runORDCAO

Here are explained the instructions to run ORCHIDEE off-line simulations as it was prepared for the post-graduate course 'Interacció suelo-atmófera y su modelado

All the necessary files are uploaded at the ftp of the course

ftp://ftp.cima.fcen.uba.ar/lluis.fita/Curso_InteraccionSueloAtmosfera/

It has been created an specific work-flow management for the course OR1proc OR 1proc, this instructions follow the use of such work-flow

Getting work-flow

1. Creation of a work-flow folder [oRWORKFLOW_1proc] (installOR)

mkdir installOR

1. Going there

cd installOR

1. Getting the files of the work-flow

wget -r -nH --cut-dirs=3 ftp://ftp.cima.fcen.uba.ar/lluis.fita/Curso_InteraccionSueloAtmosfera/TPs/components

1. ftp does not charge the execution attributes. They have to be manuallry added:

chmod u+x components/shell/run_multi-or_1proc.bash
chmod u+x components/shell/prepare_forcings.bash
chmod u+x components/ORtemplate/bin/orchideedriver

Getting forcings

Here we only will get a minimal sub-set of the available forcings, just to run a test case. Being in the folder [oRWORKFLOW_1proc]

1. Creation of the atmospheric forcing data folder structure

mkdir -p forcings/ATMOS/CRUNCEP

1. Getting 3 files of atmospheric forcing

cd forcings/ATMOS/CRUNCEP
wget -r -nH --cut-dirs=6 ftp://ftp.cima.fcen.uba.ar/lluis.fita/Curso_InteraccionSueloAtmosfera/TPs/forcings/ATMOS/CRUNCEP/cruncep_halfdeg_1989.nc
wget -r -nH --cut-dirs=6 ftp://ftp.cima.fcen.uba.ar/lluis.fita/Curso_InteraccionSueloAtmosfera/TPs/forcings/ATMOS/CRUNCEP/cruncep_halfdeg_1990.nc
wget -r -nH --cut-dirs=6 ftp://ftp.cima.fcen.uba.ar/lluis.fita/Curso_InteraccionSueloAtmosfera/TPs/forcings/ATMOS/CRUNCEP/cruncep_halfdeg_1991.nc

1. Going back to [oRWORKFLOW_1proc]

cd ../../../

1. Creation of the ancillary data folder structure

mkdir -p forcings/IGCM/SRF

1. Getting the basic ancillary data

cd forcings/IGCM/SRF
wget -r -nH --cut-dirs=6 ftp://ftp.cima.fcen.uba.ar/lluis.fita/Curso_InteraccionSueloAtmosfera/TPs/forcings/IGCM/SRF/cartepente2d_15min.nc
wget -r -nH --cut-dirs=6 ftp://ftp.cima.fcen.uba.ar/lluis.fita/Curso_InteraccionSueloAtmosfera/TPs/forcings/IGCM/SRF/soils_param.nc

1. Ohter ancillary data

mkdir PFTMAPS/CMIP6/ESA-LUH2v2/historical/15PFT.v2/
cd PFTMAPS/CMIP6/ESA-LUH2v2/historical/15PFT.v2/
wget -r -nH --cut-dirs=11 ftp://ftp.cima.fcen.uba.ar/lluis.fita/Curso_InteraccionSueloAtmosfera/TPs/forcings/IGCM/SRF/PFTMAPS/CMIP6/ESA-LUH2v2/historical/15PFT.v2/PFTmap_1990.nc
mkdir WOODHARVEST/LUH2v2/historical4
cd WOODHARVEST/LUH2v2/historical4
wget -r -nH --cut-dirs=9 ftp://ftp.cima.fcen.uba.ar/lluis.fita/Curso_InteraccionSueloAtmosfera/TPs/forcings/IGCM/SRF/WOODHARVEST/LUH2v2/historical4/woodharvest_1990.nc
mkdir SOIL
wget -r -nH --cut-dirs=7 ftp://ftp.cima.fcen.uba.ar/lluis.fita/Curso_InteraccionSueloAtmosfera/TPs/forcings/IGCM/SRF/SOIL/
soil_bulk_and_ph.nc

Running ORCHIDEE

Creation of a working directory [WORKDIR] (InteraccionSueloAtmosfera)

cd ${HOME}
mkdir InteraccionSueloAtmosfera
cd InteraccionSueloAtmosfera

1. Creation of a test folder

mkdir test
cd test

1. copying the configuration file and linkning the running script

cp ~/installOR/components/shell/or_1-proc.config ./
ln ~/installOR/components/shell/run_multi-or_1proc.bash ./

1. Editting the configuration file (or_1-proc.config). It should look like:

# scratch
scratch = false

# Period
period=1990-1990

# config
pyBIN=/usr/bin/python
OUTfolder=/home/administrador/InteraccionSueloAtmosfera/test
foldOR1proc=/home/administrador/installOR
forcingfolder=/home/administrador/installOR/forcings

# Anciliary data 1 file without year (original name of the files with the ancilliary data [folderName, since ${forcings}]@[origFilen]@[ORfilen])
filestolink=IGCM/SRF/albedo@alb_bg_modisopt_2D_ESA_v3.nc@alb_bg.nc:IGCM/SRF@cartepente2d_15min.nc@cartepente2d_15min.nc:IGCM/SRF@reftemp.nc@reftemp.nc:IGCM/SRF@routing.nc@routing.nc:IGCM/SRF/SOIL@soil_bulk_and_ph.nc@soil_bulk_and_ph.nc:IGCM/SRF@soils_param.nc@soils_param.nc

# Anciliary data 1 file with year (original name of the files with the ancilliary data [folderName, since ${forcings}]@[origFilen]@[ORfilen], [YYYY] to be changed by the correspondant year)
filestolinkyr=IGCM/SRF/PFTMAPS/CMIP6/ESA-LUH2v2/historical/15PFT.v2@PFTmap_YYYY.nc@PFTmap.nc:IGCM/SRF/WOODHARVEST/LUH2v2/historical4@woodharvest_YYYY.nc@woodharvest.nc

# Anciliary data 3 files with year-1,year,year+1 (original name of the files with the ancilliary data [folderName, since ${forcings}]@[origFilen]@[ORfilen], [YYYY] to be changed by the correspondant year-1, year, year+1)
filestolink3yr=

# Atmospheric forcing as [ForcingName]@[HeaderForcingFiles] [assuming ${forcingfolder}/ATMOS/{ForcingName}/{HeaderForcingFiles}_YYYY.nc]
atmos=CRUNCEP@cruncep_halfdeg

# Additional parameters for run.def as [paramName1]:[values1];...;[paramNameN]:[valuesN] (! for spaces)
addparams=LIMIT_WEST@-66.9598;LIMIT_EAST@-65.4598;LIMIT_SOUTH@-33.9648;LIMIT_NORTH@-32.4648;RIVER_ROUTING@n

1. Running it

nohup ./run_multi-or_1proc.bash >& run_multi_or_1proc.log &

1. When finished one should have (among others)

orout/1990/sechiba_histout_0000.nc
orout/1990/stomate_histout_0000.nc

1. Getting forcings

wget -r ftp://ftp.cima.fcen.uba.ar/lluis.fita/Curso_InteraccionSueloAtmosfera/TPs/forcings