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run_cable-pop.1000pts4848.sh
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run_cable-pop.1000pts4848.sh
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#!/usr/bin/env bash
# Explor / Pearcey / Aurora
# https://slurm.schedmd.com/sbatch.html
#SBATCH --ignore-pbs
# Name - 8 letters and digits
#SBATCH --job-name=bios9
#SBATCH --output=%x-%j.out
#SBATCH --error=%x-%j.out
# -N nodes / -n tasks (mpiexec, srun, ...)
# -c cpus_per_task (OpenMP, make -j, ...)
#SBATCH --nodes=1
#SBATCH --ntasks=4
#SBATCH --ntasks-per-node=4
# Check memory on *nix with /usr/bin/time -v ./prog
# time (day-hh:mm:ss) / memory (optional, units K,M,G,T)
#SBATCH --time=01:00:00
#SBATCH --mem=4G
#SBATCH --mail-type=FAIL,STAGE_OUT,TIME_LIMIT,INVALID_DEPEND,END
# section cuntz@explor
#SBATCH --account=oqx29
# Explor partitions (sinfo):
# https://explor.univ-lorraine.fr/new_queue/
# debug, std, gpu
#SBATCH --partition=std
# old hf partitions are cne[01-16]
# #SBATCH --constraint=HF
#SBATCH --exclude=cnf[01-08],cnh[01-02],cni[01-24],cnj[01-64],cnk[01-08]
#SBATCH [email protected]
# # section nieradzik@aurora
# #SBATCH --qos=test -t 15:00
# #SBATCH [email protected]
# Gadi
# https://opus.nci.org.au/display/Help/How+to+submit+a+job
#PBS -N mc_01
#PBS -P x45
# express / normal / copyq (2x24, cascadelake)
#PBS -q normal
# Typical for global or Aust continent at 0.25, 192 GB memory and 48 cpus,
# maybe 12 hours walltime
# Typical for small runs, fewer cpus than pixels
#PBS -l walltime=02:00:00
#PBS -l mem=48GB
#PBS -l ncpus=48
# #PBS -l jobfs=1GB
#PBS -l storage=gdata/x45
#PBS -l software=netCDF:MPI:Intel:GNU
#PBS -r y
#PBS -l wd
#PBS -j oe
#PBS -S /bin/bash
#PBS -M [email protected]
#PBS -m ae
# cuntz@explor, cuntz@mc16, cuntz@mcinra, moc801@gadi cuntz@gadi
# kna016@pearcey knauer@pearcey, jk8585@gadi knauer@gadi
# bri220@pearcey, pcb599@gadi briggs@gadi
# yc3714@gadi villalobos@gadi
# nieradzik@aurora
# inh599@gadi harman@gadi
system=inh599@gadi
# MPI run or single processor run
# nproc should fit with job tasks
dompi=1 # 0: normal run: ./cable
# 1: MPI run: mpiexec -n ${nproc} ./cable_mpi
nproc=48 # Number of cores for MPI runs
# must be same as above: SBATCH -n nproc or PBS -l ncpus=nproc
# --------------------------------------------------------------------
#
# Full Cable run with biomass spinup, POP, land-use change, etc.
#
# This script uses CRU-JRA forcing.
#
# Global meteo and land-use change data can be used with a mask giving land points.
# In step 0, the land mask can be extracted for a single point, an area
# or a number of random points can be chosen.
# Alternatively, single site met, LUH2, forcing and mask can be extracted from the global data sets.
#
# The run sequence is as follows:
# 1. Create a climate restart file using Cable's default vegetation distribution.
# 2. First phase of spinup with static land use, fixed atmospheric CO2 and
# N deposition from 1700, and 30 years of repeated meteorology.
# Zero initial biomass stocks, POP and climate.
# 3. Bring biomass stocks into equilibrium, restricting labile P and mineral N pools.
# Repeat a and b several times.
# a) Start from restart files.
# b) Use dump files for the biophysics. Quasi-equilibrium of soil and litter pools
# using an analytic steady-state solution.
# 4. Same as 3 but without any restriction on labile P and mineral N pools.
# Repeat a and b several times.
# 5. Second phase of spinup with dynamic land use, atmospheric CO2 and N deposition.
# a) Dynamic land use from 1580 to 1699, using still fixed atmospheric CO2 and
# N deposition from 1700, and 30 years of repeated meteorology.
# b) Run from 1700 to 1899 with dynmic land use, varying atmospheric CO2 and N deposition,
# but still with 30 years of repeated meteorology.
# 6. Final historical run, everything dynamic from 1900 to 2017.
# 7. Future run, everything dynamic (not all met types).
#
# Written, Matthias Cuntz, Aug 2019, following the run scripts and namelists provided by Vanessa Haverd
# Modified, Jurgen Knauer, 2020 - gm_explicit, coordination, acclimation
# - bios, plume, future runs
# Matthias Cuntz, Mar 2021 - functions into run_cable-pop_lib.sh
#
# --------------------------------------------------------------------
#ASKJK - changes in comparison to gm_acclim_coord
# 1. Removed switch Test_parallel=1 -> used [[ dompi -eq 1 ]]
# 2. ScriptsPath="${workpath}/scripts"
# but
# namelistpath="$(dirname ${workpath})/namelists"
# with
# workpath="/home/599/jk8585/CABLE_run/gm_acclim_coord/global_runs"
# cablehome="/home/599/jk8585/CABLE_code"
# -> changed to similar of ScriptsPath="$(dirname ${workpath})/scripts"
# 3. Need plume.nml, bios.nml, gm_LUT_*.nc
# 4. output%grid = "mask" (in gm_acclim_coord) or "land" (default before) [PB:Always has to be "mask"]
# 5. What should be for Run in bios.nml after 1. Climate restart?
# 6. Why is YearEnd different for plume (1849) compared to cru (1699) in 5a. First dynamic land use?
# 7. Do we need chunking in 5a, 5b, 6, and 7? [PB: unnecessary at this point, but possibly for 0.05degs]
# 8. Do we need cropping output to latlon region at the end: is this not in step 0 with ${doextractsite} -eq 1? [PB: Not needed for # BIOS
#
#ASKJK - changes in comparison to gm_acclim_coord
# --------------------------------------------------------------------
# Sequence switches
#
imeteo=0 # 0: Use global meteo, land use and mask
# 1: Use local mask, but global meteo and land use (doextractsite=1)
# 2: Use local meteo, land use and mask (doextractsite=2)
# Step 0
purge_restart=0 # 1/0: Do/Do not delete all restart files (completely new run, e.g. if settings changed)
doextractsite=0 # 0: Do not extract local meteo, land use nor mask
# 1: Do extract only mask at specific site/region (imeteo=1)
# 2: Do extract meteo, land use and mask at specific site/region (imeteo=2)
# Does not work with randompoints /= 0 but with latlon
experiment=1000ptsmpinewmet4848potstem
randompoints=0 # <0: use -1*randompoints from file ${LandMaskFilePath}/${experiment}_points.csv if existing
# 0: use latlon
# >0: generate and use randompoints random grid points from GlobalLandMaskFile
# lat,lon or latmin,latmax,lonmin,lonmax # must have . in numbers otherwise indexes taken
latlon=42.536875,-72.172602
# latlon=-34.5,-33.5,149.5,156.5
# latlon=42.5,43.5,109.5,110.5
# latlon=-44.0,-10.0,110.0,155.0 # Australia
# Step 1
doclimate=1 # 1/0: Do/Do not create climate restart file
# Step 2
dofromzero=1 # 1/0: Do/Do not first spinup phase from zero biomass stocks
# Step 3
doequi1=0 # 1/0: Do/Do not bring biomass stocks into quasi-equilibrium with restricted P and N pools
nequi1=0 # number of times to repeat steps in doequi1
# Step 4
doequi2=0 # 1/0: Do/Do not bring biomass stocks into quasi-equilibrium with unrestricted P and N pools
nequi2=4 # number of times to repeat steps in doequi2
# Step 5a
doiniluc=0 # 1/0: Do/Do not spinup with dynamic land use (5a)
# Step 5b
doinidyn=0 # 1/0: Do/Do not full dynamic spinup from 1700 to 1899 (5b)
# Step 6
dofinal=0 # 1/0: Do/Do not final run from 1900 to 2017
# Step 7
dofuture=0 # 1/0: Do/Do not future runs (plume only)
# --------------------------------------------------------------------
# Other switches
#
# MetType
mettype='bios' # 'cru', 'plume', 'bios'
degrees=0.05 # bios only: resolution of met and LUC (0.05 or 0.25)
metmodel='hadgem2' # 'hadgem2', 'ipsl' (only used if mettype='plume')
RCP='hist' # 'hist', '2.6', '4.5', '6.0', '8.5' (no future runs if RCP='hist')
# Cable
explicit_gm=0 # 1/0: explicit (finite) or implicit mesophyll conductance
use_LUTgm=1 # 1/0: Do/Do not use lookup table for parameter conversion accounting for gm (only used if explicit_gm=1)
Rubisco_params="Bernacchi_2002" # "Bernacchi_2002" or "Walker_2013"
coordinate_photosyn=1 # 1/0: Do/Do not coordinate photosynthesis
coord=F # T/F: version of photosyn. optimisation (optimised(F) or forced (T))
acclimate_photosyn=1 # 1/0: Do/Do not acclimate photosynthesis
call_pop=1 # 1/0: Do/Do not use POP population dynamics model, coupled to CASA
doc13o2=0 # 1/0: Do/Do not calculate 13C
c13o2_simple_disc=0 # 1/0: simple or full 13C leaf discrimination
# --------------------------------------------------------------------
# Setup
#
set -e
trap cleanup 1 2 3 6
pid=$$
isdir="${PWD}"
prog=$0
pprog=$(basename ${prog})
pdir=$(dirname ${prog})
tmp=${TMPDIR:-"/tmp"}
system=$(echo ${system} | tr A-Z a-z)
sys=${system#*@}
user=${system%@*}
#
# Special things on specific computer system such as loading modules
#
export mpiexecdir=
if [[ "${sys}" == "explor" ]] ; then
# prog is slurm_script
pdir=${isdir}
# # INTELMPI - load mpi module first, otherwise intel module will not prepend LD_LIBRARY_PATH
# module load intelmpi/2018.5.274
# module load intel/2018.5
# unset I_MPI_PMI_LIBRARY
# export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${HOME}/local/lib:${HOME}/local/netcdf-fortran-4.4.4-ifort2018.0/lib
# export mpiexecdir=/soft/env/soft/all/intel/2018.3/compilers_and_libraries_2018.5.274/linux/mpi/intel64/bin
# INTEL / OpenMPI - load mpi module first, otherwise intel module will not pre-pend LD_LIBRARY_PATH
module load openmpi/3.0.0/intel18
module load intel/2018.5
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/home/oqx29/shared/local.save/lib:/home/oqx29/shared/local.save/netcdf-fortran-4.4.4-ifort2018.0/lib
export mpiexecdir=/opt/soft/hf/openmpi-3.0.0-intel18/bin
# # GNU / OpenMPI
# module load gcc/6.3.0
# module load openmpi/3.0.1/gcc/6.3.0
# export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${HOME}/local/lib:${HOME}/local/netcdf-fortran-4.4.4-gfortran63/lib
# export mpiexecdir=/opt/soft/hf/openmpi/3.0.1/gcc/6.3.0/bin
if [[ ${doextractsite} -ge 1 ]] ; then module load python/intel/2019/3 ; fi
elif [[ "${sys}" == "mc16" ]] ; then
# export mpiexecdir=/usr/local/openmpi-4.1.1-gfortran/bin
export mpiexecdir=/usr/local/openmpi-4.1.1-ifort/bin
elif [[ "${sys}" == "mcinra" ]] ; then
export mpiexecdir=/usr/local/openmpi-3.1.4-gfortran/bin
# export mpiexecdir=/usr/local/openmpi-3.1.5-ifort/bin
elif [[ "${sys}" == "pearcey" ]] ; then
# prog is slurm_script
pdir=${isdir}
module del intel-cc intel-fc
module add intel-cc/16.0.1.150 intel-fc/16.0.1.150
module unload intel-mpi/5.0.1.035
module add netcdf/4.3.3.1 openmpi/1.8.8
elif [[ "${sys}" == "gadi" ]] ; then
pdir=${isdir}
. /etc/bashrc
module purge
# module load intel-compiler/2019.5.281
# module load intel-mpi/2019.5.281
# module load netcdf/4.6.3
# module load intel-compiler/2021.5.0
# module load intel-mpi/2021.5.1
# module load netcdf/4.8.0
# # module load hdf5/1.10.5
module load intel-compiler-llvm/2023.0.0
module load intel-mpi/2021.8.0
module load netcdf/4.9.2
if [[ ${doextractsite} -ge 1 ]] ; then
module load python3/3.7.4
export PYTHONPATH=${PYTHONPATH}:/g/data/x45/python/lib/python3.7/site-packages
fi
if [[ ${randompoints} -eq 0 ]] ; then module load nco/4.9.2 ; fi # needed for cropping outputs
export mpiexecdir=/apps/intel-mpi/2019.5.281/intel64/bin
elif [[ "${sys}" == "aurora" ]] ; then
pdir=${isdir}
module purge
module load intel/2020a
module load netCDF-Fortran/4.5.2
if [[ ${doextractsite} -ge 1 ]] ; then
module load GCCcore/10.3.0 Python/3.9.5
export PYTHONPATH=${PYTHONPATH} #CLN not copied!#:/g/data/x45/python/lib/python3.7/site-packages
echo 'Extraction not possible at the moment. Set Py-Path!'
exit -666
fi
export mpiexecdir=""
fi
if [[ ! -z ${mpiexecdir} ]] ; then export mpiexecdir="${mpiexecdir}/" ; fi
#
# Directories of things
#
# Naming of experiments for gm_acclim_coord experiments of Jurgen
if [[ ("${system}" == "jk8585@gadi") || ("${system}" == "knauer@gadi") ]] ; then
experiment=test_${mettype}
if [[ "${mettype}" == "plume" ]] ; then
# (TEST_)(exp|imp)_(no)coord(T|F)(_PSacclim)_(B2002|W2013)
if [[ ${explicit_gm} -eq 1 ]] ; then
if [[ ${coordinate_photosyn} -eq 1 ]] ; then
if [[ ${acclimate_photosyn} -eq 1 ]] ; then
experiment=exp_coord${coord}_PSacclim
else
experiment=exp_coord${coord}
fi
else
if [[ ${acclimate_photosyn} -eq 1 ]] ; then
experiment=exp_nocoord_PSacclim
else
experiment=exp_nocoord
fi
fi
else
if [[ ${coordinate_photosyn} -eq 1 ]] ; then
if [[ ${acclimate_photosyn} -eq 1 ]] ; then
experiment=imp_coord${coord}_PSacclim
else
experiment=imp_coord${coord}
fi
else
if [[ ${acclimate_photosyn} -eq 1 ]] ; then
experiment=imp_nocoord_PSacclim
else
experiment=imp_nocoord
fi
fi
fi
if [[ "${Rubisco_params}" == "Bernacchi_2002" ]] ; then
experiment=${experiment}_B2002
elif [[ "${Rubisco_params}" == "Walker_2013" ]] ; then
experiment=${experiment}_W2013
else
echo "unknown option for 'Rubisco_params', exiting..."
exit 1
fi
if [[ ${dompi} -ne 0 ]] ; then
experiment=TEST_${experiment}
fi
fi
fi
#
# Relative directories must be relative to the directory of this script,
# not relative to the directory from which this script is launched (if different)
# nor relative to the run path.
#
if [[ "${system}" == "cuntz@explor" ]] ; then
# Run directory: runpath="${sitepath}/run_xxx"
cablebase="/home/oqx29/zzy20/prog/cable"
sitepath="${cablebase}/runs/bios9/${experiment}"
cablehome="${cablebase}/branches/NESP2pt9_BLAZE"
cabledata="/home/oqx29/shared/cable"
metdata="/home/oqx29/shared/met_forcing"
workpath=${cablehome}
# Cable executable
if [[ ${dompi} -eq 1 ]] ; then
exe="${cablehome}/offline/cable-mpi"
else
exe="${cablehome}/offline/cable"
fi
# CABLE-AUX directory (uses offline/gridinfo_CSIRO_1x1.nc and offline/modis_phenology_csiro.txt)
aux="${cabledata}/CABLE-AUX"
# BLAZE directory
BlazeDataPath="${cabledata}/Data_BLAZE"
# Global MET, MASK, LUH
if [[ "${mettype}" == "cru" ]] ; then
# Global MASK
SurfaceFile="${aux}/offline/gridinfo_CSIRO_1x1.nc" # note that SurfaceFile does not need subsetting
# Global MET
# GlobalLandMaskFile="${aux}/offline/gridinfo_CSIRO_1x1.nc"
GlobalLandMaskFile="${cabledata}/ipbes/masks/glob_ipsl_1x1.nc"
# GlobalMetPath="${cabledata}/CRUJRA2022/daily_1deg"
GlobalMetPath="${metdata}/CRUJRA2022/daily_1deg"
# Global LUC
GlobalTransitionFilePath="${cabledata}/LUH2/GCB_2019/1deg/EXTRACT"
elif [[ "${mettype}" == "plume" ]] ; then
# Global MASK
SurfaceFile="${aux}/offline/gridinfo_CSIRO_1x1.nc" # note that SurfaceFile does not need subsetting
# Global MET
# GlobalLandMaskFile="/g/data/x45/ipbes/masks/glob_ipsl_1x1.nc"
GlobalLandMaskFile="${cabledata}/ipbes/masks/gridinfo_CSIRO_1x1.nc"
GlobalMetPath="${cabledata}/ipbes/${metmodel}/1deg"
# only in plume.nml
CO2Path="${cabledata}/ipbes/co2"
NdepPath="${cabledata}/ipbes/ndep"
# Global LUC
GlobalTransitionFilePath="${cabledata}/LUH2/GCB_2019/1deg/EXTRACT"
elif [[ "${mettype}" == "bios" ]] ; then
# Global MASK
SurfaceFile="${aux}/offline/gridinfo_CSIRO_CRU05x05_4tiles.nc" # note that SurfaceFile does not need subsetting
# Global MET
GlobalLandMaskFile="${cabledata}/BIOS3_forcing/acttest9/acttest9" # no file extension
GlobalMetPath="${cabledata}/BIOS3_forcing/acttest9/met/" # last slash is needed
ParamPath="${cabledata}/BIOS3_forcing/acttest9/params/" # only in bios.nml
# Global LUC
GlobalTransitionFilePath="${cabledata}/LUH2/v3h/${degrees}deg_aust/EXTRACT"
fi
elif [[ "${system}" == "cuntz@mc16" || "${system}" == "cuntz@mcinra" ]] ; then
# Run directory: runpath="${sitepath}/run_xxx"
cablebase="/Users/cuntz/prog/vanessa/cable"
sitepath="${cablebase}/runs/single_sites/${experiment}"
cablehome="${cablebase}/branches/NESP2pt9_BLAZE"
# Cable executable
if [[ ${dompi} -eq 1 ]] ; then
# exe="${cablehome}/branches/NESP2pt9_BLAZE/offline/cable-mpi-gfortran"
exe="${cablehome}/offline/cable-mpi-ifort"
else
exe="${cablehome}/offline/cable"
fi
# CABLE-AUX directory (uses offline/gridinfo_CSIRO_1x1.nc and offline/modis_phenology_csiro.txt)
aux="${cablebase}/CABLE-AUX"
# Global Mask, CRU, LUC
GlobalLandMaskFile="${aux}/offline/gridinfo_CSIRO_1x1.nc"
SurfaceFile="${aux}/offline/gridinfo_CSIRO_1x1.nc" # note that SurfaceFile does not need subsetting
GlobalMetPath=
GlobalTransitionFilePath=
elif [[ "${system}" == "moc801@gadi" || "${system}" == "cuntz@gadi" ]] ; then
# Run directory: runpath="${sitepath}/run_xxx"
# sitepath="/home/801/moc801/prog/cable/runs/single_sites/${experiment}"
sitepath="/scratch/x45/moc801/cable/c13"
cablehome="/home/801/moc801/prog/cable/branches/NESP2pt9_BLAZE"
workpath=${cablehome}
# Cable executable
if [[ ${dompi} -eq 1 ]] ; then
exe="${cablehome}/offline/cable-mpi"
else
exe="${cablehome}/offline/cable"
fi
# CABLE-AUX directory (uses offline/gridinfo_CSIRO_1x1.nc and offline/modis_phenology_csiro.txt)
aux="/g/data/x45/CABLE-AUX"
# BLAZE directory
BlazeDataPath="/g/data/x45/Data_BLAZE"
# Global MET, MASK, LUH
if [[ "${mettype}" == "cru" ]] ; then
# Global MASK
SurfaceFile="${aux}/offline/gridinfo_CSIRO_1x1.nc" # note that SurfaceFile does not need subsetting
# Global MET
# GlobalLandMaskFile="${aux}/offline/gridinfo_CSIRO_1x1.nc"
GlobalLandMaskFile="/g/data/x45/ipbes/masks/glob_ipsl_1x1.nc"
GlobalMetPath="/g/data/x45/CRUJRA2020/daily_1deg"
# Global LUC
GlobalTransitionFilePath="/g/data/x45/LUH2/GCB_2019/1deg/EXTRACT"
elif [[ "${mettype}" == "plume" ]] ; then
# Global MASK
SurfaceFile="${aux}/offline/gridinfo_CSIRO_1x1.nc" # note that SurfaceFile does not need subsetting
# Global MET
# GlobalLandMaskFile="/g/data/x45/ipbes/masks/glob_ipsl_1x1.nc"
GlobalLandMaskFile="/g/data/x45/ipbes/masks/gridinfo_CSIRO_1x1.nc"
GlobalMetPath="/g/data/x45/ipbes/${metmodel}/1deg"
# only in plume.nml
CO2Path="/g/data/x45/ipbes/co2"
NdepPath="/g/data/x45/ipbes/ndep"
# Global LUC
GlobalTransitionFilePath="/g/data/x45/LUH2/GCB_2019/1deg/EXTRACT"
elif [[ "${mettype}" == "bios" ]] ; then
# Global MASK
SurfaceFile="${aux}/offline/gridinfo_CSIRO_CRU05x05_4tiles.nc" # note that SurfaceFile does not need subsetting
# Global MET
GlobalLandMaskFile="/g/data/x45/BIOS3_forcing/acttest9/acttest9" # no file extension
GlobalMetPath="/g/data/x45/BIOS3_forcing/acttest9/met/" # last slash is needed
ParamPath="/g/data/x45/BIOS3_forcing/acttest9/params/" # only in bios.nml
# Global LUC
GlobalTransitionFilePath="/g/data/x45/LUH2/v3h/${degrees}deg_aust/EXTRACT"
fi
elif [[ "${system}" == "kna016@pearcey" || "${system}" == "knauer@pearcey" ]] ; then
# Run directory: runpath="${sitepath}/run_xxx"
sitepath="/OSM/CBR/OA_GLOBALCABLE/work/Juergen/CABLE_run/parallel_runs/${experiment}"
cablehome="/OSM/CBR/OA_GLOBALCABLE/work/Juergen/CABLE_code/NESP2pt9_BLAZE"
# Cable executable
if [[ ${dompi} -eq 1 ]] ; then
exe="${cablehome}/offline/cable-mpi"
else
exe="${cablehome}/offline/cable"
fi
# CABLE-AUX directory (uses offline/gridinfo_CSIRO_1x1.nc and offline/modis_phenology_csiro.txt)
aux="/OSM/CBR/OA_GLOBALCABLE/work/Vanessa/CABLE-AUX"
# Global Mask
GlobalLandMaskFile="${aux}/offline/gridinfo_CSIRO_1x1.nc"
SurfaceFile="${aux}/offline/gridinfo_CSIRO_1x1.nc" # note that SurfaceFile does not need subsetting
# Global CRU
GlobalMetPath="/OSM/CBR/OA_GLOBALCABLE/work/CRU-JRA55/crujra/daily_1deg"
# Global LUC
GlobalTransitionFilePath="/OSM/CBR/OA_GLOBALCABLE/work/LUH2/v3/1deg"
elif [[ "${system}" == "jk8585@gadi" || "${system}" == "knauer@gadi" ]] ; then
# Run directory: runpath="${sitepath}/run"
sitepath="/g/data/x45/jk8585/global_runs/gm_acclim_coord/${experiment}"
cablecode="/home/599/jk8585/CABLE_code/gm_acclim_coord"
cablehome="/home/599/jk8585/CABLE_run/gm_acclim_coord"
# Cable executable
if [[ ${dompi} -eq 1 ]] ; then
exe="${cablecode}/offline/cable-mpi"
else
exe="${cablecode}/offline/cable"
fi
# CABLE-AUX directory (uses offline/gridinfo_CSIRO_1x1.nc and offline/modis_phenology_csiro.txt)
aux="/g/data/x45/CABLE-AUX"
# Global Mask
SurfaceFile="${aux}/offline/gridinfo_CSIRO_1x1.nc" # note that SurfaceFile does not need subsetting
# Global Met
if [[ "${mettype}" == "cru" ]] ; then
GlobalLandMaskFile="/g/data/x45/ipbes/masks/glob_ipsl_1x1.nc"
GlobalMetPath="/g/data/x45/CRUJRA2020/daily_1deg"
elif [[ "${mettype}" == "plume" ]] ; then
# GlobalLandMaskFile="/g/data/x45/ipbes/masks/glob_ipsl_1x1.nc"
GlobalLandMaskFile="/g/data/x45/ipbes/masks/gridinfo_CSIRO_1x1.nc"
GlobalMetPath="/g/data/x45/ipbes/${metmodel}/1deg"
# only in plume.nml
CO2Path="/g/data/x45/ipbes/co2"
NdepPath="/g/data/x45/ipbes/ndep"
elif [[ "${mettype}" == "bios" ]] ; then
GlobalLandMaskFile="/g/data/x45/BIOS3_forcing/acttest9/acttest9" # no file extension
GlobalMetPath="/g/data/x45/BIOS3_forcing/acttest9/met/" # last slash is needed
ParamPath="/g/data/x45/BIOS3_forcing/acttest9/params/" # only in bios.nml
GlobalTransitionFilePath="/g/data/x45/LUH2/v3h/${degrees}deg_aust/EXTRACT"
fi
# Global LUC
GlobalTransitionFilePath="/g/data/x45/LUH2/GCB_2019/1deg/EXTRACT"
elif [[ "${system}" == "yc3714@gadi" || "${system}" == "villalobos@gadi" ]] ; then
# Run directory: runpath="${sitepath}/run"
sitepath="/g/data/x45/BIOS3_output/${experiment}" # Results
workpath="/home/563/yc3714/CSIRO/CABLE_run/BIOS3_blaze" # run directory
cablehome="/home/563/yc3714/CSIRO/CABLE_code/9011/NESP2pt9_BLAZE" # model home
# Cable executable
if [[ ${dompi} -eq 1 ]] ; then
exe="${cablehome}/offline/cable-mpi"
else
exe="${cablehome}/offline/cable"
fi
# CABLE-AUX directory (uses offline/gridinfo_CSIRO_1x1.nc and offline/modis_phenology_csiro.txt)
aux="/g/data/x45/CABLE-AUX"
# Global Mask
SurfaceFile="${aux}/offline/gridinfo_CSIRO_CRU05x05_4tiles.nc" # note that SurfaceFile does not need subsetting
# Global Met
if [[ "${mettype}" == "cru" ]] ; then
GlobalLandMaskFile="/g/data/x45/ipbes/masks/glob_ipsl_1x1.nc"
GlobalMetPath="/g/data/x45/CRUJRA2020/daily_1deg"
elif [[ "${mettype}" == "plume" ]] ; then
GlobalLandMaskFile="/g/data/x45/ipbes/masks/gridinfo_CSIRO_1x1.nc"
GlobalMetPath="/g/data/x45/ipbes/${metmodel}/1deg"
# only in plume.nml
CO2Path="/g/data/x45/ipbes/co2"
NdepPath="/g/data/x45/ipbes/ndep"
elif [[ "${mettype}" == "bios" ]] ; then
GlobalLandMaskFile="/g/data/x45/BIOS3_forcing/acttest9/acttest9" # no file extension
GlobalMetPath="/g/data/x45/BIOS3_forcing/acttest9/met/" # last slash is needed
ParamPath="/g/data/x45/BIOS3_forcing/acttest9/params/" # only in bios.nml
GlobalTransitionFilePath="/g/data/x45/LUH2/v3h/${degrees}deg_aust/EXTRACT"
fi
# Global LUC
# GlobalTransitionFilePath="/g/data/x45/LUH2/GCB_2019/1deg/EXTRACT"
elif [[ "${system}" == "inh599@gadi" || "${system}" == "harman@gadi" ]] ; then
# Run directory: runpath="${sitepath}/run"
#sitepath="/g/data/x45/BIOS3_output/${experiment}" # Results
sitepath="/scratch/x45/inh599/BIOStests/${experiment}" # Results
workpath="/home/599/inh599/JAC/CABLE/BLAZEruns" # run directory
cablehome="/home/599/inh599/JAC/CABLE/BLAZE_9184" # model home
# Cable executable
if [[ ${dompi} -eq 1 ]] ; then
exe="${cablehome}/offline/cable-mpi"
else
exe="${cablehome}/offline/cable"
fi
# CABLE-AUX directory (uses offline/gridinfo_CSIRO_1x1.nc and offline/modis_phenology_csiro.txt)
aux="/g/data/x45/CABLE-AUX"
BlazeDataPath="/g/data/x45/Data_BLAZE"
# Global Mask
SurfaceFile="${aux}/offline/gridinfo_CSIRO_CRU05x05_4tiles.nc" # note that SurfaceFile does not need subsetting
# Global Met
if [[ "${mettype}" == "cru" ]] ; then
GlobalLandMaskFile="/g/data/x45/ipbes/masks/glob_ipsl_1x1.nc"
GlobalMetPath="/g/data/x45/CRUJRA2020/daily_1deg"
elif [[ "${mettype}" == "plume" ]] ; then
GlobalLandMaskFile="/g/data/x45/ipbes/masks/gridinfo_CSIRO_1x1.nc"
GlobalMetPath="/g/data/x45/ipbes/${metmodel}/1deg"
# only in plume.nml
CO2Path="/g/data/x45/ipbes/co2"
NdepPath="/g/data/x45/ipbes/ndep"
elif [[ "${mettype}" == "bios" ]] ; then
#GlobalLandMaskFile="/g/data/x45/BIOS3_forcing/acttest9/acttest9" # no file extension
#GlobalMetPath="/g/data/x45/BIOS3_forcing/acttest9/met/" # last slash is needed - updated 29/3/2024
#ParamPath="/g/data/x45/BIOS3_forcing/acttest9/params/" # only in bios.nml
GlobalLandMaskFile="/g/data/x45/BIOS3_forcing/reccap1000pts/reccap1000pts" # no file extension
GlobalMetPath="/g/data/x45/BIOS3_forcing/reccap1000pts/met/" # last slash is needed - updated 29/3/2024
ParamPath="/g/data/x45/BIOS3_forcing/reccap1000pts/params/"
GlobalTransitionFilePath="/g/data/x45/LUH2/v3h/${degrees}deg_aust/EXTRACT"
fi
# Global LUC
# GlobalTransitionFilePath="/g/data/x45/LUH2/GCB_2019/1deg/EXTRACT"
elif [[ "${system}" == "bri220@pearcey" || "${system}" == "briggs@pearcey" ]] ; then
# Run directory: runpath="${sitepath}/run_xxx"
sitepath="/OSM/CBR/OA_GLOBALCABLE/work/Peter/CABLE_run/parallel_runs/${experiment}"
cablehome="/OSM/CBR/OA_GLOBALCABLE/work/Peter/CABLE_code"
# Cable executable
if [[ ${dompi} -eq 1 ]] ; then
exe="${cablehome}/NESP2pt9_BLAZE/offline/cable-mpi"
else
exe="${cablehome}/NESP2pt9_BLAZE/offline/cable"
fi
# CABLE-AUX directory (uses offline/gridinfo_CSIRO_1x1.nc and offline/modis_phenology_csiro.txt)
aux="/OSM/CBR/OA_GLOBALCABLE/work/Vanessa/CABLE-AUX"
# Global Mask
GlobalLandMaskFile="${aux}/offline/gridinfo_CSIRO_1x1.nc"
# Global CRU
GlobalMetPath="/OSM/CBR/OA_GLOBALCABLE/work/CRU-JRA55/crujra/daily_1deg"
# Global LUC
GlobalTransitionFilePath="/OSM/CBR/OA_GLOBALCABLE/work/LUH2/v3/1deg"
elif [[ "${system}" == "pcb599@gadi" || "${system}" == "briggs@gadi" ]] ; then
# Run directory: runpath="${sitepath}/run_xxx"
sitepath="/g/data/x45/BIOS3_output/${experiment}"
workpath="/home/599/pcb599/CABLE_run/BIOS3/run"
cablehome="/home/599/pcb599/CABLE_code/NESP2pt9_BLAZE"
# Cable executable
if [[ ${dompi} -eq 1 ]] ; then
exe="${cablehome}/offline/cable-mpi"
else
exe="${cablehome}/offline/cable"
fi
# CABLE-AUX directory (uses offline/gridinfo_CSIRO_1x1.nc and offline/modis_phenology_csiro.txt)
aux="/g/data/x45/CABLE-AUX"
# Global Mask
GlobalLandMaskFile="${aux}/offline/gridinfo_CSIRO_1x1.nc"
SurfaceFile="${aux}/offline/gridinfo_CSIRO_1x1.nc" # note that SurfaceFile does not need subsetting
# Global LUC
GlobalTransitionFilePath="/g/data/x45/LUH2/GCB_2019/1deg/EXTRACT"
# Global Met
if [[ "${mettype}" == 'plume' ]] ; then
GlobalMetPath="/g/data/x45/ipbes/${metmodel}/1deg"
CO2Path="/g/data/x45/ipbes/co2"
NdepPath="/g/data/x45/ipbes/ndep"
GlobalLandMaskFile="/g/data/x45/ipbes/masks/glob_ipsl_1x1.nc"
GlobalLandMaskFile="/g/data/x45/ipbes/masks/gridinfo_CSIRO_1x1.nc"
elif [[ "${mettype}" == 'bios' ]] ; then
GlobalLandMaskFile="/g/data/x45/BIOS3_forcing/acttest9/acttest9" # no file extension
GlobalMetPath="/g/data/x45/BIOS3_forcing/acttest9/met/" # last slash is needed
ParamPath="/g/data/x45/BIOS3_forcing/acttest9/params/"
GlobalTransitionFilePath="/g/data/x45/LUH2/v3h/${degrees}deg_aust/EXTRACT"
elif [[ "${mettype}" == 'cru' ]] ; then
GlobalLandMaskFile="/g/data/x45/ipbes/masks/glob_ipsl_1x1.nc"
GlobalMetPath="/g/data/x45/CRUJRA2020/daily_1deg"
fi
elif [[ "${system}" == "nieradzik@aurora" ]] ; then
# Run directory: runpath="${sitepath}/run_xxx"
sitepath="/home/x_larni/STOREDIR/RUNDIR/CABLE/${experiment}"
workpath="/home/x_larni/SRC/CABLE/NESP2pt9_BLAZE"
cablehome="/home/x_larni/SRC/CABLE/NESP2pt9_BLAZE"
# Cable executable
if [[ ${dompi} -eq 1 ]] ; then
exe="${cablehome}/offline/cable-mpi"
else
exe="${cablehome}/offline/cable"
fi
# CABLE-AUX directory (uses offline/gridinfo_CSIRO_1x1.nc and offline/modis_phenology_csiro.txt)
aux="/home/x_larni/STOREDIR/DATA/CABLE-AUX"
# Global Mask
GlobalLandMaskFile="${aux}/offline/gridinfo_CSIRO_1x1.nc"
SurfaceFile="${aux}/offline/gridinfo_CSIRO_1x1.nc" # note that SurfaceFile does not need subsetting
# Global LUC
GlobalTransitionFilePath="/g/data/x45/LUH2/GCB_2019/1deg/EXTRACT"
# Global Met
if [[ "${mettype}" == 'plume' ]] ; then
GlobalMetPath="/g/data/x45/ipbes/${metmodel}/1deg"
CO2Path="/g/data/x45/ipbes/co2"
NdepPath="/g/data/x45/ipbes/ndep"
GlobalLandMaskFile="/g/data/x45/ipbes/masks/glob_ipsl_1x1.nc"
GlobalLandMaskFile="/g/data/x45/ipbes/masks/gridinfo_CSIRO_1x1.nc"
elif [[ "${mettype}" == 'bios' ]] ; then
GlobalLandMaskFile="/home/x_larni/STOREDIR/DATA/CABLE_INPUT/acttest9/acttest9" # no file extension
GlobalMetPath="/home/x_larni/STOREDIR/DATA/CABLE_INPUT/acttest9/met/" # last slash is needed
ParamPath="/home/x_larni/STOREDIR/DATA/CABLE_INPUT/acttest9/params/"
GlobalTransitionFilePath="/home/x_larni/STOREDIR/DATA/CABLE_INPUT/LUH2/v3h/${degrees}deg_aust/EXTRACT"
elif [[ "${mettype}" == 'cru' ]] ; then
GlobalLandMaskFile="/g/data/x45/ipbes/masks/glob_ipsl_1x1.nc"
GlobalMetPath="/g/data/x45/CRUJRA2020/daily_1deg"
fi
else
echo "System not known."
exit 1
fi
# Run directory
#runpath="${sitepath}/run_20210618"
runpath="${sitepath}/run"
# Cable parameters
if [[ "${mettype}" == 'bios' ]] ; then
namelistpath="${workpath}/namelists_bios"
filename_veg="${workpath}/params_bios/def_veg_params.txt"
filename_soil="${workpath}/params_bios/def_soil_params.txt"
casafile_cnpbiome="${workpath}/params_bios/pftlookup.csv"
else
namelistpath="${workpath}/namelists"
filename_veg="${workpath}/params/def_veg_params.txt"
filename_soil="${workpath}/params/def_soil_params.txt"
casafile_cnpbiome="${workpath}/params/pftlookup.csv"
fi
# Other scripts
ScriptsPath="${cablehome}/scripts"
# Mask
LandMaskFile="${sitepath}/mask/${experiment}_landmask.nc"
# Met
if [[ "${mettype}" == 'bios' ]] ; then
MetPath="${sitepath}/met/bios_${degrees}deg"
ClimateFile="${sitepath}/mask/bios_climate_rst.nc"
if [[ "${sys}" == "gadi" ]]; then
if [[ (${doclimate} -eq 0) && (! -f ${ClimateFile}) ]] ; then
ClimateFile="/g/data/x45/BIOS3_output/bio_climate_acttest9/bios_climate_rst.nc"
fi
fi
else
MetPath="${sitepath}/met/cru_jra_1deg"
ClimateFile="${sitepath}/mask/cru_climate_rst.nc"
if [[ "${sys}" == "gadi" ]]; then
if [[ (${doclimate} -eq 0) && (! -f ${ClimateFile}) ]] ; then
ClimateFile="/g/data/x45/ipbes/cable_climate/ipsl_climate_rst_glob_1deg.nc"
fi
fi
fi
# LUC
TransitionFilePath="${sitepath}/LUH2/v3/1deg"
# gm lookup tables
gm_lut_bernacchi_2002="${cablehome}/params/gm_LUT_351x3601x7_1pt8245_Bernacchi2002.nc"
gm_lut_walker_2013="${cablehome}/params/gm_LUT_351x3601x7_1pt8245_Walker2013.nc"
# 13C
filename_d13c_atm="${cablehome}/params/graven_et_al_gmd_2017-table_s1-delta_13c-1700-2025.txt"
# --------------------------------------------------------------------
# Start Script
# --------------------------------------------------------------------
# --------------------------------------------------------------------
# Helper functions, most functions are in plumber_cable-pop_lib.sh
#
source ${pdir}/run_cable-pop_lib.sh
# usage of script
function usage()
{
printf "${pprog} [-h]\n"
printf "Runs Cable on a single grid cell with spinup, POP, land-use change, etc.\n"
printf "Behaviour of the script is controlled by switches at the top of the script (ca. line 101ff).\n"
printf "\n"
printf "Options\n"
printf " -h Prints this help screen.\n"
}
# cleanup at end or at trap
function cleanup()
{
\rm -f ${tmp}/*.${pid}*
exit 1
}
# returns argument to extract lat and lon with ncks
function nckslatlon()
{
vars=$(ncvarlist ${1})
if [[ -z $(isin latitude ${vars}) ]] ; then ilat="lat" ; else ilat="latitude" ; fi
if [[ -z $(isin longitude ${vars}) ]] ; then ilon="lon" ; else ilon="longitude" ; fi
if [[ -z $(echo ${2} | cut -f 3 -d ",") || -z $(echo ${2} | cut -f 4 -d ",") ]] ; then
iilat=$(echo ${2} | cut -f 1 -d ",")
iilon=$(echo ${2} | cut -f 2 -d ",")
echo "-d ${ilat},${iilat} -d ${ilon},${iilon}"
else
iilat1=$(echo ${2} | cut -f 1 -d ",")
iilat2=$(echo ${2} | cut -f 2 -d ",")
iilon1=$(echo ${2} | cut -f 3 -d ",")
iilon2=$(echo ${2} | cut -f 4 -d ",")
echo "-d ${ilat},${iilat1},${iilat2} -d ${ilon},${iilon1},${iilon2}"
fi
}
# --------------------------------------------------------------------------------------------------
# Preparation
#
# Get options
while getopts "h" option ; do
case ${option} in
h) usage; exit;;
*) printf "Error ${pprog}: unimplemented option.\n\n" 1>&2; usage 1>&2; exit 1;;
esac
done
shift $((${OPTIND} - 1))
#
# get directories
mkdir -p ${sitepath}/mask
pdir=$(abspath ${pdir})
cd ${pdir}
adir=$(abspath ${aux})
exe=$(absfile ${exe})
mkdir -p ${runpath}
rdir=$(abspath ${runpath})
ndir=$(abspath ${namelistpath})
sdir=$(abspath ${ScriptsPath})
#
# prepare run directory
cd ${rdir}
mkdir -p logs
mkdir -p outputs
mkdir -p restart
ln -sf ${adir}
# ln -sf ${exe}
cp ${exe} ./
iexe=$(basename ${exe})
cd ${pdir}
#
# set stacksize to unlimited if permitted, otherwise to 15 bit if possible
set +e
ulimit -s unlimited 2> /dev/null || ulimit -s 32768
set -e
# --------------------------------------------------------------------
# Info
#
t1=$(date +%s)
printf "Started at %s\n" "$(date)"
printf "\nSetup\n"
printf " Serial / Parallel\n"
printf " dompi=${dompi}\n"
printf " nproc=${nproc}\n"
printf "\n"
printf " Sequence\n"
printf " imeteo=${imeteo}\n"
printf " doextractsite=${doextractsite}\n"
printf " experiment=${experiment}\n"
printf " randompoints=${randompoints}\n"
printf " latlon=${latlon}\n"
printf " doclimate=${doclimate}\n"
printf " dofromzero=${dofromzero}\n"
printf " doequi1=${doequi1}\n"
printf " nequi1=${nequi1}\n"
printf " doequi2=${doequi2}\n"
printf " nequi2=${nequi2}\n"
printf " doiniluc=${doiniluc}\n"
printf " doinidyn=${doinidyn}\n"
printf " dofinal=${dofinal}\n"
printf " dofuture=${dofuture}\n"
printf "\n"
printf " Options\n"
printf " mettype=${mettype}\n"
printf " metmodel=${metmodel}\n"
printf " RCP=${RCP}\n"
printf " explicit_gm=${explicit_gm}\n"
printf " use_LUTgm=${use_LUTgm}\n"
printf " Rubisco_params=${Rubisco_params}\n"
printf " coordinate_photosyn=${coordinate_photosyn}\n"
printf " coord=${coord}\n"
printf " acclimate_photosyn=${acclimate_photosyn}\n"
printf " call_pop=${call_pop}\n"
printf " doc13o2=${doc13o2}\n"
printf " c13o2_simple_disc=${c13o2_simple_disc}\n"
printf "\n"
printf " Directories\n"
printf " sitepath=${sitepath}\n"
printf " cablehome=${cablehome}\n"
printf " exe=${exe}\n"
printf " aux=${aux}\n"
printf " GlobalLandMaskFile=${GlobalLandMaskFile}\n"
printf " SurfaceFile=${SurfaceFile}\n"
printf " GlobalMetPath=${GlobalMetPath}\n"
printf " GlobalTransitionFilePath=${GlobalTransitionFilePath}\n"
printf " runpath=${runpath}\n"
printf " namelistpath=${namelistpath}\n"
printf " filename_veg=${filename_veg}\n"
printf " filename_soil=${filename_soil}\n"
printf " casafile_cnpbiome=${casafile_cnpbiome}\n"
printf " LandMaskFile=${LandMaskFile}\n"
printf " MetPath=${MetPath}\n"
printf " ClimateFile=${ClimateFile}\n"
printf " TransitionFilePath=${TransitionFilePath}\n"
printf " gm_lut_bernacchi_2002=${gm_lut_bernacchi_2002}\n"
printf " gm_lut_walker_2013=${gm_lut_walker_2013}\n"
printf " filename_d13c_atm=${filename_d13c_atm}\n"
printf "\n"
# --------------------------------------------------------------------
# Prep input
#
# 0. Extract meteo, land use and mask for one specific site from global files
if [[ ${doextractsite} -ge 2 ]] ; then
set +e
xnco=$(which ncks 2> /dev/null)
set -e
if [[ -z ${xnco} ]] ; then module load nco ; fi
fi
if [[ ${doextractsite} -eq 1 ]] ; then
echo "0. Set local mask"
cd ${pdir}
# mask
LandMaskFilePath=$(dirname ${LandMaskFile})
mkdir -p ${LandMaskFilePath}
LandMaskFile=$(absfile ${LandMaskFile})
# echo $(basename ${LandMaskFile})
# generate random points if ${randompoints} > 0
if [[ ${randompoints} -ne 0 ]] ; then
dogeneraterandom=1
rpoints=${randompoints}
if [[ ${randompoints} -lt 0 ]] ; then
if [[ -f ${LandMaskFilePath}/${experiment}_points.csv ]] ; then dogeneraterandom = 0 ; fi
rpoints=$(( ${randompoints} * -1 ))
fi
# generate random points
cat > ${tmp}/sedtmp.${pid} << EOF
basepath = "${sitepath}"
gridinfo_file = "${GlobalLandMaskFile}"
outname = "${LandMaskFilePath}/${experiment}_points.csv"
EOF
applysed ${tmp}/sedtmp.${pid} ${sdir}/generate_latlonlist.py ${LandMaskFilePath}/generate_latlonlist.py
python3 ${LandMaskFilePath}/generate_latlonlist.py ${rpoints}
# set mask to generated random points
cat > ${tmp}/sedtmp.${pid} << EOF
path = "${LandMaskFilePath}"
maskfname = "${LandMaskFile}"
latlonfile = "${LandMaskFilePath}/${experiment}_points.csv"
gridinfo_file = "${GlobalLandMaskFile}"
EOF
if [[ "${mettype}" == "bios" ]] ; then
echo "res = 0.25" >> ${tmp}/sedtmp.${pid}
fi
applysed ${tmp}/sedtmp.${pid} ${sdir}/create_landmask.py ${LandMaskFilePath}/create_landmask.py
sed -i -e "s|from lnutils.*|sys.path.insert(1,'${sdir}'); from lnutils import latlon2ixjy|" ${LandMaskFilePath}/create_landmask.py
python3 ${LandMaskFilePath}/create_landmask.py
else
# # cdo -s -f nc4 -z zip sellonlatbox,-72.5,-72.0,42.5,43.0 ${GlobalLandMaskFile} ${LandMaskFile}
# ncks -O $(nckslatlon ${GlobalLandMaskFile} ${latlon}) ${GlobalLandMaskFile} ${LandMaskFile}
cat > ${tmp}/sedtmp.${pid} << EOF
path = "${LandMaskFilePath}"
maskfname = "${LandMaskFile}"
gridinfo_file = "${GlobalLandMaskFile}"
EOF
if [[ "${mettype}" == "bios" ]] ; then
echo "res = 0.25" >> ${tmp}/sedtmp.${pid}
fi
applysed ${tmp}/sedtmp.${pid} ${sdir}/create_landmask.py ${LandMaskFilePath}/create_landmask.py
sed -i -e "s|from lnutils.*|sys.path.insert(1,'${sdir}'); from lnutils import latlon2ixjy|" ${LandMaskFilePath}/create_landmask.py
python3 ${LandMaskFilePath}/create_landmask.py ${latlon}
fi
elif [[ ${doextractsite} -eq 2 ]] ; then
echo "0. Extract local meteo and mask"
cd ${pdir}
# meteorology
met_list="pre pres dlwrf dswrf spfh tmax tmin ugrd vgrd ndep"
mkdir -p ${MetPath}
MetPath=$(abspath ${MetPath})
for mm in ${met_list} ; do
echo ${GlobalMetPath}/${mm}
mkdir -p ${MetPath}/${mm}
for nc in ${GlobalMetPath}/${mm}/*.nc ; do
ff=$(basename ${nc})
echo " ${ff}"
# cdo -s -f nc4 -z zip sellonlatbox,-72.5,-72.0,42.5,43.0 ${nc} ${MetPath}/${mm}/${ff}
ncks -O $(nckslatlon ${nc} ${latlon}) ${nc} ${MetPath}/${mm}/${ff}
done
done
echo ${GlobalMetPath}/co2/*.csv
mkdir -p ${MetPath}/co2
cp ${GlobalMetPath}/co2/*.csv ${MetPath}/co2/
# land use
mkdir -p ${TransitionFilePath}
TransitionFilePath=$(abspath ${TransitionFilePath})
echo ${GlobalTransitionFilePath}
for nc in ${GlobalTransitionFilePath}/*.nc ; do
ff=$(basename ${nc})
echo " ${ff}"
# cdo -s -f nc4 -z zip sellonlatbox,-72.5,-72.0,42.5,43.0 ${nc} ${TransitionFilePath}/${ff}
ncks -O $(nckslatlon ${nc} ${latlon}) ${nc} ${TransitionFilePath}/${ff}
done
# mask
LandMaskFilePath=$(dirname ${LandMaskFile})
mkdir -p ${LandMaskFilePath}
LandMaskFile=$(absfile ${LandMaskFile})
echo $(basename ${LandMaskFile})
# cdo -s -f nc4 -z zip sellonlatbox,-72.5,-72.0,42.5,43.0 ${GlobalLandMaskFile} ${LandMaskFile}
ncks -O $(nckslatlon ${GlobalLandMaskFile} ${latlon}) ${GlobalLandMaskFile} ${LandMaskFile}
fi
# --------------------------------------------------------------------
# Prepare sequence
#
# Choose meteo, land use and mask directories and files
if [[ ${imeteo} -eq 0 ]] ; then
MetPath=$(abspath ${GlobalMetPath})
TransitionFilePath=$(abspath ${GlobalTransitionFilePath})
LandMaskFile=$(absfile ${GlobalLandMaskFile})