Updates for hpc-stack

- Remove unneeded ignores from .gitignore
- Update Externals.cfg and checkout.sh for component stack versions
- Update link_fv3gfs.sh for changed component links
- Further Hera module updates for hpc-stack

Refs: #164

.gitignore

@@ -31,6 +31,7 @@ sorc/logs
 sorc/fv3gfs.fd
 sorc/gfs_post.fd
 sorc/gfs_wafs.fd
+sorc/gldas.fd
 sorc/gsi.fd
 sorc/ufs_utils.fd
 sorc/verif-global.fd
@@ -42,14 +43,12 @@ sorc/calc_increment_ens.fd
 sorc/calc_increment_ens_ncio.fd
 sorc/emcsfc_ice_blend.fd
 sorc/emcsfc_snow2mdl.fd
-sorc/filter_topo.fd
 sorc/fregrid.fd
 sorc/gdas2gldas.fd
 sorc/getsfcensmeanp.fd
 sorc/getsigensmeanp_smooth.fd
 sorc/getsigensstatp.fd
 sorc/gfs_ncep_post.fd
-sorc/gldas.fd
 sorc/gldas2gdas.fd
 sorc/gldas_forcing.fd
 sorc/gldas_model.fd
@@ -62,21 +61,15 @@ sorc/global_gsi.fd
 sorc/interp_inc.fd
 sorc/make_hgrid.fd
 sorc/make_solo_mosaic.fd
-sorc/mkgfsnemsioctl.fd
 sorc/ncdiag_cat.fd
-sorc/nemsio_chgdate.fd
-sorc/nemsio_get.fd
-sorc/nemsio_read.fd
 sorc/nst_tf_chg.fd
-sorc/orog.fd
 sorc/oznmon_horiz.fd
 sorc/oznmon_time.fd
 sorc/radmon_angle.fd
 sorc/radmon_bcoef.fd
 sorc/radmon_bcor.fd
 sorc/radmon_time.fd
 sorc/recentersigp.fd
-sorc/shave.fd
 sorc/wafs_awc_wafavn.fd
 sorc/wafs_blending.fd
 sorc/wafs_cnvgrib2.fd
@@ -140,10 +133,10 @@ scripts/exglobal_diag.sh
 # ush symlinks
 ush/calcanl_gfs.py
 ush/calcinc_gfs.py
+ush/chgres_cube.sh
 ush/emcsfc_ice_blend.sh
 ush/emcsfc_snow.sh
 ush/fix_precip.sh
-ush/fv3gfs_chgres.sh
 ush/fv3gfs_downstream_nems.sh
 ush/fv3gfs_driver_grid.sh
 ush/fv3gfs_dwn_nems.sh

Externals.cfg

@@ -1,7 +1,7 @@
 # External sub-modules of global-workflow
 
 [FV3GFS]
-tag = GFS.v16.0.14
+hash = 06bc77ba3640358b54b6ff03f542e2ce0d3242be
 local_path = sorc/fv3gfs.fd
 repo_url = https://github.com/ufs-community/ufs-weather-model.git
 protocol = git
@@ -15,7 +15,7 @@ protocol = git
 required = True
 
 [GLDAS]
-tag = gldas_gfsv16_release.v1.13.0
+tag = gldas_gfsv16_release.v1.14.0
 local_path = sorc/gldas.fd
 repo_url = https://github.com/NOAA-EMC/GLDAS.git
 protocol = git
@@ -30,7 +30,7 @@ protocol = git
 required = True
 
 [UFS_UTILS]
-tag = ops-gfsv16.0.0
+#tag = ops-gfsv16.0.0
 local_path = sorc/ufs_utils.fd
 repo_url = https://github.com/NOAA-EMC/UFS_UTILS.git
 protocol = git

modulefiles/fv3gfs/enkf_chgres_recenter.hera

@@ -13,4 +13,7 @@ module load w3nco/2.4.1
 module load ip/3.3.3
 module load sp/2.3.3
 
+module load hdf5/1.10.6
+module load netcdf/4.7.4
+
 export FC=ifort

modulefiles/fv3gfs/enkf_chgres_recenter_nc.hera

@@ -1,15 +1,18 @@
 #%Module#####################################################
-## enkf_chgres_recenter component - hera
+## enkf_chgres_recenter_nc component - hera
 #############################################################
 
-module use -a /scratch2/NCEPDEV/nwprod/NCEPLIBS/modulefiles
-module load bacio/2.0.2
-module load w3nco/2.0.6
-module load ip/3.0.1
-module load sp/2.0.2
+module use /scratch2/NCEPDEV/nwprod/hpc-stack/libs/hpc-stack/modulefiles/stack
+module load hpc/1.1.0
+module load hpc-intel/18.0.5.274
+module load hpc-impi/2018.0.4
 
-module use /scratch1/NCEPDEV/nems/emc.nemspara/soft/modulefiles/
-module load netcdf_parallel/4.7.4.release
-module load hdf5_parallel/1.10.6.release
+module load bacio/2.4.1
+module load w3nco/2.4.1
+module load ip/3.3.3
+module load sp/2.3.3
+
+module load hdf5/1.10.6
+module load netcdf/4.7.4
 
 export FC=ifort

modulefiles/fv3gfs/gaussian_sfcanl.hera

@@ -2,17 +2,18 @@
 ## gaussian_sfcanl build module for Hera
 #############################################################
 
-module use -a /scratch2/NCEPDEV/nwprod/NCEPLIBS/modulefiles
-module load w3nco/2.0.6
-module load bacio/2.0.2
-module load nemsio/2.2.3
-module load sp/2.0.2
-module use /scratch1/NCEPDEV/nems/emc.nemspara/soft/modulefiles/
-module load netcdf_parallel/4.7.4.release
-module load hdf5_parallel/1.10.6.release
+module use /scratch2/NCEPDEV/nwprod/hpc-stack/libs/hpc-stack/modulefiles/stack
+module load hpc/1.1.0
+module load hpc-intel/18.0.5.274
+module load hpc-impi/2018.0.4
 
+module load w3nco/2.4.1
+module load bacio/2.4.1
+module load nemsio/2.5.2
+module load sp/2.3.3
 
-export NETCDF_INCLUDE="-I${NETCDF}/include"
-export NETCDF_LDFLAGS_F="-L${NETCDF}/lib -lnetcdf -lnetcdff -L${HDF5}/lib -lhdf5 -lhdf5_fortran"
+module load netcdf/4.7.4
+module load hdf5/1.10.6
 
-#export FCOMP=$FCOMP
+export NETCDF_INCLUDE="-I${NETCDF}/include"
+export NETCDF_LDFLAGS_F="-L${NETCDF}/lib -lnetcdf -lnetcdff -L${HDF5_LIBRARIES} -lhdf5 -lhdf5_fortran"

modulefiles/module_base.hera

@@ -17,8 +17,8 @@ module load gempak/7.4.2
 module load prod_util/1.2.2
 module load grib_util/1.2.2
 module load g2tmpl/1.9.1
-module load crtm/2.3.0
 
+module load crtm/2.3.0
 setenv CRTM_FIX /scratch2/NCEPDEV/nwprod/NCEPLIBS/fix/crtm_v2.3.0
 
 module load netcdf/4.7.4

modulefiles/modulefile.fv3nc2nemsio.hera

@@ -2,12 +2,16 @@
 ## Module file for fv3nc2nemsio
 #############################################################
 
-module use -a /scratch2/NCEPDEV/nwprod/NCEPLIBS/modulefiles
-module load netcdf/4.7.0
-module load hdf5/1.10.5
-module load bacio/2.0.2
-module load nemsio/2.2.3
-module load w3nco/2.0.6
+module use /scratch2/NCEPDEV/nwprod/hpc-stack/libs/hpc-stack/modulefiles/stack
+module load hpc/1.1.0
+module load hpc-intel/18.0.5.274
+module load hpc-impi/2018.0.4
+
+module load netcdf/4.7.4
+module load hdf5/1.10.6
+module load bacio/2.4.1
+module load nemsio/2.5.2
+module load w3nco/2.4.1
 
 export FCMP="ifort"
 export FFLAGS="-g -O2 -traceback"

sorc/build_fv3.sh

@@ -23,10 +23,9 @@ cd fv3gfs.fd/
 FV3=$( pwd -P )/FV3
 cd tests/
 
-if [ ${RUN_CCPP:-${1:-"NO"}} = "NO" ]; then
- ./compile.sh "$FV3" "$target" "WW3=Y 32BIT=Y" 1
- mv -f fv3_1.exe ../NEMS/exe/global_fv3gfs.x
-else
+# GFSv16 with waves
+# ./compile.sh "$FV3" "$target" "WW3=Y 32BIT=Y" 1
+# mv -f fv3_1.exe ../NEMS/exe/global_fv3gfs.x
+
  ./compile.sh "$target" "CCPP=Y 32BIT=Y SUITES=FV3_GFS_v15,FV3_GFS_v16beta" 2 NO NO
  mv -f fv3_2.exe ../NEMS/exe/global_fv3gfs.x
-fi

sorc/checkout.sh

@@ -2,17 +2,13 @@
 #set -xue
 set -x
 
-while getopts "oc" option;
+while getopts "o" option;
 do
  case $option in
   o)
    echo "Received -o flag for optional checkout of GTG, will check out GTG with EMC_post"
    checkout_gtg="YES"
    ;;
-  c)
-   echo "Received -c flag, check out ufs-weather-model develop branch with CCPP physics"  
-   run_ccpp="YES"
-   ;;
   :)
    echo "option -$OPTARG needs an argument"
    ;;
@@ -31,11 +27,7 @@ if [[ ! -d fv3gfs.fd ]] ; then
     rm -f ${topdir}/checkout-fv3gfs.log
     git clone https://github.com/ufs-community/ufs-weather-model fv3gfs.fd >> ${topdir}/checkout-fv3gfs.log 2>&1
     cd fv3gfs.fd
-    if [ ${run_ccpp:-"NO"} = "NO" ]; then
-     git checkout GFS.v16.0.14
-    else
-     git checkout b771e5be7e35eaea5ee7f762d644afccab019ed3
-    fi
+    git checkout 06bc77ba3640358b54b6ff03f542e2ce0d3242be
     git submodule update --init --recursive
     cd ${topdir}
 else
@@ -59,7 +51,7 @@ if [[ ! -d gldas.fd ]] ; then
     rm -f ${topdir}/checkout-gldas.log
     git clone https://github.com/NOAA-EMC/GLDAS.git gldas.fd >> ${topdir}/checkout-gldas.fd.log 2>&1
     cd gldas.fd
-    git checkout gldas_gfsv16_release.v1.13.0
+    git checkout gldas_gfsv16_release.v1.14.0
     cd ${topdir}
 else
     echo 'Skip.  Directory gldas.fd already exists.'

sorc/link_fv3gfs.sh

@@ -78,7 +78,7 @@ cd ${pwd}/../ush                ||exit 8
     done
     for file in emcsfc_ice_blend.sh  fv3gfs_driver_grid.sh  fv3gfs_make_orog.sh  global_cycle_driver.sh \
         emcsfc_snow.sh  fv3gfs_filter_topo.sh  global_chgres_driver.sh  global_cycle.sh \
-        fv3gfs_chgres.sh  fv3gfs_make_grid.sh  global_chgres.sh  ; do
+        chgres_cube.sh  fv3gfs_make_grid.sh  global_chgres.sh  ; do
         $LINK ../sorc/ufs_utils.fd/ush/$file                  .
     done
     for file in gldas_archive.sh  gldas_forcing.sh gldas_get_data.sh  gldas_process_data.sh gldas_liscrd.sh  gldas_post.sh ; do
@@ -295,13 +295,12 @@ cd ${pwd}/../sorc   ||   exit 8
 
     $SLINK gfs_post.fd/sorc/ncep_post.fd                                                   gfs_ncep_post.fd
 
-    $SLINK ufs_utils.fd/sorc/fre-nctools.fd/tools/shave.fd                                 shave.fd
-    for prog in filter_topo fregrid make_hgrid make_solo_mosaic ; do
+    for prog in fregrid make_hgrid make_solo_mosaic ; do
         $SLINK ufs_utils.fd/sorc/fre-nctools.fd/tools/$prog                                ${prog}.fd                                
     done
-    for prog in  global_cycle.fd   nemsio_read.fd  nemsio_chgdate.fd \
+    for prog in  global_cycle.fd \
         emcsfc_ice_blend.fd  nst_tf_chg.fd \
-        emcsfc_snow2mdl.fd   global_chgres.fd  nemsio_get.fd    orog.fd ;do
+        emcsfc_snow2mdl.fd   global_chgres.fd ;do
         $SLINK ufs_utils.fd/sorc/$prog                                                     $prog
     done