Add note on need to set MPI_TYPE_DEPTH for LILAC

Author: billsacks

doc/source/lilac/obtaining-building-and-running/index.rst

@@ -9,4 +9,5 @@
 
    obtaining-and-building-ctsm.rst
    setting-ctsm-runtime-options.rst
+   notes-on-running-ctsm.rst
    restarting.rst

doc/source/lilac/obtaining-building-and-running/notes-on-running-ctsm.rst

@@ -0,0 +1,26 @@
+.. highlight:: shell
+
+.. _notes-on-running-ctsm:
+
+=======================
+ Notes on running CTSM
+=======================
+
+.. _runtime-environment-variables:
+
+Environment variables that may need to be set at runtime
+========================================================
+
+With the MPT MPI library (which is the default MPI library on NCAR's cheyenne machine), it is important to set the environment variable ``MPI_TYPE_DEPTH`` to 16 when running CTSM (this setting is required by the Parallel IO library). Typically you should set this variable in your job submission script, using either:
+
+.. code-block:: Bash
+
+    export MPI_TYPE_DEPTH=16
+
+or:
+
+.. code-block:: Tcsh
+
+    setenv MPI_TYPE_DEPTH 16
+
+prior to running the model.

doc/source/lilac/specific-atm-models/wrf.rst

@@ -390,8 +390,11 @@ A simple PBS script to run WRF-CTSM on ``Cheyenne`` looks like this:
     #PBS -l select=2:ncpus=36:mpiprocs=36
 
     ### Run the executable
+    setenv MPI_TYPE_DEPTH 16
     mpiexec_mpt ./wrf.exe
 
+(See :numref:`runtime-environment-variables` for a description of the need to set ``MPI_TYPE_DEPTH`` on ``Cheyenne``.)
+
 To submit a batch job to the ``Cheyenne`` queues, use ``qsub`` command followed
 by the PBS script name. 
 For example, if you named this script ``run_wrf_ctsm.csh``, submit the job like this::