Merge develop into release/public-v1 (changes: PR NCAR#48 from George…

… Gayno, chgres_cube grib2 GFS data support); update submodule pointer for cmake

CMakeLists.txt

@@ -40,6 +40,7 @@ find_package(Jasper REQUIRED)
 find_package(PNG REQUIRED)
 find_package(ESMF MODULE REQUIRED)
 find_package(ZLIB REQUIRED)
+find_package(WGRIB2 REQUIRED)
 
 if(NOT TARGET landsfcutil_4)
   find_package(landsfcutil REQUIRED)

modulefiles/chgres_cube.hera

@@ -19,6 +19,9 @@ module load sfcio//v1.1.0-intel-19.0.4.243
 module load sigio/v2.1.0-intel-19.0.4.243-impi
 module load esmf/8.0.0-intel-19.0.4.243-impi
 
+export WGRIB2API_INC="/apps/wgrib2/2.0.8/intel/18.0.3.222/lib"
+export WGRIB2_LIB="/apps/wgrib2/2.0.8/intel/18.0.3.222/lib/libwgrib2.a"
+
 export FCOMP=mpiifort
 export FFLAGS="-O3 -fp-model precise -g -traceback -r8 -i4 -qopenmp -convert big_endian -assume byterecl"
 # for debugging

modulefiles/chgres_cube.jet

@@ -4,8 +4,8 @@
 
 module load intel/18.0.5.274
 module load impi/2018.4.274
-module load szip
-module load hdf5
+module load szip/2.1
+module load hdf5/1.8.9
 module load netcdf/4.2.1.1
 
 module load w3nco/v2.0.6
@@ -22,3 +22,6 @@ export FCOMP=mpiifort
 export FFLAGS="-O3 -fp-model precise -g -traceback -r8 -i4 -qopenmp -convert big_endian -assume byterecl"
 #debug
 #export FFLAGS="-O0 -g -traceback -r8 -i4 -qopenmp -convert big_endian -check bounds -warn unused -assume byterecl"
+
+export WGRIB2API_INC="/mnt/lfs3/projects/hwrfv3/Jili.Dong/wgrib2-2.0.8/grib2/lib"
+export WGRIB2_LIB="/mnt/lfs3/projects/hwrfv3/Jili.Dong/wgrib2-2.0.8/grib2/lib/libwgrib2.a"

modulefiles/chgres_cube.linux.gnu

@@ -0,0 +1,24 @@
+#############################################################
+## chgres_cube component - linux.gnu
+#############################################################
+
+export IP_INCd=${NCEPLIBS}/ip/include_d
+export NEMSIO_INC=${NCEPLIBS}/nemsio/include
+export SFCIO_INC4=${NCEPLIBS}/sfcio/include_4
+export SIGIO_INC4=${NCEPLIBS}/sigio/include_4
+
+export BACIO_LIB4=${NCEPLIBS}/bacio/lib/libbacio_v2.1.0_4.a
+export IP_LIBd=${NCEPLIBS}/ip/lib/libip_v3.0.0_d.a
+export NEMSIO_LIB=${NCEPLIBS}/nemsio/lib/libnemsio_v2.2.3.a
+export SFCIO_LIB4=${NCEPLIBS}/sfcio/lib/libsfcio_v1.1.0_4.a
+export SIGIO_LIB4=${NCEPLIBS}/sigio/lib/libsigio_v2.1.0_4.a
+export SP_LIBd=${NCEPLIBS}/sp/lib/libsp_v2.0.2_d.a
+export W3NCO_LIBd=${NCEPLIBS}/w3nco/lib/libw3nco_v2.0.6_d.a
+
+export WGRIB2API_INC=${WGRIB2_DIR}/include
+export WGRIB2_LIB=${WGRIB2_DIR}/lib/libwgrib2.a
+
+export FCOMP=mpif90
+export FFLAGS="-O3 -g -fbacktrace -fdefault-real-8 -ffree-line-length-none -fopenmp -fconvert=big-endian"
+# for debugging
+#export FFLAGS="-O0 -g -fbacktrace -fdefault-real-8 -ffree-line-length-none -fopenmp -fconvert=big-endian"

modulefiles/chgres_cube.linux.intel

@@ -0,0 +1,24 @@
+#############################################################
+## chgres_cube component - linux.intel
+#############################################################
+
+export IP_INCd=${NCEPLIBS}/ip/include_d
+export NEMSIO_INC=${NCEPLIBS}/nemsio/include
+export SFCIO_INC4=${NCEPLIBS}/sfcio/include_4
+export SIGIO_INC4=${NCEPLIBS}/sigio/include_4
+
+export BACIO_LIB4=${NCEPLIBS}/bacio/lib/libbacio_v2.1.0_4.a
+export IP_LIBd=${NCEPLIBS}/ip/lib/libip_v3.0.0_d.a
+export NEMSIO_LIB=${NCEPLIBS}/nemsio/lib/libnemsio_v2.2.3.a
+export SFCIO_LIB4=${NCEPLIBS}/sfcio/lib/libsfcio_v1.1.0_4.a
+export SIGIO_LIB4=${NCEPLIBS}/sigio/lib/libsigio_v2.1.0_4.a
+export SP_LIBd=${NCEPLIBS}/sp/lib/libsp_v2.0.2_d.a
+export W3NCO_LIBd=${NCEPLIBS}/w3nco/lib/libw3nco_v2.0.6_d.a
+
+export WGRIB2API_INC=${WGRIB2_DIR}/include
+export WGRIB2_LIB=${WGRIB2_DIR}/lib/libwgrib2.a
+
+export FCOMP=mpif90
+export FFLAGS="-O3 -fp-model source -g -traceback -r8 -i4 -qopenmp -convert big_endian -assume byterecl"
+# for debugging
+#export FFLAGS="-O0 -g -traceback -r8 -i4 -qopenmp -convert big_endian -check bounds -warn unused -assume byterecl"

modulefiles/chgres_cube.odin

@@ -0,0 +1,27 @@
+#%Module#####################################################
+## chgres build module for Odin
+#############################################################
+
+module use /oldscratch/ywang/external/modulefiles
+module load esmf/8.0.0bs30
+
+module load cray-netcdf-hdf5parallel
+module load cray-parallel-netcdf
+module load cray-hdf5-parallel
+module load w3nco/v2.0.6
+module load nemsio/v2.2.2
+module load bacio/v2.0.2
+module load sp/v2.0.2
+module load sfcio/v1.0.0
+module load sigio/v2.0.1
+
+
+export FCOMP=ftn
+export FFLAGS="-O3 -fp-model precise -g -traceback -r8 -i4 -qopenmp -convert big_endian -assume byterecl"
+export WGRIB2API_LIB="/home/larissa.reames/tmp/wgrib2-2/grib2/lib/libwgrib2_api.a"
+export WGRIB2API_INC="/home/larissa.reames/tmp/wgrib2-2/grib2/lib"
+export WGRIB2_LIB="/home/larissa.reames/tmp/wgrib2-2/grib2/lib/libwgrib2.a"
+
+
+# for debugging
+#export FFLAGS="-O0 -g -traceback -r8 -i4 -qopenmp -convert big_endian -check bounds -warn unused -assume byterecl"

modulefiles/chgres_cube.wcoss_cray

@@ -19,6 +19,9 @@ module load sfcio-intel/1.0.0
 # module load esmf/7.1.0r
 export ESMFMKFILE=/gpfs/hps3/emc/global/noscrub/George.Gayno/esmf/8_0_0_bs20/lib/esmf.mk
 
+export WGRIB2API_INC=/gpfs/hps3/emc/meso/save/Dusan.Jovic/wgrib2/include
+export WGRIB2_LIB=/gpfs/hps3/emc/meso/save/Dusan.Jovic/wgrib2/lib/libwgrib2.a
+
 export FCOMP=ftn
 export FFLAGS="-O3 -fp-model precise -g -r8 -i4 -qopenmp -convert big_endian -assume byterecl"
 # for debugging

modulefiles/chgres_cube.wcoss_dell_p3

@@ -14,6 +14,9 @@ module load bacio/2.0.2
 module load sfcio/1.0.0
 module load sigio/2.1.0
 
+export WGRIB2API_INC=/u/Wesley.Ebisuzaki/home/grib2.v2.0.8.intel/lib
+export WGRIB2_LIB=/u/Wesley.Ebisuzaki/home/grib2.v2.0.8.intel/lib/libwgrib2.a
+
 export FCOMP=mpif90
 export FFLAGS="-O3 -fp-model precise -g -traceback -r8 -i4 -qopenmp -convert big_endian -assume byterecl"
 # for debugging

parm/varmap_tables/GFSphys_var_map.txt

@@ -0,0 +1,23 @@
+dzdt                dzdt      set_to_fill   0        D
+sphum               sphum     set_to_fill   1E-7     T
+liq_wat             liq_wat   set_to_fill   0        T
+o3mr                o3mr      set_to_fill   1E-7     T
+ice_wat             ice_wat   set_to_fill   0        T
+rainwat             rainwat   set_to_fill   0        T
+snowwat             snowwat   set_to_fill   0        T
+graupel             graupel   set_to_fill   0        T
+vtype               vtype     skip          0        S
+sotype              stype     skip          0        S
+vfrac               vfrac     skip          0        S
+fricv               uustar    set_to_fill   0        S
+sfcr                zorl      set_to_fill   0.01     S
+tprcp               tprcp     set_to_fill   0.00     S
+ffmm                ffmm      set_to_fill   0.00     S
+f10m                f10m      set_to_fill   0.00     S
+soilw               smc       stop          0        S
+soill               slc       set_to_fill   0.0      S
+soilt               stc       stop          0        S
+cnwat               cnwat     set_to_fill   0.0      S
+hice                icetk     set_to_fill   1.5      S
+weasd               weasd     set_to_fill   0.0      S
+snod                snod      set_to_fill   0.0      S       	

parm/varmap_tables/README

@@ -0,0 +1,24 @@
+#######################################################
+#            Description of varmap_tables             #
+#######################################################
+
+These files, each named for the phys_suite variable set in the chgres_cube namelist, 
+control how chgres_cube, when processing grib2 files, handles variables that might
+be missing from the grib2 files. Since there are so many different version of grib2
+files, it's often uncertain what fields are available even if you know what source
+model the data is coming from. Each file contains :
+
+Line 1: number of entries in the table
+Column 1: Name the code searches for in the table. Do not change.
+Column 2: Name the code will use to save the variable in the output file. Unimplemented.
+Comumn 3: Behavior when the code can't find the variable in the input file. Options are:
+	  "skip": Don't write to output file.
+	  "set_to_fill": Set to user-specified field value (see column 4).
+	  "stop": Force an exception and stop code execution. Use this if you absolutely
+		require a field to be present.
+Column 4: If column 3 = "set_to_fill", then this value is used to fill in all points 
+	  in the input field. These values may be over-written by the code before 
+	  output depending on the variable (esp. for surface variables). Be careful
+	  with these values for surface variables. If you set this value too low 
+	  (e.g., -100000), the code may run extremely slowly due to variable replacment
+	  at "missing" points.

sorc/build_chgres_cube.sh

@@ -0,0 +1,41 @@
+#! /usr/bin/env bash
+set -eux
+
+target=${target:-"NULL"}
+
+if [[ $target == "linux.gnu" || $target == "linux.intel" ]]; then
+ unset -f module
+else
+ source ./machine-setup.sh > /dev/null 2>&1
+fi
+
+cwd=`pwd`
+
+USE_PREINST_LIBS=${USE_PREINST_LIBS:-"true"}
+if [ $USE_PREINST_LIBS = true ]; then
+  export MOD_PATH
+  source ../modulefiles/chgres_cube.$target             > /dev/null 2>&1
+else
+  export MOD_PATH=${cwd}/lib/modulefiles
+  if [ $target = wcoss_cray ]; then
+    source ../modulefiles/chgres_cube.${target}_userlib > /dev/null 2>&1
+  else
+    source ../modulefiles/chgres_cube.$target           > /dev/null 2>&1
+  fi
+fi
+
+# Check final exec folder exists
+if [ ! -d "../exec" ]; then
+  mkdir ../exec
+fi
+
+#
+# --- Chgres part
+#
+cd chgres_cube.fd
+
+make clean
+make
+make install
+
+exit

sorc/chgres_cube.fd/CMakeLists.txt

@@ -32,11 +32,13 @@ target_include_directories(${exe_name} PUBLIC
 
 target_include_directories(${exe_name}
   PRIVATE
+  ${WGRIB2_INCLUDES}
   ${NETCDF_INCLUDES}
   ${NETCDF_INCLUDES_F90}
   ${MPI_Fortran_INCLUDE_PATH})
 
 target_link_libraries(${exe_name}
+  ${WGRIB2_LIBRARIES}
   ${NETCDF_LIBRARIES_F90} ${NETCDF_LIBRARIES}
   nemsio
   sfcio_4 ${MPI_Fortran_LIBRARIES}