Remove obsolete platforms (WCOSS1, Dell, Cray, Theia) references. (#922)

Removes code related to decommissioned HPC platforms WCOSS 1 (Dell & Cray) and Theia. Some references remain in scripts outside the global-workflow repo that are cloned as part of `checkout.sh`. Scripts from the `driver` directory that were hard-wired for one of the WCOSS1 platforms are also removed.

Additionally, this commit also switches to using serial netCDF for resolutions C48. C96, C192.  Running with parallel netCDF (on Hera) gave errors when testing at C96 for the deterministic forecast.  If someone gives a very compelling reason to use parallel netCDF at these resolutions as default, I would be very interested in what they have to say.

Closes #680

docs/doxygen/compile

@@ -1,20 +1,22 @@
-#!/bin/ksh -x
+#!/bin/bash
 
-machine=${1:-${machine:-"WCOSS_C"}}
+set -ex
+
+machine=${1:-${machine:-"HERA"}}
 machine=$(echo $machine | tr '[a-z]' '[A-Z]')
 
 if [ $machine = "HERA" ]; then
     doxygen=/usr/bin/doxygen
-elif [ $machine = "WCOSS_C" ]; then
-    doxygen=/gpfs/hps3/emc/hwrf/noscrub/soft/doxygen-1.8.10/bin/doxygen
-elif [ $machine = "WCOSS" ]; then
-    doxygen=/hwrf/noscrub/soft/doxygen-1.8.10/bin/doxygen
+elif [ $machine = "ORION" ]; then
+    doxygen=/bin/doxygen
 elif [ $machine = "JET" ]; then
     doxygen=/contrib/doxygen/1.8.10/bin/doxygen
 else
-    echo "machine $machine is unrecognized, ABORT!"
-    echo "try system doxygen"
+    echo "machine $machine is unrecognized!"
+    echo "trying system doxygen"
     doxygen=$(which doxygen)
+    rc=$?
+    [[ $rc -ne 0 ]] && (echo "doxygen not found, ABORT!"; exit 1)
 fi
 
 $doxygen

docs/doxygen/mainpage.h

@@ -21,7 +21,7 @@ This is a very much a work in progress and any issues should be reported back an
 To setup an experiment, a python script <b>\c setup_expt.py</b> (located in <b>\c fv3gfs/ush</b>) can be used:
 
     $> setup_expt.py -h
-    usage: setup_expt.py [-h] [--machine {HERA,WCOSS_C}] --pslot PSLOT
+    usage: setup_expt.py [-h] --pslot PSLOT
                      [--configdir CONFIGDIR] [--idate IDATE] [--icsdir ICSDIR]
                      [--resdet RESDET] [--resens RESENS] [--comrot COMROT]
                      [--expdir EXPDIR] [--nens NENS] [--cdump CDUMP]
@@ -32,8 +32,6 @@ To setup an experiment, a python script <b>\c setup_expt.py</b> (located in <b>\
 
     optional arguments:
         -h, --help   show this help message and exit
-        --machine    machine name
-                        (default: WCOSS_C)
         --pslot      parallel experiment name [REQUIRED]
                         (default: None)
         --configdir  full path to directory containing the config files
@@ -58,8 +56,8 @@ To setup an experiment, a python script <b>\c setup_expt.py</b> (located in <b>\
 The above script creates directories <b>\c EXPDIR</b> and <b>\c COMROT</b>. It will make links for initial conditions from a location provided via the <b>\c --icsdir</b> argument for a chosen resolution for the control <b>\c --resdet</b> and the ensemble <b>\c --resens</b>. Experiment name is controlled by the input argument <b>\c --pslot</b>. The script will ask user input in case any of the directories already exist. It will copy experiment configuration files into the <b>\c EXPDIR</b> from <b>\c CONFIGDIR</b>.
 
 Sample initial conditions for a few resolutions are available at:<br>
-<b>Theia:</b> /scratch4/NCEPDEV/da/noscrub/Rahul.Mahajan/ICS<br>
-<b>WCOSS Cray:</b> /gpfs/hps/emc/da/noscrub/Rahul.Mahajan/ICS
+<b>Hera:</b> TODO: /path/here/for/initial/conditions<br>
+<b>Orion:</b> TODO: /path/here/for/initial/conditions<br>
 
 Next step is for the user to go through the individual config files (atleast <b>\c config.base</b>) and customize the experiment configuration based on user needs. A stock configuration will be provided at a later stage, but it is imperative that the user understand the steps involved in the system.
 

docs/note_fixfield.txt

@@ -2,9 +2,8 @@
 For EMC, the fix fields for running the model are not included in git repository.
 They are saved locally on all platforms
 
-Venus/Mars:  /gpfs/dell2/emc/modeling/noscrub/emc.glopara/git/fv3gfs/fix
-Surge/Luna: /gpfs/hps3/emc/global/noscrub/emc.glopara/git/fv3gfs/fix
-Hera: /scratch1/NCEPDEV/global/glopara/fix 
+Hera: /scratch1/NCEPDEV/global/glopara/fix
+Orion: /work/noaa/global/glopara/fix
 
 ------------------------------------------------------------------------------
 09/28/2018