Merge branch 'develop' into feature/warm_start

Fixes ufs-community#520.

.github/PULL_REQUEST_TEMPLATE

@@ -0,0 +1,32 @@
+- Use this template to give a detailed message describing the change you want to make to the code.
+
+- You may delete any sections labeled "optional".
+
+- If you are unclear on what should be written here, see https://github.com/NOAA-EMC/UFS_UTILS/wiki/9.-Creating-a-Pull-Request for some guidance. 
+
+- The title of this pull request should be a brief summary (ideally less than 100 characters) of the changes included in this PR. Please also include the branch to which this PR is being issued.
+
+- Use the "Preview" tab to see what your PR will look like when you hit "Create pull request"
+
+# --- Delete this line and those above before hitting "Create pull request" ---
+
+## DESCRIPTION OF CHANGES: 
+One or more paragraphs describing the problem, solution, and required changes.
+
+## TESTS CONDUCTED: 
+State whether the contingency tests were run or are pending, and if they were already run, state the result.  If contingency test baselines need to be updated as a result of this PR, please specify the machine(s) and path(s) to the new files.  Note that running the contigency tests is required for every PR and should be run at least once after all commits or changes have been made after review of the PR.  Make note of the compilers used, the platform/machine, and other relevant details as necessary.  Please also note whether new unit tests or updates to existing ones were required and their file names.
+
+## DEPENDENCIES:
+Add any links to pending PRs that are required prior to merging this PR. For example:
+
+NOAA-EMC/UFS_UTILS/pull/<pr_number>
+
+## DOCUMENTATION:
+If this PR is contributing new capabilities that need to be documented, please also include updates to the RST files in the docs/source directory as supporting material.
+
+## ISSUE: 
+If this PR is resolving or referencing one or more issues, in this repository or elsewhere, list them here. For example, "Fixes issue mentioned in #123" or "Related to bug in https://github.com/NOAA-EMC/other_repository/pull/63"
+
+## CONTRIBUTORS (optional): 
+If others have contributed to this work aside from the PR author, list them here
+

reg_tests/global_cycle/C768.lndincsnow.sh

@@ -0,0 +1,85 @@
+#!/bin/bash
+
+#------------------------------------------------------------------
+# Run global_cycle for a C768 case to test the ingest of snow
+# increments from JEDI.  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=$NWPROD
+export BASE_GSM=$NWPROD
+
+export CYCLEXEC=$BASE_GSM/exec/global_cycle
+
+export CDATE=2019073000
+export FHOUR=00
+export DELTSFC=6
+
+export CASE=C768
+
+export COMIN=$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 DO_SNO_INC=.true. # must be lower-case.
+export JCAP=1534
+export LONB=3072
+export LATB=1536
+
+export FIXgsm=$BASE_GSM/fix/fix_am
+
+export DONST="NO"
+export use_ufo=.true.
+
+export DO_SFCCYCLE=".FALSE." 
+export DO_LNDINC=".TRUE." 
+
+export VERBOSE=YES
+export CYCLVARS=FSNOL=99999.,FSNOS=99999.,
+
+$BASE_GSM/ush/global_cycle_driver.sh
+
+iret=$?
+if [ $iret -ne 0 ]; then
+  set +x
+  echo "<<< C768 LANDINC SNOW 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 $HOMEreg/baseline_data/c768.lndincsnow/$files
+    iret=$?
+    if [ $iret -ne 0 ]; then
+      test_failed=1
+    fi
+  fi
+done
+
+set +x
+if [ $test_failed -ne 0 ]; then
+  echo
+  echo "****************************************"
+  echo "<<< C768 LANDINC SNOW CYCLE TEST FAILED. >>>"
+  echo "****************************************"
+else
+  echo
+  echo "***************************************"
+  echo "<<< C768 LANDINC SNOW CYCLE TEST PASSED. >>>"
+  echo "***************************************"
+fi
+
+exit

reg_tests/global_cycle/C768.lndinc.sh → reg_tests/global_cycle/C768.lndincsoil.sh

@@ -1,8 +1,10 @@
 #!/bin/bash
 
 #------------------------------------------------------------------
-# Run global_cycle for a C768 test case.  Compare output
-# to a baseline set of files using the 'nccmp' utility.
+# Run global_cycle for a C768 case to test the ingest and
+# application of soil temperature increments from the GSI.  
+# Compare output to a baseline set of files using the 'nccmp' 
+# utility.
 #------------------------------------------------------------------
 
 set -x
@@ -50,7 +52,7 @@ $BASE_GSM/ush/global_cycle_driver.sh
 iret=$?
 if [ $iret -ne 0 ]; then
   set +x
-  echo "<<< C768 LANDINC CYCLE TEST FAILED. >>>"
+  echo "<<< C768 LANDINC SOILT CYCLE TEST FAILED. >>>"
   exit $iret
 fi
 
@@ -61,7 +63,7 @@ for files in *tile*.nc
 do
   if [ -f $files ]; then
     echo CHECK $files
-    $NCCMP -dmfqS $files $HOMEreg/baseline_data/c768.lndinc/$files
+    $NCCMP -dmfqS $files $HOMEreg/baseline_data/c768.lndincsoil/$files
     iret=$?
     if [ $iret -ne 0 ]; then
       test_failed=1
@@ -72,14 +74,14 @@ done
 set +x
 if [ $test_failed -ne 0 ]; then
   echo
-  echo "*********************************"
-  echo "<<< C768 LANDINC CYCLE TEST FAILED. >>>"
-  echo "*********************************"
+  echo "*****************************************"
+  echo "<<< C768 LANDINC SOILT CYCLE TEST FAILED. >>>"
+  echo "*****************************************"
 else
   echo
-  echo "*********************************"
-  echo "<<< C768 LANDINC CYCLE TEST PASSED. >>>"
-  echo "*********************************"
+  echo "*****************************************"
+  echo "<<< C768 LANDINC SOILT CYCLE TEST PASSED. >>>"
+  echo "*****************************************"
 fi
 
 exit

reg_tests/global_cycle/driver.hera.sh

@@ -57,13 +57,19 @@ 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.lndinc \
-      -o $LOG_FILE -e $LOG_FILE ./C768.lndinc.sh)
+TEST2=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J c768.lndincsoil \
+     -o $LOG_FILE -e $LOG_FILE ./C768.lndincsoil.sh)
+
+LOG_FILE=consistency.log03
+export DATA="${DATA_DIR}/test3"
+export COMOUT=$DATA
+TEST3=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J c768.lndincsnow \
+     -o $LOG_FILE -e $LOG_FILE ./C768.lndincsnow.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:$TEST2 << EOF
+      afterok:$TEST1:$TEST2:$TEST3 << EOF
 #!/bin/bash
 grep -a '<<<' ${LOG_FILE}*  > summary.log
 EOF

reg_tests/global_cycle/driver.jet.sh

@@ -27,8 +27,8 @@ module list
 
 export WORK_DIR="${WORK_DIR:-/lfs4/HFIP/emcda/$LOGNAME/stmp}"
 
-PROJECT_CODE="${PROJECT_CODE:-emcda}"
-QUEUE="${QUEUE:-windfall}"
+PROJECT_CODE="${PROJECT_CODE:-hfv3gfs}"
+QUEUE="${QUEUE:-batch}"
 
 #-----------------------------------------------------------------------------
 # Should not have to change anything below.
@@ -55,13 +55,19 @@ 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.lndinc \
-      --partition=xjet -o $LOG_FILE -e $LOG_FILE ./C768.lndinc.sh)
+TEST2=$(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 $LOG_FILE ./C768.lndincsoil.sh)
+
+LOG_FILE=consistency.log03
+export DATA="${DATA_DIR}/test3"
+export COMOUT=$DATA
+TEST3=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J c768.lndincsnow \
+      --partition=xjet -o $LOG_FILE -e $LOG_FILE ./C768.lndincsnow.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:$TEST2 << EOF
+       afterok:$TEST1:$TEST2:$TEST3 << EOF
 #!/bin/bash
 grep -a '<<<' ${LOG_FILE}* > ./summary.log
 EOF

reg_tests/global_cycle/driver.orion.sh

@@ -55,13 +55,19 @@ 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.lndinc \
-      -o $LOG_FILE -e $LOG_FILE ./C768.lndinc.sh)
+TEST2=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J c768.lndincsoil \
+      -o $LOG_FILE -e $LOG_FILE ./C768.lndincsoil.sh)
+
+LOG_FILE=consistency.log03
+export DATA="${DATA_DIR}/test3"
+export COMOUT=$DATA
+TEST3=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J c768.lndincsnow \
+      -o $LOG_FILE -e $LOG_FILE ./C768.lndincsnow.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:$TEST2 << EOF
+      afterok:$TEST1:$TEST2:$TEST3 << EOF
 #!/bin/bash
 grep -a '<<<' ${LOG_FILE}*  > summary.log
 EOF

reg_tests/global_cycle/driver.wcoss_cray.sh

@@ -26,7 +26,7 @@ module list
 WORK_DIR="${WORK_DIR:-/gpfs/hps3/stmp/$LOGNAME}"
 
 PROJECT_CODE="${PROJECT_CODE:-GDAS-T2O}"
-QUEUE="${QUEUE:-debug}"
+QUEUE="${QUEUE:-dev}"
 
 #-----------------------------------------------------------------------------
 # Should not have to change anything below.
@@ -59,8 +59,14 @@ bsub -e $LOG_FILE -o $LOG_FILE -q $QUEUE -P $PROJECT_CODE -J c768.fv3gfs -M 2400
 LOG_FILE=consistency.log02
 export DATA="${DATA_DIR}/test2"
 export COMOUT=$DATA
-bsub -e $LOG_FILE -o $LOG_FILE -q $QUEUE -P $PROJECT_CODE -J c768.lndinc -M 2400 -W 0:05 \
-        -extsched 'CRAYLINUX[]' "export NODES=1; $PWD/C768.lndinc.sh"
+bsub -e $LOG_FILE -o $LOG_FILE -q $QUEUE -P $PROJECT_CODE -J c768.lndincsoil -M 2400 -W 0:05 \
+        -extsched 'CRAYLINUX[]' "export NODES=1; $PWD/C768.lndincsoil.sh"
+
+LOG_FILE=consistency.log03
+export DATA="${DATA_DIR}/test3"
+export COMOUT=$DATA
+bsub -e $LOG_FILE -o $LOG_FILE -q $QUEUE -P $PROJECT_CODE -J c768.lndincsnow -M 2400 -W 0:05 \
+        -extsched 'CRAYLINUX[]' "export NODES=1; $PWD/C768.lndincsnow.sh"
 
 LOG_FILE=consistency.log
 bsub -o $LOG_FILE -q $QUEUE -P $PROJECT_CODE -J summary -R "rusage[mem=100]" -W 0:01 \

reg_tests/global_cycle/driver.wcoss_dell_p3.sh

@@ -28,7 +28,7 @@ module list
 WORK_DIR="${WORK_DIR:-/gpfs/dell1/stmp/$LOGNAME}"
 
 PROJECT_CODE="${PROJECT_CODE:-GFS-DEV}"
-QUEUE="${QUEUE:-debug}"
+QUEUE="${QUEUE:-dev}"
 
 #-----------------------------------------------------------------------------
 # Should not have to change anything below.
@@ -55,8 +55,14 @@ bsub -e $LOG_FILE -o $LOG_FILE -q $QUEUE -P $PROJECT_CODE -J c768.fv3gfs -W 0:05
 LOG_FILE=consistency.log02
 export DATA="${DATA_DIR}/test2"
 export COMOUT=$DATA
-bsub -e $LOG_FILE -o $LOG_FILE -q $QUEUE -P $PROJECT_CODE -J c768.lndinc -W 0:05 -x -n 6 \
-        -M 2400 -R "span[ptile=6]" -R "affinity[core(1)]" "$PWD/C768.lndinc.sh"
+bsub -e $LOG_FILE -o $LOG_FILE -q $QUEUE -P $PROJECT_CODE -J c768.lndincsoil -W 0:05 -x -n 6 \
+        -M 2400 -R "span[ptile=6]" -R "affinity[core(1)]" "$PWD/C768.lndincsoil.sh"
+
+LOG_FILE=consistency.log03
+export DATA="${DATA_DIR}/test3"
+export COMOUT=$DATA
+bsub -e $LOG_FILE -o $LOG_FILE -q $QUEUE -P $PROJECT_CODE -J c768.lndincsnow -W 0:05 -x -n 6 \
+        -M 2400 -R "span[ptile=6]" -R "affinity[core(1)]" "$PWD/C768.lndincsnow.sh"
 
 LOG_FILE=consistency.log
 bsub -o $LOG_FILE -q $QUEUE -P $PROJECT_CODE -J summary -R "affinity[core(1)]" -R "rusage[mem=100]" -W 0:01 \