Merge branch 'develop' into feature/srw_doc

Fixes ufs-community#643.

README.md

@@ -15,6 +15,7 @@ https://ufs-community.github.io/UFS_UTILS/.
 Utility | Programmer(s)
 --------|----------
 chgres_cube | George Gayno, Jeff Beck, Larissa Reames
+cpld_gridgen | Denise Worthen, Minsuk Ji
 emcsfc_ice_blend | George Gayno
 emcsfc_snow2mdl | George Gayno
 fre-nctools | GFDL progammer
@@ -70,6 +71,7 @@ make install
 The UFS_UTILS package contains the following utilities (under the sorc
 directory):
 - chgres_cube
+- cpld_gridgen
 - emcsfc_ice_blend
 - emcsfc_snow2mdl
 - fre-nctools

build_all.sh

@@ -15,7 +15,7 @@ export MOD_PATH
 if [[ "$target" == "linux.*" || "$target" == "macosx.*" ]]; then
  unset -f module
  set +x
- source ./modulefiles/build.$target > /dev/null 
+ source ./modulefiles/build.$target > /dev/null
  set -x
 else
  set +x

docs/user_guide.md

@@ -71,4 +71,6 @@ https://github.com/ufs-community/UFS_UTILS.
   Currently, contains the routines required by global_cycle to 
   perform data assimilation updates to land model states
 
+- <a href="cpld_gridgen/index.html">cpld_gridgen</a> - Utility to 
+  create the Fix and IC files for the S2SW and S2S applications 
 

modulefiles/build.hera.gnu.lua

@@ -22,7 +22,7 @@ load(pathJoin("hpc-mpich", mpich_ver))
 netcdf_ver=os.getenv("netcdf_ver") or "4.7.4"
 load(pathJoin("netcdf", netcdf_ver))
 
-esmf_ver=os.getenv("esmf_ver") or "8_1_1"
+esmf_ver=os.getenv("esmf_ver") or "8.2.1b04"
 load(pathJoin("esmf", esmf_ver))
 
 bacio_ver=os.getenv("bacio_ver") or "2.4.1"

modulefiles/build.hera.intel.lua

@@ -61,4 +61,7 @@ load(pathJoin("nccmp", nccmp_ver))
 esmf_ver=os.getenv("esmf_ver") or "8.2.1b04"
 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")

modulefiles/build.jet.intel.lua

@@ -58,4 +58,7 @@ load(pathJoin("g2", g2_ver))
 prod_util_ver=os.getenv("prod_util_ver") or "1.2.2"
 load(pathJoin("prod_util", prod_util_ver))
 
+nco_ver=os.getenv("nco_ver") or "4.9.3"
+load(pathJoin("nco", nco_ver))
+
 whatis("Description: UFS_UTILS build environment")

modulefiles/build.orion.intel.lua

@@ -58,4 +58,7 @@ load(pathJoin("nccmp", nccmp_ver))
 esmf_ver=os.getenv("esmf_ver") or "8.2.0"
 load(pathJoin("esmf", esmf_ver))
 
+nco_ver=os.getenv("nco_ver") or "4.9.3"
+load(pathJoin("nco", nco_ver))
+
 whatis("Description: UFS_UTILS build environment")

modulefiles/build.s4.intel.lua

@@ -0,0 +1,59 @@
+help([[
+Load environment to compile UFS_UTILS on S4 using Intel
+]])
+
+load(pathJoin("license_intel","S4"))
+prepend_path("MODULEPATH", "/data/prod/hpc-stack/modulefiles/stack")
+
+hpc_ver=os.getenv("hpc_ver") or "1.2.0"
+load(pathJoin("hpc", hpc_ver))
+
+hpc_intel_ver=os.getenv("hpc_intel_ver") or "2022.1"
+load(pathJoin("hpc-intel", hpc_intel_ver))
+
+impi_ver=os.getenv("impi_ver") or "2022.1"
+load(pathJoin("hpc-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 "3.3.3"
+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))
+
+w3nco_ver=os.getenv("w3nco_ver") or "2.4.1"
+load(pathJoin("w3nco", w3nco_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 "4.7.4"
+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 "8.2.1b04"
+load(pathJoin("esmf", esmf_ver))
+
+whatis("Description: UFS_UTILS build environment")

reg_tests/chgres_cube/driver.s4.sh

@@ -0,0 +1,224 @@
+#!/bin/bash
+
+#-----------------------------------------------------------------------------
+#
+# Run the chgres_cube consistency tests on S4.
+#
+# Set WORK_DIR to a general working location outside the UFS_UTILS directory.
+# The exact working directory (OUTDIR) will be WORK_DIR/reg_tests/chgres-cube. 
+# Set the PROJECT_CODE and QUEUE as appropriate.  To see which projects you 
+# are authorized to use, type
+# "sacctmgr show assoc Users=<USERNAME> format=account,user,qos"
+#
+# Invoke the script with no arguments.  A series of daisy-chained
+# jobs will be submitted.  To check the queue, type:
+# "squeue -u USERNAME".
+#
+# The run output will be stored in OUTDIR.  Log output from the suite
+# will be in LOG_FILE.  Once the suite has completed, a summary is
+# placed in SUM_FILE.
+#
+# A test fails when its output does not match the baseline files as
+# determined by the "nccmp" utility.  The baseline files are stored in
+# HOMEreg.
+#
+#-----------------------------------------------------------------------------
+
+set -x
+
+compiler=${compiler:-"intel"}
+
+source ../../sorc/machine-setup.sh > /dev/null 2>&1
+module use ../../modulefiles
+module load build.$target.$compiler
+module list
+
+export OUTDIR="${WORK_DIR:-/scratch/short/users/$LOGNAME}"
+export OUTDIR="${OUTDIR}/reg-tests/chgres-cube"
+
+PROJECT_CODE="${PROJECT_CODE:-star}"
+QUEUE="${QUEUE:-s4}"
+
+#-----------------------------------------------------------------------------
+# Should not have to change anything below here.  HOMEufs is the root
+# directory of your UFS_UTILS clone.  HOMEreg contains the input data
+# and baseline data for each test.
+#-----------------------------------------------------------------------------
+
+export UPDATE_BASELINE="FALSE"
+#export UPDATE_BASELINE="TRUE"
+
+if [ "$UPDATE_BASELINE" = "TRUE" ]; then
+  source ../get_hash.sh
+fi
+
+export HOMEufs=$PWD/../..
+
+export HOMEreg=/data/users/dhuber/save/nems/role.ufsutils/ufs_utils/reg_tests/chgres_cube
+
+LOG_FILE=consistency.log
+SUM_FILE=summary.log
+rm -f $LOG_FILE* $SUM_FILE
+
+export OMP_STACKSIZE=1024M
+
+export APRUN=srun
+export NCCMP=${NCCMP:-nccmp}
+rm -fr $OUTDIR
+
+#-----------------------------------------------------------------------------
+# Initialize C96 using FV3 warm restart files.
+#-----------------------------------------------------------------------------
+
+LOG_FILE=consistency.log01
+export OMP_NUM_THREADS=1   # should match cpus-per-task
+TEST1=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:15:00 -A $PROJECT_CODE -q $QUEUE -J c96.fv3.restart \
+      -o $LOG_FILE -e $LOG_FILE ./c96.fv3.restart.sh)
+
+#-----------------------------------------------------------------------------
+# Initialize C192 using FV3 tiled history files.
+#-----------------------------------------------------------------------------
+
+LOG_FILE=consistency.log02
+export OMP_NUM_THREADS=1   # should match cpus-per-task
+TEST2=$(sbatch --parsable --ntasks-per-node=6 --nodes=2 -t 0:15:00 -A $PROJECT_CODE -q $QUEUE -J c192.fv3.history \
+      -o $LOG_FILE -e $LOG_FILE ./c192.fv3.history.sh)
+
+#-----------------------------------------------------------------------------
+# Initialize C96 using FV3 gaussian nemsio files.
+#-----------------------------------------------------------------------------
+
+LOG_FILE=consistency.log03
+export OMP_NUM_THREADS=1   # should match cpus-per-task
+TEST3=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:15:00 -A $PROJECT_CODE -q $QUEUE -J c96.fv3.nemsio \
+      -o $LOG_FILE -e $LOG_FILE ./c96.fv3.nemsio.sh)
+
+#-----------------------------------------------------------------------------
+# Initialize C96 using spectral GFS sigio/sfcio files.
+#-----------------------------------------------------------------------------
+
+LOG_FILE=consistency.log04
+export OMP_NUM_THREADS=6   # should match cpus-per-task
+TEST4=$(sbatch --parsable --ntasks-per-node=3 --cpus-per-task=6 --nodes=2 -t 0:15:00 -A $PROJECT_CODE -q $QUEUE -J c96.gfs.sigio \
+      -o $LOG_FILE -e $LOG_FILE ./c96.gfs.sigio.sh)
+
+#-----------------------------------------------------------------------------
+# Initialize C96 using spectral GFS gaussian nemsio files.
+#-----------------------------------------------------------------------------
+
+LOG_FILE=consistency.log05
+export OMP_NUM_THREADS=1   # should match cpus-per-task
+TEST5=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:15:00 -A $PROJECT_CODE -q $QUEUE -J c96.gfs.nemsio \
+      -o $LOG_FILE -e $LOG_FILE ./c96.gfs.nemsio.sh)
+
+#-----------------------------------------------------------------------------
+# Initialize regional C96 using FV3 gaussian nemsio files.
+#-----------------------------------------------------------------------------
+
+LOG_FILE=consistency.log06
+export OMP_NUM_THREADS=1   # should match cpus-per-task
+TEST6=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:15:00 -A $PROJECT_CODE -q $QUEUE -J c96.regional \
+      -o $LOG_FILE -e $LOG_FILE ./c96.regional.sh)
+
+#-----------------------------------------------------------------------------
+# Initialize C96 using FV3 gaussian netcdf files.
+#-----------------------------------------------------------------------------
+
+LOG_FILE=consistency.log07
+export OMP_NUM_THREADS=1   # should match cpus-per-task
+TEST7=$(sbatch --parsable --ntasks-per-node=12 --nodes=1 -t 0:15:00 -A $PROJECT_CODE -q $QUEUE -J c96.fv3.netcdf \
+      -o $LOG_FILE -e $LOG_FILE ./c96.fv3.netcdf.sh)
+
+#-----------------------------------------------------------------------------
+# Initialize global C192 using GFS GRIB2 files.
+#-----------------------------------------------------------------------------
+
+LOG_FILE=consistency.log08
+export OMP_NUM_THREADS=1   # should match cpus-per-task
+TEST8=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J c192.gfs.grib2 \
+      -o $LOG_FILE -e $LOG_FILE ./c192.gfs.grib2.sh)
+
+#-----------------------------------------------------------------------------
+# Initialize CONUS 25-KM USING GFS GRIB2 files.
+#-----------------------------------------------------------------------------
+
+LOG_FILE=consistency.log09
+export OMP_NUM_THREADS=1   # should match cpus-per-task
+TEST9=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J 25km.conus.gfs.grib2.conus \
+      -o $LOG_FILE -e $LOG_FILE ./25km.conus.gfs.grib2.sh)
+
+#-----------------------------------------------------------------------------
+# Initialize CONUS 3-KM USING HRRR GRIB2 file WITH GFS PHYSICS.
+#-----------------------------------------------------------------------------
+
+LOG_FILE=consistency.log10
+export OMP_NUM_THREADS=1   # should match cpus-per-task
+TEST10=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:10:00 -A $PROJECT_CODE -q $QUEUE -J 3km.conus.hrrr.gfssdf.grib2.conus \
+      -o $LOG_FILE -e $LOG_FILE ./3km.conus.hrrr.gfssdf.grib2.sh)
+
+#-----------------------------------------------------------------------------
+# Initialize CONUS 3-KM USING HRRR GRIB2 file WITH GSD PHYSICS AND SFC VARS FROM FILE.
+#-----------------------------------------------------------------------------
+
+LOG_FILE=consistency.log11
+export OMP_NUM_THREADS=1   # should match cpus-per-task
+TEST11=$(sbatch --parsable --ntasks-per-node=6 --nodes=2 -t 0:10:00 -A $PROJECT_CODE -q $QUEUE -J 3km.conus.hrrr.newsfc.grib2.conus \
+      -o $LOG_FILE -e $LOG_FILE ./3km.conus.hrrr.newsfc.grib2.sh)
+
+#-----------------------------------------------------------------------------
+# Initialize CONUS 13-KM USING NAM GRIB2 file WITH GFS PHYSICS .
+#-----------------------------------------------------------------------------
+
+LOG_FILE=consistency.log12
+export OMP_NUM_THREADS=1   # should match cpus-per-task
+TEST12=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J 13km.conus.nam.grib2.conus \
+      -o $LOG_FILE -e $LOG_FILE ./13km.conus.nam.grib2.sh)
+
+#-----------------------------------------------------------------------------
+# Initialize CONUS 13-KM USING RAP GRIB2 file WITH GSD PHYSICS .
+#-----------------------------------------------------------------------------
+
+LOG_FILE=consistency.log13
+export OMP_NUM_THREADS=1   # should match cpus-per-task
+TEST13=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J 13km.conus.rap.grib2.conus \
+      -o $LOG_FILE -e $LOG_FILE ./13km.conus.rap.grib2.sh)
+
+#-----------------------------------------------------------------------------
+# Initialize CONUS 13-KM NA USING NCEI GFS GRIB2 file WITH GFS PHYSICS .
+#-----------------------------------------------------------------------------
+
+LOG_FILE=consistency.log14
+export OMP_NUM_THREADS=1   # should match cpus-per-task
+TEST14=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J 13km.na.gfs.ncei.grib2.conus \
+      -o $LOG_FILE -e $LOG_FILE ./13km.na.gfs.ncei.grib2.sh)
+
+#-----------------------------------------------------------------------------
+# Initialize C96 WAM IC using FV3 gaussian netcdf files.
+#-----------------------------------------------------------------------------
+
+LOG_FILE=consistency.log15
+export OMP_NUM_THREADS=1   # should match cpus-per-task
+TEST15=$(sbatch --parsable --ntasks-per-node=12 --nodes=1 -t 0:15:00 -A $PROJECT_CODE -q $QUEUE -J c96.fv3.netcdf2wam \
+      -o $LOG_FILE -e $LOG_FILE ./c96.fv3.netcdf2wam.sh)
+
+#-----------------------------------------------------------------------------
+# Initialize CONUS 25-KM USING  GFS PGRIB2+BGRIB2 files.
+#-----------------------------------------------------------------------------
+
+LOG_FILE=consistency.log16
+export OMP_NUM_THREADS=1   # should match cpus-per-task
+TEST16=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J 25km.conus.gfs.pbgrib2.conus \
+      -o $LOG_FILE -e $LOG_FILE ./25km.conus.gfs.pbgrib2.sh)
+
+#-----------------------------------------------------------------------------
+# Create summary log.
+#-----------------------------------------------------------------------------
+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:$TEST4:$TEST5:$TEST6:$TEST7:$TEST8:$TEST9:$TEST10:$TEST11:$TEST12:$TEST13:$TEST14:$TEST15:$TEST16 << EOF
+#!/bin/bash
+grep -a '<<<' $LOG_FILE*  > $SUM_FILE
+EOF
+
+exit 0