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<div class="section" id="compiling-and-running-the-model">
<span id="run"></span><h1>Compiling and running the model<a class="headerlink" href="#compiling-and-running-the-model" title="Permalink to this headline">¶</a></h1>
<p><a class="reference external" href="https://github.com/kaizhangpnl/kaizhangpnl.github.io/blob/master/source/run.rst">Github</a>
<a class="reference external" href="https://kaizhangpnl.github.io/run.html">Spinx</a></p>
<p>First of all, please read</p>
<p><a class="reference external" href="https://e3sm.org/model/running-e3sm/e3sm-quick-start/">E3SM Quick Start</a></p>
<p>Since EAMv1 is a descendant of CAM5, they share a lot of functionalities. Users are
encouraged to read the <a class="reference external" href="http://www.cesm.ucar.edu/models/cesm1.2/cam/docs/ug5_3/">CAM5.3 user’s guide</a>
to obtain more useful information.</p>
<div class="section" id="run-script">
<h2>Run script<a class="headerlink" href="#run-script" title="Permalink to this headline">¶</a></h2>
<p>A <a class="reference external" href="https://github.com/E3SM-Project/E3SM/blob/master/run_e3sm.template.csh">runscript</a>
is available in the E3SM model source code directory (parallel to “cime” and “compoment”).
For E3SM project members, more example scripts can be found <a class="reference external" href="https://github.com/E3SM-Project/SimulationScripts/">here (internal)</a>.</p>
<p>It takes several minutes to compile and a dozen of minutes (or more) to run and generate
log files, so it’s good time to grab a coffee and read an abstract!</p>
</div>
<div class="section" id="creating-a-new-case">
<h2>Creating a new case<a class="headerlink" href="#creating-a-new-case" title="Permalink to this headline">¶</a></h2>
<p>A new case is often created for each simulation</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>./create_newcase -case $temp_case_scripts_dir \
-mach $newcase_machine \
-compset $compset \
-res $resolution \
-project $project \
-pecount $std_proc_configuration
</pre></div>
</div>
</div>
<div class="section" id="setting-compsets">
<h2>Setting compsets<a class="headerlink" href="#setting-compsets" title="Permalink to this headline">¶</a></h2>
<p>Available compsets for E3SM can be found in:</p>
<blockquote>
<div><a class="reference external" href="https://github.com/E3SM-Project/E3SM/blob/master/cime/config/e3sm/allactive/config_compsets.xml">cime/config/e3sm/allactive/config_compsets.xml</a></div></blockquote>
<p>Available compsets for EAM can be found in:</p>
<blockquote>
<div><a class="reference external" href="https://github.com/E3SM-Project/E3SM/blob/master/components/cam/cime_config/config_compsets.xml">components/cam/cime_config/config_compsets.xml</a></div></blockquote>
<p>The most frequently used compsets are listed below:</p>
<ul>
<li><p class="first"><code class="docutils literal notranslate"><span class="pre">FC5AV1C-04P2</span></code> <a class="reference external" href="https://github.com/E3SM-Project/E3SM/blob/master/components/cam/bld/namelist_files/use_cases/2000_cam5_av1c-04p2.xml">namelist setup</a></p>
<p>V1 atmosphere-only simulation with present-day external forcing. Tuning settings are for the ne30L72 resolution.</p>
<p>The present-day external forcing (so-called “year 2000”, mean of 1995-2005) will be used.
The anthropogenic aerosol emissions and greenhouse gas concentration are constant.
The atmosphere model is coupled with the ELM land model (similar to CLM4.5), and
driven by prescribed climatological SST / sea ice cover.</p>
<p>Note that the tuning setting is slightly different from that used in the DECK simulations. See <a class="reference external" href="https://kaizhangpnl.github.io/flow.html#list-of-tuning-parameters">List of tuning parameters</a> for details.</p>
</li>
<li><p class="first"><code class="docutils literal notranslate"><span class="pre">F1850C5AV1C-04P2</span></code> <a class="reference external" href="https://github.com/E3SM-Project/E3SM/blob/master/components/cam/bld/namelist_files/use_cases/1850_cam5_av1c-04p2.xml">namelist setup</a></p>
<p>V1 atmosphere-only simulation with pre-industrial external forcing. Tuning settings are for the ne30L72 resolution.</p>
</li>
<li><p class="first"><code class="docutils literal notranslate"><span class="pre">FC5</span></code> <a class="reference external" href="https://github.com/E3SM-Project/E3SM/blob/master/components/cam/bld/namelist_files/use_cases/2000_cam5_cosp.xml">namelist setup</a></p>
<p>V0-like atmosphere-only simulation with present-day external forcing. Tuning settings are for the <code class="docutils literal notranslate"><span class="pre">ne30L30</span></code> resolution.
Note that some tuning parameters need to be changed for version 0.3.</p>
</li>
<li><p class="first"><code class="docutils literal notranslate"><span class="pre">F1850C5</span></code> <a class="reference external" href="https://github.com/E3SM-Project/E3SM/blob/master/components/cam/bld/namelist_files/use_cases/1850_cam5.xml">namelist setup</a></p>
<p>V0-like atmosphere-only simulation with pre-industrial external forcing. Tuning settings are for the <code class="docutils literal notranslate"><span class="pre">ne30L30</span></code> resolution.
Note that some tuning parameters need to be changed for version 0.3.</p>
</li>
<li><p class="first"><code class="docutils literal notranslate"><span class="pre">FC5AV1C-H01C</span></code> <a class="reference external" href="https://github.com/E3SM-Project/E3SM/blob/master/components/cam/bld/namelist_files/use_cases/2000_cam5_av1c-h01c.xml">namelist setup</a></p>
<p>High-resolution (ne120L72) V1 atmosphere-only simulation with present-day external forcing.</p>
</li>
<li><p class="first"><code class="docutils literal notranslate"><span class="pre">F1850C5AV1C-H01C</span></code> <a class="reference external" href="https://github.com/E3SM-Project/E3SM/blob/master/components/cam/bld/namelist_files/use_cases/2000_cam5_av1c-h01c.xml">namelist setup</a></p>
<p>High-resolution (ne120L72) V1 atmosphere-only simulation with pre-industrial external forcing.</p>
</li>
<li><p class="first"><code class="docutils literal notranslate"><span class="pre">F20TRC5-CMIP6</span></code> <a class="reference external" href="https://github.com/E3SM-Project/E3SM/blob/master/components/cam/bld/namelist_files/use_cases/20TR_cam5_CMIP6.xml">namelist setup</a></p>
<p>V1 atmosphere-only simulation with time-varying 20th-century external forcing from CMIP6.</p>
</li>
</ul>
<p>More information on the DECK compsets is available <a class="reference external" href="https://acme-climate.atlassian.net/wiki/spaces/ATM/pages/110100741/DECK+compsets">here</a>.</p>
</div>
<div class="section" id="changing-spatial-resolutions">
<h2>Changing spatial resolutions<a class="headerlink" href="#changing-spatial-resolutions" title="Permalink to this headline">¶</a></h2>
<p>To change the horizontal resolution, set</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="nb">set</span> <span class="n">resolution</span> <span class="o">=</span> <span class="n">ne30_ne30</span> <span class="p">(</span><span class="ow">or</span> <span class="n">ne4_ne4</span><span class="p">,</span> <span class="n">ne11_ne11</span><span class="p">,</span> <span class="n">ne16_ne16</span><span class="p">,</span> <span class="n">ne120_ne120</span><span class="p">)</span>
</pre></div>
</div>
<p>before executing “create_newcase”</p>
</div>
<div class="section" id="debugging-mode">
<h2>Debugging mode<a class="headerlink" href="#debugging-mode" title="Permalink to this headline">¶</a></h2>
<p>Before compiling the code</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">./</span><span class="n">xmlchange</span> <span class="o">-</span><span class="n">file</span> <span class="n">env_build</span><span class="o">.</span><span class="n">xml</span> <span class="o">-</span><span class="nb">id</span> <span class="n">DEBUG</span> <span class="o">-</span><span class="n">val</span> <span class="s2">"TRUE"</span>
</pre></div>
</div>
</div>
<div class="section" id="sanity-check-for-state-variables">
<h2>Sanity-check for state variables<a class="headerlink" href="#sanity-check-for-state-variables" title="Permalink to this headline">¶</a></h2>
<ul>
<li><p class="first">Namelist change</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">cat</span> <span class="o"><<</span><span class="n">EOF</span> <span class="o">>></span> <span class="n">user_nl_cam</span>
<span class="n">state_debug_checks</span> <span class="o">=</span> <span class="o">.</span><span class="n">true</span><span class="o">.</span>
<span class="n">EOF</span>
</pre></div>
</div>
</li>
</ul>
<p>The model will check if the state variables are within a plausible range
(e.g. temperature above zero) when physics_upstate is called.
Note that this sanity-check will be switched on automatically when the model is
running in debugging mode.</p>
</div>
<div class="section" id="switching-on-cosp-simulator">
<h2>Switching on COSP simulator<a class="headerlink" href="#switching-on-cosp-simulator" title="Permalink to this headline">¶</a></h2>
<ul>
<li><p class="first">Configuration</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">./</span><span class="n">xmlchange</span> <span class="o">-</span><span class="n">append</span> <span class="o">-</span><span class="n">file</span> <span class="n">env_build</span><span class="o">.</span><span class="n">xml</span> <span class="o">-</span><span class="nb">id</span> <span class="n">CAM_CONFIG_OPTS</span> <span class="o">-</span><span class="n">val</span> <span class="s2">"-cosp"</span>
</pre></div>
</div>
</li>
<li><p class="first">Namelist change</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>cat <<EOF >> user_nl_cam
docosp = .true. !!! needed for some versions of E3SM
cosp_lite = .true.
EOF
</pre></div>
</div>
</li>
</ul>
<p>If cosp_lite = true, the COSP cloud simulators are run to produce
select output for the AMWG diagnostics package.
sets cosp_ncolumns=10 and cosp_nradsteps=3
(appropriate for COSP statistics derived from seasonal averages),
and runs MISR, ISCCP, MODIS, and CALIPSO lidar simulators
(cosp_lmisr_sim=.true.,cosp_lisccp_sim=.true.,
cosp_lmodis_sim=.true.,cosp_llidar_sim=.true.).
This default logical is set in cospsimulator_intr.F90.</p>
<p>More detailed information on how to configure the COSP output can be found in the
source code <a class="reference external" href="https://github.com/E3SM-Project/E3SM/blob/master/components/cam/src/physics/cam/cospsimulator_intr.F90">cospsimulator_intr.F90</a>.</p>
</div>
<div class="section" id="single-column-model-scm-simulations">
<h2>Single column model (SCM) simulations<a class="headerlink" href="#single-column-model-scm-simulations" title="Permalink to this headline">¶</a></h2>
<p>EAM can run in the single column mode.
Some instructions on how to configure and run a single column model can be found
<a class="reference external" href="https://acme-climate.atlassian.net/wiki/spaces/Docs/pages/128294958/Running+the+ACME+Single+Column+Model">here</a>. (internal)</p>
<p>A runscript template can be found <a class="reference external" href="https://github.com/kaizhangpnl/kaizhangpnl.github.io/blob/master/source/scm_runscript.rst">here</a>.</p>
<p>IOP forcing data to drive the SCM can be found
<a class="reference external" href="https://acme-climate.atlassian.net/wiki/spaces/Docs/pages/127456636/ACME+Single-Column+Model+Case+Library">here</a>. (internal) or
from the E3SM input data server <a class="reference external" href="https://acme-svn2.ornl.gov/acme-repo/acme/inputdata/atm/cam/scam/iop/">here</a>.</p>
</div>
<div class="section" id="output-data-in-specified-regions">
<h2>Output data in specified regions<a class="headerlink" href="#output-data-in-specified-regions" title="Permalink to this headline">¶</a></h2>
<p>This functionality is inherited from CESM:</p>
<p>“List of columns or contiguous columns at which the fincl1 fields will be
output. Individual columns are specified as a string using a longitude
degree (greater or equal to 0.) followed by a single character
(e)ast/(w)est identifer, an underscore ‘_’ , and a latitude degree followed
by a single character (n)orth/(s)outh identifier. For example, ‘10e_20n’
would pick the model column closest to 10 degrees east longitude by 20
degrees north latitude. A group of contiguous columns can be specified
using bounding latitudes and longitudes separated by a colon. For example,
‘10e:20e_15n:20n’ would select the model columns which fall with in the
longitude range from 10 east to 20 east and the latitude range from 15
north to 20 north.”</p>
<p>Namelist change:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>cat <<EOF >> user_nl_cam
fincl2 = 'U','V','T','Q','PS'
fincl2lonlat = '210e:330e_15n:65n' ! CONUS
EOF
</pre></div>
</div>
<p>To post-process the regional output on the unstructured spectral element grid,
please follow the guide available
<a class="reference external" href="https://acme-climate.atlassian.net/wiki/spaces/SIM/pages/754286611/Regridding+E3SM+Data+with+ncremap">here</a>
(currently internal).</p>
</div>
<div class="section" id="output-data-at-a-certain-local-time">
<h2>Output data at a certain local time<a class="headerlink" href="#output-data-at-a-certain-local-time" title="Permalink to this headline">¶</a></h2>
<p>The following example shows how to sample data within a local time window (+- 1h near 10:30am):</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">cat</span> <span class="o"><<</span><span class="n">EOF</span> <span class="o">>></span> <span class="n">user_nl_cam</span>
<span class="n">nhtfrq</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span><span class="o">-</span><span class="mi">24</span>
<span class="n">mfilt</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span><span class="mi">1</span>
<span class="n">lcltod_start</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span><span class="mi">34200</span>
<span class="n">lcltod_stop</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span><span class="mi">41400</span>
<span class="n">avgflag_pertape</span><span class="p">(</span><span class="mi">2</span><span class="p">)</span> <span class="o">=</span> <span class="s1">'L'</span>
<span class="n">fincl2</span> <span class="o">=</span> <span class="s1">'CLOUD'</span><span class="p">,</span> <span class="s1">'LWP'</span>
<span class="n">EOF</span>
</pre></div>
</div>
<p>The model will sample and average all the data in the two hours and output the data one
file per day.</p>
</div>
<div class="section" id="frequently-used-namelist-options">
<h2>Frequently-used namelist options<a class="headerlink" href="#frequently-used-namelist-options" title="Permalink to this headline">¶</a></h2>
<p>The following namelist options are frequently used for detailed diagnostics:</p>
<ul>
<li><p class="first">Switch for diagnostic output of the aerosol tendencies</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">history_aerosol</span> <span class="o">=</span> <span class="o">.</span><span class="n">true</span><span class="o">.</span>
</pre></div>
</div>
</li>
<li><p class="first">Switch for diagnostic output of the aerosol optics</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">history_aero_optics</span> <span class="o">=</span> <span class="o">.</span><span class="n">true</span><span class="o">.</span>
</pre></div>
</div>
</li>
<li><p class="first">Produce output for the AMWG diagnostic package</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">history_amwg</span> <span class="o">=</span> <span class="o">.</span><span class="n">true</span><span class="o">.</span>
</pre></div>
</div>
</li>
<li><p class="first">Switch for water/heat budget analysis output</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">history_budget</span> <span class="o">=</span> <span class="o">.</span><span class="n">true</span><span class="o">.</span>
</pre></div>
</div>
</li>
<li><p class="first">Switch for the AMWG variability diagnostics output</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">history_vdiag</span> <span class="o">=</span> <span class="o">.</span><span class="n">true</span><span class="o">.</span>
</pre></div>
</div>
</li>
<li><p class="first">Switch for verbose (mostly aerosol-related) history output</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">history_verbose</span> <span class="o">=</span> <span class="o">.</span><span class="n">true</span><span class="o">.</span>
</pre></div>
</div>
</li>
</ul>
</div>
<div class="section" id="other-options">
<h2>Other options<a class="headerlink" href="#other-options" title="Permalink to this headline">¶</a></h2>
<p>The complete namelist options are listed in:</p>
<blockquote>
<div><a class="reference external" href="https://github.com/E3SM-Project/E3SM/blob/master/components/cam/bld/namelist_files/namelist_definition.xml">components/cam/bld/namelist_files/namelist_definition.xml</a></div></blockquote>
</div>
<div class="section" id="specific-setup-for-constance-pnnl">
<h2>Specific setup for Constance (PNNL)<a class="headerlink" href="#specific-setup-for-constance-pnnl" title="Permalink to this headline">¶</a></h2>
<p>Add the following to your .cshrc file:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>limit coredumpsize unlimited
limit stacksize unlimited
module load python/2.7.8
module load intel/15.0.1
module load mvapich2/2.1
module load netcdf/4.3.2
module load mkl/15.0.1
setenv MKL_PATH $MLIB_LIB
setenv NETCDF_HOME /share/apps/netcdf/4.3.2/intel/15.0.1
</pre></div>
</div>
<p>A script to configure and make the model on constance is available
<a class="reference external" href="https://github.com/kaizhangpnl/kaizhangpnl.github.io/tree/master/source/make_e3sm_atm.csh">here</a>.</p>
<p>And contact Balwinder Singh for accessing the E3SM input file directory on Constance.</p>
</div>
<div class="section" id="reference">
<h2>Reference<a class="headerlink" href="#reference" title="Permalink to this headline">¶</a></h2>
<p>Documentation from <a class="reference external" href="http://www.cesm.ucar.edu/models/cesm1.2/cam/docs/ug5_3/">CAM5.3</a>.</p>
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<ul>
<li><a class="reference internal" href="#">Compiling and running the model</a><ul>
<li><a class="reference internal" href="#run-script">Run script</a></li>
<li><a class="reference internal" href="#creating-a-new-case">Creating a new case</a></li>
<li><a class="reference internal" href="#setting-compsets">Setting compsets</a></li>
<li><a class="reference internal" href="#changing-spatial-resolutions">Changing spatial resolutions</a></li>
<li><a class="reference internal" href="#debugging-mode">Debugging mode</a></li>
<li><a class="reference internal" href="#sanity-check-for-state-variables">Sanity-check for state variables</a></li>
<li><a class="reference internal" href="#switching-on-cosp-simulator">Switching on COSP simulator</a></li>
<li><a class="reference internal" href="#single-column-model-scm-simulations">Single column model (SCM) simulations</a></li>
<li><a class="reference internal" href="#output-data-in-specified-regions">Output data in specified regions</a></li>
<li><a class="reference internal" href="#output-data-at-a-certain-local-time">Output data at a certain local time</a></li>
<li><a class="reference internal" href="#frequently-used-namelist-options">Frequently-used namelist options</a></li>
<li><a class="reference internal" href="#other-options">Other options</a></li>
<li><a class="reference internal" href="#specific-setup-for-constance-pnnl">Specific setup for Constance (PNNL)</a></li>
<li><a class="reference internal" href="#reference">Reference</a></li>
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