gfs_post.sh

#! /usr/bin/env bash

################################################################################
####  UNIX Script Documentation Block
#                      .                                             .
# Script name:         gfs_post.sh           
# Script description:  Posts the global pressure GRIB file
#
# Author:        Mark Iredell       Org: NP23         Date: 1999-05-01
#
# Abstract: This script reads a single global GFS IO file and (optionally)
#   a global flux file and creates a global pressure GRIB file.
#   The resolution and generating code of the output GRIB file can also
#   be set in the argument list.
#
# Script history log:
# 1999-05-01  Mark Iredell
# 2007-04-04  Huiya Chuang: Modify the script to run unified post
# 2012-06-04  Jun Wang: add grib2 option
# 2015-03-20  Lin Gan: add Perl for Post XML performance upgrade
# 2016-02-08  Lin Gan: Modify to use Vertical Structure
# 2018-02-05  Wen Meng: For EE2 standard, create gfs_post.sh based
#                  global_post.sh and change EXECglobal to EXECgfs;
#                  Remove legacy setting for reading non-nemsio model output
#                  and generating grib1 data
# 2019-06-02  Wen Meng: Remove the links of gfs fix files. 
# 2021-06-11  Yali Mao: Instead of err_chk, 'exit $err' for wafsfile
#                  if POSTGPEXEC fails
#
# Usage:  global_postgp.sh SIGINP FLXINP FLXIOUT PGBOUT PGIOUT IGEN
#
#   Input script positional parameters:
#     1             Input sigma file
#                   defaults to $SIGINP
#     2             Input flux file
#                   defaults to $FLXINP
#     3             Output flux index file
#                   defaults to $FLXIOUT
#     4             Output pressure GRIB file
#                   defaults to $PGBOUT
#     5             Output pressure GRIB index file
#                   defaults to $PGIOUT, then to none
#     8             Model generating code,
#                   defaults to $IGEN, then to input sigma generating code
#
#   Imported Shell Variables:
#     SIGINP        Input sigma file
#                   overridden by $1
#     FLXINP        Input flux file
#                   overridden by $2
#     FLXIOUT       Output flux index file
#                   overridden by $3
#     PGBOUT        Output pressure GRIB file
#                   overridden by $4. If not defined,
#                   post will use the filename specified in
#                   the control file
#     PGIOUT        Output pressure GRIB index file
#                   overridden by $5; defaults to none
#     IGEN          Model generating code
#                   overridden by $8; defaults to input sigma generating code
##### Moorthi: Add new imported shell variable for running chgres
#     CHGRESSH      optional: the script to run chgres
#		    default to to ${USHglobal}/global_chgres.sh
#     SIGLEVEL      optional: the coordinate text file
#		    default to to /nwprod/fix/global_hyblev.l${LEVS}.txt
##### Chuang: Add new imported Shell Variable for post
#     OUTTYP        Output file type read in by post 
#                   1: if user has a sigma file and needs post to run chgres to convert to gfs io file
#                   2: if user already has a gfs io file
#                   3: if user uses post to read sigma file directly
#                   0: if user wishes to generate both gfsio and sigma files
#                   4: if user uses post to read nemsio file directly
#     VDATE         Verifying date 10 digits yyyymmddhh
#     GFSOUT        Optional, output file name from chgres which is input file name to post 
#                   if model already runs gfs io, make sure GFSOUT is linked to the gfsio file
#     CTLFILE       Optional, Your version of control file if not using operational one
#     OVERPARMEXEC  Optional, the executable for changing Grib KPDS ID
#		    default to to ${EXECglobal}/overparm_grib 
#     CHGRESTHREAD  Optional, speed up chgres by using multiple threads 
#		    default to 1
#     FILTER        Optional, set to 1 to filter SLP and 500 mb height using copygb
#     D3DINP        Optional, Inout D3D file, if not defined, post will run
#                   without processing D3D file
#     D3DOUT        Optional, output D3D file, if not defined, post will
#                   use the file name specified in the control file
#     IPVOUT        Optional, output IPV file, if not defined, post will
#                   use the file name specified in the control file
#    GENPSICHI      Optional, set to YES will generate psi and chi and
#                   append it to the end of PGBOUT.  Default to NO
#    GENPSICHIEXE   Optional, specify where executable is for generating
#                   psi and chi.
########################################################################       
#     EXECUTIL      Directory for utility executables
#                   defaults to /nwprod/util/exec
#     USHUTIL       Directory for utility scripts
#                   defaults to /nwprod/util/ush
#     EXECglobal    Directory for global executables
#                   defaults to /nwprod/exec
#     USHglobal     Directory for global scripts
#                   defaults to /nwprod/ush
#     DATA          working directory
#                   (if nonexistent will be made, used and deleted)
#                   defaults to current working directory
#     MP            Multi-processing type ("p" or "s")
#                   defaults to "p", or "s" if LOADL_STEP_TYPE is not PARALLEL
#     XC            Suffix to add to executables
#                   defaults to none
#     POSTGPEXEC    Global post executable
#                   defaults to ${EXECglobal}/upp.x
#     GRBINDEX      GRIB index maker
#                   defaults to ${EXECUTIL}/grbindex$XC
#     POSTGPLIST    File containing further namelist inputs
#                   defaults to /dev/null
#     INISCRIPT     Preprocessing script
#                   defaults to none
#     LOGSCRIPT     Log posting script
#                   defaults to none
#     ERRSCRIPT     Error processing script
#                   defaults to 'eval [[ $err = 0 ]]'
#     ENDSCRIPT     Postprocessing script
#                   defaults to none
#     POSTGPVARS    Other namelist inputs to the global post executable
#                   such as IDRT,KO,PO,KTT,KT,PT,KZZ,ZZ,
#                           NCPUS,MXBIT,IDS,POB,POT,MOO,MOOA,MOW,MOWA,
#                           ICEN,ICEN2,IENST,IENSI
#                   defaults to none set
#     NTHREADS      Number of threads
#                   defaults to 1
#     NTHSTACK      Size of stack per thread
#                   defaults to 64000000
#     VERBOSE       Verbose flag (YES or NO)
#                   defaults to NO
#     PGMOUT        Executable standard output
#                   defaults to $pgmout, then to '&1'
#     PGMERR        Executable standard error
#                   defaults to $pgmerr, then to '&1'
#     pgmout        Executable standard output default
#     pgmerr        Executable standard error default
#     REDOUT        standard output redirect ('1>' or '1>>')
#                   defaults to '1>', or to '1>>' to append if $PGMOUT is a file
#     REDERR        standard error redirect ('2>' or '2>>')
#                   defaults to '2>', or to '2>>' to append if $PGMERR is a file
#
#   Exported Shell Variables:
#     PGM           Current program name
#     pgm
#     ERR           Last return code
#     err
#
#   Modules and files referenced:
#     scripts    : $INISCRIPT
#                  $LOGSCRIPT
#                  $ERRSCRIPT
#                  $ENDSCRIPT
#
#     programs   : $POSTGPEXEC
#                  $GRBINDEX
#
#     input data : $1 or $SIGINP
#                  $2 or $SFCINP
#                  $POSTGPLIST
#
#     output data: $3 or $FLXIOUT
#                  $4 or $PGBOUT
#                  $5 or $PGIOUT
#                  $PGMOUT
#                  $PGMERR
#
#     scratch    : ${DATA}/postgp.inp.sig
#                  ${DATA}/postgp.inp.flx
#                  ${DATA}/postgp.out.pgb
#
# Remarks:
#
#   Condition codes
#      0 - no problem encountered
#     >0 - some problem encountered
#
#   Control variable resolution priority
#     1 Command line argument.
#     2 Environment variable.
#     3 Inline default.
#
# Attributes:
#   Language: POSIX shell
#   Machine: IBM SP
#
####
################################################################################
#  Set environment.
source "${HOMEgfs}/ush/preamble.sh"

#  Command line arguments.
export SIGINP=${1:-${SIGINP:-}}
export FLXINP=${2:-${FLXINP:-}}
export FLXIOUT=${3:-${FLXIOUT:-}}
export PGBOUT=${4:-${PGBOUT:-}}
#export PGIOUT=${5:-${PGIOUT}}
export PGIOUT=${PGIOUT:-pgb.idx}
export IO=${6:-${IO:-0}}
export JO=${7:-${JO:-0}}
export IGEN=${8:-${IGEN:-0}}
#  Directories.
export NWPROD=${NWPROD:-/nwprod}
#export EXECUTIL=${EXECUTIL:-${NWPROD}/util/exec}
export USHUTIL=${USHUTIL:-${NWPROD}/util/ush}
export EXECgfs=${EXECgfs:-${NWPROD}/exec}
export USHgfs=${USHgfs:-${NWPROD}/ush}
export DATA=${DATA:-$(pwd)}
#  Filenames.
export MP=${MP:-$([[ ${LOADL_STEP_TYPE:-SERIAL} = PARALLEL ]]&&echo "p"||echo "s")}
export XC=${XC:-}
export POSTGPEXEC=${POSTGPEXEC:-${EXECgfs}/upp.x}
export OVERPARMEXEC=${OVERPARMEXEC:-${EXECgfs}/overparm_grib}
export POSTGPLIST=${POSTGPLIST:-/dev/null}
export INISCRIPT=${INISCRIPT:-}
# Ignore warning about single quote not subtituting now
# shellcheck disable=SC2016
export ERRSCRIPT=${ERRSCRIPT:-'eval (( err == 0 ))'}
# shellcheck disable=
export LOGSCRIPT=${LOGSCRIPT:-}
export ENDSCRIPT=${ENDSCRIPT:-}
export GFSOUT=${GFSOUT:-gfsout}
export CTLFILE=${CTLFILE:-${NWPROD}/parm/gfs_cntrl.parm}
export GRIBVERSION=${GRIBVERSION:-'grib1'}
#  Other variables.
export POSTGPVARS=${POSTGPVARS}
export NTHREADS=${NTHREADS:-1}
export NTHSTACK=${NTHSTACK:-64000000}
export PGMOUT=${PGMOUT:-${pgmout:-'&1'}}
export PGMERR=${PGMERR:-${pgmerr:-'&2'}}
export CHGRESTHREAD=${CHGRESTHREAD:-1}
export FILTER=${FILTER:-0}
export GENPSICHI=${GENPSICHI:-NO}
export GENPSICHIEXE=${GENPSICHIEXE:-${EXECgfs}/genpsiandchi}
export ens=${ens:-NO}
#export D3DINP=${D3DINP:-/dev/null}
l="$(echo "${PGMOUT}" | xargs | cut -c1)"
[[ ${l} = '&' ]]&&a=''||a='>'
export REDOUT=${REDOUT:-'1>'${a}}
l="$(echo "${PGMERR}" | xargs | cut -c1)"
[[ ${l} = '&' ]]&&a=''||a='>'
export REDERR=${REDERR:-'2>'${a}}
################################################################################

# Chuang: Run chgres if OUTTYP=1 or 0

export APRUN=${APRUNP:-${APRUN:-""}}

# exit if NEMSINP does not exist
if (( OUTTYP == 4 )) ; then
	if [ ! -s "${NEMSINP}" ] || [ ! -s "${FLXINP}"  ] ; then
		echo "model files not found, exitting"
		exit 111
	fi
fi

export SIGHDR=${SIGHDR:-${NWPROD}/exec/global_sighdr} 
export IDRT=${IDRT:-4}

# run post to read file if OUTTYP=4
if (( OUTTYP == 4 )) ; then
  export MODEL_OUT_FORM=${MODEL_OUT_FORM:-netcdfpara}
  export GFSOUT=${NEMSINP}
fi

# allow threads to use threading in Jim's sp lib
# but set default to 1 
export OMP_NUM_THREADS=${OMP_NUM_THREADS:-1}

pwd=$(pwd)
if [[ -d "${DATA}" ]]; then
	mkdata=NO
else
	mkdir -p "${DATA}"
	mkdata=YES
fi
cd "${DATA}" || exit 99
################################################################################
#  Post GRIB
export PGM=${POSTGPEXEC}
export pgm=${PGM}
${LOGSCRIPT}
cat <<-EOF >postgp.inp.nml$$
	&NAMPGB
	${POSTGPVARS}
EOF

cat <<-EOF >>postgp.inp.nml$$
	/
EOF

if [[ "${VERBOSE}" = "YES" ]]; then
	cat postgp.inp.nml$$
fi

# making the time stamp format for ncep post
YY=$(echo "${VDATE}" | cut -c1-4)
MM=$(echo "${VDATE}" | cut -c5-6)
DD=$(echo "${VDATE}" | cut -c7-8)
HH=$(echo "${VDATE}" | cut -c9-10)
export YY MM DD HH

cat > itag <<-EOF
	&model_inputs
	fileName='${GFSOUT}'
	IOFORM='${MODEL_OUT_FORM}'
	grib='${GRIBVERSION}'
	DateStr='${YY}-${MM}-${DD}_${HH}:00:00'
	MODELNAME='GFS'
	fileNameFlux='${FLXINP}'
	/
EOF

cat postgp.inp.nml$$ >> itag

cat itag

rm -f fort.*

#ln -sf $SIGINP     postgp.inp.sig$$
#ln -sf $FLXINP     postgp.inp.flx$$
#ln -sf $PGBOUT     postgp.out.pgb$$

# change model generating Grib number 
if [ "${GRIBVERSION}" = "grib2" ]; then
	cp "${POSTGRB2TBL}" .
	cp "${PostFlatFile}" ./postxconfig-NT.txt
	if [ "${ens}" = "YES" ] ; then
		sed < "${PostFlatFile}" -e "s#negatively_pert_fcst#${ens_pert_type}#" > ./postxconfig-NT.txt
	fi
	#  cp ${CTLFILE} postcntrl.xml
fi
CTL=$(basename "${CTLFILE}")
export CTL

ln -sf griddef.out fort.110
cp "${PARMpost}/nam_micro_lookup.dat" ./eta_micro_lookup.dat

echo "gfs_post.sh OMP_NUM_THREADS= ${OMP_NUM_THREADS}"
${APRUN:-mpirun.lsf} "${POSTGPEXEC}" < itag > "outpost_gfs_${VDATE}_${CTL}"

export ERR=$?
export err=${ERR}

if (( err != 0 )) ; then
	if [ "${PGBOUT}" = "wafsfile" ] ; then
		exit "${err}"
	fi
fi
${ERRSCRIPT} || exit 2

if [ "${FILTER}" = "1" ] ; then
	# Filter SLP and 500 mb height using copygb, change GRIB ID, and then
	# cat the filtered fields to the pressure GRIB file, from Iredell

	if [ "${GRIBVERSION}" = "grib2" ]; then
		if [ "${ens}" = "YES" ] ; then
			"${COPYGB2}" -x -i'4,0,80' -k'1 3 0 7*-9999 101 0 0' "${PGBOUT}" tfile
			export err=$?; err_chk
		else
			"${COPYGB2}" -x -i'4,0,80' -k'0 3 0 7*-9999 101 0 0' "${PGBOUT}" tfile
			export err=$?; err_chk
		fi
		${WGRIB2} tfile -set_byte 4 11 1 -grib prmsl
		export err=$?; err_chk
		if [ "${ens}" = "YES" ] ; then
			"${COPYGB2}" -x -i'4,1,5' -k'1 3 5 7*-9999 100 0 50000' "${PGBOUT}" tfile
			export err=$?; err_chk
		else
			"${COPYGB2}" -x -i'4,1,5' -k'0 3 5 7*-9999 100 0 50000' "${PGBOUT}" tfile
			export err=$?; err_chk
		fi
		${WGRIB2} tfile -set_byte 4 11 193 -grib h5wav
		export err=$?; err_chk

		#cat $PGBOUT prmsl h5wav >> $PGBOUT
		#wm
		#  cat  prmsl h5wav >> $PGBOUT
		[[ -f prmsl ]] && rm prmsl
		[[ -f h5wav ]] && rm h5wav
		[[ -f tfile ]] && rm tfile
	fi
fi

################################################################################
#  Make GRIB index file
if [[ -n "${PGIOUT}" ]]; then
	if [ "${GRIBVERSION}" = "grib2" ]; then
		${GRB2INDEX} "${PGBOUT}" "${PGIOUT}"
	fi
fi
if [[ -r ${FLXINP} && -n ${FLXIOUT} && ${OUTTYP} -le 3 ]]; then
	${GRBINDEX} "${FLXINP}" "${FLXIOUT}"
fi
################################################################################
# generate psi and chi
echo "GENPSICHI = ${GENPSICHI}"
if [ "${GENPSICHI}" = "YES" ] ; then
	#echo "PGBOUT PGIOUT=" $PGBOUT $PGIOUT
	#echo "YY MM=" $YY $MM
	export psichifile=./psichi.grb
	${GENPSICHIEXE} < postgp.inp.nml$$
	rc=$?
	if (( rc != 0 )); then
		echo "Nonzero return code rc=${rc}"
		exit 3
	fi
	cat ./psichi.grb >> "${PGBOUT}"
fi
################################################################################
#  Postprocessing
cd "${pwd}" || exit 2
[[ "${mkdata}" = "YES" ]] && rmdir "${DATA}"

exit "${err}"