/usr/bin/ncremap is in nco 4.5.4-1build1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
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# Purpose: Regrid (subsets of) variables from netCDF files
# Regrids all input files (possibly on different grids) to a single specified output grid
# Copyright (C) 2015-2016 Charlie Zender
# This file is part of NCO, the netCDF Operators. NCO is free software.
# You may redistribute and/or modify NCO under the terms of the
# GNU General Public License (GPL) Version 3.
# As a special exception to the terms of the GPL, you are permitted
# to link the NCO source code with the HDF, netCDF, OPeNDAP, and UDUnits
# libraries and to distribute the resulting executables under the terms
# of the GPL, but in addition obeying the extra stipulations of the
# HDF, netCDF, OPeNDAP, and UDUnits licenses.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
# See the GNU General Public License for more details.
# The original author of this software, Charlie Zender, seeks to improve
# it with your suggestions, contributions, bug-reports, and patches.
# Please contact the NCO project at http://nco.sf.net or write to
# Charlie Zender
# Department of Earth System Science
# University of California, Irvine
# Irvine, CA 92697-3100
# Source: https://github.com/nco/nco/tree/master/data/ncremap
# Prerequisites: Bash, NCO, ESMF_RegridWeightGen
# Script could use other shells, e.g., dash (Debian default) after re-writing function definition and looping constructs
# Script could use other weight-generators, e.g., TempestRemap by re-writing map-file command
# Script runs in one of four modes:
# 1. Free-will: Infer source and destination grids to generate map-file, then regrid
# 2. Old Grid: Use known-good destination grid to generate map-file then regrid
# 3. New Grid: Generate source-grid from ncks parameter string
# 4. Pre-Destination: Apply supplied map-file to all input files
# By default, ncremap deletes any intermediate grids and map-file that it generates
# Use Free-Will, Old-Grid, or New-Grid mode to process Swath-Like-Data (SLD) where each input may be a granule on a new grid, yet all inputs are to be regridded to the same output grid
# Use Pre-Destination mode to post-process models or analyses where all files are converted from the same source grid to the same destination grid so the map-file can be pre-generated and never change
# Additional Documentation:
# Configure paths at High-Performance Computer Centers (HPCCs) based on ${HOSTNAME}
if [ -z "${HOSTNAME}" ]; then
if [ -f /bin/hostname ] && [ -x /bin/hostname ] ; then
export HOSTNAME=`/bin/hostname`
elif [ -f /usr/bin/hostname ] && [ -x /usr/bin/hostname ] ; then
export HOSTNAME=`/usr/bin/hostname`
fi # !hostname
fi # HOSTNAME
# Default input and output directory is ${DATA}
if [ -z "${DATA}" ]; then
case "${HOSTNAME}" in
cooley* | cc* ) DATA="/projects/HiRes_EarthSys/${USER}" ; ;; # ALCF cooley compute nodes named ccNNN
edison* | hopper* | nid* ) DATA="${SCRATCH}" ; ;; # NERSC edison compute nodes named nidNNNNN
pileus* ) DATA="/lustre/atlas/proj-shared/cli115/${USER}" ; ;; # OLCF CADES
rhea* ) DATA="/lustre/atlas/proj-shared/cli115/${USER}" ; ;; # OLCF rhea compute nodes named rheaNNN
* ) DATA='/tmp' ; ;; # Other
esac # !HOSTNAME
fi # DATA
# Test cases (examples for Charlie's machines):
# ls ${DATA}/sld/raw/*.nc | ncremap -a conserve -D 0 -d ${DATA}/dstmch90/dstmch90_clm.nc -O ~/rgr
# ncremap -a conserve -v FSNT -I ${DATA}/ne30/raw -s ${DATA}/grids/ne30np4_pentagons.091226.nc -d ${DATA}/dstmch90/dstmch90_clm.nc -O ~/rgr
# ls ${DATA}/essgcm14/essgcm14*cam*0007*.nc | ncremap -a conserve -M -d ${DATA}/dstmch90/dstmch90_clm.nc -O ~/rgr
# ncremap -a conserve -v FSNT -I ${DATA}/ -s ${DATA}/grids/ne30np4_pentagons.091226.nc -d ${DATA}/dstmch90/dstmch90_clm.nc -O ~/rgr
# ncremap -i AIRS.2014.10.01.202.L2.TSurfStd.Regrid010.1DLatLon.hole.nc -d ${DATA}/dstmch90/dstmch90_clm.nc -O ~/rgr
# ncremap -v TSurfAir -i ${DATA}/hdf/AIRS.2015.01.15.001.L2.RetStd.v6.0.11.0.G15015142014.hdf -g ${DATA}/grids/180x360_SCRIP.20150901.nc -O ~/rgr
# ncremap -v CloudFrc_A -i ${DATA}/hdf/AIRS.2002.08.01.L3.RetStd_H031.v4.0.21.0.G06104133732.hdf -g ${DATA}/grids/180x360_SCRIP.20150901.nc -O ~/rgr
# ncremap -i ${DATA}/hdf/MOD04_L2.A2000055.0005.006.2014307165927.hdf -g ${DATA}/grids/180x360_SCRIP.20150901.nc -O ~/rgr
# ncremap -i ${DATA}/hdf/OMI-Aura_L2-OMIAuraSO2_2012m1222-o44888_v01-00-2014m0107t114720.h5 -g ${DATA}/grids/180x360_SCRIP.20150901.nc -O ~/rgr
# ncremap -v T -i ${DATA}/hdf/wrfout_v2_Lambert_notime.nc -g ${DATA}/grids/180x360_SCRIP.20150901.nc -O ~/rgr
# ncremap -v StepTwoO3 -i ${DATA}/hdf/OMI-Aura_L2-OMTO3_2015m0731t0034-o58727_v003-2015m0731t080836.he5.nc -d ${DATA}/hdf/cam_time.nc -O ~/rgr
# ncremap -v TSurfStd -i ${DATA}/sld/raw/AIRS.2014.10.01.202.L2.TSurfStd.Regrid010.1DLatLon.hole.nc -G "--rgr grd_ttl='Default internally-generated grid' --rgr grid=~/rgr/ncremap_tmp_grd_dst.nc --rgr latlon=100,100 --rgr snwe=30.0,70.0,-130.0,-90.0" -O ~/rgr
# ncremap -x TSurfStd_ct -i ${DATA}/sld/raw/AIRS.2014.10.01.202.L2.TSurfStd.Regrid010.1DLatLon.hole.nc -g ${DATA}/grids/180x360_SCRIP.20150901.nc -O ~/rgr
# ncremap -i ${DATA}/hdf/cice_hi_flt.nc -g ${DATA}/grids/180x360_SCRIP.20150901.nc -O ~/rgr
# ncremap -i ${DATA}/hdf/cam_time.nc -g ${DATA}/grids/180x360_SCRIP.20150901.nc -O ~/rgr
# CESM & ACME:
# ncremap -i ${DATA}/ne120/raw/b1850c5_m2a.cam.h0.0060-01.nc -g ${DATA}/grids/180x360_SCRIP.20150901.nc -O ~/rgr
# ncremap -i ${DATA}/ne120/raw/b1850c5_m2a.clm2.h0.0060-01.nc -g ${DATA}/grids/180x360_SCRIP.20150901.nc -O ~/rgr
# ncremap -i ${DATA}/ne120/raw/b1850c5_m2a.cice.h.0060-01.nc -g ${DATA}/grids/180x360_SCRIP.20150901.nc -O ~/rgr
# ncremap -i ${DATA}/ne120/raw/b1850c5_m2a.pop.h.0060-01.nc -g ${DATA}/grids/180x360_SCRIP.20150901.nc -O ~/rgr
# ncremap -i ${DATA}/ne120/raw/b1850c5_m2a.rtm.h0.0060-01.nc -g ${DATA}/grids/180x360_SCRIP.20150901.nc -O ~/rgr
# ACME benchmarks:
# ncremap -v FSNT,AODVIS -i ${DATA}/ne30/raw/famipc5_ne30_v0.3_00003.cam.h0.1979-01.nc -m map_ne30np4_to_fv129x256_aave.150418.nc -O ~/rgr
# ncremap -v FSNT,AODVIS -i ${DATA}/ne30/raw/famipc5_ne30_v0.3_00003.cam.h0.1979-01.nc -m map_ne30np4_to_fv129x256_aave.20150901.nc -O ~/rgr
# ncremap -v FSNT,AODVIS -w esmf -i ${DATA}/ne30/raw/famipc5_ne30_v0.3_00003.cam.h0.1979-01.nc -s ${DATA}/grids/ne30np4_pentagons.091226.nc -g ${DATA}/grids/129x256_SCRIP.20150901.nc -O ~/rgr
# ncremap -v FSNT,AODVIS -w tempest -i ${DATA}/ne30/raw/famipc5_ne30_v0.3_00003.cam.h0.1979-01.nc -s ${DATA}/grids/ne30np4_pentagons.091226.nc -g ${DATA}/grids/129x256_SCRIP.20150901.nc -O ~/rgr
# Debugging and Benchmarking:
# ncremap -D 1 -i ${DATA}/sld/raw/AIRS.2014.10.01.202.L2.TSurfStd.Regrid010.1DLatLon.hole.nc -d ${DATA}/dstmch90/dstmch90_clm.nc -O ~/rgr > ~/ncremap.out 2>&1 &
# dbg_lvl: 0 = Quiet, print basic status during evaluation
# 1 = Print configuration, full commands, and status to output during evaluation
# 2 = As in dbg_lvl=1, but _do not evaluate commands_
# 3 = As in dbg_lvl=1, and pass debug level through to NCO/ncks
# thr_nbr: Thread number to use in NCO regridder, '-t 1' for one thread, '-t 2' for two threads...
# Set script name and run directory
drc_pwd=${PWD}
spt_nm=$(basename ${0}) # [sng] Script name
nco_version=$(ncks --version 2>&1 >/dev/null | grep NCO | awk '{print $5}')
# Set fonts for legibility
fnt_nrm=`tput sgr0` # Normal
fnt_bld=`tput bold` # Bold
fnt_rvr=`tput smso` # Reverse
# Defaults for command-line options and some derived variables
# Modify these defaults to save typing later
alg_typ='conserve' # [nbr] Algorithm for ESMF interpolation (bilinear|patch|neareststod|nearestdtos|conserve)
dbg_lvl=0 # [nbr] Debugging level
#drc_in="${drc_pwd}" # [sng] Input file directory
drc_in='' # [sng] Input file directory
drc_in_xmp='~/drc_in' # [sng] Input file directory for examples
drc_out="${drc_pwd}" # [sng] Output file directory
drc_out_xmp="~/rgr" # [sng] Output file directory for examples
dst_fl='' # [sng] Destination file
dst_xmp='dst.nc' # [sng] Destination file for examples
#esmf_opt='--src_regional --dst_regional --ignore_unmapped' # [sng] ESMF_RegridWeightGen options
esmf_opt='--ignore_unmapped' # [sng] ESMF_RegridWeightGen options
#fml_nm='' # [sng] Family name (e.g., 'amip', 'control', 'experiment')
fl_nbr=0 # [nbr] Number of files to remap
gaa_sng="--gaa rgr_script=${spt_nm} --gaa rgr_hostname=${HOSTNAME} --gaa rgr_version=${nco_version}" # [sng] Global attributes to add
grd_dst='' # [sng] Destination grid-file
grd_dst_glb="${DATA}/grids/180x360_SCRIP.20150901.nc" # [sng] Grid-file (destination) global
grd_dst_xmp='grd_dst.nc' # [sng] Destination grid-file for examples
grd_sng='' # [sng] Grid string
grd_src='' # [sng] Source grid-file
grd_src_xmp='grd_src.nc' # [sng] Source grid-file for examples
hdr_pad='1000' # [B] Pad at end of header section
in_fl='' # [sng] Input file
#in_fl='AIRS.2014.10.01.202.L2.TSurfStd.Regrid010.1DLatLon.hole.nc' # [sng] Input file
in_xmp='in.nc' # [sng] Input file for examples
map_fl='' # [sng] Map-file
map_xmp='map.nc' # [sng] Map-file for examples
mlt_map_flg='Yes' # [sng] Multi-map flag
mpi_flg='No' # [sng] Parallelize over nodes
msh_fl='' # [sng] Mesh-file (for Tempest)
nco_opt='-O --no_tmp_fl' # [sng] NCO defaults (e.g., '-O -6 -t 1')
nco_usr='' # [sng] NCO user-configurable options (e.g., '-D 1')
out_fl='' # [sng] Output file
out_xmp='out.nc' # [sng] Output file for examples
par_typ='' # [sng] Parallelism type
rgr_opt='--rgr lat_nm_out=lat --rgr lon_nm_out=lon' # [sng] Regridding options (e.g., '--rgr col_nm=lndgrid')
tps_opt='' # [sng] TempestRemap options
thr_nbr=2 # [nbr] Thread number for regridder
#var_lst='FSNT,AODVIS' # [sng] Variables to process (empty means all)
tmp_out_fl='ncremap_grd_tmp.nc' # [sng] Temporary output file
var_lst='' # [sng] Variables to process (empty means all)
var_xmp='FSNT' # [sng] Variable list for examples
wgt_gnr='esmf' # [sng] Weight-generator program
xtn_var='' # [sng] Extensive variables (e.g., 'TSurfStd_ct')
function fnc_usg_prn { # NB: dash supports fnc_nm (){} syntax, not function fnc_nm{} syntax
# Print usage
printf "\nQuick documentation for ${fnt_bld}${spt_nm}${fnt_nrm} (more at http://nco.sf.net/nco.html#ncremap)\n\n"
printf "${fnt_rvr}Basic usage:${fnt_nrm} ${fnt_bld}$spt_nm -i in_fl -d dst_fl -o out_fl${fnt_nrm}\n\n"
echo "Command-line options:"
echo "${fnt_rvr}-a${fnt_nrm} ${fnt_bld}alg_typ${fnt_nrm} Algorithm for ESMF weight generation (default ${fnt_bld}${alg_typ}${fnt_nrm})"
echo "${fnt_rvr}-d${fnt_nrm} ${fnt_bld}dst_fl${fnt_nrm} Data file to infer destination grid from (empty means none, i.e., use grd_fl, grd_sng or map_fl)) (default ${fnt_bld}${dst_fl}${fnt_nrm})"
echo "${fnt_rvr}-D${fnt_nrm} ${fnt_bld}dbg_lvl${fnt_nrm} Debugging level (default ${fnt_bld}${dbg_lvl}${fnt_nrm})"
echo "${fnt_rvr}-E${fnt_nrm} ${fnt_bld}esmf_opt${fnt_nrm} ESMF ESMF_RegridWeightGen options (default ${fnt_bld}${esmf_opt}${fnt_nrm})"
# echo "${fnt_rvr}-f${fnt_nrm} ${fnt_bld}fml_nm${fnt_nrm} Family name (empty means none) (default ${fnt_bld}${fml_nm}${fnt_nrm})"
echo "${fnt_rvr}-g${fnt_nrm} ${fnt_bld}grd_dst${fnt_nrm} Grid-file (destination) (empty means none, i.e., infer from dst_fl or use grd_sng or map_fl) (default ${fnt_bld}${grd_dst}${fnt_nrm})"
echo "${fnt_rvr}-G${fnt_nrm} ${fnt_bld}grd_sng${fnt_nrm} Grid generation argument string (empty means none) (default ${fnt_bld}${grd_sng}${fnt_nrm})"
echo "${fnt_rvr}-I${fnt_nrm} ${fnt_bld}drc_in${fnt_nrm} Input directory (empty means none) (default ${fnt_bld}${drc_in}${fnt_nrm})"
echo "${fnt_rvr}-i${fnt_nrm} ${fnt_bld}in_fl${fnt_nrm} Input file (empty means use stdin or drc_in) (default ${fnt_bld}${in_fl}${fnt_nrm})"
echo "${fnt_rvr}-M${fnt_nrm} Multi-map-file toggle (unset means generate one map-file per input file)"
echo "${fnt_rvr}-m${fnt_nrm} ${fnt_bld}map_fl${fnt_nrm} Map-file (empty means generate internally) (default ${fnt_bld}${map_fl}${fnt_nrm})"
echo "${fnt_rvr}-n${fnt_nrm} ${fnt_bld}nco_opt${fnt_nrm} NCO options (empty means none) (default ${fnt_bld}${nco_opt}${fnt_nrm})"
echo "${fnt_rvr}-O${fnt_nrm} ${fnt_bld}drc_out${fnt_nrm} Output directory (default ${fnt_bld}${drc_out}${fnt_nrm})"
echo "${fnt_rvr}-o${fnt_nrm} ${fnt_bld}out_fl${fnt_nrm} Output-file (regridded file) (empty copies Input filename) (default ${fnt_bld}${out_fl}${fnt_nrm})"
echo "${fnt_rvr}-p${fnt_nrm} ${fnt_bld}par_typ${fnt_nrm} Parallelism type (default ${fnt_bld}${par_typ}${fnt_nrm})"
echo "${fnt_rvr}-R${fnt_nrm} ${fnt_bld}rgr_opt${fnt_nrm} Regridding options (empty means none) (default ${fnt_bld}${rgr_opt}${fnt_nrm})"
echo "${fnt_rvr}-s${fnt_nrm} ${fnt_bld}grd_src${fnt_nrm} Grid-file (source) (empty means infer or use map_fl) (default ${fnt_bld}${grd_src}${fnt_nrm})"
echo "${fnt_rvr}-t${fnt_nrm} ${fnt_bld}thr_nbr${fnt_nrm} Thread number for regridder (default ${fnt_bld}${thr_nbr}${fnt_nrm})"
echo "${fnt_rvr}-T${fnt_nrm} ${fnt_bld}tps_opt${fnt_nrm} TempestRemap GenerateOfflineMap options (default ${fnt_bld}${tps_opt}${fnt_nrm})"
echo "${fnt_rvr}-v${fnt_nrm} ${fnt_bld}var_lst${fnt_nrm} Variable list (empty means all) (default ${fnt_bld}${var_lst}${fnt_nrm})"
echo "${fnt_rvr}-w${fnt_nrm} ${fnt_bld}wgt_gnr${fnt_nrm} Weight-generator (default ${fnt_bld}${wgt_gnr}${fnt_nrm})"
echo "${fnt_rvr}-x${fnt_nrm} ${fnt_bld}xtn_var${fnt_nrm} Extensive variables (empty means none) (default ${fnt_bld}${xtn_var}${fnt_nrm})"
printf "\n"
printf "Examples: ${fnt_bld}$spt_nm -i ${in_xmp} -m ${map_xmp} -o ${out_xmp} ${fnt_nrm}\n"
printf " ${fnt_bld}$spt_nm -i ${in_xmp} -d ${dst_xmp} -o ${out_xmp} ${fnt_nrm}\n"
printf " ${fnt_bld}$spt_nm -i ${in_xmp} -g ${grd_dst_xmp} -o ${out_xmp} ${fnt_nrm}\n"
printf " ${fnt_bld}$spt_nm -a bilinear -i ${in_xmp} -d ${dst_xmp} -o ${out_xmp} ${fnt_nrm}\n"
printf " ${fnt_bld}$spt_nm -a conserve -i ${in_xmp} -d ${dst_xmp} -o ${out_xmp} ${fnt_nrm}\n"
printf " ${fnt_bld}$spt_nm -w tempest -i ${in_xmp} -d ${dst_xmp} -o ${out_xmp} ${fnt_nrm}\n"
printf " ${fnt_bld}$spt_nm -v ${var_xmp} -i ${in_xmp} -m ${map_xmp} -o ${out_xmp} ${fnt_nrm}\n"
printf " ${fnt_bld}$spt_nm -I ${drc_in_xmp} -m ${map_xmp} -O ${drc_out_xmp} ${fnt_nrm}\n"
printf " ${fnt_bld}$spt_nm -M -I ${drc_in_xmp} -d ${dst_xmp} -O ${drc_out_xmp} ${fnt_nrm}\n"
printf " ${fnt_bld}$spt_nm -M -I ${drc_in_xmp} -g ${grd_dst_xmp} -O ${drc_out_xmp} ${fnt_nrm}\n"
printf " ${fnt_bld}$spt_nm -I ${drc_in_xmp} -s ${grd_src_xmp} -d ${dst_xmp} -O ${drc_out_xmp} ${fnt_nrm}\n"
printf " ${fnt_bld}$spt_nm -I ${drc_in_xmp} -s ${grd_src_xmp} -g ${grd_dst_xmp} -O ${drc_out_xmp} ${fnt_nrm}\n"
printf " ${fnt_bld}$spt_nm -I ${drc_in_xmp} -d ${dst_xmp} -O ${drc_out_xmp} ${fnt_nrm}\n"
printf " ${fnt_bld}$spt_nm -I ${drc_in_xmp} -g ${grd_dst_xmp} -O ${drc_out_xmp} ${fnt_nrm}\n"
printf " ${fnt_bld}ls mdl*2005*nc | $spt_nm -m ${map_xmp} -O ${drc_out_xmp} ${fnt_nrm}\n"
printf " ${fnt_bld}ls mdl*2005*nc | $spt_nm -d ${dst_xmp} -O ${drc_out_xmp} ${fnt_nrm}\n"
exit 1
} # end fnc_usg_prn()
function dst_is_grd {
# Is destination grid specified as SCRIP grid-file?
# Usage: dst_is_grd ${fl}
fl=${1}
flg='Yes'
#flg='No'
} # end dst_is_grd()
# Check argument number and complain accordingly
arg_nbr=$#
#printf "\ndbg: Number of arguments: ${arg_nbr}"
if [ ${arg_nbr} -eq 0 ]; then
fnc_usg_prn
fi # !arg_nbr
# Parse command-line options:
# http://stackoverflow.com/questions/402377/using-getopts-in-bash-shell-script-to-get-long-and-short-command-line-options
# http://tuxtweaks.com/2014/05/bash-getopts
cmd_ln="${@}"
while getopts :a:D:d:E:f:g:G:h:I:i:Mm:n:O:o:p:R:s:T:t:v:w:x: OPT; do
case ${OPT} in
a) alg_typ=${OPTARG} ;; # Algorithm
D) dbg_lvl=${OPTARG} ;; # Debugging level
d) dst_fl=${OPTARG} ;; # Destination file
E) esmf_opt=${OPTARG} ;; # ESMF options
# f) fml_nm=${OPTARG} ;; # Family name
g) grd_dst=${OPTARG} ;; # Destination grid-file
G) grd_sng=${OPTARG} ;; # Grid generation string
I) drc_in=${OPTARG} ;; # Input directory
i) in_fl=${OPTARG} ;; # Input file
M) mlt_map_flg='No' ;; # Multi-map flag
m) map_fl=${OPTARG} ;; # Map-file
n) nco_usr=${OPTARG} ;; # NCO options
O) drc_out=${OPTARG} ;; # Output directory
o) out_fl=${OPTARG} ;; # Output file
p) par_typ=${OPTARG} ;; # Parallelism type
R) rgr_opt=${OPTARG} ;; # Regridding options
s) grd_src=${OPTARG} ;; # Source grid-file
T) tps_opt=${OPTARG} ;; # Tempest options
t) thr_usr=${OPTARG} ;; # Thread number
v) var_lst=${OPTARG} ;; # Variables
w) wgt_usr=${OPTARG} ;; # Weight-generator
x) xtn_var=${OPTARG} ;; # Extensive variables
\?) # Unrecognized option
printf "\nERROR: Option ${fnt_bld}-$OPTARG${fnt_nrm} not allowed"
fnc_usg_prn ;;
esac
done
shift $((OPTIND-1)) # Advance one argument
# Derived variables
grd_dst_dfl="${drc_out}/ncremap_tmp_grd_dst.nc" # [sng] Grid-file (destination) default
grd_src_dfl="${drc_out}/ncremap_tmp_grd_src.nc" # [sng] Grid-file (source) default
tmp_out_fl="${drc_out}/${tmp_out_fl}" # [sng] Temporary output file
if [ ${alg_typ} = 'bilinear' ] || [ ${alg_typ} = 'bln' ] ; then
# ESMF algorithms are bilinear|patch|neareststod|nearestdtos|conserve
alg_opt='bilinear'
elif [ ${alg_typ} = 'conserve' ] || [ ${alg_typ} = 'conservative' ] || [ ${alg_typ} = 'cns' ] ; then
alg_opt='conserve'
elif [ ${alg_typ} = 'nearestdtos' ] || [ ${alg_typ} = 'nds' ] || [ ${alg_typ} = 'dtos' ] ; then
alg_opt='nearestdtos'
elif [ ${alg_typ} = 'neareststod' ] || [ ${alg_typ} = 'nsd' ] || [ ${alg_typ} = 'stod' ] ; then
alg_opt='nearestdtos'
elif [ ${alg_typ} = 'patch' ] || [ ${alg_typ} = 'pch' ] || [ ${alg_typ} = 'ptc' ] ; then
alg_opt='patch'
fi # !alg_typ
if [ -z "${drc_in}" ]; then
drc_in="${drc_pwd}"
else # !drc_in
drc_in_usr_flg='Yes'
fi # !drc_in
if [ ${dbg_lvl} -ge 2 ]; then
nco_opt="-D ${dbg_lvl} ${nco_opt}"
fi # !dbg_lvl
if [ -n "${nco_usr}" ]; then
nco_opt="${nco_usr} ${nco_opt}"
fi # !var_lst
if [ -n "${gaa_sng}" ]; then
nco_opt="${nco_opt} ${gaa_sng}"
fi # !var_lst
if [ -n "${hdr_pad}" ]; then
nco_opt="${nco_opt} --hdr_pad=${hdr_pad}"
fi # !hdr_pad
if [ -n "${var_lst}" ]; then
nco_var_lst="-v ${var_lst}"
fi # !var_lst
if [ -n "${xtn_var}" ]; then
rgr_opt="${rgr_opt} --xtn=${xtn_var}"
fi # !var_lst
if [ -n "${par_typ}" ]; then
if [ "${par_typ}" != 'bck' ] && [ "${par_typ}" != 'mpi' ] && [ "${par_typ}" != 'nil' ]; then
echo "ERROR: Invalid -p par_typ option = ${par_typ}"
echo "HINT: Valid par_typ arguments are 'bck', 'mpi', and 'nil'"
exit 1
fi # !par_typ
fi # !par_typ
if [ "${par_typ}" = 'bck' ]; then
par_opt=' &'
elif [ "${par_typ}" = 'mpi' ]; then
mpi_flg='Yes'
par_opt=' &'
fi # !par_typ
if [ -n "${out_fl}" ]; then
out_usr_flg='Yes'
fi # !out_fl
if [ -n "${thr_usr}" ]; then
thr_nbr="${thr_usr}"
fi # !thr_usr
if [ -n "${wgt_usr}" ]; then
wgt_gnr="${wgt_usr}"
fi # !wgt_usr
if [ "${wgt_gnr}" != 'esmf' ] && [ "${wgt_gnr}" != 'tempest' ] ; then
echo "ERROR: Invalid -w wgt_gnr option = ${wgt_gnr}"
echo "HINT: Valid wgt_gnr arguments are 'esmf' and 'tempest'"
exit 1
fi # !wgt_gnr
if [ -n "${in_fl}" ]; then
# Single file argument
fl_in[${fl_nbr}]=${in_fl}
let fl_nbr=${fl_nbr}+1
else # !in_fl
# Detecting input on stdin:
# http://stackoverflow.com/questions/2456750/detect-presence-of-stdin-contents-in-shell-script
# ls ${DATA}/ne30/raw/famipc5*1979*.nc | ncremap -D 1 -m ${DATA}/maps/map_ne30np4_to_fv129x256_aave.20150901.nc -O ~/rgr
if [ -t 0 ]; then
if [ "${drc_in_usr_flg}" = 'Yes' ]; then
for fl in "${drc_in}"/*.nc "${drc_in}"/*.nc3 "${drc_in}"/*.nc4 "${drc_in}"/*.cdf "${drc_in}"/*.hdf "${drc_in}"/*.he5 "${drc_in}"/*.h5 ; do
if [ -f "${fl}" ]; then
fl_in[${fl_nbr}]=${fl}
let fl_nbr=${fl_nbr}+1
fi # !file
done
else # !drc_in
echo "ERROR: Must specify input file with -i or with stdin"
echo "HINT: Pipe file list to script via stdin with, e.g., 'ls *.nc | ${spt_nm}'"
exit 1
fi # !drc_in
else
# Input awaits on unit 0, i.e., on stdin
while read -r line; do # NeR05 p. 179
fl_in[${fl_nbr}]=${line}
let fl_nbr=${fl_nbr}+1
done < /dev/stdin
fi # stdin
fi # !in_fl
if [ -n "${dst_fl}" ]; then
if [ ! -e "${dst_fl}" ]; then
echo "ERROR: Unable to find specified destination-file ${dst_fl}"
echo "HINT: Supply the full path-name for the destination-file"
exit 1
fi # ! -e
dst_usr_flg='Yes'
fi # !dst_fl
if [ -n "${grd_dst}" ]; then
if [ ! -e "${grd_dst}" ]; then
echo "ERROR: Unable to find specified destination grid-file ${grd_dst}"
echo "HINT: Supply the full path-name for the destination grid, or generate one automatically with -G"
exit 1
fi # ! -e
grd_dst_usr_flg='Yes'
else
grd_dst=${grd_dst_dfl} # [sng] Grid-file default
fi # !grd_dst
if [ -n "${grd_src}" ]; then
if [ ! -e "${grd_src}" ]; then
echo "ERROR: Unable to find specified source grid-file ${grd_src}"
exit 1
fi # ! -e
grd_src_usr_flg='Yes'
else
grd_src=${grd_src_dfl} # [sng] Grid-file default
fi # !grd_src
if [ -z "${grd_sng}" ]; then
grd_sng_dfl="--rgr grd_ttl='Default internally-generated grid' --rgr grid=${grd_dst_dfl} --rgr latlon=100,100 --rgr snwe=30.0,70.0,-130.0,-90.0" # [sng] Grid string default
grd_sng="${grd_sng_dfl}"
else
grd_sng_usr_flg='Yes'
fi # !grd_sng
if [ -n "${map_fl}" ]; then
if [ ! -e "${map_fl}" ]; then
echo "ERROR: Unable to find specified regrid map ${map_fl}"
echo "HINT: Supply the full path-name for the regridding map"
exit 1
fi # ! -e
map_usr_flg='Yes'
else
if [ "${wgt_gnr}" = 'esmf' ]; then
map_fl_dfl="${drc_out}/ncremap_tmp_map_${wgt_gnr}_${alg_opt}.nc" # [sng] Map-file default
fi # !esmf
if [ "${wgt_gnr}" = 'tempest' ]; then
map_fl_dfl="${drc_out}/ncremap_tmp_map_${wgt_gnr}.nc" # [sng] Map-file default
msh_fl_dfl="${drc_out}/ncremap_tmp_msh_ovr_${wgt_gnr}.g" # [sng] Mesh-file default
msh_fl=${msh_fl_dfl}
fi # !tempest
map_fl=${map_fl_dfl}
fi # !map_fl
# Print initial state
if [ ${dbg_lvl} -ge 2 ]; then
printf "dbg: alg_opt = ${alg_opt}\n"
printf "dbg: dbg_lvl = ${dbg_lvl}\n"
printf "dbg: drc_in = ${drc_in}\n"
printf "dbg: drc_out = ${drc_out}\n"
printf "dbg: dst_fl = ${dst_fl}\n"
# printf "dbg: fml_nm = ${fml_nm}\n"
printf "dbg: gaa_sng = ${gaa_sng}\n"
printf "dbg: grd_dst = ${grd_dst}\n"
printf "dbg: grd_sng = ${grd_sng}\n"
printf "dbg: grd_src = ${grd_src}\n"
printf "dbg: hdr_pad = ${hdr_pad}\n"
printf "dbg: in_fl = ${in_fl}\n"
printf "dbg: map_fl = ${map_fl}\n"
printf "dbg: mlt_map = ${mlt_map_flg}\n"
printf "dbg: mpi_flg = ${mpi_flg}\n"
printf "dbg: nco_opt = ${nco_opt}\n"
printf "dbg: nd_nbr = ${nd_nbr}\n"
printf "dbg: out_fl = ${out_fl}\n"
printf "dbg: par_typ = ${par_typ}\n"
printf "dbg: thr_nbr = ${thr_nbr}\n"
printf "dbg: var_lst = ${var_lst}\n"
printf "Asked to regrid ${fl_nbr} files:\n"
for ((fl_idx=0;fl_idx<${fl_nbr};fl_idx++)); do
printf "${fl_in[${fl_idx}]}\n"
done # !fl_idx
fi # !dbg
if [ ${dbg_lvl} -ge 2 ]; then
if [ ${mpi_flg} = 'Yes' ]; then
for ((nd_idx=0;nd_idx<${nd_nbr};nd_idx++)); do
printf "dbg: nd_nm[${nd_idx}] = ${nd_nm[${nd_idx}]}\n"
done # !nd
fi # !mpi
fi # !dbg
# Create output directory
mkdir -p ${drc_out}
# Human-readable summary
if [ ${dbg_lvl} -ge 1 ]; then
printf "NCO regridder invoked with command:\n"
echo "${spt_nm} ${cmd_ln}"
fi # !dbg
date_srt=$(date +"%s")
if [ -f 'PET0.RegridWeightGen.Log' ]; then
printf "${spt_nm}: Removing PET0.RegridWeightGen.Log file from current directory before running\n"
/bin/rm -f PET0.RegridWeightGen.Log
fi # !PETO
printf "Started processing at `date`.\n"
printf "NCO version is ${nco_version}\n"
if [ "${map_usr_flg}" = 'Yes' ] && [ -n "${wgt_usr}" ] ; then
printf "${spt_nm}: ERROR Specifying both '-m map_fl' and '-w wgt_gnr' is not allowed (the weight-generator is unnecessary)\n"
exit 1
fi # wgt_usr
if [ "${grd_src_usr_flg}" = 'Yes' ]; then
if [ "${map_usr_flg}" = 'Yes' ]; then
printf "${spt_nm}: ERROR Specifying both '-s grd_src' and '-m map_fl' is ambiguous and forbidden\n"
exit 1
fi # !map_usr_flg
fi # !grd_src_usr_flg
if [ "${dst_usr_flg}" = 'Yes' ]; then
if [ "${map_usr_flg}" = 'Yes' ]; then
printf "${spt_nm}: ERROR Specify either '-d dst_fl' or '-m map_fl' not both\n"
exit 1
fi # !map_usr_flg
if [ "${grd_dst_usr_flg}" = 'Yes' ]; then
printf "${spt_nm}: ERROR Specify either '-d dst_fl' or '-g grd_dst' not both\n"
exit 1
fi # !grd_dst_usr_flg
else # !dst_usr_flg
if [ "${grd_dst_usr_flg}" = 'Yes' ]; then
if [ "${map_usr_flg}" = 'Yes' ]; then
printf "${spt_nm}: ERROR Specify either '-g grd_dst' or '-m map_fl' not both\n"
exit 1
fi # !map_usr_flg
else
if [ "${map_usr_flg}" != 'Yes' ] && [ "${grd_sng_usr_flg}" != 'Yes' ] ; then
printf "${spt_nm}: ERROR Must use one of '-d dst_fl', '-g grd_dst', '-G grd_sng', or '-m map_fl'\n"
exit 1
fi # !map_usr_flg
fi # !grd_dst_usr_flg
fi # !dst_usr_flg
# Generate destination grid, if necessary, once (only) before loop over input files
# Block 1: Destination grid
# Unlike source grid, same destination grid is used for all files
# Generate destination grid at most one-time
# Eventually we will allow destination grid to be provided as grid-file, map-file, or data-file
# Currently we require user to know (and specify) means by which destination grid is provided
if [ "${map_usr_flg}" = 'Yes' ]; then
printf "Source and destination grids will both be read from supplied map-file ${map_fl}\n"
else # !map_usr_flg
fl_idx=0 # [idx] Current file index
if [ "${dst_usr_flg}" = 'Yes' ]; then
# Block 1 Loop 1: Generate, check, and store (but do not yet execute) commands
# Infer destination grid-file from data file
printf "Destination grid will be inferred from data-file ${dst_fl} and stored as ${grd_dst}\n"
cmd_dst[${fl_idx}]="ncks ${nco_opt} --rgr nfr=y --rgr grid=${grd_dst} ${dst_fl} ${tmp_out_fl}"
else # !dst_usr_flg
if [ "${grd_dst_usr_flg}" = 'Yes' ]; then
printf "Destination grid supplied by user as ${grd_dst}\n"
else
if [ "${grd_sng_usr_flg}" = 'Yes' ]; then
printf "Destination grid will be generated from NCO grid string ${grd_sng}\n"
cmd_dst[${fl_idx}]="ncks ${nco_opt} ${grd_sng} ${fl_in[0]} ${tmp_out_fl}"
else
printf "${spt_nm}: ERROR Grid string grd_sng not provided\n"
exit 1
fi # !grd_sng_usr_flg
fi # !grd_dst_usr_flg
fi # !dst_usr_flg
if [ "${dst_usr_flg}" = 'Yes' ] || [ "${grd_dst_usr_flg}" != 'Yes' ]; then
# Block 1 Loop 2: Execute and/or echo commands
if [ ${dbg_lvl} -ge 1 ]; then
echo ${cmd_dst[${fl_idx}]}
fi # !dbg
if [ ${dbg_lvl} -ne 2 ]; then
eval ${cmd_dst[${fl_idx}]}
if [ $? -ne 0 ]; then
printf "${spt_nm}: ERROR Failed to generate destination grid. Debug this:\n${cmd_dst[${fl_idx}]}\n"
exit 1
fi # !err
if [ "${grd_sng_usr_flg}" = 'Yes' ]; then
/bin/rm -f ${tmp_out_fl}
fi # !grd_sng_usr_flg
fi # !dbg
fi # !dst_usr_flg || grd_dst_usr_flg
printf "Weight-generation type: ${wgt_gnr}\n"
if [ "${wgt_gnr}" = 'esmf' ]; then
printf "ESMF's ESMF_RegridWeightGen will generate map-file internally and store it as ${map_fl}\n"
printf "Algorithm used to generate weights in map-file is: ${alg_opt}\n"
fi # !esmf
if [ "${wgt_gnr}" = 'tempest' ]; then
printf "TempestRemap's GenerateOverlapMesh and GenerateOfflineMap will generate map-file internally and store it as ${map_fl}\n"
fi # !tempest
if [ ${fl_nbr} -ge 2 ]; then
if [ "${mlt_map_flg}" = 'Yes' ]; then
printf "Input files assumed to use unique input grids, one map-file will be generated per input file\n"
else # !mlt_map_flg
printf "Input files assumed to use same input grid, only one map-file will be generated\n"
fi # !mlt_map_flg
fi # !fl_nbr
fi # !map_usr
# If user provides source gridfile, assume it applies to every input file
# Do not infer source gridfiles from input files within file loop
# Generate map-file once outside of file loop, and re-use it for every input file
if [ "${grd_src_usr_flg}" = 'Yes' ]; then
printf "Source grid supplied by user as ${grd_src}\n"
fl_idx=0
if [ "${wgt_gnr}" = 'esmf' ]; then
cmd_map[${fl_idx}]="ESMF_RegridWeightGen -s ${grd_src} -d ${grd_dst} -w ${map_fl} --method ${alg_opt} ${esmf_opt} > /dev/null"
fi # !esmf
if [ "${wgt_gnr}" = 'tempest' ]; then
cmd_msh[${fl_idx}]="GenerateOverlapMesh --a ${grd_src} --b ${grd_dst} --out ${msh_fl} > /dev/null"
cmd_map[${fl_idx}]="GenerateOfflineMap --in_mesh ${grd_src} --out_mesh ${grd_dst} --ov_mesh ${msh_fl} --out_map ${map_fl} ${tps_opt} > /dev/null"
# 20160101: TempestRemap programs have false positive error returns (failures reported as successes) so remove old map/mesh before generating new
/bin/rm -f ${msh_fl} ${map_fl}
if [ ${dbg_lvl} -ge 1 ]; then
echo ${cmd_msh[${fl_idx}]}
fi # !dbg
if [ ${dbg_lvl} -ne 2 ]; then
eval ${cmd_msh[${fl_idx}]}
if [ $? -ne 0 ] || [ ! -f ${msh_fl} ] ; then
printf "${spt_nm}: ERROR Failed to generate mesh-file. Debug this:\n${cmd_msh[${fl_idx}]}\n"
exit 1
fi # !err
fi # !dbg
fi # !tempest
if [ ${dbg_lvl} -ge 1 ]; then
echo ${cmd_map[${fl_idx}]}
fi # !dbg
if [ ${dbg_lvl} -ne 2 ]; then
eval ${cmd_map[${fl_idx}]}
if [ $? -ne 0 ] || [ ! -f ${map_fl} ] ; then
printf "${spt_nm}: ERROR Failed to generate map-file. Debug this:\n${cmd_map[${fl_idx}]}\n"
if [ "${wgt_gnr}" = 'esmf' ]; then
printf "${spt_nm}: HINT When ESMF fails to generate map-files, it often puts additional debugging information in the file named PET0.RegridWeightGen.Log in the invocation directory (${drc_pwd})\n"
fi # !esmf
exit 1
fi # !err
fi # !dbg
# Set map_usr_flg to 'Yes' here to avoid re-generating map within file loop
map_usr_flg='Yes'
fi # !grd_src_usr_flg
# Begin loop over input files
for ((fl_idx=0;fl_idx<${fl_nbr};fl_idx++)); do
in_fl=${fl_in[${fl_idx}]}
if [ "$(basename ${in_fl})" = "${in_fl}" ]; then
in_fl="${drc_pwd}/${in_fl}"
fi # !basename
if [ "${out_usr_flg}" = 'Yes' ]; then
if [ ${fl_nbr} -ge 2 ]; then
echo "ERROR: Single output filename specified with -o for multiple input files"
echo "HINT: For multiple input files use -O option to specify output directory and do not use -o option. Output files will have same name as input files, but will be in different directory."
exit 1
fi # !fl_nbr
else # !out_usr_flg
out_fl="${drc_out}/$(basename ${in_fl})" # [sng] Output-file default
fi # !out_fl
if [ "${in_fl}" = "${out_fl}" ]; then
echo "ERROR: Input file = Output file = ${in_fl}"
echo "HINT: To prevent inadvertent data loss, ${spt_nm} insists that Input file and Output filenames differ"
exit 1
fi # !basename
# Generate new map unless map-file was supplied or already-generated (as indicated by map_usr_flg)
if [ "${map_usr_flg}" != 'Yes' ]; then
# Block 2: Source grid
# Block 2 Loop 1: Source gridfile command
if [ ! -e "${in_fl}" ]; then
echo "${spt_nm}: ERROR Unable to find Input file ${in_fl}"
echo "HINT: All files implied to exist must be in the directory specified by their filename or in ${drc_in} before ${spt_nm} will proceed"
exit 1
fi # ! -e
# Infer source grid-file from input data file
cmd_src[${fl_idx}]="ncks ${nco_opt} --rgr nfr=y --rgr grid=${grd_src} ${in_fl} ${tmp_out_fl}"
# Block 2 Loop 2: Execute and/or echo commands
if [ ${dbg_lvl} -ge 1 ]; then
echo ${cmd_src[${fl_idx}]}
fi # !dbg
if [ ${dbg_lvl} -ne 2 ]; then
eval ${cmd_src[${fl_idx}]}
if [ $? -ne 0 ]; then
printf "${spt_nm}: ERROR Failed to generate source grid. Debug this:\n${cmd_src[${fl_idx}]}\n"
exit 1
fi # !err
fi # !dbg
# Block 3: Source->destination maps
# Block 3 Loop 1: Map-file commands
printf "Grid(src): ${grd_src}\n"
printf "Grid(dst): ${grd_dst}\n"
printf "Map-File : ${map_fl}\n"
if [ "${wgt_gnr}" = 'esmf' ]; then
cmd_map[${fl_idx}]="ESMF_RegridWeightGen -s ${grd_src} -d ${grd_dst} -w ${map_fl} --method ${alg_opt} ${esmf_opt} > /dev/null"
fi # !esmf
if [ "${wgt_gnr}" = 'tempest' ]; then
printf "Mesh-File: ${msh_fl}\n"
cmd_msh[${fl_idx}]="GenerateOverlapMesh --a ${grd_src} --b ${grd_dst} --out ${msh_fl} ${tps_opt} > /dev/null"
cmd_map[${fl_idx}]="GenerateOfflineMap --in_mesh ${grd_src} --out_mesh ${grd_dst} --ov_mesh ${msh_fl} --out_map ${map_fl} ${tps_opt} > /dev/null"
# 20160101: TempestRemap programs have false negative error returns (failures reported as successes) so remove old map/mesh before generating new
/bin/rm -f ${msh_fl} ${map_fl}
if [ ${dbg_lvl} -ge 1 ]; then
echo ${cmd_msh[${fl_idx}]}
fi # !dbg
if [ ${dbg_lvl} -ne 2 ]; then
eval ${cmd_msh[${fl_idx}]}
if [ $? -ne 0 ] || [ ! -f ${msh_fl} ] ; then
printf "${spt_nm}: ERROR Failed to generate mesh-file. Debug this:\n${cmd_msh[${fl_idx}]}\n"
exit 1
fi # !err
fi # !dbg
fi # !tempest
# Block 3 Loop 2: Execute and/or echo commands
if [ ${dbg_lvl} -ge 1 ]; then
echo ${cmd_map[${fl_idx}]}
fi # !dbg
if [ ${dbg_lvl} -ne 2 ]; then
eval ${cmd_map[${fl_idx}]}
if [ $? -ne 0 ] || [ ! -f ${map_fl} ] ; then
printf "${spt_nm}: ERROR Failed to generate map-file. Debug this:\n${cmd_map[${fl_idx}]}\n"
if [ "${wgt_gnr}" = 'esmf' ]; then
printf "${spt_nm}: HINT When ESMF fails to generate map-files, it often puts additional debugging information in the file named PET0.RegridWeightGen.Log in the invocation directory (${drc_pwd})\n"
fi # !esmf
exit 1
fi # !err
fi # !dbg
# Prevent creating new source gridfile and map-file after first iteration
if [ "${mlt_map_flg}" = 'No' ] && [ ${fl_idx} -eq 0 ] ; then
map_usr_flg='Yes'
fi # !mlt_map_flg
fi # !map_usr_flg
# Block 4: Regrid
printf "Input : ${in_fl}\n"
printf "Output: ${out_fl}\n"
cmd_rgr[${fl_idx}]="ncks -t ${thr_nbr} ${nco_opt} ${nco_var_lst} ${rgr_opt} --map=${map_fl} ${in_fl} ${out_fl}"
# Block 4 Loop 2: Execute and/or echo commands
if [ ${dbg_lvl} -ge 1 ]; then
echo ${cmd_rgr[${fl_idx}]}
fi # !dbg
if [ ${dbg_lvl} -ne 2 ]; then
eval ${cmd_rgr[${fl_idx}]}
if [ -z "${par_opt}" ]; then
eval ${cmd_rgr[${fl_idx}]}
if [ $? -ne 0 ]; then
printf "${spt_nm}: ERROR Failed to regrid. cmd_rgr[${fl_idx}] failed. Debug this:\n${cmd_rgr[${fl_idx}]}\n"
exit 1
fi # !err
else # !par_typ
eval ${cmd_rgr[${fl_idx}]} ${par_opt}
rgr_pid[${fl_idx}]=$!
fi # !par_typ
fi # !dbg
done # !fl_idx
# wait() for parallel regridding, if any, to finish
if [ -n "${par_opt}" ]; then
for ((fl_idx=0;fl_idx<${fl_nbr};fl_idx++)); do
wait ${rgr_pid[${fl_idx}]}
if [ $? -ne 0 ]; then
printf "${spt_nm}: ERROR Failed to regrid. cmd_rgr[${fl_idx}] failed. Debug this:\n${cmd_rgr[${fl_idx}]}\n"
exit 1
fi # !err
done # !fl_idx
fi # !par_typ
date_end=$(date +"%s")
printf "Completed processing of ${fl_nbr} file(s) at `date`.\n"
date_dff=$((date_end-date_srt))
echo "Quick plots of results from last regridded file:"
echo "ncview ${out_fl} &"
echo "panoply ${out_fl} &"
echo "Elapsed time $((date_dff/60))m$((date_dff % 60))s"
exit 0
|