Updated documentation for building out of box capability for CESM on …

…keeling. (#13)

* Add files via upload

* Add files via upload

Updated out of box capability page for CESM:
Removed cp commands from inaccessible directory
Copy-paste instructions for important code blocks

* Update out_of_box_cesm.rst

Changed method of updating configuration files for Machines and Compilers to copy and paste code blocks.
Previous directory was not accessible to copy from.
Instructions to check file paths for config_machines.xml

docs/source/cesm/out_of_box_cesm.rst

@@ -12,7 +12,7 @@ Machine Configuration
 Here, specifications, compilers, and other configurations for various machines at places
 like NCAR are located. We will need to replicate these conditions for keeling.
 
-Try ``cp /data/keeling/a/mailes2/CESM/cesm1_2_1/scripts/ccsm_utils/Machines/config_machines.xml .`` and edit $HOME to your home directory in the following entries:
+Navigate to the file ``/CESM/cesm1_2_1/scripts/ccsm_utils/Machines/config_machines.xml`` and edit $HOME to your home directory in the following entries:
 
 * RUNDIR
 * EXEROOT
@@ -52,13 +52,12 @@ Format should look like below.
 In place of each $HOME variable, put your home directory. Any path with $CASE in it will
 automatically create the desired directories for each case when called. You may need to
 create the Baseline and long term archiving (DOUT_L_MSROOT) directories yourself
-though.
+though. Be sure to check that all the file paths match the directories in your system.
 
 Machine compilers
 =================
-Try ``cp /data/keeling/a/mailes2/CESM/cesm1_2_1/scripts/ccsm_utils/Machines/config_compilers.xml .``
-
-Make sure the keeling entry (below the intel entry) looks like below.
+In the file ``CESM/cesm1_2_1/scripts/ccsm_utils/Machines/config_compilers.xml``,
+paste the code block and check that the keeling entry (below the intel entry) looks like below.
 
 .. code-block:: xml
 
@@ -78,13 +77,15 @@ Copy the userdefined file:
 
 Make batch
 ============
-Try ``cp /data/keeling/a/mailes2/CESM/cesm1_2_1/scripts/ccsm_utils/Machines/mkbatch.keeling .``
+In the file ``CESM/cesm1_2_1/scripts/ccsm_utils/Machines/mkbatch.keeling``
+
+Copy and paste any of the missing chunks of code below:
 
-Check the time limit is set to one day:
+1. Check the time limit is set to one day:
 
 ``set tlimit = "1-00:00:00"``
 
-Under the first USERDEFINED section, it should look like below.
+2. Under the first USERDEFINED section, it should look like below.
 
 .. code-block:: xml
 
@@ -103,7 +104,7 @@ Under the first USERDEFINED section, it should look like below.
 
 Change ``--mail-user`` to your own email.
 
-The according PBS lines should look like the following:
+3. The according PBS lines should look like the following:
 
 .. code-block:: xml
 
@@ -112,7 +113,7 @@ The according PBS lines should look like the following:
    ##PBS -l nodes=${nodes}:ppn=${taskpernode}
    ##PBS -l walltime=${tlimit}
 
-And the BSUB lines:
+4. And the BSUB lines:
 
 .. code-block:: xml
 
@@ -121,14 +122,14 @@ And the BSUB lines:
    ...
    ###BSUB -W ${tlimit}
 
-Under the second USERDEFINED section, the MPI exec and run lines should look like this:
+5. Under the second USERDEFINED section, the MPI exec and run lines should look like this:
 
 .. code-block:: console 
 
    #mpiexec -n ${maxtasks} \$EXEROOT/cesm.exe >&! cesm.log.\$LID
    mpirun -np ${maxtasks} \$EXEROOT/cesm.exe >&! cesm.log.\$LID
 
-Make sure env_mach_specific.keeling and mkbatch.keeling are executable!
+Make sure env_mach_specific.keeling and mkbatch.keeling are executable! (ll)
 
 Running a case
 ===============