Merge branch 'develop' into feature/dev-wcoss2

* develop:
  change gdasechgres dependency to just gdasefcs01 instead of gdasefmn (#933)
  Remove obsolete platforms (WCOSS1, Dell, Cray, Theia) references. (#922)
  Optimize DA clone, build, and link (#931)

Author: KateFriedman-NOAA

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