Improve repository build script (#819)

Update the build_all.sh script to do a "submodule update" if
necessary before building.

Update build instructions in README.md.

Update the rt.sh script to remove the recursive clone as submodules
are now handled by the build script.

Fixes #818.

README.md

@@ -59,20 +59,21 @@ It also uses the following repositories:
 
 ## Installing
 
-On Orion, Jet, Hera and WCOSS2, invoke the build script:
+On Orion, Jet, Hera and WCOSS2 do the following:
+
+1) Set the 'fixed' directories using the `link_fixdirs.sh`
+script in `./fix`. Usage: `./link_fixdirs.sh $RUN_ENVIR $machine`,
+where `$RUN_ENVIR` is "emc" or "nco" (most developers
+should choose "emc") and `$machine` is the platform. Example:
 
 ```
-./build_all.sh
+./link_fixdirs.sh emc hera
 ```
 
-Otherwise, do:
+2) Then, invoke the build script:
 
 ```
-mkdir build
-cd build
-cmake -DCMAKE_INSTALL_PREFIX=/path/to/install ..
-make -j2
-make install
+./build_all.sh
 ```
 
 ## Contents

build_all.sh

@@ -26,6 +26,13 @@ else
  set -x
 fi
 
+# Ensure the submodules have been initialized.
+
+if [[ ! -d ./ccpp-physics/physics ]]; then
+  git submodule init
+  git submodule update
+fi
+
 # The unit test data download is part of the build system. Not all machines can
 # access the EMC ftp site, so turn off the build (-DBUILD_TESTING=OFF) of the units tests accordingly.
 # Those with access to the EMC ftp site are: Orion and Hera.

fix/link_fixdirs.sh

@@ -1,7 +1,15 @@
 #!/bin/bash
 set -ex
 
-#--Make symbolic links to 'fixed' directories.
+# Set up the 'fixed' directories. 
+# 
+# This script takes two arguments:
+#
+#  $RUN_ENVIR - Either 'emc' (creates links) or
+#               'nco' (copies data).
+#
+#  $machine - is the machine. Choices are:
+#             'wcoss2', 'hera', 'jet', 'orion', 's4'
 
 RUN_ENVIR=${1}
 machine=${2}

reg_tests/rt.sh

@@ -1,4 +1,4 @@
-#!/bin/bash -l
+#!/bin/bash
 
 ulimit -s unlimited
 
@@ -16,7 +16,7 @@ cd ${WORK_DIR}
 rm -f reg_test_results.txt
 rm -rf UFS_UTILS
 
-git clone --recursive https://github.com/ufs-community/UFS_UTILS.git
+git clone https://github.com/ufs-community/UFS_UTILS.git
 rc=$?
 
 # Check to see if the clone was successful. Previously, it has