Merge branch 'develop' into cleanup/oro_script

Fixes ufs-community#932.

README.md

@@ -59,7 +59,7 @@ It also uses the following repositories:
 
 ## Installing
 
-On Orion, Hercules, Jet, Hera and WCOSS2 do the following:
+On Orion, Hercules, Jet, Hera, S4, Gaea 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`,

fix/link_fixdirs.sh

@@ -9,15 +9,15 @@ set -ex
 #               'nco' (copies data).
 #
 #  $machine - is the machine. Choices are:
-#             'wcoss2', 'hera', 'jet', 'orion', 'hercules', 's4'
+#             'wcoss2', 'hera', 'jet', 'orion', 'hercules', 's4', 'gaea'
 
 RUN_ENVIR=${1}
 machine=${2}
 
 if [ $# -lt 2 ]; then
     set +x
     echo '***ERROR*** must specify two arguements: (1) RUN_ENVIR, (2) machine'
-    echo ' Syntax: link_fv3gfs.sh ( nco | emc ) ( wcoss2 |  hera  | jet | orion | hercules | s4 )'
+    echo ' Syntax: link_fv3gfs.sh ( nco | emc ) ( wcoss2 |  hera  | jet | orion | hercules | s4 | gaea )'
     exit 1
 fi
 
@@ -28,10 +28,10 @@ if [ $RUN_ENVIR != emc -a $RUN_ENVIR != nco ]; then
     exit 1
 fi
 
-if [ $machine != wcoss2 -a $machine != hera -a $machine != jet -a $machine != orion -a $machine != s4 -a $machine != hercules ]; then
+if [ $machine != wcoss2 -a $machine != hera -a $machine != jet -a $machine != orion -a $machine != s4 -a $machine != hercules -a $machine != gaea ]; then
     set +x
     echo '***ERROR*** unsupported machine'
-    echo 'Syntax: link_fv3gfs.sh ( nco | emc ) ( wcoss2 | hera | jet | orion | hercules | s4 )'
+    echo 'Syntax: link_fv3gfs.sh ( nco | emc ) ( wcoss2 | hera | jet | orion | hercules | s4 | gaea )'
     exit 1
 fi
 
@@ -54,6 +54,8 @@ elif [ $machine = "wcoss2" ]; then
     FIX_DIR="/lfs/h2/emc/global/noscrub/emc.global/FIX/fix"
 elif [ $machine = "s4" ]; then
     FIX_DIR="/data/prod/glopara/fix"
+elif [ $machine = "gaea" ]; then
+    FIX_DIR="/gpfs/f5/epic/proj-shared/global/glopara/data/fix"
 fi
 
 am_ver=${am_ver:-20220805}

modulefiles/build.gaea.intel.lua

@@ -0,0 +1,66 @@
+help([[
+Load environment to compile UFS_UTILS on Gaea using Intel
+]])
+
+prepend_path("MODULEPATH", "/sw/rdtn/modulefiles")
+load("hsi")
+
+prepend_path("MODULEPATH", "/ncrc/proj/epic/spack-stack/spack-stack-1.6.0/envs/unified-env/install/modulefiles/Core")
+
+stack_intel_ver=os.getenv("stack_intel_ver") or "2023.1.0"
+load(pathJoin("stack-intel", stack_intel_ver))
+
+stack_cray_mpich_ver=os.getenv("stack_cray_mpich_ver") or "8.1.25"
+load(pathJoin("stack-cray-mpich", stack_cray_mpich_ver))
+
+cmake_ver=os.getenv("cmake_ver") or "3.23.1"
+load(pathJoin("cmake", cmake_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 "4.3.0"
+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 "2.5.0"
+load(pathJoin("sp", sp_ver))
+
+w3emc_ver=os.getenv("w3emc_ver") or "2.10.0"
+load(pathJoin("w3emc", w3emc_ver))
+
+-- Uncomment when CHGRES_ALL is ON
+--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 "1.2.13"
+load(pathJoin("zlib", zlib_ver))
+
+png_ver=os.getenv("png_ver") or "1.6.37"
+load(pathJoin("libpng", png_ver))
+
+netcdf_c_ver=os.getenv("netcdf_c_ver") or "4.9.2"
+load(pathJoin("netcdf-c", netcdf_c_ver))
+
+netcdf_fortran_ver=os.getenv("netcdf_fortran_ver") or "4.6.1"
+load(pathJoin("netcdf-fortran", netcdf_fortran_ver))
+
+nccmp_ver=os.getenv("nccmp_ver") or "1.9.0.1"
+load(pathJoin("nccmp", nccmp_ver))
+
+esmf_ver=os.getenv("esmf_ver") or "8.6.0"
+load(pathJoin("esmf", esmf_ver))
+
+nco_ver=os.getenv("nco_ver") or "5.0.6"
+load(pathJoin("nco", nco_ver))
+
+whatis("Description: UFS_UTILS build environment")
+

reg_tests/global_cycle/C192.lndincsoilnoahmp.sh → reg_tests/global_cycle/C192.gsi_lndincsoilnoahmp.sh

@@ -29,8 +29,6 @@ export OCNRES=99999
 
 export COMIN=$HOMEreg/input_data_noahmp
 
-export LND_SOI_FILE=$COMIN/sfcincr_gsi
-
 export JCAP=1534
 export LONB=3072
 export LATB=1536
@@ -40,6 +38,7 @@ export use_ufo=.true.
 
 export DO_SFCCYCLE=".FALSE." 
 export DO_LNDINC=".TRUE." 
+export DO_SOI_INC_GSI=".true."
 
 export VERBOSE=YES
 export CYCLVARS=FSNOL=-2.,FSNOS=99999.,
@@ -49,7 +48,7 @@ $HOMEgfs/ush/global_cycle_driver.sh
 iret=$?
 if [ $iret -ne 0 ]; then
   set +x
-  echo "<<< C192 LANDINC SOIL NOAHMP CYCLE TEST FAILED. >>>"
+  echo "<<< C192 GSI based LANDINC SOIL NOAHMP CYCLE TEST FAILED. >>>"
   exit $iret
 fi
 
@@ -60,7 +59,19 @@ for files in *tile*.nc
 do
   if [ -f $files ]; then
     echo CHECK $files
-    $NCCMP -dmfqS $files $HOMEreg/baseline_data/c192.lndincsoilnoahmp/$files
+    $NCCMP -dmfqS $files $HOMEreg/baseline_data/c192.gsi_lndincsoilnoahmp/$files
+    iret=$?
+    if [ $iret -ne 0 ]; then
+      test_failed=1
+    fi
+  fi
+done
+
+for files in *gaussian_interp*
+do
+  if [ -f $files ]; then
+    echo CHECK $files
+    $NCCMP -dmfqS $files $HOMEreg/baseline_data/c192.gsi_lndincsoilnoahmp/$files
     iret=$?
     if [ $iret -ne 0 ]; then
       test_failed=1
@@ -72,15 +83,15 @@ set +x
 if [ $test_failed -ne 0 ]; then
   echo
   echo "**********************************************"
-  echo "<<< C192 LANDINC SOIL-NOAHMP CYCLE TEST FAILED. >>>"
+  echo "<<< C192 GSI based LANDINC SOIL-NOAHMP CYCLE TEST FAILED. >>>"
   echo "**********************************************"
   if [ "$UPDATE_BASELINE" = "TRUE" ]; then
     $HOMEgfs/reg_tests/update_baseline.sh $HOMEreg "c192.lndincsoilnoahmp" $commit_num
   fi
 else
   echo
   echo "*****************************************"
-  echo "<<< C192 LANDINC SOIL-NOAHMP CYCLE TEST PASSED. >>>"
+  echo "<<< C192 GSI based LANDINC SOIL-NOAHMP CYCLE TEST PASSED. >>>"
   echo "*****************************************"
 fi
 

reg_tests/global_cycle/C192.jedi_lndincsoilnoahmp.sh

@@ -0,0 +1,88 @@
+#!/bin/bash
+
+#------------------------------------------------------------------
+# Run global_cycle for a C192 case to test the ingest and
+# application of soil moisture and temperature increments
+# on the cubed-sphere grid into Noah-MP restarts, which
+# yields (almost) identical results as compared with the GSI case 
+# given the same day of increments on two different grids.
+# Compare output to a baseline set of files using the 'nccmp' 
+# utility.
+#------------------------------------------------------------------
+
+set -x
+
+NCCMP=${NCCMP:-$(which nccmp)}
+
+export MAX_TASKS_CY=6
+
+export HOMEgfs=$NWPROD
+
+export FIXgfs=$HOMEreg/fix
+
+export CYCLEXEC=$HOMEgfs/exec/global_cycle
+
+export CDATE=2019073000
+export FHOUR=00
+export DELTSFC=6
+
+export CASE=C192
+export OCNRES=99999
+
+export COMIN=$HOMEreg/input_data_noahmp
+
+export JCAP=1534
+export LONB=3072
+export LATB=1536
+
+export DONST="NO"
+export use_ufo=.true.
+
+export DO_SFCCYCLE=".FALSE." 
+export DO_LNDINC=".TRUE." 
+export DO_SOI_INC_JEDI=".true."
+
+export VERBOSE=YES
+export CYCLVARS=FSNOL=-2.,FSNOS=99999.,
+
+$HOMEgfs/ush/global_cycle_driver.sh
+
+iret=$?
+if [ $iret -ne 0 ]; then
+  set +x
+  echo "<<< C192 JEDI based LANDINC SOIL NOAHMP CYCLE TEST FAILED. >>>"
+  exit $iret
+fi
+
+test_failed=0
+
+cd $DATA
+for files in *tile*.nc
+do
+  if [ -f $files ]; then
+    echo CHECK $files
+    $NCCMP -dmfqS $files $HOMEreg/baseline_data/c192.jedi_lndincsoilnoahmp/$files
+    iret=$?
+    if [ $iret -ne 0 ]; then
+      test_failed=1
+    fi
+  fi
+done
+
+set +x
+if [ $test_failed -ne 0 ]; then
+  echo
+  echo "**********************************************"
+  echo "<<< C192 JEDI based LANDINC SOIL-NOAHMP CYCLE TEST FAILED. >>>"
+  echo "**********************************************"
+  if [ "$UPDATE_BASELINE" = "TRUE" ]; then
+    $HOMEgfs/reg_tests/update_baseline.sh $HOMEreg "c192.jedi_lndincsoilnoahmp" $commit_num
+  fi
+else
+  echo
+  echo "*****************************************"
+  echo "<<< C192 JEDI based LANDINC SOIL-NOAHMP CYCLE TEST PASSED. >>>"
+  echo "*****************************************"
+fi
+
+exit

reg_tests/global_cycle/C768.lndincsnow.sh

@@ -31,7 +31,8 @@ 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 DO_SNO_INC=.true. # must be lower-case.
+export DO_SNO_INC_JEDI=.true. # must be lower-case.
+export DO_SOI_INC_JEDI=.false.
 export JCAP=1534
 export LONB=3072
 export LATB=1536

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 c192.lndincsoilnoahmp \
-     -o $LOG_FILE -e $LOG_FILE ./C192.lndincsoilnoahmp.sh)
+TEST2=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J c192.gsi_lndincsoilnoahmp \
+     -o $LOG_FILE -e $LOG_FILE ./C192.gsi_lndincsoilnoahmp.sh)
 
 LOG_FILE=consistency.log03
 export DATA="${DATA_DIR}/test3"
@@ -79,10 +79,16 @@ export COMOUT=$DATA
 TEST4=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J c48.noahmp.frac \
       -o $LOG_FILE -e $LOG_FILE ./C48.noahmp.fracgrid.sh)
 
+LOG_FILE=consistency.log05
+export DATA="${DATA_DIR}/test5"
+export COMOUT=$DATA
+TEST5=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J c192.jedi_lndincsoilnoahmp \
+     -o $LOG_FILE -e $LOG_FILE ./C192.jedi_lndincsoilnoahmp.sh)
+
 LOG_FILE=consistency.log
 sbatch --nodes=1 -t 0:01:00 -A $PROJECT_CODE -J chgres_summary -o $LOG_FILE -e $LOG_FILE \
       --open-mode=append -q $QUEUE -d\
-      afterok:$TEST1:$TEST2:$TEST3:$TEST4 << EOF
+      afterok:$TEST1:$TEST2:$TEST3:$TEST4:$TEST5 << EOF
 #!/bin/bash
 grep -a '<<<' ${LOG_FILE}*  > summary.log
 EOF

reg_tests/global_cycle/driver.hercules.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 c192.lndincsoilnoahmp \
-      -o $LOG_FILE -e $LOG_FILE ./C192.lndincsoilnoahmp.sh)
+TEST2=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J c192.gsi_lndincsoilnoahmp \
+      -o $LOG_FILE -e $LOG_FILE ./C192.gsi_lndincsoilnoahmp.sh)
 
 LOG_FILE=consistency.log03
 export DATA="${DATA_DIR}/test3"
@@ -79,10 +79,16 @@ export COMOUT=$DATA
 TEST4=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J c48.noahmp.frac \
       -o $LOG_FILE -e $LOG_FILE ./C48.noahmp.fracgrid.sh)
 
+LOG_FILE=consistency.log05
+export DATA="${DATA_DIR}/test5"
+export COMOUT=$DATA
+TEST5=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J c192.jedi_lndincsoilnoahmp \
+     -o $LOG_FILE -e $LOG_FILE ./C192.jedi_lndincsoilnoahmp.sh)
+
 LOG_FILE=consistency.log
 sbatch --nodes=1 -t 0:01:00 -A $PROJECT_CODE -J chgres_summary -o $LOG_FILE -e $LOG_FILE \
       --open-mode=append -q $QUEUE -d\
-      afterok:$TEST1:$TEST2:$TEST3:$TEST4 << EOF
+      afterok:$TEST1:$TEST2:$TEST3:$TEST4:$TEST5 << EOF
 #!/bin/bash
 grep -a '<<<' ${LOG_FILE}*  > summary.log
 EOF

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 c192.lndincsoilnoahmp \
-      --partition=xjet -o $LOG_FILE -e $LOG_FILE ./C192.lndincsoilnoahmp.sh)
+TEST2=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J c192.gsi_lndincsoilnoahmp \
+      --partition=xjet -o $LOG_FILE -e $LOG_FILE ./C192.gsi_lndincsoilnoahmp.sh)
 
 LOG_FILE=consistency.log03
 export DATA="${DATA_DIR}/test3"
@@ -77,10 +77,16 @@ export COMOUT=$DATA
 TEST4=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J c48.noahmp.frac \
       --partition=xjet -o $LOG_FILE -e $LOG_FILE ./C48.noahmp.fracgrid.sh)
 
+LOG_FILE=consistency.log05
+export DATA="${DATA_DIR}/test5"
+export COMOUT=$DATA
+TEST5=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J c192.jedi_lndincsoilnoahmp \
+     -o $LOG_FILE -e $LOG_FILE ./C192.jedi_lndincsoilnoahmp.sh)
+
 LOG_FILE=consistency.log
 sbatch --partition=xjet --nodes=1  -t 0:01:00 -A $PROJECT_CODE -J summary -o $LOG_FILE -e $LOG_FILE \
        --open-mode=append -q $QUEUE -d\
-       afterok:$TEST1:$TEST2:$TEST3:$TEST4 << EOF
+       afterok:$TEST1:$TEST2:$TEST3:$TEST4:$TEST5 << EOF
 #!/bin/bash
 grep -a '<<<' ${LOG_FILE}* > ./summary.log
 EOF