Unify build system

Combines the checkout and build from the standard and coupled workflows
system that checks out the current UFS.

The model source directory is now ufs_model.fd rather than fv3gfs.fd or
ufs_coupled.fd. The build script is renamed build_ufs.sh and the link
script is renamed to simply link.sh.

The checkout script checks out the same UFS version (current as of
2021 Jul 20) for all applications, removing the coupled option from the
coupled branch. A new option, -m, allows the user to specify a different
model hash to check out. Checkout log files are now placed in the logs
directory like the build logs in order to keep the sorc directory clean.

Two new options are added to the build_all script: -c to build the
coupled (S2SW) app, and -a to build the aerosol (ATMAERO) app. Without
either argument, the traditional (ATMW) app is built. If either option
is provided, the cpl_build.cfg file controls which executables are built;
otherwise fv3gfs_build.cfg is still used. The build_ufs script corre-
spondingly accepts the same options.

The reg2grb2 source directory is copied over from the coupled model and
cmake files for workflow_utils are updated correspondingly to build.
Additionally, the build_workflow_utils modulefiles are updated to use the
ncio module in hpc-stack and the hack that cloned and built it as part of
the workflow_utils build is removed.

The build_ww3prepost script is updated to make the code more easily main-
tained and the corresponding modulefiles are updated to remove unnecessary
modules.

The link script is updated to the new fix location (ending in fix_NEW)
removes links with targets that no longer exist. A new third argument to
link, coupled, is added to additionally link files needed by the coupled
system.

Note that while the checkout, build, and link have all been tested and
complete without error, the workflow is otherwise untested and may not
work until additional updates are made to use the current UFS.

Refs: NOAA-EMC#366, NOAA-EMC#368, NOAA-EMC#374

.gitignore

@@ -30,7 +30,7 @@ parm/wafs
 #--------------------------------------------
 sorc/*log
 sorc/logs
-sorc/fv3gfs.fd
+sorc/ufs_model.fd
 sorc/gfs_post.fd
 sorc/gfs_wafs.fd
 sorc/gldas.fd

modulefiles/modulefile.ww3.hera

@@ -13,20 +13,7 @@ module load jasper/2.0.25
 module load zlib/1.2.11
 module load png/1.6.35
 
-module load hdf5/1.10.6
-module load netcdf/4.7.4
-module load pio/2.5.2
-module load esmf/8_1_1
-module load fms/2020.04.03
-
 module load bacio/2.4.1
-module load crtm/2.3.0
 module load g2/3.4.1
-module load g2tmpl/1.9.1
-module load ip/3.3.3
-module load nemsio/2.5.2
-module load sp/2.3.3
-module load w3emc/2.7.3
-module load w3nco/2.4.1
-module load wgrib2/2.0.8
-module load upp/10.0.6
+
+module load netcdf/4.7.4

modulefiles/modulefile.ww3.orion

@@ -14,20 +14,7 @@ module load jasper/2.0.25
 module load zlib/1.2.11
 module load png/1.6.35
 
-module load hdf5/1.10.6
-module load netcdf/4.7.4
-module load pio/2.5.2
-module load esmf/8_1_1
-module load fms/2020.04.03
-
 module load bacio/2.4.1
-module load crtm/2.3.0
 module load g2/3.4.1
-module load g2tmpl/1.9.1
-module load ip/3.3.3
-module load nemsio/2.5.2
-module load sp/2.3.3
-module load w3emc/2.7.3
-module load w3nco/2.4.1
-module load wgrib2/2.0.8
-module load upp/10.0.6
+
+module load netcdf/4.7.4

modulefiles/modulefile.ww3.wcoss_dell_p3

@@ -9,20 +9,7 @@ module load jasper/2.0.25
 module load zlib/1.2.11
 module load png/1.6.35
 
-module load hdf5/1.10.6
-module load netcdf/4.7.4
-module load pio/2.5.2
-module load esmf/8_1_1
-module load fms/2020.04.03
-
 module load bacio/2.4.1
-module load crtm/2.3.0
 module load g2/3.4.1
-module load g2tmpl/1.9.1
-module load ip/3.3.3
-module load nemsio/2.5.2
-module load sp/2.3.3
-module load w3emc/2.7.3
-module load w3nco/2.4.1
-module load wgrib2/2.0.8
-module load upp/10.0.6
+
+module load netcdf/4.7.4

modulefiles/workflow_utils.hera

@@ -20,7 +20,9 @@ module load sp/2.3.3
 module load ip/3.3.3
 module load nemsio/2.5.2
 module load nemsiogfs/2.5.3
-#module load ncio/1.0.0
+module load ncio/1.0.0
+module load landsfcutil/2.4.1
+module load wgrib2/2.0.8
 module load sigio/2.3.2
 module load g2/3.4.1
 module load bufr/11.4.0

modulefiles/workflow_utils.orion

@@ -20,7 +20,9 @@ module load sp/2.3.3
 module load ip/3.3.3
 module load nemsio/2.5.2
 module load nemsiogfs/2.5.3
-#module load ncio/1.0.0
+module load ncio/1.0.0
+module load landsfcutil/2.4.1
+module load wgrib2/2.0.8
 module load sigio/2.3.2
 module load g2/3.4.1
 module load bufr/11.4.0

modulefiles/workflow_utils.wcoss_dell_p3

@@ -20,7 +20,9 @@ module load sp/2.3.3
 module load ip/3.3.3
 module load nemsio/2.5.2
 module load nemsiogfs/2.5.3
-#module load ncio/1.0.0
+module load ncio/1.0.0
+module load landsfcutil/2.4.1
+module load wgrib2/2.0.8
 module load sigio/2.3.2
 module load g2/3.4.1
 module load bufr/11.4.0

sorc/CMakeLists.txt

@@ -51,17 +51,19 @@ find_package(sp REQUIRED)
 find_package(ip REQUIRED)
 find_package(ncio REQUIRED)
 find_package(nemsio REQUIRED)
-find_package(nemsiogfs REQUIRED)
 find_package(sigio REQUIRED)
 find_package(g2 REQUIRED)
 find_package(bufr REQUIRED)
+find_package(landsfcutil REQUIRED)
+find_package(wgrib2 REQUIRED)
 
 add_subdirectory(enkf_chgres_recenter.fd)
 add_subdirectory(enkf_chgres_recenter_nc.fd)
 add_subdirectory(fv3nc2nemsio.fd)
 add_subdirectory(regrid_nemsio.fd)
 add_subdirectory(gaussian_sfcanl.fd)
 add_subdirectory(gfs_bufr.fd)
+add_subdirectory(reg2grb2.fd)
 add_subdirectory(tocsbufr.fd)
 add_subdirectory(fbwndgfs.fd)
 add_subdirectory(vint.fd)

sorc/build_all.sh

@@ -9,6 +9,25 @@ set +x
 #                   Anything other than "true"  will use libraries locally.
 #------------------------------------
 
+_build_ufs_options=""
+
+while getopts "ac" option;do
+ case $option in
+  a)
+   echo "Received -a flag, building ufs-weather-model for ATMAERO app"
+   echo "skipping builds not needed for prototype runs"
+   _build_ufs_options=-a
+   break
+   ;;
+  c)
+   echo "Received -c flag, building ufs-weather-model for S2SW app"
+   echo "skipping builds not needed for prototype runs"
+   _build_ufs_options=-c
+   break
+   ;;
+ esac
+done
+
 export USE_PREINST_LIBS="true"
 
 #------------------------------------
@@ -37,28 +56,14 @@ source ./machine-setup.sh > /dev/null 2>&1
 #------------------------------------
 # INCLUDE PARTIAL BUILD 
 #------------------------------------
-
-. ./partial_build.sh
+. ./partial_build.sh $@
 
 #------------------------------------
 # Exception Handling Init
 #------------------------------------
 ERRSCRIPT=${ERRSCRIPT:-'eval [[ $err = 0 ]]'}
 err=0
 
-#------------------------------------
-# build fv3
-#------------------------------------
-$Build_fv3gfs && {
-echo " .... Building fv3 .... "
-./build_fv3.sh > $logs_dir/build_fv3.log 2>&1
-rc=$?
-if [[ $rc -ne 0 ]] ; then
-    echo "Fatal error in building fv3."
-    echo "The log file is in $logs_dir/build_fv3.log"
-fi
-((err+=$rc))
-}
 
 #------------------------------------
 # build WW3 pre & post execs 
@@ -74,6 +79,20 @@ fi
 ((err+=$rc))
 }
 
+#------------------------------------
+# build forecast model 
+#------------------------------------
+$Build_ufs_model && {
+    echo " .... Building forecast model .... "
+    ./build_ufs.sh ${_build_ufs_options} > $logs_dir/build_ufs.log 2>&1
+    rc=$?
+    if [[ $rc -ne 0 ]] ; then
+        echo "Fatal error in building UFS model."
+        echo "The log file is in $logs_dir/build_ufs.log"
+    fi
+    ((err+=$rc))
+}
+
 #------------------------------------
 # build gsi
 #------------------------------------

sorc/build_ufs.sh

@@ -0,0 +1,49 @@
+#! /usr/bin/env bash
+set -eux
+
+# Build ATMW by default
+APP="ATMW"
+CCPP_SUITES="FV3_GFS_v16,FV3_GFS_v16_RRTMGP,FV3_GFS_v16_ugwpv1"
+
+while getopts "ac" option; do
+  case "${option}" in
+    a)
+      APP="ATMAERO"
+      CCPP_SUITES="FV3_GFS_v16,FV3_GFS_v16_ugwpv1"
+      shift
+      ;;
+    c)
+      APP="S2SW"
+      CCPP_SUITES="FV3_GFS_v16_coupled,FV3_GFS_v16_couplednsst,FV3_GFS_v16_coupled_nsstNoahmpUGWPv1"
+      shift
+      ;;
+    *)
+      echo "Unrecognized option: ${1}"
+      exit 1
+      ;;
+  esac
+done
+
+source ./machine-setup.sh > /dev/null 2>&1
+cwd=$(pwd)
+
+# Remove previous build directory if it exists
+if [ -d ufs_model.fd/build ]; then
+  rm -R ufs_model.fd/build
+fi
+
+# Set target platform
+case "${target}" in
+  hera|orion|stampede)
+    target=${target}.intel
+    ;;
+esac
+
+MOD_PATH=$cwd/ufs_model.fd/modulefiles
+
+module purge
+
+cd ufs_model.fd/
+module use ${MOD_PATH}
+module load ufs_${target}
+CMAKE_FLAGS="-DAPP=${APP} -DCCPP_SUITES=${CCPP_SUITES}" ./build.sh

sorc/build_workflow_utils.sh

@@ -5,35 +5,19 @@ set -eux
 readonly UTILS_DIR=$(cd "$(dirname "$($cmd -f -n "${BASH_SOURCE[0]}" )" )" && pwd -P)
 
 # Adapt for global-workflow structure.
-target=${target:-"NULL"}
+source ${UTILS_DIR}/machine-setup.sh > /dev/null 2>&1
 modulefile=${UTILS_DIR}/../modulefiles/workflow_utils.$target
 if [[ -f $modulefile ]]; then
   set +x
-  source ${UTILS_DIR}/machine-setup.sh > /dev/null 2>&1
   source $modulefile
   module list
   set -x
+else
+  echo "FATAL: modulefile $modulefile not found!"
+  exit 1
 fi
 # End adaptation
 
-# Begin hack
-# In place until nceplibs-ncio is in hpc-stack and available as a module
-# After nceplibs-ncio is in hpc-stack, add the following line to
-# ${UTILS_DIR}/../modulefiles/workflow_utils.<platform>
-# "module load ncio/<ncio-version>"
-# and remove this hack
-
-[[ -d nceplibs-ncio ]] && rm -rf nceplibs-ncio
-git clone -b develop https://github.com/noaa-emc/nceplibs-ncio
-cd nceplibs-ncio
-mkdir -p build && cd build
-cmake -DCMAKE_INSTALL_PREFIX=../install ..
-make -j ${BUILD_JOBS:-4} VERBOSE=${BUILD_VERBOSE:-}
-make install
-cd ../..
-export ncio_ROOT=$PWD/nceplibs-ncio/install
-# End hack
-
 BUILD_DIR=${BUILD_DIR:-${UTILS_DIR}/build}
 [[ -d $BUILD_DIR ]] && rm -rf $BUILD_DIR
 mkdir -p ${BUILD_DIR}