIME.scripts.create_test module": [[13, "cime-scripts-create-test-module"]], "CIME.scripts.query_config module": [[13, "cime-scripts-query-config-module"]], "CIME.scripts.query_testlists module": [[13, "cime-scripts-query-testlists-module"]], "CIME.simple_compare module": [[0, "cime-simple-compare-module"]], "CIME.test_scheduler module": [[0, "cime-test-scheduler-module"]], "CIME.test_status module": [[0, "cime-test-status-module"]], "CIME.test_utils module": [[0, "cime-test-utils-module"]], "CIME.tests package": [[14, "cime-tests-package"]], "CIME.tests.base module": [[14, "cime-tests-base-module"]], "CIME.tests.case_fake module": [[14, "module-CIME.tests.case_fake"]], "CIME.tests.custom_assertions_test_status module": [[14, "cime-tests-custom-assertions-test-status-module"]], "CIME.tests.scripts_regression_tests module": [[14, "cime-tests-scripts-regression-tests-module"]], "CIME.tests.test_sys_bless_tests_results module": [[14, "cime-tests-test-sys-bless-tests-results-module"]], "CIME.tests.test_sys_build_system module": [[14, "cime-tests-test-sys-build-system-module"]], "CIME.tests.test_sys_cime_case module": [[14, "cime-tests-test-sys-cime-case-module"]], "CIME.tests.test_sys_cime_performance module": [[14, "cime-tests-test-sys-cime-performance-module"]], "CIME.tests.test_sys_create_newcase module": [[14, "cime-tests-test-sys-create-newcase-module"]], "CIME.tests.test_sys_full_system module": [[14, "cime-tests-test-sys-full-system-module"]], "CIME.tests.test_sys_grid_generation module": [[14, "cime-tests-test-sys-grid-generation-module"]], "CIME.tests.test_sys_jenkins_generic_job module": [[14, "cime-tests-test-sys-jenkins-generic-job-module"]], "CIME.tests.test_sys_manage_and_query module": [[14, "cime-tests-test-sys-manage-and-query-module"]], "CIME.tests.test_sys_query_config module": [[14, "cime-tests-test-sys-query-config-module"]], "CIME.tests.test_sys_run_restart module": [[14, "cime-tests-test-sys-run-restart-module"]], "CIME.tests.test_sys_save_timings module": [[14, "cime-tests-test-sys-save-timings-module"]], "CIME.tests.test_sys_single_submit module": [[14, "cime-tests-test-sys-single-submit-module"]], "CIME.tests.test_sys_test_scheduler module": [[14, "cime-tests-test-sys-test-scheduler-module"]], "CIME.tests.test_sys_unittest module": [[14, "cime-tests-test-sys-unittest-module"]], "CIME.tests.test_sys_user_concurrent_mods module": [[14, "cime-tests-test-sys-user-concurrent-mods-module"]], "CIME.tests.test_sys_wait_for_tests module": [[14, "cime-tests-test-sys-wait-for-tests-module"]], "CIME.tests.test_unit_aprun module": [[14, "cime-tests-test-unit-aprun-module"]], "CIME.tests.test_unit_baselines_performance module": [[14, "cime-tests-test-unit-baselines-performance-module"]], "CIME.tests.test_unit_bless_test_results module": [[14, "cime-tests-test-unit-bless-test-results-module"]], "CIME.tests.test_unit_case module": [[14, "cime-tests-test-unit-case-module"]], "CIME.tests.test_unit_case_fake module": [[14, "module-CIME.tests.test_unit_case_fake"]], "CIME.tests.test_unit_case_run module": [[14, "cime-tests-test-unit-case-run-module"]], "CIME.tests.test_unit_case_setup module": [[14, "cime-tests-test-unit-case-setup-module"]], "CIME.tests.test_unit_compare_test_results module": [[14, "cime-tests-test-unit-compare-test-results-module"]], "CIME.tests.test_unit_compare_two module": [[14, "cime-tests-test-unit-compare-two-module"]], "CIME.tests.test_unit_config module": [[14, "cime-tests-test-unit-config-module"]], "CIME.tests.test_unit_cs_status module": [[14, "cime-tests-test-unit-cs-status-module"]], "CIME.tests.test_unit_custom_assertions_test_status module": [[14, "cime-tests-test-unit-custom-assertions-test-status-module"]], "CIME.tests.test_unit_doctest module": [[14, "cime-tests-test-unit-doctest-module"]], "CIME.tests.test_unit_expected_fails_file module": [[14, "cime-tests-test-unit-expected-fails-file-module"]], "CIME.tests.test_unit_grids module": [[14, "cime-tests-test-unit-grids-module"]], "CIME.tests.test_unit_hist_utils module": [[14, "cime-tests-test-unit-hist-utils-module"]], "CIME.tests.test_unit_nmlgen module": [[14, "cime-tests-test-unit-nmlgen-module"]], "CIME.tests.test_unit_paramgen module": [[14, "module-CIME.tests.test_unit_paramgen"]], "CIME.tests.test_unit_system_tests module": [[14, "cime-tests-test-unit-system-tests-module"]], "CIME.tests.test_unit_test_status module": [[14, "cime-tests-test-unit-test-status-module"]], "CIME.tests.test_unit_two_link_to_case2_output module": [[14, "cime-tests-test-unit-two-link-to-case2-output-module"]], "CIME.tests.test_unit_user_mod_support module": [[14, "cime-tests-test-unit-user-mod-support-module"]], "CIME.tests.test_unit_user_nl_utils module": [[14, "module-CIME.tests.test_unit_user_nl_utils"]], "CIME.tests.test_unit_utils module": [[14, "cime-tests-test-unit-utils-module"]], "CIME.tests.test_unit_xml_archive_base module": [[14, "cime-tests-test-unit-xml-archive-base-module"]], "CIME.tests.test_unit_xml_env_batch module": [[14, "cime-tests-test-unit-xml-env-batch-module"]], "CIME.tests.test_unit_xml_env_mach_specific module": [[14, "cime-tests-test-unit-xml-env-mach-specific-module"]], "CIME.tests.test_unit_xml_machines module": [[14, "cime-tests-test-unit-xml-machines-module"]], "CIME.tests.test_unit_xml_namelist_definition module": [[14, "cime-tests-test-unit-xml-namelist-definition-module"]], "CIME.tests.test_unit_xml_tests module": [[14, "cime-tests-test-unit-xml-tests-module"]], "CIME.tests.utils module": [[14, "cime-tests-utils-module"]], "CIME.user_mod_support module": [[0, "cime-user-mod-support-module"]], "CIME.utils module": [[0, "cime-utils-module"]], "CIME.wait_for_tests module": [[0, "cime-wait-for-tests-module"]], "CIMEROOT/config/cesm": [[103, "cimeroot-config-cesm"]], "CIMEROOT/config/config_headers.xml": [[104, "cimeroot-config-config-headers-xml"]], "CIMEROOT/config/config_tests.xml": [[104, "cimeroot-config-config-tests-xml"]], "CIMEROOT/config/e3sm": [[107, "cimeroot-config-e3sm"]], "CIMEROOT/src/components/data_comps/datm/cime_config": [[102, "cimeroot-src-components-data-comps-datm-cime-config"]], "CIMEROOT/src/components/data_comps/desp/cime_config": [[108, "cimeroot-src-components-data-comps-desp-cime-config"]], "CIMEROOT/src/components/data_comps/dice/cime_config": [[114, "cimeroot-src-components-data-comps-dice-cime-config"]], "CIMEROOT/src/components/data_comps/dlnd/cime_config": [[110, "cimeroot-src-components-data-comps-dlnd-cime-config"]], "CIMEROOT/src/components/data_comps/docn/cime_config": [[112, "cimeroot-src-components-data-comps-docn-cime-config"]], "CIMEROOT/src/components/data_comps/drof/cime_config": [[113, "cimeroot-src-components-data-comps-drof-cime-config"]], "CIMEROOT/src/components/data_comps/dwav/cime_config": [[115, "cimeroot-src-components-data-comps-dwav-cime-config"]], "CIMEROOT/src/components/stub_comps/satm/cime_config": [[102, "cimeroot-src-components-stub-comps-satm-cime-config"]], "CIMEROOT/src/components/stub_comps/sesp/cime_config": [[108, "cimeroot-src-components-stub-comps-sesp-cime-config"]], "CIMEROOT/src/components/stub_comps/sglc/cime_config": [[111, "cimeroot-src-components-stub-comps-sglc-cime-config"]], "CIMEROOT/src/components/stub_comps/sice/cime_config": [[114, "cimeroot-src-components-stub-comps-sice-cime-config"]], "CIMEROOT/src/components/stub_comps/slnd/cime_config": [[110, "cimeroot-src-components-stub-comps-slnd-cime-config"]], "CIMEROOT/src/components/stub_comps/socn/cime_config": [[112, "cimeroot-src-components-stub-comps-socn-cime-config"]], "CIMEROOT/src/components/stub_comps/srof/cime_config": [[113, "cimeroot-src-components-stub-comps-srof-cime-config"]], "CIMEROOT/src/components/stub_comps/swav/cime_config": [[115, "cimeroot-src-components-stub-comps-swav-cime-config"]], "CIMEROOT/src/components/xcpl_comps/xatm/cime_config": [[102, "cimeroot-src-components-xcpl-comps-xatm-cime-config"]], "CIMEROOT/src/components/xcpl_comps/xglc/cime_config": [[111, "cimeroot-src-components-xcpl-comps-xglc-cime-config"]], "CIMEROOT/src/components/xcpl_comps/xice/cime_config": [[114, "cimeroot-src-components-xcpl-comps-xice-cime-config"]], "CIMEROOT/src/components/xcpl_comps/xlnd/cime_config": [[110, "cimeroot-src-components-xcpl-comps-xlnd-cime-config"]], "CIMEROOT/src/components/xcpl_comps/xocn/cime_config": [[112, "cimeroot-src-components-xcpl-comps-xocn-cime-config"]], 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\ No newline at end of file
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"building-pfunit"]], "CAM": [[79, "cam"]], "CCS and your environment": [[90, "ccs-and-your-environment"]], "CESM Coupled Model XML Files": [[104, "cesm-coupled-model-xml-files"]], "CESM Linux and Mac Support": [[94, "cesm-linux-and-mac-support"]], "CESM-ECT (CESM Ensemble Consistency Test):": [[75, "cesm-ect-cesm-ensemble-consistency-test"]], "CICE": [[79, "cice"]], "CIME": [[15, "cime"]], "CIME Atmosphere Data and Stub XML Files": [[103, "cime-atmosphere-data-and-stub-xml-files"]], "CIME ESP Data and Stub XML Files": [[109, "cime-esp-data-and-stub-xml-files"]], "CIME Land Data and Stub XML Files": [[111, "cime-land-data-and-stub-xml-files"]], "CIME Land Ice Data and Stub XML Files": [[112, "cime-land-ice-data-and-stub-xml-files"]], "CIME Load Balancing Tool": [[77, "cime-load-balancing-tool"]], "CIME Ocean Data and Stub XML Files": [[113, "cime-ocean-data-and-stub-xml-files"]], "CIME River Runoff Data and Stub XML Files": [[114, "cime-river-runoff-data-and-stub-xml-files"]], "CIME Sea Ice Data and Stub XML Files": [[115, "cime-sea-ice-data-and-stub-xml-files"]], "CIME Wave Data and Stub XML Files": [[116, "cime-wave-data-and-stub-xml-files"]], "CIME config": [[81, "cime-config"]], "CIME config and hooks": [[81, "cime-config-and-hooks"]], "CIME directory content": [[82, "id2"]], "CIME directory in a climate model": [[82, "id1"]], "CIME documentation": [[74, "cime-documentation"]], "CIME hooks": [[81, "cime-hooks"]], "CIME package": [[0, "cime-package"]], "CIME user config directory": [[80, "cime-user-config-directory"]], "CIME.BuildTools package": [[1, "cime-buildtools-package"]], "CIME.BuildTools.configure module": [[1, "cime-buildtools-configure-module"]], "CIME.Servers package": [[2, "cime-servers-package"]], "CIME.Servers.ftp module": [[2, "cime-servers-ftp-module"]], "CIME.Servers.generic_server module": [[2, "cime-servers-generic-server-module"]], "CIME.Servers.gftp module": [[2, "cime-servers-gftp-module"]], "CIME.Servers.svn module": [[2, "cime-servers-svn-module"]], "CIME.Servers.wget module": [[2, "cime-servers-wget-module"]], "CIME.SystemTests package": [[3, "cime-systemtests-package"]], "CIME.SystemTests.dae module": [[3, "cime-systemtests-dae-module"]], "CIME.SystemTests.eri module": [[3, "cime-systemtests-eri-module"]], "CIME.SystemTests.erio module": [[3, "cime-systemtests-erio-module"]], "CIME.SystemTests.erp module": [[3, "cime-systemtests-erp-module"]], "CIME.SystemTests.err module": [[3, "cime-systemtests-err-module"]], "CIME.SystemTests.erri module": [[3, "cime-systemtests-erri-module"]], "CIME.SystemTests.ers module": [[3, "cime-systemtests-ers-module"]], "CIME.SystemTests.ers2 module": [[3, "cime-systemtests-ers2-module"]], "CIME.SystemTests.ert module": [[3, "cime-systemtests-ert-module"]], "CIME.SystemTests.funit module": [[3, "cime-systemtests-funit-module"]], "CIME.SystemTests.homme module": [[3, "cime-systemtests-homme-module"]], "CIME.SystemTests.hommebaseclass module": [[3, "cime-systemtests-hommebaseclass-module"]], "CIME.SystemTests.hommebfb module": [[3, "cime-systemtests-hommebfb-module"]], "CIME.SystemTests.icp module": [[3, "cime-systemtests-icp-module"]], "CIME.SystemTests.irt module": [[3, "cime-systemtests-irt-module"]], "CIME.SystemTests.ldsta module": [[3, "cime-systemtests-ldsta-module"]], "CIME.SystemTests.mcc module": [[3, "cime-systemtests-mcc-module"]], "CIME.SystemTests.mvk module": [[3, "cime-systemtests-mvk-module"]], "CIME.SystemTests.nck module": [[3, "cime-systemtests-nck-module"]], "CIME.SystemTests.ncr module": [[3, "cime-systemtests-ncr-module"]], "CIME.SystemTests.nodefail module": [[3, "cime-systemtests-nodefail-module"]], "CIME.SystemTests.pea module": [[3, "cime-systemtests-pea-module"]], "CIME.SystemTests.pem module": [[3, "cime-systemtests-pem-module"]], "CIME.SystemTests.pet module": [[3, "cime-systemtests-pet-module"]], "CIME.SystemTests.pfs module": [[3, "cime-systemtests-pfs-module"]], "CIME.SystemTests.pgn module": [[3, "cime-systemtests-pgn-module"]], "CIME.SystemTests.pre module": [[3, "cime-systemtests-pre-module"]], "CIME.SystemTests.rep module": [[3, "cime-systemtests-rep-module"]], "CIME.SystemTests.restart_tests module": [[3, "cime-systemtests-restart-tests-module"]], "CIME.SystemTests.reuseinitfiles module": [[3, "cime-systemtests-reuseinitfiles-module"]], "CIME.SystemTests.seq module": [[3, "cime-systemtests-seq-module"]], "CIME.SystemTests.sms module": [[3, "cime-systemtests-sms-module"]], "CIME.SystemTests.system_tests_common module": [[3, "cime-systemtests-system-tests-common-module"]], "CIME.SystemTests.system_tests_compare_n module": [[3, "cime-systemtests-system-tests-compare-n-module"]], "CIME.SystemTests.system_tests_compare_two module": [[3, "cime-systemtests-system-tests-compare-two-module"]], "CIME.SystemTests.test_utils package": [[4, "cime-systemtests-test-utils-package"]], "CIME.SystemTests.test_utils.user_nl_utils module": [[4, "module-CIME.SystemTests.test_utils.user_nl_utils"]], "CIME.SystemTests.tsc module": [[3, "cime-systemtests-tsc-module"]], "CIME.Tools package": [[5, "cime-tools-package"]], "CIME.Tools.generate_cylc_workflow module": [[5, "cime-tools-generate-cylc-workflow-module"]], "CIME.Tools.standard_script_setup module": [[5, "cime-tools-standard-script-setup-module"]], "CIME.Tools.testreporter module": [[5, "cime-tools-testreporter-module"]], "CIME.XML package": [[6, "cime-xml-package"]], "CIME.XML.archive module": [[6, "cime-xml-archive-module"]], "CIME.XML.archive_base module": [[6, "cime-xml-archive-base-module"]], "CIME.XML.batch module": [[6, "cime-xml-batch-module"]], "CIME.XML.component module": [[6, "cime-xml-component-module"]], "CIME.XML.compsets module": [[6, "cime-xml-compsets-module"]], "CIME.XML.entry_id module": [[6, "cime-xml-entry-id-module"]], "CIME.XML.env_archive module": [[6, "cime-xml-env-archive-module"]], "CIME.XML.env_base module": [[6, "cime-xml-env-base-module"]], "CIME.XML.env_batch module": [[6, "cime-xml-env-batch-module"]], "CIME.XML.env_build module": [[6, "cime-xml-env-build-module"]], "CIME.XML.env_case module": [[6, "cime-xml-env-case-module"]], "CIME.XML.env_mach_pes module": [[6, "cime-xml-env-mach-pes-module"]], "CIME.XML.env_mach_specific module": [[6, "cime-xml-env-mach-specific-module"]], "CIME.XML.env_run module": [[6, "cime-xml-env-run-module"]], "CIME.XML.env_test module": [[6, "cime-xml-env-test-module"]], "CIME.XML.env_workflow module": [[6, "cime-xml-env-workflow-module"]], "CIME.XML.expected_fails_file module": [[6, "cime-xml-expected-fails-file-module"]], "CIME.XML.files module": [[6, "cime-xml-files-module"]], "CIME.XML.generic_xml module": [[6, "cime-xml-generic-xml-module"]], "CIME.XML.grids module": [[6, "cime-xml-grids-module"]], "CIME.XML.headers module": [[6, "cime-xml-headers-module"]], "CIME.XML.inputdata module": [[6, "cime-xml-inputdata-module"]], "CIME.XML.machines module": [[6, "cime-xml-machines-module"]], "CIME.XML.namelist_definition module": [[6, "cime-xml-namelist-definition-module"]], "CIME.XML.pes module": [[6, "cime-xml-pes-module"]], "CIME.XML.pio module": [[6, "cime-xml-pio-module"]], "CIME.XML.standard_module_setup module": [[6, "cime-xml-standard-module-setup-module"]], "CIME.XML.stream module": [[6, "cime-xml-stream-module"]], "CIME.XML.test_reporter module": [[6, "cime-xml-test-reporter-module"]], "CIME.XML.testlist module": [[6, "cime-xml-testlist-module"]], "CIME.XML.tests module": [[6, "cime-xml-tests-module"]], "CIME.XML.testspec module": [[6, "cime-xml-testspec-module"]], "CIME.XML.workflow module": [[6, "cime-xml-workflow-module"]], "CIME.aprun module": [[0, "cime-aprun-module"]], "CIME.baselines package": [[7, "cime-baselines-package"]], "CIME.baselines.performance module": [[7, "cime-baselines-performance-module"]], "CIME.bless_test_results module": [[0, "cime-bless-test-results-module"]], "CIME.build module": [[0, "cime-build-module"]], "CIME.build_scripts package": [[8, "cime-build-scripts-package"]], "CIME.buildlib module": [[0, "cime-buildlib-module"]], "CIME.buildnml module": [[0, "cime-buildnml-module"]], "CIME.case package": [[9, "cime-case-package"]], "CIME.case.case module": [[9, "cime-case-case-module"]], "CIME.case.case_clone module": [[9, "cime-case-case-clone-module"]], "CIME.case.case_cmpgen_namelists module": [[9, "cime-case-case-cmpgen-namelists-module"]], "CIME.case.case_run module": [[9, "cime-case-case-run-module"]], "CIME.case.case_setup module": [[9, "cime-case-case-setup-module"]], "CIME.case.case_st_archive module": [[9, "cime-case-case-st-archive-module"]], "CIME.case.case_submit module": [[9, "cime-case-case-submit-module"]], "CIME.case.case_test module": [[9, "cime-case-case-test-module"]], "CIME.case.check_input_data module": [[9, "cime-case-check-input-data-module"]], "CIME.case.preview_namelists module": [[9, "cime-case-preview-namelists-module"]], "CIME.code_checker module": [[0, "cime-code-checker-module"]], "CIME.compare_namelists module": [[0, "cime-compare-namelists-module"]], "CIME.compare_test_results module": [[0, "cime-compare-test-results-module"]], "CIME.config module": [[0, "cime-config-module"]], "CIME.cs_status module": [[0, "cime-cs-status-module"]], "CIME.cs_status_creator module": [[0, "cime-cs-status-creator-module"]], "CIME.data package": [[10, "cime-data-package"]], "CIME.data.config package": [[11, "cime-data-config-package"]], "CIME.data.templates package": [[12, "cime-data-templates-package"]], "CIME.date module": [[0, "cime-date-module"]], "CIME.expected_fails module": [[0, "cime-expected-fails-module"]], "CIME.get_tests module": [[0, "cime-get-tests-module"]], "CIME.get_timing module": [[0, "cime-get-timing-module"]], "CIME.hist_utils module": [[0, "cime-hist-utils-module"]], "CIME.jenkins_generic_job module": [[0, "cime-jenkins-generic-job-module"]], "CIME.locked_files module": [[0, "cime-locked-files-module"]], "CIME.namelist module": [[0, "cime-namelist-module"]], "CIME.nmlgen module": [[0, "cime-nmlgen-module"]], "CIME.provenance module": [[0, "cime-provenance-module"]], "CIME.scripts package": [[13, "cime-scripts-package"]], "CIME.scripts.create_clone module": [[13, "cime-scripts-create-clone-module"]], "CIME.scripts.create_newcase module": [[13, "cime-scripts-create-newcase-module"]], "CIME.scripts.create_test module": [[13, "cime-scripts-create-test-module"]], "CIME.scripts.query_config module": [[13, "cime-scripts-query-config-module"]], "CIME.scripts.query_testlists module": [[13, "cime-scripts-query-testlists-module"]], "CIME.simple_compare module": [[0, "cime-simple-compare-module"]], "CIME.test_scheduler module": [[0, "cime-test-scheduler-module"]], "CIME.test_status module": [[0, "cime-test-status-module"]], "CIME.test_utils module": [[0, "cime-test-utils-module"]], "CIME.tests package": [[14, "cime-tests-package"]], "CIME.tests.base module": [[14, "cime-tests-base-module"]], "CIME.tests.case_fake module": [[14, "module-CIME.tests.case_fake"]], "CIME.tests.custom_assertions_test_status module": [[14, "cime-tests-custom-assertions-test-status-module"]], "CIME.tests.scripts_regression_tests module": [[14, "cime-tests-scripts-regression-tests-module"]], "CIME.tests.test_sys_bless_tests_results module": [[14, "cime-tests-test-sys-bless-tests-results-module"]], "CIME.tests.test_sys_build_system module": [[14, "cime-tests-test-sys-build-system-module"]], "CIME.tests.test_sys_cime_case module": [[14, "cime-tests-test-sys-cime-case-module"]], "CIME.tests.test_sys_cime_performance module": [[14, "cime-tests-test-sys-cime-performance-module"]], "CIME.tests.test_sys_create_newcase module": [[14, "cime-tests-test-sys-create-newcase-module"]], "CIME.tests.test_sys_full_system module": [[14, "cime-tests-test-sys-full-system-module"]], "CIME.tests.test_sys_grid_generation module": [[14, "cime-tests-test-sys-grid-generation-module"]], "CIME.tests.test_sys_jenkins_generic_job module": [[14, "cime-tests-test-sys-jenkins-generic-job-module"]], "CIME.tests.test_sys_manage_and_query module": [[14, "cime-tests-test-sys-manage-and-query-module"]], "CIME.tests.test_sys_query_config module": [[14, "cime-tests-test-sys-query-config-module"]], "CIME.tests.test_sys_run_restart module": [[14, "cime-tests-test-sys-run-restart-module"]], "CIME.tests.test_sys_save_timings module": [[14, "cime-tests-test-sys-save-timings-module"]], "CIME.tests.test_sys_single_submit module": [[14, "cime-tests-test-sys-single-submit-module"]], "CIME.tests.test_sys_test_scheduler module": [[14, "cime-tests-test-sys-test-scheduler-module"]], "CIME.tests.test_sys_unittest module": [[14, "cime-tests-test-sys-unittest-module"]], "CIME.tests.test_sys_user_concurrent_mods module": [[14, "cime-tests-test-sys-user-concurrent-mods-module"]], "CIME.tests.test_sys_wait_for_tests module": [[14, "cime-tests-test-sys-wait-for-tests-module"]], "CIME.tests.test_unit_aprun module": [[14, "cime-tests-test-unit-aprun-module"]], "CIME.tests.test_unit_baselines_performance module": [[14, "cime-tests-test-unit-baselines-performance-module"]], "CIME.tests.test_unit_bless_test_results module": [[14, "cime-tests-test-unit-bless-test-results-module"]], "CIME.tests.test_unit_case module": [[14, "cime-tests-test-unit-case-module"]], "CIME.tests.test_unit_case_fake module": [[14, "module-CIME.tests.test_unit_case_fake"]], "CIME.tests.test_unit_case_run module": [[14, "cime-tests-test-unit-case-run-module"]], "CIME.tests.test_unit_case_setup module": [[14, "cime-tests-test-unit-case-setup-module"]], "CIME.tests.test_unit_compare_test_results module": [[14, "cime-tests-test-unit-compare-test-results-module"]], "CIME.tests.test_unit_compare_two module": [[14, "cime-tests-test-unit-compare-two-module"]], "CIME.tests.test_unit_config module": [[14, "cime-tests-test-unit-config-module"]], "CIME.tests.test_unit_cs_status module": [[14, "cime-tests-test-unit-cs-status-module"]], "CIME.tests.test_unit_custom_assertions_test_status module": [[14, "cime-tests-test-unit-custom-assertions-test-status-module"]], "CIME.tests.test_unit_doctest module": [[14, "cime-tests-test-unit-doctest-module"]], "CIME.tests.test_unit_expected_fails_file module": [[14, "cime-tests-test-unit-expected-fails-file-module"]], "CIME.tests.test_unit_grids module": [[14, "cime-tests-test-unit-grids-module"]], "CIME.tests.test_unit_hist_utils module": [[14, "cime-tests-test-unit-hist-utils-module"]], "CIME.tests.test_unit_locked_files module": [[14, "cime-tests-test-unit-locked-files-module"]], "CIME.tests.test_unit_nmlgen module": [[14, "cime-tests-test-unit-nmlgen-module"]], "CIME.tests.test_unit_paramgen module": [[14, "module-CIME.tests.test_unit_paramgen"]], "CIME.tests.test_unit_system_tests module": [[14, "cime-tests-test-unit-system-tests-module"]], "CIME.tests.test_unit_test_status module": [[14, "cime-tests-test-unit-test-status-module"]], "CIME.tests.test_unit_two_link_to_case2_output module": [[14, "cime-tests-test-unit-two-link-to-case2-output-module"]], "CIME.tests.test_unit_user_mod_support module": [[14, "cime-tests-test-unit-user-mod-support-module"]], "CIME.tests.test_unit_user_nl_utils module": [[14, "module-CIME.tests.test_unit_user_nl_utils"]], "CIME.tests.test_unit_utils module": [[14, "cime-tests-test-unit-utils-module"]], "CIME.tests.test_unit_xml_archive_base module": [[14, "cime-tests-test-unit-xml-archive-base-module"]], "CIME.tests.test_unit_xml_env_batch module": [[14, "cime-tests-test-unit-xml-env-batch-module"]], "CIME.tests.test_unit_xml_env_mach_specific module": [[14, "cime-tests-test-unit-xml-env-mach-specific-module"]], "CIME.tests.test_unit_xml_machines module": [[14, "cime-tests-test-unit-xml-machines-module"]], "CIME.tests.test_unit_xml_namelist_definition module": [[14, "cime-tests-test-unit-xml-namelist-definition-module"]], "CIME.tests.test_unit_xml_tests module": [[14, "cime-tests-test-unit-xml-tests-module"]], "CIME.tests.utils module": [[14, "cime-tests-utils-module"]], "CIME.user_mod_support module": [[0, "cime-user-mod-support-module"]], "CIME.utils module": [[0, "cime-utils-module"]], "CIME.wait_for_tests module": [[0, "cime-wait-for-tests-module"]], "CIMEROOT/config/cesm": [[104, "cimeroot-config-cesm"]], "CIMEROOT/config/config_headers.xml": [[105, "cimeroot-config-config-headers-xml"]], "CIMEROOT/config/config_tests.xml": [[105, "cimeroot-config-config-tests-xml"]], "CIMEROOT/config/e3sm": [[108, "cimeroot-config-e3sm"]], "CIMEROOT/src/components/data_comps/datm/cime_config": [[103, "cimeroot-src-components-data-comps-datm-cime-config"]], "CIMEROOT/src/components/data_comps/desp/cime_config": [[109, "cimeroot-src-components-data-comps-desp-cime-config"]], "CIMEROOT/src/components/data_comps/dice/cime_config": [[115, "cimeroot-src-components-data-comps-dice-cime-config"]], "CIMEROOT/src/components/data_comps/dlnd/cime_config": [[111, "cimeroot-src-components-data-comps-dlnd-cime-config"]], "CIMEROOT/src/components/data_comps/docn/cime_config": [[113, "cimeroot-src-components-data-comps-docn-cime-config"]], "CIMEROOT/src/components/data_comps/drof/cime_config": [[114, "cimeroot-src-components-data-comps-drof-cime-config"]], "CIMEROOT/src/components/data_comps/dwav/cime_config": [[116, "cimeroot-src-components-data-comps-dwav-cime-config"]], "CIMEROOT/src/components/stub_comps/satm/cime_config": [[103, "cimeroot-src-components-stub-comps-satm-cime-config"]], "CIMEROOT/src/components/stub_comps/sesp/cime_config": [[109, "cimeroot-src-components-stub-comps-sesp-cime-config"]], "CIMEROOT/src/components/stub_comps/sglc/cime_config": [[112, "cimeroot-src-components-stub-comps-sglc-cime-config"]], "CIMEROOT/src/components/stub_comps/sice/cime_config": [[115, "cimeroot-src-components-stub-comps-sice-cime-config"]], "CIMEROOT/src/components/stub_comps/slnd/cime_config": [[111, "cimeroot-src-components-stub-comps-slnd-cime-config"]], "CIMEROOT/src/components/stub_comps/socn/cime_config": [[113, "cimeroot-src-components-stub-comps-socn-cime-config"]], "CIMEROOT/src/components/stub_comps/srof/cime_config": [[114, "cimeroot-src-components-stub-comps-srof-cime-config"]], "CIMEROOT/src/components/stub_comps/swav/cime_config": [[116, "cimeroot-src-components-stub-comps-swav-cime-config"]], "CIMEROOT/src/components/xcpl_comps/xatm/cime_config": [[103, "cimeroot-src-components-xcpl-comps-xatm-cime-config"]], "CIMEROOT/src/components/xcpl_comps/xglc/cime_config": [[112, "cimeroot-src-components-xcpl-comps-xglc-cime-config"]], "CIMEROOT/src/components/xcpl_comps/xice/cime_config": [[115, "cimeroot-src-components-xcpl-comps-xice-cime-config"]], "CIMEROOT/src/components/xcpl_comps/xlnd/cime_config": [[111, "cimeroot-src-components-xcpl-comps-xlnd-cime-config"]], "CIMEROOT/src/components/xcpl_comps/xocn/cime_config": [[113, "cimeroot-src-components-xcpl-comps-xocn-cime-config"]], "CIMEROOT/src/components/xcpl_comps/xrof/cime_config": [[114, "cimeroot-src-components-xcpl-comps-xrof-cime-config"]], "CIMEROOT/src/components/xcpl_comps/xwav/cime_config": [[116, "cimeroot-src-components-xcpl-comps-xwav-cime-config"]], "CIMEROOT/src/drivers/mct/cime_config": [[107, "cimeroot-src-drivers-mct-cime-config"]], "CIMEROOT/src/drivers/mct/cime_config/namelist_definition_*.xml": [[107, "cimeroot-src-drivers-mct-cime-config-namelist-definition-xml"]], "CISM": [[79, "cism"]], "CLM": [[79, "clm"]], "Calling case.build": [[78, "calling-case-build"]], "Calling case.setup": [[96, "calling-case-setup"]], "Calling case.submit": [[95, "calling-case-submit"]], "Calling create_newcase": [[87, "calling-create-newcase"]], "Case Resource Allocation": [[93, "case-resource-allocation"]], "Cloning a Case": [[84, "cloning-a-case"]], "Common XML Files": [[105, "common-xml-files"]], "Comparing a baseline": [[97, "comparing-a-baseline"]], "Compiler settings": [[91, "compiler-settings"]], "Component sets": [[86, "component-sets"]], "Component specific settings in a compset": [[86, "component-specific-settings-in-a-compset"]], "Components": [[85, "components"]], "Compset longname": [[86, "compset-longname"]], "Configuration": [[85, "configuration"]], "Configuring the Case Control System": [[89, "configuring-the-case-control-system"]], "Controlling output data": [[95, "controlling-output-data"]], "Controlling processors and threads": [[93, "controlling-processors-and-threads"]], "Controlling timers": [[98, "controlling-timers"]], "Coupling": [[73, "coupling"]], "Create_test output": [[97, "create-test-output"]], "Creating New Compsets": [[86, "creating-new-compsets"]], "Creating a Case": [[87, "creating-a-case"]], "Creating a baseline": [[97, "creating-a-baseline"]], "Creating or obtaining a summary file:": [[75, "creating-or-obtaining-a-summary-file"]], "Creating test runs:": [[75, "creating-test-runs"]], "Customizing CESM active component-specific namelist settings": [[79, "customizing-cesm-active-component-specific-namelist-settings"]], "Customizing data model input variable and stream files": [[79, "customizing-data-model-input-variable-and-stream-files"]], "Customizing driver input variables": [[79, "customizing-driver-input-variables"]], "Customizing your input variables": [[79, "customizing-your-input-variables"]], "Data Assimilation and other External Processing": [[95, "data-assimilation-and-other-external-processing"]], "Data Assimilation scripts": [[95, "data-assimilation-scripts"]], "Data Atmosphere (DATM)": [[79, "data-atmosphere-datm"]], "Data Land (DLND)": [[79, "data-land-dlnd"]], "Data Ocean (DOCN)": [[79, "data-ocean-docn"]], "Data River (DROF)": [[79, "data-river-drof"]], "Data Sea-ice (DICE)": [[79, "data-sea-ice-dice"]], "Data, Stub and Driver Component XML Files": [[106, "data-stub-and-driver-component-xml-files"]], "Defining a test class in order to define setUp and tearDown methods": [[100, "defining-a-test-class-in-order-to-define-setup-and-teardown-methods"]], "Defining the machine": [[91, "defining-the-machine"]], "Development": [[73, "development"], [102, "development"]], "Directory content": [[82, "directory-content"]], "Discovering available pre-defined compsets with query_config": [[90, "discovering-available-pre-defined-compsets-with-query-config"]], "Distributed Input Data Repositories": [[95, "distributed-input-data-repositories"]], "Documentation of the unit test build system": [[100, "documentation-of-the-unit-test-build-system"]], "Driver XML Files": [[107, "driver-xml-files"]], "E3SM Coupled Model XML Files": [[108, "e3sm-coupled-model-xml-files"]], "Entries in env_mach_pes.xml": [[93, "id3"]], "Extending the Load Balancing Tool": [[77, "extending-the-load-balancing-tool"]], "Files and Directories": [[73, "files-and-directories"]], "Finding more documentation and examples": [[100, "finding-more-documentation-and-examples"]], "Fortran Unit Testing": [[100, "fortran-unit-testing"]], "General": [[73, "general"]], "General guidelines for writing unit tests": [[100, "general-guidelines-for-writing-unit-tests"]], "Glossary": [[73, "glossary"]], "Grid longname": [[88, "grid-longname"]], "How does CIME load customizations?": [[81, "how-does-cime-load-customizations"]], "How to add unit testing support on your machine": [[100, "how-to-add-unit-testing-support-on-your-machine"]], "How to write a new unit test": [[100, "how-to-write-a-new-unit-test"]], "Indices and tables": [[70, "indices-and-tables"], [76, "indices-and-tables"], [89, "indices-and-tables"]], "Input data": [[78, "input-data"], [95, "input-data"]], "Introduction": [[71, "introduction"], [90, "introduction"], [100, "introduction"]], "Key Terms and concepts": [[90, "key-terms-and-concepts"]], "Locked files in your case directory": [[87, "locked-files-in-your-case-directory"]], "Long-term archiving": [[95, "long-term-archiving"]], "MOSART": [[79, "mosart"]], "Main 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diff --git a/versions/master/html/users_guide/cime-dir.html b/versions/master/html/users_guide/cime-dir.html
index 27781998cf6..fa8e149d7cc 100644
--- a/versions/master/html/users_guide/cime-dir.html
+++ b/versions/master/html/users_guide/cime-dir.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>10. Directory content &mdash; CIME master documentation</title>
+  <title>11. Directory content &mdash; CIME master documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
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@@ -23,7 +23,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
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     <link rel="next" title="Building a Coupled Model with CIME" href="../build_cpl/index.html" />
-    <link rel="prev" title="9. Workflows" href="workflows.html" /> 
+    <link rel="prev" title="10. Workflows" href="workflows.html" /> 
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@@ -53,15 +53,16 @@
 <li class="toctree-l1"><a class="reference internal" href="index.html">Using the Case Control System</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="index.html#configuring-the-case-control-system">Configuring the Case Control System</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="cime-internals.html">1. Main Configuration File</a></li>
-<li class="toctree-l2"><a class="reference internal" href="compsets.html">2. Component sets</a></li>
-<li class="toctree-l2"><a class="reference internal" href="grids.html">3. Model grids</a></li>
-<li class="toctree-l2"><a class="reference internal" href="machine.html">4. Defining the machine</a></li>
-<li class="toctree-l2"><a class="reference internal" href="pes-threads.html">5. Controlling processors and threads</a></li>
-<li class="toctree-l2"><a class="reference internal" href="porting-cime.html">6. Porting and validating CIME on a new platform</a></li>
-<li class="toctree-l2"><a class="reference internal" href="unit_testing.html">7. Fortran Unit Testing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="multi-instance.html">8. Multi-instance component functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="workflows.html">9. Workflows</a></li>
-<li class="toctree-l2 current"><a class="current reference internal" href="#">10. Directory content</a></li>
+<li class="toctree-l2"><a class="reference internal" href="components.html">2. Components</a></li>
+<li class="toctree-l2"><a class="reference internal" href="compsets.html">3. Component sets</a></li>
+<li class="toctree-l2"><a class="reference internal" href="grids.html">4. Model grids</a></li>
+<li class="toctree-l2"><a class="reference internal" href="machine.html">5. Defining the machine</a></li>
+<li class="toctree-l2"><a class="reference internal" href="pes-threads.html">6. Controlling processors and threads</a></li>
+<li class="toctree-l2"><a class="reference internal" href="porting-cime.html">7. Porting and validating CIME on a new platform</a></li>
+<li class="toctree-l2"><a class="reference internal" href="unit_testing.html">8. Fortran Unit Testing</a></li>
+<li class="toctree-l2"><a class="reference internal" href="multi-instance.html">9. Multi-instance component functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="workflows.html">10. Workflows</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">11. Directory content</a></li>
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@@ -91,7 +92,7 @@
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           <li class="breadcrumb-item"><a href="index.html">Using the Case Control System</a></li>
-      <li class="breadcrumb-item active"><span class="section-number">10. </span>Directory content</li>
+      <li class="breadcrumb-item active"><span class="section-number">11. </span>Directory content</li>
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@@ -102,7 +103,7 @@
            <div itemprop="articleBody">
              
   <section id="directory-content">
-<span id="cime-dir"></span><h1><span class="section-number">10. </span>Directory content<a class="headerlink" href="#directory-content" title="Link to this heading"></a></h1>
+<span id="cime-dir"></span><h1><span class="section-number">11. </span>Directory content<a class="headerlink" href="#directory-content" title="Link to this heading"></a></h1>
 <p>If you use CIME as part of a climate model or standalone, the content of the <strong>cime</strong> directory is the same.</p>
 <p>If you are using it as part of a climate model, <strong>cime</strong> is usually one of the first subdirectories under the main directory.</p>
 <table class="docutils align-default" id="id1">
@@ -195,7 +196,7 @@
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index f557ecde435..b7b6516f57a 100644
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@@ -53,15 +53,16 @@
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-<li class="toctree-l2"><a class="reference internal" href="multi-instance.html">8. Multi-instance component functionality</a></li>
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-<li class="toctree-l2"><a class="reference internal" href="cime-dir.html">10. Directory content</a></li>
+<li class="toctree-l2"><a class="reference internal" href="components.html">2. Components</a></li>
+<li class="toctree-l2"><a class="reference internal" href="compsets.html">3. Component sets</a></li>
+<li class="toctree-l2"><a class="reference internal" href="grids.html">4. Model grids</a></li>
+<li class="toctree-l2"><a class="reference internal" href="machine.html">5. Defining the machine</a></li>
+<li class="toctree-l2"><a class="reference internal" href="pes-threads.html">6. Controlling processors and threads</a></li>
+<li class="toctree-l2"><a class="reference internal" href="porting-cime.html">7. Porting and validating CIME on a new platform</a></li>
+<li class="toctree-l2"><a class="reference internal" href="unit_testing.html">8. Fortran Unit Testing</a></li>
+<li class="toctree-l2"><a class="reference internal" href="multi-instance.html">9. Multi-instance component functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="workflows.html">10. Workflows</a></li>
+<li class="toctree-l2"><a class="reference internal" href="cime-dir.html">11. Directory content</a></li>
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new file mode 100644
index 00000000000..4b189fdd248
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+<!DOCTYPE html>
+<html class="writer-html5" lang="en" data-content_root="../">
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+<li class="toctree-l1"><a class="reference internal" href="../what_cime/index.html">What is CIME?</a></li>
+<li class="toctree-l1"><a class="reference internal" href="index.html">Using the Case Control System</a></li>
+<li class="toctree-l1 current"><a class="reference internal" href="index.html#configuring-the-case-control-system">Configuring the Case Control System</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="cime-internals.html">1. Main Configuration File</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">2. Components</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#configuration">2.1. Configuration</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#triggering-a-rebuild">2.2. Triggering a rebuild</a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="compsets.html">3. Component sets</a></li>
+<li class="toctree-l2"><a class="reference internal" href="grids.html">4. Model grids</a></li>
+<li class="toctree-l2"><a class="reference internal" href="machine.html">5. Defining the machine</a></li>
+<li class="toctree-l2"><a class="reference internal" href="pes-threads.html">6. Controlling processors and threads</a></li>
+<li class="toctree-l2"><a class="reference internal" href="porting-cime.html">7. Porting and validating CIME on a new platform</a></li>
+<li class="toctree-l2"><a class="reference internal" href="unit_testing.html">8. Fortran Unit Testing</a></li>
+<li class="toctree-l2"><a class="reference internal" href="multi-instance.html">9. Multi-instance component functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="workflows.html">10. Workflows</a></li>
+<li class="toctree-l2"><a class="reference internal" href="cime-dir.html">11. Directory content</a></li>
+<li class="toctree-l2"><a class="reference internal" href="index.html#indices-and-tables">Indices and tables</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="../build_cpl/index.html">Building a Coupled Model with CIME</a></li>
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+          <li class="breadcrumb-item"><a href="index.html">Using the Case Control System</a></li>
+      <li class="breadcrumb-item active"><span class="section-number">2. </span>Components</li>
+      <li class="wy-breadcrumbs-aside">
+            <a href="../_sources/users_guide/components.rst.txt" rel="nofollow"> View page source</a>
+      </li>
+  </ul>
+  <hr/>
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+             
+  <section id="components">
+<span id="id1"></span><h1><span class="section-number">2. </span>Components<a class="headerlink" href="#components" title="Link to this heading"></a></h1>
+<p>A single component in the smallest unit within a model. Multiple components make up a component set.</p>
+<section id="configuration">
+<h2><span class="section-number">2.1. </span>Configuration<a class="headerlink" href="#configuration" title="Link to this heading"></a></h2>
+<p>The configuration for a component can be found under <cite>cime_config</cite> in the component directory.</p>
+<p>Example contents of a components <cite>config_component.xml</cite>.</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>&lt;?xml version=&quot;1.0&quot;?&gt;
+
+&lt;?xml-stylesheet type=&quot;text/xsl&quot; href=&quot;entry_id.xsl&quot; ?&gt;
+
+&lt;entry_id version=&quot;3.0&quot;&gt;
+  &lt;description&gt;
+    &lt;desc atm=&quot;SATM&quot;&gt;Stub atm component&lt;/desc&gt;
+  &lt;/description&gt;
+
+  &lt;entry id=&quot;COMP_ATM&quot;&gt;
+    &lt;type&gt;char&lt;/type&gt;
+    &lt;valid_values&gt;satm&lt;/valid_values&gt;
+    &lt;default_value&gt;satm&lt;/default_value&gt;
+    &lt;group&gt;case_comp&lt;/group&gt;
+    &lt;file&gt;env_case.xml&lt;/file&gt;
+    &lt;desc&gt;Name of atmosphere component&lt;/desc&gt;
+  &lt;/entry&gt;
+
+
+  &lt;help&gt;
+    =========================================
+    SATM naming conventions in compset name
+    =========================================
+  &lt;/help&gt;
+
+&lt;/entry_id&gt;
+</pre></div>
+</div>
+</section>
+<section id="triggering-a-rebuild">
+<h2><span class="section-number">2.2. </span>Triggering a rebuild<a class="headerlink" href="#triggering-a-rebuild" title="Link to this heading"></a></h2>
+<p>It’s the responsibility of a component to define which settings will require a component to be rebuilt.</p>
+<p>These triggers can be defined as follows.</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">&lt;</span><span class="n">entry</span> <span class="nb">id</span><span class="o">=</span><span class="s2">&quot;REBUILD_TRIGGER_ATM&quot;</span><span class="o">&gt;</span>
+  <span class="o">&lt;</span><span class="nb">type</span><span class="o">&gt;</span><span class="n">char</span><span class="o">&lt;/</span><span class="nb">type</span><span class="o">&gt;</span>
+  <span class="o">&lt;</span><span class="n">default_value</span><span class="o">&gt;</span><span class="n">NTASKS</span><span class="p">,</span><span class="n">NTHREADS</span><span class="p">,</span><span class="n">NINST</span><span class="o">&lt;/</span><span class="n">default_value</span><span class="o">&gt;</span>
+  <span class="o">&lt;</span><span class="n">group</span><span class="o">&gt;</span><span class="n">rebuild_triggers</span><span class="o">&lt;/</span><span class="n">group</span><span class="o">&gt;</span>
+  <span class="o">&lt;</span><span class="n">file</span><span class="o">&gt;</span><span class="n">env_build</span><span class="o">.</span><span class="n">xml</span><span class="o">&lt;/</span><span class="n">file</span><span class="o">&gt;</span>
+  <span class="o">&lt;</span><span class="n">desc</span><span class="o">&gt;</span><span class="n">Settings</span> <span class="n">that</span> <span class="n">will</span> <span class="n">trigger</span> <span class="n">a</span> <span class="n">rebuild</span><span class="o">&lt;/</span><span class="n">desc</span><span class="o">&gt;</span>
+<span class="o">&lt;/</span><span class="n">entry</span><span class="o">&gt;</span>
+</pre></div>
+</div>
+<p>If a user was to change <cite>NTASKS</cite>, <cite>NTHREADS</cite>, or <cite>NINST</cite> in a case using the component, then a rebuild would be required before the case could be submitted again.</p>
+</section>
+</section>
+
+
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+          <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
+        <a href="cime-internals.html" class="btn btn-neutral float-left" title="1. Main Configuration File" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
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diff --git a/versions/master/html/users_guide/compsets.html b/versions/master/html/users_guide/compsets.html
index b01f969d39e..11aaec53035 100644
--- a/versions/master/html/users_guide/compsets.html
+++ b/versions/master/html/users_guide/compsets.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>2. Component sets &mdash; CIME master documentation</title>
+  <title>3. Component sets &mdash; CIME master documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
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@@ -22,8 +22,8 @@
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-    <link rel="next" title="3. Model grids" href="grids.html" />
-    <link rel="prev" title="1. Main Configuration File" href="cime-internals.html" /> 
+    <link rel="next" title="4. Model grids" href="grids.html" />
+    <link rel="prev" title="2. Components" href="components.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -53,20 +53,21 @@
 <li class="toctree-l1"><a class="reference internal" href="index.html">Using the Case Control System</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="index.html#configuring-the-case-control-system">Configuring the Case Control System</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="cime-internals.html">1. Main Configuration File</a></li>
-<li class="toctree-l2 current"><a class="current reference internal" href="#">2. Component sets</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="#compset-longname">2.1. Compset longname</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#component-specific-settings-in-a-compset">2.2. Component specific settings in a compset</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#creating-new-compsets">2.3. Creating New Compsets</a></li>
+<li class="toctree-l2"><a class="reference internal" href="components.html">2. Components</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">3. Component sets</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#compset-longname">3.1. Compset longname</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#component-specific-settings-in-a-compset">3.2. Component specific settings in a compset</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#creating-new-compsets">3.3. Creating New Compsets</a></li>
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="grids.html">3. Model grids</a></li>
-<li class="toctree-l2"><a class="reference internal" href="machine.html">4. Defining the machine</a></li>
-<li class="toctree-l2"><a class="reference internal" href="pes-threads.html">5. Controlling processors and threads</a></li>
-<li class="toctree-l2"><a class="reference internal" href="porting-cime.html">6. Porting and validating CIME on a new platform</a></li>
-<li class="toctree-l2"><a class="reference internal" href="unit_testing.html">7. Fortran Unit Testing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="multi-instance.html">8. Multi-instance component functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="workflows.html">9. Workflows</a></li>
-<li class="toctree-l2"><a class="reference internal" href="cime-dir.html">10. Directory content</a></li>
+<li class="toctree-l2"><a class="reference internal" href="grids.html">4. Model grids</a></li>
+<li class="toctree-l2"><a class="reference internal" href="machine.html">5. Defining the machine</a></li>
+<li class="toctree-l2"><a class="reference internal" href="pes-threads.html">6. Controlling processors and threads</a></li>
+<li class="toctree-l2"><a class="reference internal" href="porting-cime.html">7. Porting and validating CIME on a new platform</a></li>
+<li class="toctree-l2"><a class="reference internal" href="unit_testing.html">8. Fortran Unit Testing</a></li>
+<li class="toctree-l2"><a class="reference internal" href="multi-instance.html">9. Multi-instance component functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="workflows.html">10. Workflows</a></li>
+<li class="toctree-l2"><a class="reference internal" href="cime-dir.html">11. Directory content</a></li>
 <li class="toctree-l2"><a class="reference internal" href="index.html#indices-and-tables">Indices and tables</a></li>
 </ul>
 </li>
@@ -96,7 +97,7 @@
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       <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
           <li class="breadcrumb-item"><a href="index.html">Using the Case Control System</a></li>
-      <li class="breadcrumb-item active"><span class="section-number">2. </span>Component sets</li>
+      <li class="breadcrumb-item active"><span class="section-number">3. </span>Component sets</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/users_guide/compsets.rst.txt" rel="nofollow"> View page source</a>
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@@ -107,7 +108,7 @@
            <div itemprop="articleBody">
              
   <section id="component-sets">
-<span id="compsets"></span><h1><span class="section-number">2. </span>Component sets<a class="headerlink" href="#component-sets" title="Link to this heading"></a></h1>
+<span id="compsets"></span><h1><span class="section-number">3. </span>Component sets<a class="headerlink" href="#component-sets" title="Link to this heading"></a></h1>
 <p>In CIME, multiple components can define compsets that are targeted to their model development needs.</p>
 <p>Each component supports a set of compset longnames that are used in testing and supported in out of the box configurations.</p>
 <p>To determine if the compset name to <a class="reference external" href="../Tools_user/create_newcase.html">create_newcase</a> is a supported component, CIME looks in the <strong>config_files.xml</strong> file and parses the
@@ -139,7 +140,7 @@
 is defined, using the above example, in <code class="docutils literal notranslate"><span class="pre">$SRCROOT/components/cam/cime_config/config_compsets.xml</span></code>
 In a compset where all components are prognostic, the primary component will be <strong>allactive</strong>.</p>
 <section id="compset-longname">
-<span id="defining-compsets"></span><h2><span class="section-number">2.1. </span>Compset longname<a class="headerlink" href="#compset-longname" title="Link to this heading"></a></h2>
+<span id="defining-compsets"></span><h2><span class="section-number">3.1. </span>Compset longname<a class="headerlink" href="#compset-longname" title="Link to this heading"></a></h2>
 <p>Each config_compsets.xml file has a list of allowed component sets in the form of a longname and an alias.</p>
 <p>A compset longname has this form:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">TIME_ATM</span><span class="p">[</span><span class="o">%</span><span class="n">phys</span><span class="p">]</span><span class="n">_LND</span><span class="p">[</span><span class="o">%</span><span class="n">phys</span><span class="p">]</span><span class="n">_ICE</span><span class="p">[</span><span class="o">%</span><span class="n">phys</span><span class="p">]</span><span class="n">_OCN</span><span class="p">[</span><span class="o">%</span><span class="n">phys</span><span class="p">]</span><span class="n">_ROF</span><span class="p">[</span><span class="o">%</span><span class="n">phys</span><span class="p">]</span><span class="n">_GLC</span><span class="p">[</span><span class="o">%</span><span class="n">phys</span><span class="p">]</span><span class="n">_WAV</span><span class="p">[</span><span class="o">%</span><span class="n">phys</span><span class="p">]</span><span class="n">_ESP</span><span class="p">[</span><span class="n">_BGC</span><span class="o">%</span><span class="n">phys</span><span class="p">]</span>
@@ -166,7 +167,7 @@
 <strong>All</strong> data models have a %phys option that corresponds to the data model mode.</p>
 </section>
 <section id="component-specific-settings-in-a-compset">
-<span id="defining-component-specific-compset-settings"></span><h2><span class="section-number">2.2. </span>Component specific settings in a compset<a class="headerlink" href="#component-specific-settings-in-a-compset" title="Link to this heading"></a></h2>
+<span id="defining-component-specific-compset-settings"></span><h2><span class="section-number">3.2. </span>Component specific settings in a compset<a class="headerlink" href="#component-specific-settings-in-a-compset" title="Link to this heading"></a></h2>
 <p>Every model component also contains a <strong>config_component.xml</strong> file that has two functions:</p>
 <ol class="arabic simple">
 <li><p>Specifying the component-specific definitions of what can appear after the <code class="docutils literal notranslate"><span class="pre">%</span></code> in the compset longname, (for example, <code class="docutils literal notranslate"><span class="pre">DOM</span></code> in <code class="docutils literal notranslate"><span class="pre">DOCN%DOM</span></code>).</p></li>
@@ -217,7 +218,7 @@
 <p>To list the possible values, use the <a class="reference external" href="../Tools_user/query_config.html">query_config –component datm</a> command.</p>
 </section>
 <section id="creating-new-compsets">
-<span id="id1"></span><h2><span class="section-number">2.3. </span>Creating New Compsets<a class="headerlink" href="#creating-new-compsets" title="Link to this heading"></a></h2>
+<span id="id1"></span><h2><span class="section-number">3.3. </span>Creating New Compsets<a class="headerlink" href="#creating-new-compsets" title="Link to this heading"></a></h2>
 <p>A description of how CIME interprets a compset name is given in the section <a class="reference internal" href="#defining-compsets"><span class="std std-ref">Compset longname</span></a> .</p>
 <p>To create a new compset, you will at a minimum have to:</p>
 <ol class="arabic simple">
@@ -283,8 +284,8 @@
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-        <a href="grids.html" class="btn btn-neutral float-right" title="3. Model grids" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
+        <a href="components.html" class="btn btn-neutral float-left" title="2. Components" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
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index ab3400013ea..88d61f5c7ac 100644
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   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>3. Model grids &mdash; CIME master documentation</title>
+  <title>4. Model grids &mdash; CIME master documentation</title>
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 <li class="toctree-l1"><a class="reference internal" href="index.html">Using the Case Control System</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="index.html#configuring-the-case-control-system">Configuring the Case Control System</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="cime-internals.html">1. Main Configuration File</a></li>
-<li class="toctree-l2"><a class="reference internal" href="compsets.html">2. Component sets</a></li>
-<li class="toctree-l2 current"><a class="current reference internal" href="#">3. Model grids</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="#grid-longname">3.1. Grid longname</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#adding-grids">3.2. Adding grids</a></li>
+<li class="toctree-l2"><a class="reference internal" href="components.html">2. Components</a></li>
+<li class="toctree-l2"><a class="reference internal" href="compsets.html">3. Component sets</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">4. Model grids</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#grid-longname">4.1. Grid longname</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#adding-grids">4.2. Adding grids</a></li>
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="machine.html">4. Defining the machine</a></li>
-<li class="toctree-l2"><a class="reference internal" href="pes-threads.html">5. Controlling processors and threads</a></li>
-<li class="toctree-l2"><a class="reference internal" href="porting-cime.html">6. Porting and validating CIME on a new platform</a></li>
-<li class="toctree-l2"><a class="reference internal" href="unit_testing.html">7. Fortran Unit Testing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="multi-instance.html">8. Multi-instance component functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="workflows.html">9. Workflows</a></li>
-<li class="toctree-l2"><a class="reference internal" href="cime-dir.html">10. Directory content</a></li>
+<li class="toctree-l2"><a class="reference internal" href="machine.html">5. Defining the machine</a></li>
+<li class="toctree-l2"><a class="reference internal" href="pes-threads.html">6. Controlling processors and threads</a></li>
+<li class="toctree-l2"><a class="reference internal" href="porting-cime.html">7. Porting and validating CIME on a new platform</a></li>
+<li class="toctree-l2"><a class="reference internal" href="unit_testing.html">8. Fortran Unit Testing</a></li>
+<li class="toctree-l2"><a class="reference internal" href="multi-instance.html">9. Multi-instance component functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="workflows.html">10. Workflows</a></li>
+<li class="toctree-l2"><a class="reference internal" href="cime-dir.html">11. Directory content</a></li>
 <li class="toctree-l2"><a class="reference internal" href="index.html#indices-and-tables">Indices and tables</a></li>
 </ul>
 </li>
@@ -95,7 +96,7 @@
   <ul class="wy-breadcrumbs">
       <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
           <li class="breadcrumb-item"><a href="index.html">Using the Case Control System</a></li>
-      <li class="breadcrumb-item active"><span class="section-number">3. </span>Model grids</li>
+      <li class="breadcrumb-item active"><span class="section-number">4. </span>Model grids</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/users_guide/grids.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -106,7 +107,7 @@
            <div itemprop="articleBody">
              
   <section id="model-grids">
-<span id="grids"></span><h1><span class="section-number">3. </span>Model grids<a class="headerlink" href="#model-grids" title="Link to this heading"></a></h1>
+<span id="grids"></span><h1><span class="section-number">4. </span>Model grids<a class="headerlink" href="#model-grids" title="Link to this heading"></a></h1>
 <p>CIME looks at the xml node <code class="docutils literal notranslate"><span class="pre">GRIDS_SPEC_FILE</span></code> in  <strong>$CIMEROOT/config/$models/config_files.xml</strong> file to identify supported out-of-the-box model grids for the target model.</p>
 <p>The node has the following contents:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span>&lt;entry id=&quot;GRIDS_SPEC_FILE&quot;&gt;
@@ -120,7 +121,7 @@
 </pre></div>
 </div>
 <section id="grid-longname">
-<h2><span class="section-number">3.1. </span>Grid longname<a class="headerlink" href="#grid-longname" title="Link to this heading"></a></h2>
+<h2><span class="section-number">4.1. </span>Grid longname<a class="headerlink" href="#grid-longname" title="Link to this heading"></a></h2>
 <p>CIME model grids generally are associated with a specific combination of atmosphere, land, land-ice, river-runoff and ocean/ice grids. The naming convention for these grids uses only atmosphere, land, and ocean/ice grid specifications.</p>
 <p>A model grid longname has the form:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">a</span><span class="o">%</span><span class="n">name_l</span><span class="o">%</span><span class="n">name_oi</span><span class="o">%</span><span class="n">name_r</span><span class="o">%</span><span class="n">name_m</span><span class="o">%</span><span class="n">mask_g</span><span class="o">%</span><span class="n">name_w</span><span class="o">%</span><span class="n">name</span>
@@ -163,7 +164,7 @@ <h2><span class="section-number">3.1. </span>Grid longname<a class="headerlink"
 </ul>
 </section>
 <section id="adding-grids">
-<span id="adding-cases"></span><h2><span class="section-number">3.2. </span>Adding grids<a class="headerlink" href="#adding-grids" title="Link to this heading"></a></h2>
+<span id="adding-cases"></span><h2><span class="section-number">4.2. </span>Adding grids<a class="headerlink" href="#adding-grids" title="Link to this heading"></a></h2>
 <dl id="adding-a-grid">
 <dt>CIME supports numerous out-of-the box model resolutions. To see the grids that are supported, call <a class="reference external" href="../Tools_user/query_config.html">query_config</a> as shown below.</dt><dd><div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">&gt;</span> <span class="n">query_config</span> <span class="o">--</span><span class="n">grids</span>
 </pre></div>
@@ -310,8 +311,8 @@ <h2><span class="section-number">3.1. </span>Grid longname<a class="headerlink"
            </div>
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="compsets.html" class="btn btn-neutral float-left" title="2. Component sets" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
-        <a href="machine.html" class="btn btn-neutral float-right" title="4. Defining the machine" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
+        <a href="compsets.html" class="btn btn-neutral float-left" title="3. Component sets" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+        <a href="machine.html" class="btn btn-neutral float-right" title="5. Defining the machine" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
     </div>
 
   <hr/>
diff --git a/versions/master/html/users_guide/index.html b/versions/master/html/users_guide/index.html
index cc18b8e444e..ef535b0f965 100644
--- a/versions/master/html/users_guide/index.html
+++ b/versions/master/html/users_guide/index.html
@@ -66,15 +66,16 @@
 </li>
 <li class="toctree-l1"><a class="reference internal" href="#configuring-the-case-control-system">Configuring the Case Control System</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="cime-internals.html">1. Main Configuration File</a></li>
-<li class="toctree-l2"><a class="reference internal" href="compsets.html">2. Component sets</a></li>
-<li class="toctree-l2"><a class="reference internal" href="grids.html">3. Model grids</a></li>
-<li class="toctree-l2"><a class="reference internal" href="machine.html">4. Defining the machine</a></li>
-<li class="toctree-l2"><a class="reference internal" href="pes-threads.html">5. Controlling processors and threads</a></li>
-<li class="toctree-l2"><a class="reference internal" href="porting-cime.html">6. Porting and validating CIME on a new platform</a></li>
-<li class="toctree-l2"><a class="reference internal" href="unit_testing.html">7. Fortran Unit Testing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="multi-instance.html">8. Multi-instance component functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="workflows.html">9. Workflows</a></li>
-<li class="toctree-l2"><a class="reference internal" href="cime-dir.html">10. Directory content</a></li>
+<li class="toctree-l2"><a class="reference internal" href="components.html">2. Components</a></li>
+<li class="toctree-l2"><a class="reference internal" href="compsets.html">3. Component sets</a></li>
+<li class="toctree-l2"><a class="reference internal" href="grids.html">4. Model grids</a></li>
+<li class="toctree-l2"><a class="reference internal" href="machine.html">5. Defining the machine</a></li>
+<li class="toctree-l2"><a class="reference internal" href="pes-threads.html">6. Controlling processors and threads</a></li>
+<li class="toctree-l2"><a class="reference internal" href="porting-cime.html">7. Porting and validating CIME on a new platform</a></li>
+<li class="toctree-l2"><a class="reference internal" href="unit_testing.html">8. Fortran Unit Testing</a></li>
+<li class="toctree-l2"><a class="reference internal" href="multi-instance.html">9. Multi-instance component functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="workflows.html">10. Workflows</a></li>
+<li class="toctree-l2"><a class="reference internal" href="cime-dir.html">11. Directory content</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#indices-and-tables">Indices and tables</a></li>
 </ul>
 </li>
@@ -191,54 +192,59 @@
 <div class="toctree-wrapper compound">
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="cime-internals.html">1. Main Configuration File</a></li>
-<li class="toctree-l1"><a class="reference internal" href="compsets.html">2. Component sets</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="compsets.html#compset-longname">2.1. Compset longname</a></li>
-<li class="toctree-l2"><a class="reference internal" href="compsets.html#component-specific-settings-in-a-compset">2.2. Component specific settings in a compset</a></li>
-<li class="toctree-l2"><a class="reference internal" href="compsets.html#creating-new-compsets">2.3. Creating New Compsets</a></li>
+<li class="toctree-l1"><a class="reference internal" href="components.html">2. Components</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="components.html#configuration">2.1. Configuration</a></li>
+<li class="toctree-l2"><a class="reference internal" href="components.html#triggering-a-rebuild">2.2. Triggering a rebuild</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="grids.html">3. Model grids</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="grids.html#grid-longname">3.1. Grid longname</a></li>
-<li class="toctree-l2"><a class="reference internal" href="grids.html#adding-grids">3.2. Adding grids</a></li>
+<li class="toctree-l1"><a class="reference internal" href="compsets.html">3. Component sets</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="compsets.html#compset-longname">3.1. Compset longname</a></li>
+<li class="toctree-l2"><a class="reference internal" href="compsets.html#component-specific-settings-in-a-compset">3.2. Component specific settings in a compset</a></li>
+<li class="toctree-l2"><a class="reference internal" href="compsets.html#creating-new-compsets">3.3. Creating New Compsets</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="machine.html">4. Defining the machine</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="machine.html#config-machines-xml-machine-specific-file">4.1. config_machines.xml - machine specific file</a></li>
-<li class="toctree-l2"><a class="reference internal" href="machine.html#batch-system-definition">4.2. Batch system definition</a></li>
-<li class="toctree-l2"><a class="reference internal" href="machine.html#config-batch-xml-batch-directives">4.3. config_batch.xml - batch directives</a></li>
-<li class="toctree-l2"><a class="reference internal" href="machine.html#compiler-settings">4.4. Compiler settings</a></li>
-<li class="toctree-l2"><a class="reference internal" href="machine.html#config-compilers-xml-compiler-paths-and-options-deprecated-use-cmake-macros">4.5. config_compilers.xml - compiler paths and options <strong>DEPRECATED use cmake_macros</strong></a></li>
+<li class="toctree-l1"><a class="reference internal" href="grids.html">4. Model grids</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="grids.html#grid-longname">4.1. Grid longname</a></li>
+<li class="toctree-l2"><a class="reference internal" href="grids.html#adding-grids">4.2. Adding grids</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="pes-threads.html">5. Controlling processors and threads</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="pes-threads.html#pe-settings-for-a-case">5.1. pe-settings for a case</a></li>
-<li class="toctree-l2"><a class="reference internal" href="pes-threads.html#setting-the-pe-layout">5.2. Setting the PE layout</a></li>
-<li class="toctree-l2"><a class="reference internal" href="pes-threads.html#case-resource-allocation">5.3. Case Resource Allocation</a></li>
-<li class="toctree-l2"><a class="reference internal" href="pes-threads.html#optimizing-processor-layout">5.4. Optimizing processor layout</a></li>
+<li class="toctree-l1"><a class="reference internal" href="machine.html">5. Defining the machine</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="machine.html#config-machines-xml-machine-specific-file">5.1. config_machines.xml - machine specific file</a></li>
+<li class="toctree-l2"><a class="reference internal" href="machine.html#batch-system-definition">5.2. Batch system definition</a></li>
+<li class="toctree-l2"><a class="reference internal" href="machine.html#config-batch-xml-batch-directives">5.3. config_batch.xml - batch directives</a></li>
+<li class="toctree-l2"><a class="reference internal" href="machine.html#compiler-settings">5.4. Compiler settings</a></li>
+<li class="toctree-l2"><a class="reference internal" href="machine.html#config-compilers-xml-compiler-paths-and-options-deprecated-use-cmake-macros">5.5. config_compilers.xml - compiler paths and options <strong>DEPRECATED use cmake_macros</strong></a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="porting-cime.html">6. Porting and validating CIME on a new platform</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="porting-cime.html#required-libraries-packages">6.1. Required libraries/packages</a></li>
-<li class="toctree-l2"><a class="reference internal" href="porting-cime.html#an-mpi-example">6.2. An MPI example</a></li>
-<li class="toctree-l2"><a class="reference internal" href="porting-cime.html#cesm-linux-and-mac-support">6.3. CESM Linux and Mac Support</a></li>
-<li class="toctree-l2"><a class="reference internal" href="porting-cime.html#steps-for-porting">6.4. Steps for porting</a></li>
-<li class="toctree-l2"><a class="reference internal" href="porting-cime.html#validating-a-cesm-port-with-prognostic-components">6.5. Validating a CESM port with prognostic components</a></li>
-<li class="toctree-l2"><a class="reference internal" href="porting-cime.html#performance-tuning-of-a-cesm-port">6.6. Performance tuning of a CESM port</a></li>
+<li class="toctree-l1"><a class="reference internal" href="pes-threads.html">6. Controlling processors and threads</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="pes-threads.html#pe-settings-for-a-case">6.1. pe-settings for a case</a></li>
+<li class="toctree-l2"><a class="reference internal" href="pes-threads.html#setting-the-pe-layout">6.2. Setting the PE layout</a></li>
+<li class="toctree-l2"><a class="reference internal" href="pes-threads.html#case-resource-allocation">6.3. Case Resource Allocation</a></li>
+<li class="toctree-l2"><a class="reference internal" href="pes-threads.html#optimizing-processor-layout">6.4. Optimizing processor layout</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="unit_testing.html">7. Fortran Unit Testing</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="unit_testing.html#introduction">7.1. Introduction</a></li>
-<li class="toctree-l2"><a class="reference internal" href="unit_testing.html#running-cime-s-fortran-unit-tests">7.2. Running CIME’s Fortran unit tests</a></li>
-<li class="toctree-l2"><a class="reference internal" href="unit_testing.html#how-to-add-unit-testing-support-on-your-machine">7.3. How to add unit testing support on your machine</a></li>
-<li class="toctree-l2"><a class="reference internal" href="unit_testing.html#how-to-write-a-new-unit-test">7.4. How to write a new unit test</a></li>
-<li class="toctree-l2"><a class="reference internal" href="unit_testing.html#general-guidelines-for-writing-unit-tests">7.5. General guidelines for writing unit tests</a></li>
-<li class="toctree-l2"><a class="reference internal" href="unit_testing.html#more-details-on-writing-pfunit-based-unit-tests">7.6. More details on writing pFUnit-based unit tests</a></li>
-<li class="toctree-l2"><a class="reference internal" href="unit_testing.html#finding-more-documentation-and-examples">7.7. Finding more documentation and examples</a></li>
+<li class="toctree-l1"><a class="reference internal" href="porting-cime.html">7. Porting and validating CIME on a new platform</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="porting-cime.html#required-libraries-packages">7.1. Required libraries/packages</a></li>
+<li class="toctree-l2"><a class="reference internal" href="porting-cime.html#an-mpi-example">7.2. An MPI example</a></li>
+<li class="toctree-l2"><a class="reference internal" href="porting-cime.html#cesm-linux-and-mac-support">7.3. CESM Linux and Mac Support</a></li>
+<li class="toctree-l2"><a class="reference internal" href="porting-cime.html#steps-for-porting">7.4. Steps for porting</a></li>
+<li class="toctree-l2"><a class="reference internal" href="porting-cime.html#validating-a-cesm-port-with-prognostic-components">7.5. Validating a CESM port with prognostic components</a></li>
+<li class="toctree-l2"><a class="reference internal" href="porting-cime.html#performance-tuning-of-a-cesm-port">7.6. Performance tuning of a CESM port</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="multi-instance.html">8. Multi-instance component functionality</a></li>
-<li class="toctree-l1"><a class="reference internal" href="workflows.html">9. Workflows</a></li>
-<li class="toctree-l1"><a class="reference internal" href="cime-dir.html">10. Directory content</a></li>
+<li class="toctree-l1"><a class="reference internal" href="unit_testing.html">8. Fortran Unit Testing</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="unit_testing.html#introduction">8.1. Introduction</a></li>
+<li class="toctree-l2"><a class="reference internal" href="unit_testing.html#running-cime-s-fortran-unit-tests">8.2. Running CIME’s Fortran unit tests</a></li>
+<li class="toctree-l2"><a class="reference internal" href="unit_testing.html#how-to-add-unit-testing-support-on-your-machine">8.3. How to add unit testing support on your machine</a></li>
+<li class="toctree-l2"><a class="reference internal" href="unit_testing.html#how-to-write-a-new-unit-test">8.4. How to write a new unit test</a></li>
+<li class="toctree-l2"><a class="reference internal" href="unit_testing.html#general-guidelines-for-writing-unit-tests">8.5. General guidelines for writing unit tests</a></li>
+<li class="toctree-l2"><a class="reference internal" href="unit_testing.html#more-details-on-writing-pfunit-based-unit-tests">8.6. More details on writing pFUnit-based unit tests</a></li>
+<li class="toctree-l2"><a class="reference internal" href="unit_testing.html#finding-more-documentation-and-examples">8.7. Finding more documentation and examples</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="multi-instance.html">9. Multi-instance component functionality</a></li>
+<li class="toctree-l1"><a class="reference internal" href="workflows.html">10. Workflows</a></li>
+<li class="toctree-l1"><a class="reference internal" href="cime-dir.html">11. Directory content</a></li>
 </ul>
 </div>
 <section id="indices-and-tables">
diff --git a/versions/master/html/users_guide/machine.html b/versions/master/html/users_guide/machine.html
index 20adc3a4e9a..5867fd790c6 100644
--- a/versions/master/html/users_guide/machine.html
+++ b/versions/master/html/users_guide/machine.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>4. Defining the machine &mdash; CIME master documentation</title>
+  <title>5. Defining the machine &mdash; CIME master documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../_static/custom.css" />
@@ -22,8 +22,8 @@
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="5. Controlling processors and threads" href="pes-threads.html" />
-    <link rel="prev" title="3. Model grids" href="grids.html" /> 
+    <link rel="next" title="6. Controlling processors and threads" href="pes-threads.html" />
+    <link rel="prev" title="4. Model grids" href="grids.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -53,22 +53,23 @@
 <li class="toctree-l1"><a class="reference internal" href="index.html">Using the Case Control System</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="index.html#configuring-the-case-control-system">Configuring the Case Control System</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="cime-internals.html">1. Main Configuration File</a></li>
-<li class="toctree-l2"><a class="reference internal" href="compsets.html">2. Component sets</a></li>
-<li class="toctree-l2"><a class="reference internal" href="grids.html">3. Model grids</a></li>
-<li class="toctree-l2 current"><a class="current reference internal" href="#">4. Defining the machine</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="#config-machines-xml-machine-specific-file">4.1. config_machines.xml - machine specific file</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#batch-system-definition">4.2. Batch system definition</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#config-batch-xml-batch-directives">4.3. config_batch.xml - batch directives</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#compiler-settings">4.4. Compiler settings</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#config-compilers-xml-compiler-paths-and-options-deprecated-use-cmake-macros">4.5. config_compilers.xml - compiler paths and options <strong>DEPRECATED use cmake_macros</strong></a></li>
+<li class="toctree-l2"><a class="reference internal" href="components.html">2. Components</a></li>
+<li class="toctree-l2"><a class="reference internal" href="compsets.html">3. Component sets</a></li>
+<li class="toctree-l2"><a class="reference internal" href="grids.html">4. Model grids</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">5. Defining the machine</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#config-machines-xml-machine-specific-file">5.1. config_machines.xml - machine specific file</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#batch-system-definition">5.2. Batch system definition</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#config-batch-xml-batch-directives">5.3. config_batch.xml - batch directives</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#compiler-settings">5.4. Compiler settings</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#config-compilers-xml-compiler-paths-and-options-deprecated-use-cmake-macros">5.5. config_compilers.xml - compiler paths and options <strong>DEPRECATED use cmake_macros</strong></a></li>
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="pes-threads.html">5. Controlling processors and threads</a></li>
-<li class="toctree-l2"><a class="reference internal" href="porting-cime.html">6. Porting and validating CIME on a new platform</a></li>
-<li class="toctree-l2"><a class="reference internal" href="unit_testing.html">7. Fortran Unit Testing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="multi-instance.html">8. Multi-instance component functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="workflows.html">9. Workflows</a></li>
-<li class="toctree-l2"><a class="reference internal" href="cime-dir.html">10. Directory content</a></li>
+<li class="toctree-l2"><a class="reference internal" href="pes-threads.html">6. Controlling processors and threads</a></li>
+<li class="toctree-l2"><a class="reference internal" href="porting-cime.html">7. Porting and validating CIME on a new platform</a></li>
+<li class="toctree-l2"><a class="reference internal" href="unit_testing.html">8. Fortran Unit Testing</a></li>
+<li class="toctree-l2"><a class="reference internal" href="multi-instance.html">9. Multi-instance component functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="workflows.html">10. Workflows</a></li>
+<li class="toctree-l2"><a class="reference internal" href="cime-dir.html">11. Directory content</a></li>
 <li class="toctree-l2"><a class="reference internal" href="index.html#indices-and-tables">Indices and tables</a></li>
 </ul>
 </li>
@@ -98,7 +99,7 @@
   <ul class="wy-breadcrumbs">
       <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
           <li class="breadcrumb-item"><a href="index.html">Using the Case Control System</a></li>
-      <li class="breadcrumb-item active"><span class="section-number">4. </span>Defining the machine</li>
+      <li class="breadcrumb-item active"><span class="section-number">5. </span>Defining the machine</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/users_guide/machine.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -109,7 +110,7 @@
            <div itemprop="articleBody">
              
   <section id="defining-the-machine">
-<span id="machine"></span><h1><span class="section-number">4. </span>Defining the machine<a class="headerlink" href="#defining-the-machine" title="Link to this heading"></a></h1>
+<span id="machine"></span><h1><span class="section-number">5. </span>Defining the machine<a class="headerlink" href="#defining-the-machine" title="Link to this heading"></a></h1>
 <p>CIME looks at the xml node <code class="docutils literal notranslate"><span class="pre">MACHINE_SPEC_FILE</span></code> in the <strong>config_files.xml</strong> file to identify supported out-of-the-box machines for the target model. The node has the following contents:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span>&lt;entry id=&quot;MACHINES_SPEC_FILE&quot;&gt;
   &lt;type&gt;char&lt;/type&gt;
@@ -123,7 +124,7 @@
 </div>
 <p>You can supplement what is in the MACHINES_SPEC_FILE by adding a config_machines.xml file to your CIME config directory.</p>
 <section id="config-machines-xml-machine-specific-file">
-<span id="machinefile"></span><h2><span class="section-number">4.1. </span>config_machines.xml - machine specific file<a class="headerlink" href="#config-machines-xml-machine-specific-file" title="Link to this heading"></a></h2>
+<span id="machinefile"></span><h2><span class="section-number">5.1. </span>config_machines.xml - machine specific file<a class="headerlink" href="#config-machines-xml-machine-specific-file" title="Link to this heading"></a></h2>
 <p>Each <code class="docutils literal notranslate"><span class="pre">&lt;machine&gt;</span></code> tag requires the following input:</p>
 <ul>
 <li><p><code class="docutils literal notranslate"><span class="pre">DESC</span></code>: a text description of the machine</p></li>
@@ -208,7 +209,7 @@
 </ul>
 </section>
 <section id="batch-system-definition">
-<h2><span class="section-number">4.2. </span>Batch system definition<a class="headerlink" href="#batch-system-definition" title="Link to this heading"></a></h2>
+<h2><span class="section-number">5.2. </span>Batch system definition<a class="headerlink" href="#batch-system-definition" title="Link to this heading"></a></h2>
 <p>CIME looks at the xml node <code class="docutils literal notranslate"><span class="pre">BATCH_SPEC_FILE</span></code> in the <strong>config_files.xml</strong> file to identify supported out-of-the-box batch system details for the target model. The node has the following contents:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span>&lt;entry id=&quot;BATCH_SPEC_FILE&quot;&gt;
   &lt;type&gt;char&lt;/type&gt;
@@ -222,7 +223,7 @@ <h2><span class="section-number">4.2. </span>Batch system definition<a class="he
 </div>
 </section>
 <section id="config-batch-xml-batch-directives">
-<span id="batchfile"></span><h2><span class="section-number">4.3. </span>config_batch.xml - batch directives<a class="headerlink" href="#config-batch-xml-batch-directives" title="Link to this heading"></a></h2>
+<span id="batchfile"></span><h2><span class="section-number">5.3. </span>config_batch.xml - batch directives<a class="headerlink" href="#config-batch-xml-batch-directives" title="Link to this heading"></a></h2>
 <p>The <strong>config_batch.xml</strong> schema is defined in <strong>$CIMEROOT/config/xml_schemas/config_batch.xsd</strong>.</p>
 <p>CIME supports these batch systems: pbs, cobalt, lsf and slurm.</p>
 <p>The entries in <strong>config_batch.xml</strong> are hierarchical.</p>
@@ -243,7 +244,7 @@ <h2><span class="section-number">4.2. </span>Batch system definition<a class="he
 <p>In addition, there is <strong>case.test</strong> job that is used by the CIME system test workflow.</p>
 </section>
 <section id="compiler-settings">
-<span id="defining-compiler-settings"></span><h2><span class="section-number">4.4. </span>Compiler settings<a class="headerlink" href="#compiler-settings" title="Link to this heading"></a></h2>
+<span id="defining-compiler-settings"></span><h2><span class="section-number">5.4. </span>Compiler settings<a class="headerlink" href="#compiler-settings" title="Link to this heading"></a></h2>
 <p>CIME looks at the xml element <code class="docutils literal notranslate"><span class="pre">CMAKE_MACROS_DIR</span></code> in the <strong>config_files.xml</strong> file to identify supported out-of-the-box compiler details for the target model. The node has the following contents:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span>&lt;entry id=&quot;CMAKE_MACROS_DIR&quot;&gt;
   &lt;type&gt;char&lt;/type&gt;
@@ -257,7 +258,7 @@ <h2><span class="section-number">4.2. </span>Batch system definition<a class="he
 <p>Additional compilers are made avilable by adding cmake macros files to the directory pointed to by CMAKE_MACROS_DIR or to your $HOME/.cime directory.</p>
 </section>
 <section id="config-compilers-xml-compiler-paths-and-options-deprecated-use-cmake-macros">
-<span id="compilerfile"></span><h2><span class="section-number">4.5. </span>config_compilers.xml - compiler paths and options <strong>DEPRECATED use cmake_macros</strong><a class="headerlink" href="#config-compilers-xml-compiler-paths-and-options-deprecated-use-cmake-macros" title="Link to this heading"></a></h2>
+<span id="compilerfile"></span><h2><span class="section-number">5.5. </span>config_compilers.xml - compiler paths and options <strong>DEPRECATED use cmake_macros</strong><a class="headerlink" href="#config-compilers-xml-compiler-paths-and-options-deprecated-use-cmake-macros" title="Link to this heading"></a></h2>
 <p>The <strong>config_compilers.xml</strong> file defines compiler flags for building CIME (and also CESM and E3SM prognostic CIME-driven components).</p>
 <ol class="arabic simple">
 <li><p>General compiler flags (e.g., for the gnu compiler) that are machine- and componen-independent are listed first.</p></li>
@@ -296,8 +297,8 @@ <h2><span class="section-number">4.2. </span>Batch system definition<a class="he
            </div>
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diff --git a/versions/master/html/users_guide/multi-instance.html b/versions/master/html/users_guide/multi-instance.html
index 797d2b3e871..a2de4ebb566 100644
--- a/versions/master/html/users_guide/multi-instance.html
+++ b/versions/master/html/users_guide/multi-instance.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>8. Multi-instance component functionality &mdash; CIME master documentation</title>
+  <title>9. Multi-instance component functionality &mdash; CIME master documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
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+    <link rel="next" title="10. Workflows" href="workflows.html" />
+    <link rel="prev" title="8. Fortran Unit Testing" href="unit_testing.html" /> 
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 <body class="wy-body-for-nav"> 
@@ -53,15 +53,16 @@
 <li class="toctree-l1"><a class="reference internal" href="index.html">Using the Case Control System</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="index.html#configuring-the-case-control-system">Configuring the Case Control System</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="cime-internals.html">1. Main Configuration File</a></li>
-<li class="toctree-l2"><a class="reference internal" href="compsets.html">2. Component sets</a></li>
-<li class="toctree-l2"><a class="reference internal" href="grids.html">3. Model grids</a></li>
-<li class="toctree-l2"><a class="reference internal" href="machine.html">4. Defining the machine</a></li>
-<li class="toctree-l2"><a class="reference internal" href="pes-threads.html">5. Controlling processors and threads</a></li>
-<li class="toctree-l2"><a class="reference internal" href="porting-cime.html">6. Porting and validating CIME on a new platform</a></li>
-<li class="toctree-l2"><a class="reference internal" href="unit_testing.html">7. Fortran Unit Testing</a></li>
-<li class="toctree-l2 current"><a class="current reference internal" href="#">8. Multi-instance component functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="workflows.html">9. Workflows</a></li>
-<li class="toctree-l2"><a class="reference internal" href="cime-dir.html">10. Directory content</a></li>
+<li class="toctree-l2"><a class="reference internal" href="components.html">2. Components</a></li>
+<li class="toctree-l2"><a class="reference internal" href="compsets.html">3. Component sets</a></li>
+<li class="toctree-l2"><a class="reference internal" href="grids.html">4. Model grids</a></li>
+<li class="toctree-l2"><a class="reference internal" href="machine.html">5. Defining the machine</a></li>
+<li class="toctree-l2"><a class="reference internal" href="pes-threads.html">6. Controlling processors and threads</a></li>
+<li class="toctree-l2"><a class="reference internal" href="porting-cime.html">7. Porting and validating CIME on a new platform</a></li>
+<li class="toctree-l2"><a class="reference internal" href="unit_testing.html">8. Fortran Unit Testing</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">9. Multi-instance component functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="workflows.html">10. Workflows</a></li>
+<li class="toctree-l2"><a class="reference internal" href="cime-dir.html">11. Directory content</a></li>
 <li class="toctree-l2"><a class="reference internal" href="index.html#indices-and-tables">Indices and tables</a></li>
 </ul>
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@@ -91,7 +92,7 @@
   <ul class="wy-breadcrumbs">
       <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
           <li class="breadcrumb-item"><a href="index.html">Using the Case Control System</a></li>
-      <li class="breadcrumb-item active"><span class="section-number">8. </span>Multi-instance component functionality</li>
+      <li class="breadcrumb-item active"><span class="section-number">9. </span>Multi-instance component functionality</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/users_guide/multi-instance.rst.txt" rel="nofollow"> View page source</a>
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@@ -102,7 +103,7 @@
            <div itemprop="articleBody">
              
   <section id="multi-instance-component-functionality">
-<span id="multi-instance"></span><h1><span class="section-number">8. </span>Multi-instance component functionality<a class="headerlink" href="#multi-instance-component-functionality" title="Link to this heading"></a></h1>
+<span id="multi-instance"></span><h1><span class="section-number">9. </span>Multi-instance component functionality<a class="headerlink" href="#multi-instance-component-functionality" title="Link to this heading"></a></h1>
 <p>The CIME coupling infrastructure is capable of running multiple
 component instances (ensembles) under one model executable.  There are
 two modes of ensemble capability, single driver in which all component
@@ -195,8 +196,8 @@
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           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
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+        <a href="unit_testing.html" class="btn btn-neutral float-left" title="8. Fortran Unit Testing" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
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diff --git a/versions/master/html/users_guide/pes-threads.html b/versions/master/html/users_guide/pes-threads.html
index 65e7ea328ce..edd9b4382bc 100644
--- a/versions/master/html/users_guide/pes-threads.html
+++ b/versions/master/html/users_guide/pes-threads.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>5. Controlling processors and threads &mdash; CIME master documentation</title>
+  <title>6. Controlling processors and threads &mdash; CIME master documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
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@@ -22,8 +22,8 @@
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
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-    <link rel="next" title="6. Porting and validating CIME on a new platform" href="porting-cime.html" />
-    <link rel="prev" title="4. Defining the machine" href="machine.html" /> 
+    <link rel="next" title="7. Porting and validating CIME on a new platform" href="porting-cime.html" />
+    <link rel="prev" title="5. Defining the machine" href="machine.html" /> 
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@@ -53,21 +53,22 @@
 <li class="toctree-l1"><a class="reference internal" href="index.html">Using the Case Control System</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="index.html#configuring-the-case-control-system">Configuring the Case Control System</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="cime-internals.html">1. Main Configuration File</a></li>
-<li class="toctree-l2"><a class="reference internal" href="compsets.html">2. Component sets</a></li>
-<li class="toctree-l2"><a class="reference internal" href="grids.html">3. Model grids</a></li>
-<li class="toctree-l2"><a class="reference internal" href="machine.html">4. Defining the machine</a></li>
-<li class="toctree-l2 current"><a class="current reference internal" href="#">5. Controlling processors and threads</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="#pe-settings-for-a-case">5.1. pe-settings for a case</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#setting-the-pe-layout">5.2. Setting the PE layout</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#case-resource-allocation">5.3. Case Resource Allocation</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#optimizing-processor-layout">5.4. Optimizing processor layout</a></li>
+<li class="toctree-l2"><a class="reference internal" href="components.html">2. Components</a></li>
+<li class="toctree-l2"><a class="reference internal" href="compsets.html">3. Component sets</a></li>
+<li class="toctree-l2"><a class="reference internal" href="grids.html">4. Model grids</a></li>
+<li class="toctree-l2"><a class="reference internal" href="machine.html">5. Defining the machine</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">6. Controlling processors and threads</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#pe-settings-for-a-case">6.1. pe-settings for a case</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#setting-the-pe-layout">6.2. Setting the PE layout</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#case-resource-allocation">6.3. Case Resource Allocation</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#optimizing-processor-layout">6.4. Optimizing processor layout</a></li>
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="porting-cime.html">6. Porting and validating CIME on a new platform</a></li>
-<li class="toctree-l2"><a class="reference internal" href="unit_testing.html">7. Fortran Unit Testing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="multi-instance.html">8. Multi-instance component functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="workflows.html">9. Workflows</a></li>
-<li class="toctree-l2"><a class="reference internal" href="cime-dir.html">10. Directory content</a></li>
+<li class="toctree-l2"><a class="reference internal" href="porting-cime.html">7. Porting and validating CIME on a new platform</a></li>
+<li class="toctree-l2"><a class="reference internal" href="unit_testing.html">8. Fortran Unit Testing</a></li>
+<li class="toctree-l2"><a class="reference internal" href="multi-instance.html">9. Multi-instance component functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="workflows.html">10. Workflows</a></li>
+<li class="toctree-l2"><a class="reference internal" href="cime-dir.html">11. Directory content</a></li>
 <li class="toctree-l2"><a class="reference internal" href="index.html#indices-and-tables">Indices and tables</a></li>
 </ul>
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@@ -97,7 +98,7 @@
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       <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
           <li class="breadcrumb-item"><a href="index.html">Using the Case Control System</a></li>
-      <li class="breadcrumb-item active"><span class="section-number">5. </span>Controlling processors and threads</li>
+      <li class="breadcrumb-item active"><span class="section-number">6. </span>Controlling processors and threads</li>
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@@ -108,7 +109,7 @@
            <div itemprop="articleBody">
              
   <section id="controlling-processors-and-threads">
-<span id="pesthreads"></span><h1><span class="section-number">5. </span>Controlling processors and threads<a class="headerlink" href="#controlling-processors-and-threads" title="Link to this heading"></a></h1>
+<span id="pesthreads"></span><h1><span class="section-number">6. </span>Controlling processors and threads<a class="headerlink" href="#controlling-processors-and-threads" title="Link to this heading"></a></h1>
 <p>Once a compset and resolution for a case has been defined, CIME
 provides ways to define the processor layout the case will use.</p>
 <p>CIME cases have significant flexibility with respect to the layout of
@@ -118,7 +119,7 @@
 communicator.  In addition, the driver runs on the union of all
 processors and controls the sequencing and hardware partitioning.</p>
 <section id="pe-settings-for-a-case">
-<span id="defining-pes"></span><h2><span class="section-number">5.1. </span>pe-settings for a case<a class="headerlink" href="#pe-settings-for-a-case" title="Link to this heading"></a></h2>
+<span id="defining-pes"></span><h2><span class="section-number">6.1. </span>pe-settings for a case<a class="headerlink" href="#pe-settings-for-a-case" title="Link to this heading"></a></h2>
 <p>CIME looks at the xml element <code class="docutils literal notranslate"><span class="pre">PES_SPEC_FILE</span></code> in the <strong>$CIMEROOT/config/$model/config_files.xml</strong> file to determine where
 to find the supported out-of-the-box model pe-settings for the primary component (See <a class="reference internal" href="compsets.html#compsets"><span class="std std-ref">Compsets</span></a> for definition of primary component.)</p>
 <p>When your run <a class="reference external" href="../Tools_user/create_newcase.html">create_newcase</a>, CIME identifies the primary component and the setting of the <code class="docutils literal notranslate"><span class="pre">PES_SPEC_FILE</span></code> in the standard output.</p>
@@ -167,7 +168,7 @@
 <p>When <a class="reference external" href="../Tools_user/create_newcase.html">create_newcase</a>  is called, it outputs the matches that are found in determining the best out-of-the-box pe-layout.</p>
 </section>
 <section id="setting-the-pe-layout">
-<h2><span class="section-number">5.2. </span>Setting the PE layout<a class="headerlink" href="#setting-the-pe-layout" title="Link to this heading"></a></h2>
+<h2><span class="section-number">6.2. </span>Setting the PE layout<a class="headerlink" href="#setting-the-pe-layout" title="Link to this heading"></a></h2>
 <p>Optimizing the throughput and efficiency of a CIME experiment often
 involves customizing the processor (PE) layout. (See <a class="reference internal" href="#optimizing-processor-layout"><span class="std std-ref">load
 balancing</span></a>.)  CIME provides significant
@@ -249,7 +250,7 @@ <h2><span class="section-number">5.2. </span>Setting the PE layout<a class="head
 </div>
 </section>
 <section id="case-resource-allocation">
-<h2><span class="section-number">5.3. </span>Case Resource Allocation<a class="headerlink" href="#case-resource-allocation" title="Link to this heading"></a></h2>
+<h2><span class="section-number">6.3. </span>Case Resource Allocation<a class="headerlink" href="#case-resource-allocation" title="Link to this heading"></a></h2>
 <p>Resources for your case will be allocated according to the following logic.</p>
 <ul class="simple">
 <li><p><code class="docutils literal notranslate"><span class="pre">NTASKS</span></code> * <code class="docutils literal notranslate"><span class="pre">NTHRDS</span></code> is the total number of hardware processors allocated to a component.</p></li>
@@ -281,7 +282,7 @@ <h2><span class="section-number">5.3. </span>Case Resource Allocation<a class="h
 and job submit commands for your case.</p>
 </section>
 <section id="optimizing-processor-layout">
-<span id="id2"></span><h2><span class="section-number">5.4. </span>Optimizing processor layout<a class="headerlink" href="#optimizing-processor-layout" title="Link to this heading"></a></h2>
+<span id="id2"></span><h2><span class="section-number">6.4. </span>Optimizing processor layout<a class="headerlink" href="#optimizing-processor-layout" title="Link to this heading"></a></h2>
 <p>Load balancing is the practice of specifying a processor layout for a given model configuration
 (compset, grid, and so on) to maximize simulation speed while minimizing processor idle time.
 For a fixed total number of processors, the goal of this optimization is to achieve maximum throughput.
@@ -378,8 +379,8 @@ <h2><span class="section-number">5.3. </span>Case Resource Allocation<a class="h
            </div>
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index df3e115af38..4946650cddf 100644
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+++ b/versions/master/html/users_guide/porting-cime.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
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-  <title>6. Porting and validating CIME on a new platform &mdash; CIME master documentation</title>
+  <title>7. Porting and validating CIME on a new platform &mdash; CIME master documentation</title>
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@@ -53,23 +53,24 @@
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 <li class="toctree-l1 current"><a class="reference internal" href="index.html#configuring-the-case-control-system">Configuring the Case Control System</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="cime-internals.html">1. Main Configuration File</a></li>
-<li class="toctree-l2"><a class="reference internal" href="compsets.html">2. Component sets</a></li>
-<li class="toctree-l2"><a class="reference internal" href="grids.html">3. Model grids</a></li>
-<li class="toctree-l2"><a class="reference internal" href="machine.html">4. Defining the machine</a></li>
-<li class="toctree-l2"><a class="reference internal" href="pes-threads.html">5. Controlling processors and threads</a></li>
-<li class="toctree-l2 current"><a class="current reference internal" href="#">6. Porting and validating CIME on a new platform</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="#required-libraries-packages">6.1. Required libraries/packages</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#an-mpi-example">6.2. An MPI example</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#cesm-linux-and-mac-support">6.3. CESM Linux and Mac Support</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#steps-for-porting">6.4. Steps for porting</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#validating-a-cesm-port-with-prognostic-components">6.5. Validating a CESM port with prognostic components</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#performance-tuning-of-a-cesm-port">6.6. Performance tuning of a CESM port</a></li>
+<li class="toctree-l2"><a class="reference internal" href="components.html">2. Components</a></li>
+<li class="toctree-l2"><a class="reference internal" href="compsets.html">3. Component sets</a></li>
+<li class="toctree-l2"><a class="reference internal" href="grids.html">4. Model grids</a></li>
+<li class="toctree-l2"><a class="reference internal" href="machine.html">5. Defining the machine</a></li>
+<li class="toctree-l2"><a class="reference internal" href="pes-threads.html">6. Controlling processors and threads</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">7. Porting and validating CIME on a new platform</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#required-libraries-packages">7.1. Required libraries/packages</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#an-mpi-example">7.2. An MPI example</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#cesm-linux-and-mac-support">7.3. CESM Linux and Mac Support</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#steps-for-porting">7.4. Steps for porting</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#validating-a-cesm-port-with-prognostic-components">7.5. Validating a CESM port with prognostic components</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#performance-tuning-of-a-cesm-port">7.6. Performance tuning of a CESM port</a></li>
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="unit_testing.html">7. Fortran Unit Testing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="multi-instance.html">8. Multi-instance component functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="workflows.html">9. Workflows</a></li>
-<li class="toctree-l2"><a class="reference internal" href="cime-dir.html">10. Directory content</a></li>
+<li class="toctree-l2"><a class="reference internal" href="unit_testing.html">8. Fortran Unit Testing</a></li>
+<li class="toctree-l2"><a class="reference internal" href="multi-instance.html">9. Multi-instance component functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="workflows.html">10. Workflows</a></li>
+<li class="toctree-l2"><a class="reference internal" href="cime-dir.html">11. Directory content</a></li>
 <li class="toctree-l2"><a class="reference internal" href="index.html#indices-and-tables">Indices and tables</a></li>
 </ul>
 </li>
@@ -99,7 +100,7 @@
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       <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
           <li class="breadcrumb-item"><a href="index.html">Using the Case Control System</a></li>
-      <li class="breadcrumb-item active"><span class="section-number">6. </span>Porting and validating CIME on a new platform</li>
+      <li class="breadcrumb-item active"><span class="section-number">7. </span>Porting and validating CIME on a new platform</li>
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             <a href="../_sources/users_guide/porting-cime.rst.txt" rel="nofollow"> View page source</a>
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@@ -110,11 +111,11 @@
            <div itemprop="articleBody">
              
   <section id="porting-and-validating-cime-on-a-new-platform">
-<span id="porting"></span><h1><span class="section-number">6. </span>Porting and validating CIME on a new platform<a class="headerlink" href="#porting-and-validating-cime-on-a-new-platform" title="Link to this heading"></a></h1>
+<span id="porting"></span><h1><span class="section-number">7. </span>Porting and validating CIME on a new platform<a class="headerlink" href="#porting-and-validating-cime-on-a-new-platform" title="Link to this heading"></a></h1>
 <p>One of the first steps for many users is getting CIME-based models running on their local machine.
 This section describes that process.</p>
 <section id="required-libraries-packages">
-<h2><span class="section-number">6.1. </span>Required libraries/packages<a class="headerlink" href="#required-libraries-packages" title="Link to this heading"></a></h2>
+<h2><span class="section-number">7.1. </span>Required libraries/packages<a class="headerlink" href="#required-libraries-packages" title="Link to this heading"></a></h2>
 <p>The machine needs to have:</p>
 <ul class="simple">
 <li><p>a functioning MPI environment (unless you plan to run on a single core with the CIME mpi-serial library).</p></li>
@@ -125,7 +126,7 @@ <h2><span class="section-number">6.1. </span>Required libraries/packages<a class
 <p>If you are using MPI, make sure you can run a basic MPI parallel program on your machine before you attempt a CIME port. You can use this <a class="reference internal" href="#mpi-example"><span class="std std-ref">MPI example</span></a> to check.</p>
 </section>
 <section id="an-mpi-example">
-<span id="mpi-example"></span><h2><span class="section-number">6.2. </span>An MPI example<a class="headerlink" href="#an-mpi-example" title="Link to this heading"></a></h2>
+<span id="mpi-example"></span><h2><span class="section-number">7.2. </span>An MPI example<a class="headerlink" href="#an-mpi-example" title="Link to this heading"></a></h2>
 <p>It is usually very helpful to assure that you can run a basic mpi parallel program on your machine prior to attempting a CIME port.
 Understanding how to compile and run the program fhello_world_mpi.F90 shown here could potentially save many hours of frustration.</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">program</span> <span class="n">fhello_world_mpi</span><span class="o">.</span><span class="n">F90</span>
@@ -169,12 +170,12 @@ <h2><span class="section-number">6.1. </span>Required libraries/packages<a class
 </div>
 </section>
 <section id="cesm-linux-and-mac-support">
-<h2><span class="section-number">6.3. </span>CESM Linux and Mac Support<a class="headerlink" href="#cesm-linux-and-mac-support" title="Link to this heading"></a></h2>
+<h2><span class="section-number">7.3. </span>CESM Linux and Mac Support<a class="headerlink" href="#cesm-linux-and-mac-support" title="Link to this heading"></a></h2>
 <p>The distribution of CESM includes machines called <strong>homebrew</strong> and <strong>centos7-linux</strong> in the file <strong>$CIMEROOT/config/cesm/machines/config_machines.xml</strong>.
 Please see the instructions in the file to create the directory structure and use these generic machine definitions.</p>
 </section>
 <section id="steps-for-porting">
-<h2><span class="section-number">6.4. </span>Steps for porting<a class="headerlink" href="#steps-for-porting" title="Link to this heading"></a></h2>
+<h2><span class="section-number">7.4. </span>Steps for porting<a class="headerlink" href="#steps-for-porting" title="Link to this heading"></a></h2>
 <p>Porting CIME involves several steps. The first step is to define your machine. You can do this in one of two ways:</p>
 <ol class="arabic">
 <li><p>You can edit <strong>$CIMEROOT/config/$model/machines/config_machines.xml</strong> and add an appropriate section for your machine.</p></li>
@@ -213,7 +214,7 @@ <h2><span class="section-number">6.4. </span>Steps for porting<a class="headerli
 <p>After running those steps correctly, you are ready to try a case at your target compset and resolution.</p>
 </section>
 <section id="validating-a-cesm-port-with-prognostic-components">
-<h2><span class="section-number">6.5. </span>Validating a CESM port with prognostic components<a class="headerlink" href="#validating-a-cesm-port-with-prognostic-components" title="Link to this heading"></a></h2>
+<h2><span class="section-number">7.5. </span>Validating a CESM port with prognostic components<a class="headerlink" href="#validating-a-cesm-port-with-prognostic-components" title="Link to this heading"></a></h2>
 <p>The following port validation is recommended for any new machine.
 Carrying out these steps does not guarantee the model is running
 properly in all cases nor that the model is scientifically valid on
@@ -255,7 +256,7 @@ <h2><span class="section-number">6.5. </span>Validating a CESM port with prognos
 </ol>
 </section>
 <section id="performance-tuning-of-a-cesm-port">
-<h2><span class="section-number">6.6. </span>Performance tuning of a CESM port<a class="headerlink" href="#performance-tuning-of-a-cesm-port" title="Link to this heading"></a></h2>
+<h2><span class="section-number">7.6. </span>Performance tuning of a CESM port<a class="headerlink" href="#performance-tuning-of-a-cesm-port" title="Link to this heading"></a></h2>
 <p>Once you have performed the verification that your port is successful,
 you will want to determine the optimal pe-layout for your target
 configurations (i.e. compset/resolution combinations).  See the file
@@ -284,8 +285,8 @@ <h2><span class="section-number">6.6. </span>Performance tuning of a CESM port<a
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 <li class="toctree-l2"><a class="reference internal" href="cime-internals.html">1. Main Configuration File</a></li>
-<li class="toctree-l2"><a class="reference internal" href="compsets.html">2. Component sets</a></li>
-<li class="toctree-l2"><a class="reference internal" href="grids.html">3. Model grids</a></li>
-<li class="toctree-l2"><a class="reference internal" href="machine.html">4. Defining the machine</a></li>
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-<li class="toctree-l2"><a class="reference internal" href="porting-cime.html">6. Porting and validating CIME on a new platform</a></li>
-<li class="toctree-l2 current"><a class="current reference internal" href="#">7. Fortran Unit Testing</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="#introduction">7.1. Introduction</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="#what-is-a-unit-test">7.1.1. What is a unit test?</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#overview-of-unit-test-support-in-cime">7.1.2. Overview of unit test support in CIME</a></li>
+<li class="toctree-l2"><a class="reference internal" href="components.html">2. Components</a></li>
+<li class="toctree-l2"><a class="reference internal" href="compsets.html">3. Component sets</a></li>
+<li class="toctree-l2"><a class="reference internal" href="grids.html">4. Model grids</a></li>
+<li class="toctree-l2"><a class="reference internal" href="machine.html">5. Defining the machine</a></li>
+<li class="toctree-l2"><a class="reference internal" href="pes-threads.html">6. Controlling processors and threads</a></li>
+<li class="toctree-l2"><a class="reference internal" href="porting-cime.html">7. Porting and validating CIME on a new platform</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">8. Fortran Unit Testing</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#introduction">8.1. Introduction</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="#what-is-a-unit-test">8.1.1. What is a unit test?</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#overview-of-unit-test-support-in-cime">8.1.2. Overview of unit test support in CIME</a></li>
 </ul>
 </li>
-<li class="toctree-l3"><a class="reference internal" href="#running-cime-s-fortran-unit-tests">7.2. Running CIME’s Fortran unit tests</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#how-to-add-unit-testing-support-on-your-machine">7.3. How to add unit testing support on your machine</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="#building-pfunit">7.3.1. Building pFUnit</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#adding-to-the-appropriate-cmake-file">7.3.2. Adding to the appropriate cmake file</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#running-cime-s-fortran-unit-tests">8.2. Running CIME’s Fortran unit tests</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#how-to-add-unit-testing-support-on-your-machine">8.3. How to add unit testing support on your machine</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="#building-pfunit">8.3.1. Building pFUnit</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#adding-to-the-appropriate-cmake-file">8.3.2. Adding to the appropriate cmake file</a></li>
 </ul>
 </li>
-<li class="toctree-l3"><a class="reference internal" href="#how-to-write-a-new-unit-test">7.4. How to write a new unit test</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#general-guidelines-for-writing-unit-tests">7.5. General guidelines for writing unit tests</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#more-details-on-writing-pfunit-based-unit-tests">7.6. More details on writing pFUnit-based unit tests</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="#assertion-methods">7.6.1. Assertion methods</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#defining-a-test-class-in-order-to-define-setup-and-teardown-methods">7.6.2. Defining a test class in order to define setUp and tearDown methods</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#more-on-test-teardown">7.6.3. More on test teardown</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#how-to-write-a-new-unit-test">8.4. How to write a new unit test</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#general-guidelines-for-writing-unit-tests">8.5. General guidelines for writing unit tests</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#more-details-on-writing-pfunit-based-unit-tests">8.6. More details on writing pFUnit-based unit tests</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="#assertion-methods">8.6.1. Assertion methods</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#defining-a-test-class-in-order-to-define-setup-and-teardown-methods">8.6.2. Defining a test class in order to define setUp and tearDown methods</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#more-on-test-teardown">8.6.3. More on test teardown</a></li>
 </ul>
 </li>
-<li class="toctree-l3"><a class="reference internal" href="#finding-more-documentation-and-examples">7.7. Finding more documentation and examples</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="#more-detailed-examples-in-cime">7.7.1. More detailed examples in CIME</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#other-pfunit-documentation-sources">7.7.2. Other pFUnit documentation sources</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#documentation-of-the-unit-test-build-system">7.7.3. Documentation of the unit test build system</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#finding-more-documentation-and-examples">8.7. Finding more documentation and examples</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="#more-detailed-examples-in-cime">8.7.1. More detailed examples in CIME</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#other-pfunit-documentation-sources">8.7.2. Other pFUnit documentation sources</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#documentation-of-the-unit-test-build-system">8.7.3. Documentation of the unit test build system</a></li>
 </ul>
 </li>
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="multi-instance.html">8. Multi-instance component functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="workflows.html">9. Workflows</a></li>
-<li class="toctree-l2"><a class="reference internal" href="cime-dir.html">10. Directory content</a></li>
+<li class="toctree-l2"><a class="reference internal" href="multi-instance.html">9. Multi-instance component functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="workflows.html">10. Workflows</a></li>
+<li class="toctree-l2"><a class="reference internal" href="cime-dir.html">11. Directory content</a></li>
 <li class="toctree-l2"><a class="reference internal" href="index.html#indices-and-tables">Indices and tables</a></li>
 </ul>
 </li>
@@ -118,7 +119,7 @@
   <ul class="wy-breadcrumbs">
       <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
           <li class="breadcrumb-item"><a href="index.html">Using the Case Control System</a></li>
-      <li class="breadcrumb-item active"><span class="section-number">7. </span>Fortran Unit Testing</li>
+      <li class="breadcrumb-item active"><span class="section-number">8. </span>Fortran Unit Testing</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/users_guide/unit_testing.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -129,11 +130,11 @@
            <div itemprop="articleBody">
              
   <section id="fortran-unit-testing">
-<span id="unit-testing"></span><h1><span class="section-number">7. </span>Fortran Unit Testing<a class="headerlink" href="#fortran-unit-testing" title="Link to this heading"></a></h1>
+<span id="unit-testing"></span><h1><span class="section-number">8. </span>Fortran Unit Testing<a class="headerlink" href="#fortran-unit-testing" title="Link to this heading"></a></h1>
 <section id="introduction">
-<h2><span class="section-number">7.1. </span>Introduction<a class="headerlink" href="#introduction" title="Link to this heading"></a></h2>
+<h2><span class="section-number">8.1. </span>Introduction<a class="headerlink" href="#introduction" title="Link to this heading"></a></h2>
 <section id="what-is-a-unit-test">
-<h3><span class="section-number">7.1.1. </span>What is a unit test?<a class="headerlink" href="#what-is-a-unit-test" title="Link to this heading"></a></h3>
+<h3><span class="section-number">8.1.1. </span>What is a unit test?<a class="headerlink" href="#what-is-a-unit-test" title="Link to this heading"></a></h3>
 <p>A unit test is a fast, self-verifying test of a small piece of code.
 A single unit test typically covers 10s to 100s of lines of code; a single function or small module, for example.
 It typically runs in milliseconds and produces a simple pass/fail result.</p>
@@ -147,7 +148,7 @@ <h3><span class="section-number">7.1.1. </span>What is a unit test?<a class="hea
 </ul>
 </section>
 <section id="overview-of-unit-test-support-in-cime">
-<h3><span class="section-number">7.1.2. </span>Overview of unit test support in CIME<a class="headerlink" href="#overview-of-unit-test-support-in-cime" title="Link to this heading"></a></h3>
+<h3><span class="section-number">8.1.2. </span>Overview of unit test support in CIME<a class="headerlink" href="#overview-of-unit-test-support-in-cime" title="Link to this heading"></a></h3>
 <p>CIME comes with a set of tools to support building and running unit tests.
 These consist of:</p>
 <ol class="arabic simple">
@@ -158,7 +159,7 @@ <h3><span class="section-number">7.1.2. </span>Overview of unit test support in
 </section>
 </section>
 <section id="running-cime-s-fortran-unit-tests">
-<span id="running-unit-tests"></span><h2><span class="section-number">7.2. </span>Running CIME’s Fortran unit tests<a class="headerlink" href="#running-cime-s-fortran-unit-tests" title="Link to this heading"></a></h2>
+<span id="running-unit-tests"></span><h2><span class="section-number">8.2. </span>Running CIME’s Fortran unit tests<a class="headerlink" href="#running-cime-s-fortran-unit-tests" title="Link to this heading"></a></h2>
 <p>These instructions assume that you are using a machine that already has pFUnit installed, along with the necessary support in CIME.
 If that is not the case, see <a class="reference internal" href="#adding-machine-support"><span class="std std-ref">How to add unit testing support on your machine</span></a>.</p>
 <p>From the top-level CIME directory, you can run all of CIME’s Fortran unit tests by running:</p>
@@ -198,7 +199,7 @@ <h3><span class="section-number">7.1.2. </span>Overview of unit test support in
 <p>These unit tests are run automatically as part of <strong>scripts_regression_tests</strong> on machines that have a serial build of pFUnit available for the default compiler.</p>
 </section>
 <section id="how-to-add-unit-testing-support-on-your-machine">
-<span id="adding-machine-support"></span><h2><span class="section-number">7.3. </span>How to add unit testing support on your machine<a class="headerlink" href="#how-to-add-unit-testing-support-on-your-machine" title="Link to this heading"></a></h2>
+<span id="adding-machine-support"></span><h2><span class="section-number">8.3. </span>How to add unit testing support on your machine<a class="headerlink" href="#how-to-add-unit-testing-support-on-your-machine" title="Link to this heading"></a></h2>
 <p>The following instructions assume that you have ported CIME to your
 machine by following the instructions in
 <a class="reference internal" href="porting-cime.html"><span class="doc">Porting and validating CIME on a new platform</span></a>.  If you have done that, you can add
@@ -206,7 +207,7 @@ <h3><span class="section-number">7.1.2. </span>Overview of unit test support in
 pointing to the build in your ** <em>MACH*_*COMPILER</em>.cmake** file. Those
 processes are described in the following sections.</p>
 <section id="building-pfunit">
-<h3><span class="section-number">7.3.1. </span>Building pFUnit<a class="headerlink" href="#building-pfunit" title="Link to this heading"></a></h3>
+<h3><span class="section-number">8.3.1. </span>Building pFUnit<a class="headerlink" href="#building-pfunit" title="Link to this heading"></a></h3>
 <p>Follow the instructions below to build pFUnit using the default compiler on your machine.
 That is the default for <strong>run_tests.py</strong> and that is required for <strong>scripts_regression_tests.py</strong> to run the unit tests on your machine.
 For the CMake step, we typically build with <code class="docutils literal notranslate"><span class="pre">-DSKIP_MPI=YES</span></code>, <code class="docutils literal notranslate"><span class="pre">-DSKIP_OPENMP=YES</span></code> and <code class="docutils literal notranslate"><span class="pre">-DCMAKE_INSTALL_PREFIX</span></code> set to the directory where you want pFUnit to be installed.
@@ -261,7 +262,7 @@ <h3><span class="section-number">7.3.1. </span>Building pFUnit<a class="headerli
 Make sure to choose a different installation directory for each build by setting the <code class="docutils literal notranslate"><span class="pre">PFUNIT</span></code> variable differently.</p>
 </section>
 <section id="adding-to-the-appropriate-cmake-file">
-<h3><span class="section-number">7.3.2. </span>Adding to the appropriate cmake file<a class="headerlink" href="#adding-to-the-appropriate-cmake-file" title="Link to this heading"></a></h3>
+<h3><span class="section-number">8.3.2. </span>Adding to the appropriate cmake file<a class="headerlink" href="#adding-to-the-appropriate-cmake-file" title="Link to this heading"></a></h3>
 <p>After you build pFUnit, tell CIME about your build or builds.
 To do this, specify the appropriate path using the <code class="docutils literal notranslate"><span class="pre">PFUNIT_PATH</span></code> CMake variable in the ** <em>MACH*_*COMPILER</em>.cmake** file.
 For a build with no MPI or openMP support (as recommended above), the block should look like this (with the actual path replaced with the PFUNIT path you specified when doing the build):</p>
@@ -276,7 +277,7 @@ <h3><span class="section-number">7.3.2. </span>Adding to the appropriate cmake f
 </section>
 </section>
 <section id="how-to-write-a-new-unit-test">
-<h2><span class="section-number">7.4. </span>How to write a new unit test<a class="headerlink" href="#how-to-write-a-new-unit-test" title="Link to this heading"></a></h2>
+<h2><span class="section-number">8.4. </span>How to write a new unit test<a class="headerlink" href="#how-to-write-a-new-unit-test" title="Link to this heading"></a></h2>
 <div class="admonition-todo admonition" id="id1">
 <p class="admonition-title">Todo</p>
 <p>Need to write this section. This will draw on some of the information in sections 3 and 4 of <a class="reference external" href="https://github.com/NCAR/cesm_unit_test_tutorial">https://github.com/NCAR/cesm_unit_test_tutorial</a> (though without the clm and cam stuff).</p>
@@ -284,7 +285,7 @@ <h2><span class="section-number">7.4. </span>How to write a new unit test<a clas
 <p>It should also introduce the role of .pf files, which are referenced several paragraphs later as if already explained.</p>
 </section>
 <section id="general-guidelines-for-writing-unit-tests">
-<h2><span class="section-number">7.5. </span>General guidelines for writing unit tests<a class="headerlink" href="#general-guidelines-for-writing-unit-tests" title="Link to this heading"></a></h2>
+<h2><span class="section-number">8.5. </span>General guidelines for writing unit tests<a class="headerlink" href="#general-guidelines-for-writing-unit-tests" title="Link to this heading"></a></h2>
 <p>Unit tests typically test a small piece of code, on the order of 10-100 lines, as in a single function or small class.</p>
 <p>Good unit tests are <strong>“FIRST”</strong>:
 (<a class="reference external" href="https://pragprog.com/magazines/2012-01/unit-tests-are-first">https://pragprog.com/magazines/2012-01/unit-tests-are-first</a>):</p>
@@ -317,9 +318,9 @@ <h2><span class="section-number">7.5. </span>General guidelines for writing unit
 for your tests, not for your helper routines.</p>
 </section>
 <section id="more-details-on-writing-pfunit-based-unit-tests">
-<h2><span class="section-number">7.6. </span>More details on writing pFUnit-based unit tests<a class="headerlink" href="#more-details-on-writing-pfunit-based-unit-tests" title="Link to this heading"></a></h2>
+<h2><span class="section-number">8.6. </span>More details on writing pFUnit-based unit tests<a class="headerlink" href="#more-details-on-writing-pfunit-based-unit-tests" title="Link to this heading"></a></h2>
 <section id="assertion-methods">
-<h3><span class="section-number">7.6.1. </span>Assertion methods<a class="headerlink" href="#assertion-methods" title="Link to this heading"></a></h3>
+<h3><span class="section-number">8.6.1. </span>Assertion methods<a class="headerlink" href="#assertion-methods" title="Link to this heading"></a></h3>
 <p>pFUnit provides many assertion methods that you can use in the Verify step.
 Here are some of the most useful:</p>
 <table class="docutils align-default">
@@ -364,7 +365,7 @@ <h3><span class="section-number">7.6.1. </span>Assertion methods<a class="header
 file and line number of the failed assertion.</p>
 </section>
 <section id="defining-a-test-class-in-order-to-define-setup-and-teardown-methods">
-<h3><span class="section-number">7.6.2. </span>Defining a test class in order to define setUp and tearDown methods<a class="headerlink" href="#defining-a-test-class-in-order-to-define-setup-and-teardown-methods" title="Link to this heading"></a></h3>
+<h3><span class="section-number">8.6.2. </span>Defining a test class in order to define setUp and tearDown methods<a class="headerlink" href="#defining-a-test-class-in-order-to-define-setup-and-teardown-methods" title="Link to this heading"></a></h3>
 <p>As noted in the comments in <strong>test_circle.pf</strong>, defining a test class is optional.
 However, defining a minimal test class as shown here with <code class="docutils literal notranslate"><span class="pre">TestCircle</span></code> allows you
 use some pFUnit features such as the setUp and tearDown methods.</p>
@@ -423,7 +424,7 @@ <h3><span class="section-number">7.6.2. </span>Defining a test class in order to
 </div>
 </section>
 <section id="more-on-test-teardown">
-<h3><span class="section-number">7.6.3. </span>More on test teardown<a class="headerlink" href="#more-on-test-teardown" title="Link to this heading"></a></h3>
+<h3><span class="section-number">8.6.3. </span>More on test teardown<a class="headerlink" href="#more-on-test-teardown" title="Link to this heading"></a></h3>
 <p>As stated in <a class="reference internal" href="#defining-a-test-class-in-order-to-define-setup-and-teardown-methods">Defining a test class in order to define setUp and tearDown methods</a>,
 code in the tearDown method is executed after each test, often to do cleanup operations.</p>
 <p>Using the tearDown method is recommended because tests abort if an assertion fails.
@@ -456,9 +457,9 @@ <h3><span class="section-number">7.6.3. </span>More on test teardown<a class="he
 </section>
 </section>
 <section id="finding-more-documentation-and-examples">
-<h2><span class="section-number">7.7. </span>Finding more documentation and examples<a class="headerlink" href="#finding-more-documentation-and-examples" title="Link to this heading"></a></h2>
+<h2><span class="section-number">8.7. </span>Finding more documentation and examples<a class="headerlink" href="#finding-more-documentation-and-examples" title="Link to this heading"></a></h2>
 <section id="more-detailed-examples-in-cime">
-<h3><span class="section-number">7.7.1. </span>More detailed examples in CIME<a class="headerlink" href="#more-detailed-examples-in-cime" title="Link to this heading"></a></h3>
+<h3><span class="section-number">8.7.1. </span>More detailed examples in CIME<a class="headerlink" href="#more-detailed-examples-in-cime" title="Link to this heading"></a></h3>
 <p>There are many examples of unit tests in CIME, some simple and some quite complex.
 You can find them by looking for files with the “.pf” extension:</p>
 <div class="highlight-shell notranslate"><div class="highlight"><pre><span></span>&gt;<span class="w"> </span>find<span class="w"> </span>.<span class="w"> </span>--name<span class="w"> </span><span class="s1">&#39;*.pf&#39;</span>
@@ -468,11 +469,11 @@ <h3><span class="section-number">7.7.1. </span>More detailed examples in CIME<a
 <strong>CMakeLists.txt</strong> files throughout the source tree.</p>
 </section>
 <section id="other-pfunit-documentation-sources">
-<h3><span class="section-number">7.7.2. </span>Other pFUnit documentation sources<a class="headerlink" href="#other-pfunit-documentation-sources" title="Link to this heading"></a></h3>
+<h3><span class="section-number">8.7.2. </span>Other pFUnit documentation sources<a class="headerlink" href="#other-pfunit-documentation-sources" title="Link to this heading"></a></h3>
 <p>Unfortunately, the documentation inside the pFUnit repository (in the documentation and Examples directories) is out-of-date (at least as of April, 2023): much of this documentation refers to version 3 of pFUnit, which differs in some ways from version 4. However, some working examples are provided in <a class="reference external" href="https://github.com/Goddard-Fortran-Ecosystem/pFUnit_demos">https://github.com/Goddard-Fortran-Ecosystem/pFUnit_demos</a>.</p>
 </section>
 <section id="documentation-of-the-unit-test-build-system">
-<h3><span class="section-number">7.7.3. </span>Documentation of the unit test build system<a class="headerlink" href="#documentation-of-the-unit-test-build-system" title="Link to this heading"></a></h3>
+<h3><span class="section-number">8.7.3. </span>Documentation of the unit test build system<a class="headerlink" href="#documentation-of-the-unit-test-build-system" title="Link to this heading"></a></h3>
 <p>The CMake build infrastructure is in <strong>$CIMEROOT/CIME/non_py/src/CMake</strong>.</p>
 <p>The infrastructure for building and running tests with <strong>run_tests.py</strong> is in
 <strong>$CIMEROOT/scripts/fortran_unit_testing</strong>. That directory also contains general
@@ -486,8 +487,8 @@ <h3><span class="section-number">7.7.3. </span>Documentation of the unit test bu
            </div>
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
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diff --git a/versions/master/html/users_guide/workflows.html b/versions/master/html/users_guide/workflows.html
index 1fbf7ad4ae9..7bec0d18949 100644
--- a/versions/master/html/users_guide/workflows.html
+++ b/versions/master/html/users_guide/workflows.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>9. Workflows &mdash; CIME master documentation</title>
+  <title>10. Workflows &mdash; CIME master documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../_static/custom.css" />
@@ -22,8 +22,8 @@
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="10. Directory content" href="cime-dir.html" />
-    <link rel="prev" title="8. Multi-instance component functionality" href="multi-instance.html" /> 
+    <link rel="next" title="11. Directory content" href="cime-dir.html" />
+    <link rel="prev" title="9. Multi-instance component functionality" href="multi-instance.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -53,15 +53,16 @@
 <li class="toctree-l1"><a class="reference internal" href="index.html">Using the Case Control System</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="index.html#configuring-the-case-control-system">Configuring the Case Control System</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="cime-internals.html">1. Main Configuration File</a></li>
-<li class="toctree-l2"><a class="reference internal" href="compsets.html">2. Component sets</a></li>
-<li class="toctree-l2"><a class="reference internal" href="grids.html">3. Model grids</a></li>
-<li class="toctree-l2"><a class="reference internal" href="machine.html">4. Defining the machine</a></li>
-<li class="toctree-l2"><a class="reference internal" href="pes-threads.html">5. Controlling processors and threads</a></li>
-<li class="toctree-l2"><a class="reference internal" href="porting-cime.html">6. Porting and validating CIME on a new platform</a></li>
-<li class="toctree-l2"><a class="reference internal" href="unit_testing.html">7. Fortran Unit Testing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="multi-instance.html">8. Multi-instance component functionality</a></li>
-<li class="toctree-l2 current"><a class="current reference internal" href="#">9. Workflows</a></li>
-<li class="toctree-l2"><a class="reference internal" href="cime-dir.html">10. Directory content</a></li>
+<li class="toctree-l2"><a class="reference internal" href="components.html">2. Components</a></li>
+<li class="toctree-l2"><a class="reference internal" href="compsets.html">3. Component sets</a></li>
+<li class="toctree-l2"><a class="reference internal" href="grids.html">4. Model grids</a></li>
+<li class="toctree-l2"><a class="reference internal" href="machine.html">5. Defining the machine</a></li>
+<li class="toctree-l2"><a class="reference internal" href="pes-threads.html">6. Controlling processors and threads</a></li>
+<li class="toctree-l2"><a class="reference internal" href="porting-cime.html">7. Porting and validating CIME on a new platform</a></li>
+<li class="toctree-l2"><a class="reference internal" href="unit_testing.html">8. Fortran Unit Testing</a></li>
+<li class="toctree-l2"><a class="reference internal" href="multi-instance.html">9. Multi-instance component functionality</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">10. Workflows</a></li>
+<li class="toctree-l2"><a class="reference internal" href="cime-dir.html">11. Directory content</a></li>
 <li class="toctree-l2"><a class="reference internal" href="index.html#indices-and-tables">Indices and tables</a></li>
 </ul>
 </li>
@@ -91,7 +92,7 @@
   <ul class="wy-breadcrumbs">
       <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
           <li class="breadcrumb-item"><a href="index.html">Using the Case Control System</a></li>
-      <li class="breadcrumb-item active"><span class="section-number">9. </span>Workflows</li>
+      <li class="breadcrumb-item active"><span class="section-number">10. </span>Workflows</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/users_guide/workflows.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -102,7 +103,7 @@
            <div itemprop="articleBody">
              
   <section id="workflows">
-<span id="id1"></span><h1><span class="section-number">9. </span>Workflows<a class="headerlink" href="#workflows" title="Link to this heading"></a></h1>
+<span id="id1"></span><h1><span class="section-number">10. </span>Workflows<a class="headerlink" href="#workflows" title="Link to this heading"></a></h1>
 <p>Currently, there are three kinds of workflow controls available in CIME.</p>
 <ol class="arabic">
 <li><p>Multiple jobs workflow</p>
@@ -198,8 +199,8 @@
            </div>
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="multi-instance.html" class="btn btn-neutral float-left" title="8. Multi-instance component functionality" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
-        <a href="cime-dir.html" class="btn btn-neutral float-right" title="10. Directory content" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
+        <a href="multi-instance.html" class="btn btn-neutral float-left" title="9. Multi-instance component functionality" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+        <a href="cime-dir.html" class="btn btn-neutral float-right" title="11. Directory content" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
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