Merge branch 'develop' into bugfix/bnu_soil

Fixes ufs-community#821.

build_all.sh

@@ -8,49 +8,72 @@
 
 set -eux
 
+# Get the root of the cloned ufs-utils directory
+if [[ $(uname -s) == Darwin ]]; then
+  readonly DIR_ROOT=$(cd "$(dirname "$(greadlink -f -n "${BASH_SOURCE[0]}" )" )" && pwd -P)
+else
+  readonly DIR_ROOT=$(cd "$(dirname "$(readlink -f -n "${BASH_SOURCE[0]}" )" )" && pwd -P)
+fi
+
+# User Options
 target=${target:-"NULL"}
 compiler=${compiler:-"intel"}
-export MOD_PATH
+PW_CSP=${PW_CSP:-} # TODO: This is an implementation from EPIC and consistent with the UFS WM build system.
 
 if [[ "$target" == "linux.*" || "$target" == "macosx.*" ]]; then
- unset -f module
- set +x
- source ./modulefiles/build.$target > /dev/null
- set -x
+  unset -f module
+  set +x
+  source "${DIR_ROOT}/modulefiles/build.${target}" > /dev/null
+  set -x
 else
- set +x
- source ./sorc/machine-setup.sh
- module use ./modulefiles
- module load build.$target.$compiler > /dev/null
- module list
+  set +x
+  source "${DIR_ROOT}/sorc/machine-setup.sh"
+  if [[ "${target}" == "noaacloud" ]]; then
+    #TODO: This will need to be revisited once the EPIC supported-stacks come online.
+    #TODO: This is a hack due to how the spack-stack module files are generated; there may be a better way to do this.
+    source /contrib/global-workflow/spack-stack/envs/spack_2021.0.3.env
+  else
+    module use "${DIR_ROOT}/modulefiles"
+  fi
+  module load "build.$target.$compiler" > /dev/null
+  module list
  set -x
 fi
 
 # Ensure the submodules have been initialized.
 
-if [[ ! -d ./ccpp-physics/physics ]]; then
+if [[ ! -d "${DIR_ROOT}/ccpp-physics/physics" ]]; then
+  cd "${DIR_ROOT}"
   git submodule init
   git submodule update
 fi
 
+# Collect BUILD Options
+CMAKE_FLAGS+=" -DCMAKE_BUILD_TYPE=${BUILD_TYPE:-Release}"
+
+# Install options; destination for built executables, libraries, CMake Package config
+CMAKE_FLAGS+=" -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX:-${DIR_ROOT}} -DCMAKE_INSTALL_BINDIR=${INSTALL_BINDIR:-exec}"
+
+# Testing options
 # 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.
-
-CMAKE_FLAGS="-DCMAKE_INSTALL_PREFIX=../ -DCMAKE_INSTALL_BINDIR=exec -DBUILD_TESTING=OFF"
+CMAKE_FLAGS+=" -DBUILD_TESTING=${BUILD_TESTING:-OFF}"
 
 # Allow users of this script to provide CMake options e.g. -DGFS=ON|OFF to build GFS specific utilities only
 CMAKE_OPTS=${CMAKE_OPTS:-}
 
-rm -fr ./build
-mkdir ./build && cd ./build
+# Re-use or create a new BUILD_DIR (Default: create new BUILD_DIR)
+BUILD_DIR=${BUILD_DIR:-"${DIR_ROOT}/build"}
+[[ ${BUILD_CLEAN:-"YES"} =~ [yYtT] ]] && rm -rf "$BUILD_DIR"
+mkdir -p "${BUILD_DIR}" && cd "${BUILD_DIR}"
 
-cmake .. ${CMAKE_FLAGS} ${CMAKE_OPTS}
+cmake ${CMAKE_FLAGS} ${CMAKE_OPTS} "${DIR_ROOT}"
 
-make -j ${BUILD_JOBS:-8} VERBOSE=${BUILD_VERBOSE:-}
+make -j "${BUILD_JOBS:-8}" VERBOSE="${BUILD_VERBOSE:-}"
 make install
 
 #ctest
 #ctest -I 4,5
 
-exit
+exit 0

modulefiles/build.noaacloud.intel.lua

@@ -0,0 +1,59 @@
+help([[ 
+Load environment to compile UFS_UTILS on NOAA CSPs using Intel
+]])
+
+cmake_ver=os.getenv("cmake_ver") or "3.16.1"
+load(pathJoin("cmake", cmake_ver))
+
+hpc_intel_ver=os.getenv("hpc_intel_ver") or "2021.3.0"
+load(pathJoin("intel", hpc_intel_ver))
+
+impi_ver=os.getenv("impi_ver") or "2021.3.0"
+load(pathJoin("impi", impi_ver))
+
+bacio_ver=os.getenv("bacio_ver") or "2.4.1"
+load(pathJoin("bacio", bacio_ver))
+
+g2_ver=os.getenv("g2_ver") or "3.4.5"
+load(pathJoin("g2", g2_ver))
+
+ip_ver=os.getenv("ip_ver") or "4.0.0"
+load(pathJoin("ip", ip_ver))
+
+nemsio_ver=os.getenv("nemsio_ver") or "2.5.4"
+load(pathJoin("nemsio", nemsio_ver))
+
+sp_ver=os.getenv("sp_ver") or "2.3.3"
+load(pathJoin("sp", sp_ver))
+
+w3emc_ver=os.getenv("w3emc_ver") or "2.9.2"
+load(pathJoin("w3emc", w3emc_ver))
+
+sfcio_ver=os.getenv("sfcio_ver") or "1.4.1"
+load(pathJoin("sfcio", sfcio_ver))
+
+sigio_ver=os.getenv("sigio_ver") or "2.3.2"
+load(pathJoin("sigio", sigio_ver))
+
+zlib_ver=os.getenv("zlib_ver") or "1.2.11"
+load(pathJoin("zlib", zlib_ver))
+
+png_ver=os.getenv("png_ver") or "1.6.35"
+load(pathJoin("libpng", png_ver))
+
+hdf5_ver=os.getenv("hdf5_ver") or "1.10.6"
+load(pathJoin("hdf5", hdf5_ver))
+
+netcdf_ver=os.getenv("netcdf_ver") or "4.6.1"
+load(pathJoin("netcdf", netcdf_ver))
+
+nccmp_ver=os.getenv("nccmp_ver") or "1.8.9.0"
+load(pathJoin("nccmp", nccmp_ver))
+
+esmf_ver=os.getenv("esmf_ver") or "8.4.0b08"
+load(pathJoin("esmf", esmf_ver))
+
+nco_ver=os.getenv("nco_ver") or "4.9.1"
+load(pathJoin("nco", nco_ver))
+
+whatis("Description: UFS_UTILS build environment")

reg_tests/global_cycle/C768.lndincsoil.sh → reg_tests/global_cycle/C192.lndincsoilnoahmp.sh

@@ -1,8 +1,9 @@
 #!/bin/bash
 
 #------------------------------------------------------------------
-# Run global_cycle for a C768 case to test the ingest and
-# application of soil temperature increments from the GSI.  
+# Run global_cycle for a C192 case to test the ingest and
+# application of soil moisture and temperature increments
+# from the GSI, into Noah-MP restarts.
 # Compare output to a baseline set of files using the 'nccmp' 
 # utility.
 #------------------------------------------------------------------
@@ -22,13 +23,9 @@ export CDATE=2019073000
 export FHOUR=00
 export DELTSFC=6
 
-export CASE=C768
+export CASE=C192
 
-export COMIN=$HOMEreg/input_data
-export FNTSFA=$COMIN/gdas.t00z.rtgssthr.grb
-export FNSNOA=$COMIN/gdas.t00z.snogrb_t1534.3072.1536
-export FNACNA=$COMIN/gdas.t00z.seaice.5min.blend.grb
-export NST_FILE=$COMIN/gdas.t00z.dtfanl.nc
+export COMIN=$HOMEreg/input_data_noahmp
 
 export LND_SOI_FILE=$COMIN/sfcincr_gsi
 
@@ -52,7 +49,7 @@ $BASE_GSM/ush/global_cycle_driver.sh
 iret=$?
 if [ $iret -ne 0 ]; then
   set +x
-  echo "<<< C768 LANDINC SOILT CYCLE TEST FAILED. >>>"
+  echo "<<< C192 LANDINC SOIL NOAHMP CYCLE TEST FAILED. >>>"
   exit $iret
 fi
 
@@ -63,7 +60,7 @@ for files in *tile*.nc
 do
   if [ -f $files ]; then
     echo CHECK $files
-    $NCCMP -dmfqS $files $HOMEreg/baseline_data/c768.lndincsoil/$files
+    $NCCMP -dmfqS $files $HOMEreg/baseline_data/c192.lndincsoilnoahmp/$files
     iret=$?
     if [ $iret -ne 0 ]; then
       test_failed=1
@@ -75,15 +72,15 @@ set +x
 if [ $test_failed -ne 0 ]; then
   echo
   echo "*****************************************"
-  echo "<<< C768 LANDINC SOILT CYCLE TEST FAILED. >>>"
+  echo "<<< C192 LANDINC SOIL-NOAHP CYCLE TEST FAILED. >>>"
   echo "*****************************************"
   if [ "$UPDATE_BASELINE" = "TRUE" ]; then
-    $BASE_GSM/reg_tests/update_baseline.sh $HOMEreg "c768.lndincsoil" $commit_num
+    $BASE_GSM/reg_tests/update_baseline.sh $HOMEreg "c192.lndincsoilnoahmp" $commit_num
   fi
 else
   echo
   echo "*****************************************"
-  echo "<<< C768 LANDINC SOILT CYCLE TEST PASSED. >>>"
+  echo "<<< C192 LANDINC SOIL-NOAHMP CYCLE TEST PASSED. >>>"
   echo "*****************************************"
 fi
 

reg_tests/global_cycle/driver.hera.sh

@@ -64,8 +64,8 @@ TEST1=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_C
 LOG_FILE=consistency.log02
 export DATA="${DATA_DIR}/test2"
 export COMOUT=$DATA
-TEST2=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J c768.lndincsoil \
-     -o $LOG_FILE -e $LOG_FILE ./C768.lndincsoil.sh)
+TEST2=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J c192.lndincsoilnoahmp \
+     -o $LOG_FILE -e $LOG_FILE ./C192.lndincsoilnoahmp.sh)
 
 LOG_FILE=consistency.log03
 export DATA="${DATA_DIR}/test3"

reg_tests/global_cycle/driver.jet.sh

@@ -62,8 +62,8 @@ TEST1=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_C
 LOG_FILE=consistency.log02
 export DATA="${DATA_DIR}/test2"
 export COMOUT=$DATA
-TEST2=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J c768.lndincsoil \
-      --partition=xjet -o $LOG_FILE -e $LOG_FILE ./C768.lndincsoil.sh)
+TEST2=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J c192.lndincsoilnoahmp \
+      --partition=xjet -o $LOG_FILE -e $LOG_FILE ./C192.lndincsoilnoahmp.sh)
 
 LOG_FILE=consistency.log03
 export DATA="${DATA_DIR}/test3"

reg_tests/global_cycle/driver.orion.sh

@@ -62,8 +62,8 @@ TEST1=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_C
 LOG_FILE=consistency.log02
 export DATA="${DATA_DIR}/test2"
 export COMOUT=$DATA
-TEST2=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J c768.lndincsoil \
-      -o $LOG_FILE -e $LOG_FILE ./C768.lndincsoil.sh)
+TEST2=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J c192.lndincsoilnoahmp \
+      -o $LOG_FILE -e $LOG_FILE ./C192.lndincsoilnoahmp.sh)
 
 LOG_FILE=consistency.log03
 export DATA="${DATA_DIR}/test3"

reg_tests/global_cycle/driver.wcoss2.sh

@@ -69,7 +69,7 @@ TEST1=$(qsub -V -o ${LOG_FILE}01 -e ${LOG_FILE}01 -q $QUEUE -A $PROJECT_CODE -l
 export DATA="${DATA_DIR}/test2"
 export COMOUT=$DATA
 TEST2=$(qsub -V -o ${LOG_FILE}02 -e ${LOG_FILE}02 -q $QUEUE -A $PROJECT_CODE -l walltime=00:05:00 \
-        -N c768.lndincsoil -l select=1:ncpus=12:mem=8GB $PWD/C768.lndincsoil.sh)
+        -N c192.lndincsoilnoahmp -l select=1:ncpus=12:mem=8GB $PWD/C192.lndincsoilnoahmp.sh)
 
 export DATA="${DATA_DIR}/test3"
 export COMOUT=$DATA