Merge remote-tracking branch 'origin/develop' into feature/ss_180

* origin/develop: Update the C192 default ocean resolution in the gdas_init utility (ufs-community#980) Use HPC-stack libraries on WCOSS2 (ufs-community#975) Fix compiler warning in fre-nctools.fd (ufs-community#969) Fix Gnu compilation on Hera (ufs-community#965) Update fixed data directory path for Gaea (ufs-community#972)
DavidHuber-NOAA · Sep 9, 2024 · d3bb0ea · d3bb0ea
2 parents fb6eb56 + 5de880a
commit d3bb0ea
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diff --git a/fix/link_fixdirs.sh b/fix/link_fixdirs.sh
@@ -55,7 +55,7 @@ elif [ $machine = "wcoss2" ]; then
 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"
+    FIX_DIR="/gpfs/f5/ufs-ard/world-shared/global/glopara/data/fix"
 fi
 
 am_ver=${am_ver:-20220805}

diff --git a/modulefiles/build.hera.gnu.lua b/modulefiles/build.hera.gnu.lua
@@ -5,12 +5,12 @@ Load environment to compile UFS_UTILS on Hera using Gnu
 hpss_ver=os.getenv("hpss_ver") or ""
 load(pathJoin("hpss", hpss_ver))
 
-prepend_path("MODULEPATH", "/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.6.0/envs/unified-env-rocky8/install/modulefiles/Core")
+prepend_path("MODULEPATH", "/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.6.0/envs/unified-env-rocky8-ompi416/install/modulefiles/Core")
 
 stack_gcc_ver=os.getenv("stack_gcc_ver") or "9.2"
 load(pathJoin("stack-gcc", gnu_ver))
 
-stack_openmpi_ver=os.getenv("stack_openmpi_ver") or "4.1.5"
+stack_openmpi_ver=os.getenv("stack_openmpi_ver") or "4.1.6"
 load(pathJoin("stack-openmpi", stack_openmpi_ver))
 
 cmake_ver=os.getenv("cmake_ver") or "3.23.1"
@@ -41,22 +41,13 @@ load(pathJoin("w3emc", w3emc_ver))
 sigio_ver=os.getenv("sigio_ver") or "2.3.2"
 load(pathJoin("sigio", sigio_ver))
 
-hdf5_ver=os.getenv("hdf5_ver") or "1.14.0"
-load(pathJoin("hdf5", hdf5_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"
+nccmp_ver=os.getenv("nccmp_ver") or "1.9.1"
 load(pathJoin("nccmp", nccmp_ver))
 
-esmf_ver=os.getenv("esmf_ver") or "8.6.0"
+esmf_ver=os.getenv("esmf_ver") or "8.5.0"
 load(pathJoin("esmf", esmf_ver))
 
-nco_ver=os.getenv("nco_ver") or "5.0.6"
+nco_ver=os.getenv("nco_ver") or "5.1.6"
 load(pathJoin("nco", nco_ver))
 
 whatis("Description: UFS_UTILS build environment")
diff --git a/modulefiles/build.wcoss2.intel.lua b/modulefiles/build.wcoss2.intel.lua
@@ -14,7 +14,7 @@ load(pathJoin("craype", craype_ver))
 intel_ver=os.getenv("intel_ver") or "19.1.3.304"
 load(pathJoin("intel", intel_ver))
 
-cray_mpich_ver=os.getenv("cray_mpich_ver") or "8.1.7"
+cray_mpich_ver=os.getenv("cray_mpich_ver") or "8.1.12"
 load(pathJoin("cray-mpich", cray_mpich_ver))
 
 libjpeg_ver=os.getenv("libjpeg_ver") or "9c"
@@ -26,11 +26,11 @@ load(pathJoin("zlib", zlib_ver))
 libpng_ver=os.getenv("libpng_ver") or "1.6.37"
 load(pathJoin("libpng", libpng_ver))
 
-hdf5_ver=os.getenv("hdf5_ver") or "1.10.6"
-load(pathJoin("hdf5", hdf5_ver))
+hdf5_ver=os.getenv("hdf5_ver") or "1.14.0"
+load(pathJoin("hdf5-C", hdf5_ver))
 
-netcdf_ver=os.getenv("netcdf_ver") or "4.7.4"
-load(pathJoin("netcdf", netcdf_ver))
+netcdf_ver=os.getenv("netcdf_ver") or "4.9.2"
+load(pathJoin("netcdf-C", netcdf_ver))
 
 bacio_ver=os.getenv("bacio_ver") or "2.4.1"
 load(pathJoin("bacio", bacio_ver))
@@ -42,13 +42,13 @@ load(pathJoin("bacio", bacio_ver))
 w3emc_ver=os.getenv("w3emc_ver") or "2.9.2"
 load(pathJoin("w3emc", w3emc_ver))
 
-nemsio_ver=os.getenv("nemsio_ver") or "2.5.2"
+nemsio_ver=os.getenv("nemsio_ver") or "2.5.4"
 load(pathJoin("nemsio", nemsio_ver))
 
 sigio_ver=os.getenv("sigio_ver") or "2.3.2"
 load(pathJoin("sigio", sigio_ver))
 
-sp_ver=os.getenv("sp_ver") or "2.3.3"
+sp_ver=os.getenv("sp_ver") or "2.4.0"
 load(pathJoin("sp", sp_ver))
 
 ip_ver=os.getenv("ip_ver") or "4.0.0"
@@ -57,20 +57,22 @@ load(pathJoin("ip", ip_ver))
 g2_ver=os.getenv("g2_ver") or "3.4.5"
 load(pathJoin("g2", g2_ver))
 
--- for mpiexec command
+-- Needed for mpiexec command.
 cray_pals_ver=os.getenv("cray_pals_ver") or "1.2.2"
 load(pathJoin("cray-pals", cray_pals_ver))
 
+-- Needed at runtime for nco utilities.
 udunits_ver=os.getenv("udunits_ver") or "2.2.28"
 load(pathJoin("udunits", udunits_ver))
 
+-- Needed at runtime for nco utilities.
 gsl_ver=os.getenv("gsl_ver") or "2.7"
 load(pathJoin("gsl", gsl_ver))
 
-nco_ver=os.getenv("nco_ver") or "4.9.7"
+nco_ver=os.getenv("nco_ver") or "5.0.6"
 load(pathJoin("nco", nco_ver))
 
-esmf_ver=os.getenv("esmf_ver") or "8.4.1"
-load(pathJoin("esmf", esmf_ver))
+esmf_ver=os.getenv("esmf_ver") or "8.6.0"
+load(pathJoin("esmf-C", esmf_ver))
 
 whatis("Description: UFS_UTILS build environment")
diff --git a/reg_tests/chgres_cube/13km.conus.nam.grib2.sh b/reg_tests/chgres_cube/13km.conus.nam.grib2.sh
@@ -34,6 +34,8 @@ export TRACERS_INPUT=""
 
 export OMP_NUM_THREADS_CH=${OMP_NUM_THREADS:-1}
 
+NCCMP=${NCCMP:-$(which nccmp)}
+
 #-----------------------------------------------------------------------------
 # Invoke chgres program.
 #-----------------------------------------------------------------------------

diff --git a/reg_tests/chgres_cube/13km.conus.rap.grib2.sh b/reg_tests/chgres_cube/13km.conus.rap.grib2.sh
@@ -42,6 +42,8 @@ export GEOGRID_FILE_INPUT=${HOMEufs}/fix/am/geo_em.d01.nc_RAPX
 
 export OMP_NUM_THREADS_CH=${OMP_NUM_THREADS:-1}
 
+NCCMP=${NCCMP:-$(which nccmp)}
+
 #-----------------------------------------------------------------------------
 # Invoke chgres program.
 #-----------------------------------------------------------------------------

diff --git a/reg_tests/chgres_cube/13km.na.gfs.ncei.grib2.sh b/reg_tests/chgres_cube/13km.na.gfs.ncei.grib2.sh
@@ -30,6 +30,8 @@ export CDATE=2019080100
 
 export OMP_NUM_THREADS_CH=${OMP_NUM_THREADS:-1}
 
+NCCMP=${NCCMP:-$(which nccmp)}
+
 #-----------------------------------------------------------------------------
 # Invoke chgres program.
 #-----------------------------------------------------------------------------

diff --git a/reg_tests/chgres_cube/25km.conus.gfs.grib2.sh b/reg_tests/chgres_cube/25km.conus.gfs.grib2.sh
@@ -32,6 +32,8 @@ export CDATE=2019110400
 
 export OMP_NUM_THREADS_CH=${OMP_NUM_THREADS:-1}
 
+NCCMP=${NCCMP:-$(which nccmp)}
+
 #-----------------------------------------------------------------------------
 # Invoke chgres program.
 #-----------------------------------------------------------------------------

diff --git a/reg_tests/chgres_cube/25km.conus.gfs.pbgrib2.sh b/reg_tests/chgres_cube/25km.conus.gfs.pbgrib2.sh
@@ -31,6 +31,8 @@ export CDATE=2021062718
 
 export OMP_NUM_THREADS_CH=${OMP_NUM_THREADS:-1}
 
+NCCMP=${NCCMP:-$(which nccmp)}
+
 #-----------------------------------------------------------------------------
 # Invoke chgres program.
 #-----------------------------------------------------------------------------

diff --git a/reg_tests/chgres_cube/3km.conus.hrrr.gfssdf.grib2.sh b/reg_tests/chgres_cube/3km.conus.hrrr.gfssdf.grib2.sh
@@ -36,6 +36,8 @@ export GEOGRID_FILE_INPUT=${HOMEufs}/fix/am/geo_em.d01.nc_HRRRX
 
 export OMP_NUM_THREADS_CH=${OMP_NUM_THREADS:-1}
 
+NCCMP=${NCCMP:-$(which nccmp)}
+
 #-----------------------------------------------------------------------------
 # Invoke chgres program.
 #-----------------------------------------------------------------------------

diff --git a/reg_tests/chgres_cube/3km.conus.hrrr.newsfc.grib2.sh b/reg_tests/chgres_cube/3km.conus.hrrr.newsfc.grib2.sh
@@ -42,6 +42,8 @@ export GEOGRID_FILE_INPUT=${HOMEufs}/fix/am/geo_em.d01.nc_HRRRX
 
 export OMP_NUM_THREADS_CH=${OMP_NUM_THREADS:-1}
 
+NCCMP=${NCCMP:-$(which nccmp)}
+
 #-----------------------------------------------------------------------------
 # Invoke chgres program.
 #-----------------------------------------------------------------------------

diff --git a/reg_tests/chgres_cube/driver.wcoss2.sh b/reg_tests/chgres_cube/driver.wcoss2.sh
@@ -29,6 +29,9 @@ compiler=${compiler:-"intel"}
 source ../../sorc/machine-setup.sh > /dev/null 2>&1
 module use ../../modulefiles
 module load build.$target.$compiler
+# load nccmp
+module load netcdf
+module load nccmp
 module list
 
 export OUTDIR="${WORK_DIR:-/lfs/h2/emc/stmp/$LOGNAME}"
@@ -60,8 +63,6 @@ rm -f $LOG_FILE* $SUM_FILE
 
 export OMP_STACKSIZE=1024M
 
-export NCCMP=/lfs/h2/emc/global/noscrub/George.Gayno/util/nccmp/nccmp-1.8.5.0/src/nccmp
-#export NCCMP=${NCCMP:-nccmp}
 rm -fr $OUTDIR
 
 this_dir=$PWD
@@ -163,7 +164,7 @@ TEST10=$(qsub -V -o $LOG_FILE -e $LOG_FILE -q $QUEUE -A $PROJECT_CODE -l walltim
 LOG_FILE=consistency.log11
 export APRUN="mpiexec -n 12 -ppn 12 --cpu-bind core"
 TEST11=$(qsub -V -o $LOG_FILE -e $LOG_FILE -q $QUEUE -A $PROJECT_CODE -l walltime=00:05:00 \
-        -N c96.fv3.netcdf2wam -l select=1:ncpus=12:ompthreads=1:mem=75GB $PWD/c96.fv3.netcdf2wam.sh)
+        -N c96.fv3.netcdf2wam -l select=1:ncpus=12:ompthreads=1:mem=80GB $PWD/c96.fv3.netcdf2wam.sh)
 
 #-----------------------------------------------------------------------------
 # Initialize CONUS 25-KM USING  GFS PGRIB2+BGRIB2 files.

diff --git a/reg_tests/cpld_gridgen/parm/grid.nml.IN b/reg_tests/cpld_gridgen/parm/grid.nml.IN
@@ -1,4 +1,4 @@
-& grid_nml
+&grid_nml
 ni=NI_GLB
 nj=NJ_GLB
 dirsrc='FIXDIR'

diff --git a/reg_tests/cpld_gridgen/rt.sh b/reg_tests/cpld_gridgen/rt.sh
@@ -131,7 +131,7 @@ if [[ $target = wcoss2 ]]; then
     export APRUN="mpiexec -n 1 -ppn 1 --cpu-bind core"
     QUEUE=${QUEUE:-dev}
     SBATCH_COMMAND="./cpld_gridgen.sh"
-    NCCMP=/lfs/h2/emc/global/noscrub/George.Gayno/util/nccmp/nccmp-1.8.5.0/src/nccmp
+    NCCMP=nccmp
 elif [[ $target = hera ]]; then
     STMP=${STMP:-/scratch1/NCEPDEV/stmp4/$USER}
     export MOM6_FIXDIR=/scratch1/NCEPDEV/global/glopara/fix/mom6/20220805
@@ -217,6 +217,10 @@ fi
 
 module use $PATHTR/modulefiles
 module load build.$target.$compiler
+if [[ $target = wcoss2 ]]; then
+  module load netcdf
+  module load nccmp
+fi
 module list
 
 if [[ $CREATE_BASELINE = true ]]; then

diff --git a/reg_tests/global_cycle/driver.wcoss2.sh b/reg_tests/global_cycle/driver.wcoss2.sh
@@ -25,6 +25,8 @@ compiler=${compiler:-"intel"}
 source ../../sorc/machine-setup.sh > /dev/null 2>&1
 module use ../../modulefiles
 module load build.$target.$compiler
+module load netcdf
+module load nccmp
 module list
 
 WORK_DIR="${WORK_DIR:-/lfs/h2/emc/stmp/$LOGNAME}"
@@ -56,8 +58,6 @@ export NWPROD=$PWD/../..
 
 reg_dir=$PWD
 
-export NCCMP=/lfs/h2/emc/global/noscrub/George.Gayno/util/nccmp/nccmp-1.8.5.0/src/nccmp
-
 LOG_FILE=consistency.log
 rm -f ${LOG_FILE}*
 

diff --git a/reg_tests/grid_gen/driver.orion.sh b/reg_tests/grid_gen/driver.orion.sh
@@ -62,7 +62,7 @@ rm -fr $WORK_DIR
 #-----------------------------------------------------------------------------
 
 LOG_FILE1=${LOG_FILE}01
-TEST1=$(sbatch --parsable --ntasks-per-node=24 --nodes=1 -t 0:15:00 -A $PROJECT_CODE -q $QUEUE -J c96.uniform \
+TEST1=$(sbatch --parsable --ntasks-per-node=24 --nodes=1 -t 0:20:00 -A $PROJECT_CODE -q $QUEUE -J c96.uniform \
       -o $LOG_FILE1 -e $LOG_FILE1 ./c96.uniform.sh)
 
 #-----------------------------------------------------------------------------

diff --git a/reg_tests/grid_gen/driver.wcoss2.sh b/reg_tests/grid_gen/driver.wcoss2.sh
@@ -24,6 +24,8 @@ compiler=${compiler:-"intel"}
 source ../../sorc/machine-setup.sh > /dev/null 2>&1
 module use ../../modulefiles
 module load build.$target.$compiler
+module load netcdf
+module load nccmp
 module list
 
 set -x
@@ -44,8 +46,6 @@ if [ "$UPDATE_BASELINE" = "TRUE" ]; then
   source ../get_hash.sh
 fi
 
-export NCCMP=/lfs/h2/emc/global/noscrub/George.Gayno/util/nccmp/nccmp-1.8.5.0/src/nccmp
-
 LOG_FILE=consistency.log
 rm -f ${LOG_FILE}
 SUM_FILE=summary.log

diff --git a/reg_tests/ocnice_prep/rt.sh b/reg_tests/ocnice_prep/rt.sh
@@ -130,8 +130,8 @@ if [[ $target = wcoss2 ]]; then
     ACCOUNT=${ACCOUNT:-GFS-DEV}
     export APRUN="mpiexec -n 1 -ppn 1 --cpu-bind core"
     QUEUE=${QUEUE:-dev}
+    NCCMP=nccmp
     SBATCH_COMMAND="./ocnice_prep.sh"
-    NCCMP=/lfs/h2/emc/global/noscrub/George.Gayno/util/nccmp/nccmp-1.8.5.0/src/nccmp
 elif [[ $target = hera ]]; then
     STMP=${STMP:-/scratch1/NCEPDEV/stmp4/$USER}
     BASELINE_ROOT=/scratch1/NCEPDEV/nems/role.ufsutils/ufs_utils/reg_tests/ocnice_prep/baseline_data
@@ -221,6 +221,10 @@ fi
 
 module use $PATHTR/modulefiles
 module load build.$target.$compiler
+if [[ $target = wcoss2 ]]; then
+  module load netcdf
+  module load nccmp/1.8.9.0
+fi
 module list
 
 if [[ $CREATE_BASELINE = true ]]; then

diff --git a/reg_tests/weight_gen/driver.wcoss2.sh b/reg_tests/weight_gen/driver.wcoss2.sh
@@ -35,6 +35,8 @@ compiler=${compiler:-"intel"}
 source ../../sorc/machine-setup.sh > /dev/null 2>&1
 module use ../../modulefiles
 module load build.$target.$compiler
+module load netcdf
+module load nccmp
 module list
 
 export DATA="${WORK_DIR:-/lfs/h2/emc/stmp/$LOGNAME}"
@@ -54,8 +56,6 @@ fi
 export HOMEreg=/lfs/h2/emc/nems/noscrub/emc.nems/UFS_UTILS/reg_tests/weight_gen
 export HOMEufs=$PBS_O_WORKDIR/../..
 
-export NCCMP=/lfs/h2/emc/global/noscrub/George.Gayno/util/nccmp/nccmp-1.8.5.0/src/nccmp
-
 ./weight_gen.sh
 
 exit 0
diff --git a/sorc/chgres_cube.fd/program_setup.F90 b/sorc/chgres_cube.fd/program_setup.F90
@@ -296,7 +296,7 @@ subroutine read_setup_namelist(filename)
      print*,'- INPUT DATA FROM SPECTRAL GFS GAUSSIAN NEMSIO FILE.'
    case ("gfs_sigio")
      print*,'- INPUT DATA FROM SPECTRAL GFS SIGIO/SFCIO FILE.'
-#endif()
+#endif
    case ("gaussian_netcdf")
      print*,'- INPUT DATA FROM FV3 GAUSSIAN NETCDF FILE.'
    case ("grib2")

diff --git a/sorc/fre-nctools.fd/shared_lib/mosaic_util.h b/sorc/fre-nctools.fd/shared_lib/mosaic_util.h
@@ -63,6 +63,8 @@ void initNode(struct Node *node);
 void addEnd(struct Node *list, double x, double y, double z, int intersect, double u, int inbound, int inside);
 int addIntersect(struct Node *list, double x, double y, double z, int intersect, double u1, double u2, 
                 int inbound, int is1, int ie1, int is2, int ie2);
+void insertIntersect(struct Node *list, double x, double y, double z, double u1, double u2, int inbound,
+                 double x2, double y2, double z2);
 int length(struct Node *list);
 int samePoint(double x1, double y1, double z1, double x2, double y2, double z2);
 int sameNode(struct Node node1, struct Node node2);

diff --git a/sorc/global_cycle.fd/cycle.f90 b/sorc/global_cycle.fd/cycle.f90
@@ -154,7 +154,15 @@ PROGRAM SFC_DRV
  PRINT*,"READ NAMCYC NAMELIST."
 
  CALL BAOPENR(36, "fort.36", IERR)
- READ(36, NML=NAMCYC)
+ IF (IERR /= 0) THEN
+   PRINT*,'FATAL ERROR READING FORT.36 NAMELIST. IERR: ', IERR
+   CALL MPI_ABORT(MPI_COMM_WORLD, 32, IERR) 
+ ENDIF
+ READ(36, NML=NAMCYC, IOSTAT=IERR)
+ IF (IERR /= 0) THEN
+   PRINT*,'FATAL ERROR READING FORT.36 NAMELIST. IERR: ', IERR
+   CALL MPI_ABORT(MPI_COMM_WORLD, 33, IERR) 
+ ENDIF
 !IF (MYRANK==0) WRITE(6,NAMCYC)
 
  IF (MAX_TASKS < 99999 .AND. MYRANK > (MAX_TASKS - 1)) THEN
@@ -412,7 +420,15 @@ SUBROUTINE SFCDRV(LUGB, IDIM,JDIM,LENSFC,LSOIL,DELTSFC,  &
  INPUT_NML_FILE = "NULL"
 
  CALL BAOPENR(37, "fort.37", IERR)
- READ (37, NML=NAMSFCD)
+ IF (IERR /= 0) THEN
+   PRINT*,'FATAL ERROR OPENING FORT.37 NAMELIST. IERR: ', IERR
+   CALL MPI_ABORT(MPI_COMM_WORLD, 30, IERR) 
+ ENDIF
+ READ (37, NML=NAMSFCD, IOSTAT=IERR)
+ IF (IERR /= 0) THEN
+   PRINT*,'FATAL ERROR READING FORT.37 NAMELIST. IERR: ', IERR
+   CALL MPI_ABORT(MPI_COMM_WORLD, 31, IERR) 
+ ENDIF
 
  PRINT*
  PRINT*,'IN ROUTINE SFCDRV,IDIM=',IDIM,'JDIM=',JDIM,'FH=',FH

diff --git a/ush/global_cycle.sh b/ush/global_cycle.sh
@@ -379,7 +379,7 @@ cat << EOF > fort.36
  &NAMCYC
   idim=$CRES, jdim=$CRES, lsoil=$LSOIL,
   iy=$iy, im=$im, id=$id, ih=$ih, fh=$FHOUR,
-  deltsfc=$DELTSFC,ialb=$IALB,use_ufo=$use_ufo,donst=$DONST,
+  deltsfc=$DELTSFC,ialb=$IALB,use_ufo=$use_ufo,donst="$DONST",
   do_sfccycle=$DO_SFCCYCLE,do_lndinc=$DO_LNDINC,isot=$ISOT,ivegsrc=$IVEGSRC,
   zsea1_mm=$zsea1,zsea2_mm=$zsea2,MAX_TASKS=$MAX_TASKS_CY,
   frac_grid=$FRAC_GRID

diff --git a/util/gdas_init/set_fixed_files.sh b/util/gdas_init/set_fixed_files.sh
@@ -10,7 +10,7 @@ if [ ${CTAR} == 'C48' ] ; then
 elif [ ${CTAR} == 'C96' ]; then
   OCNRES='500'
 elif [ ${CTAR} == 'C192' ]; then
-  OCNRES='050'
+  OCNRES='025'
 elif [ ${CTAR} == 'C384' ]; then
   OCNRES='025'
 elif [ ${CTAR} == 'C768' ]; then