ORCHIDEE/OR4L OR4L

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OR4L

L. Fita's work-flow management for ORCHIDEE model

ORCHIDEE work-flow management is done via 3 scripts (these are the specifics for hydra [CIMA cluster]):

  • EXPERIMENTparameters.txt: General ASCII file which configures the experiment and chain of simulations (chunks). This is the unique file to modify
  • run_experiments.pbs: PBS-queue job which prepares the experiment of the environment
  • run_OR.pbs: PBS-queue job which launch the ORCHIDEE model and a range the output

An experiment which contains a period of simulation is divided by chunks small pieces of times which are manageable by the model. The work-flow follows these steps using run_experiments.pbs:

  1. Copy and link all the required files for a given chunk of the whole period of simulation following the content of EXPERIMENTparameters.txt
  2. Launches run_OR.pbs which will simulated the period of the given chunk
  3. Launches the next run_experiments.pbs (which waits until the end of run_OR.pbs)

All the scripts are located in hydra at: 

/share/tools/work-flows/OR4L/hydra

EXPERIMENTSparameters.txt

This ASCII file configures all the simulation. It assumes:

  • Required files, forcings, storage, compiled version of the code might be at different machines.
  • There is a folder with a given template version of the run.def which will be used and changed accordingly to the requirement of the experiments
  1. Experiment name

ExpName = DiPolo

  1. Simulation name

SimName = OKstomate_CRUNCEP_spinup

  1. python binary

pyBIN=/home/lluis.fita/bin/anaconda2/bin/python

  1. Start from the beginning (keeping folder structure)

scratch = false

  1. Experiment starting date

exp_start_date = 19580101000000

  1. Experiment ending date

exp_end_date = 20150101000000

  1. Chunk Length [N]@[unit]
  2. [unit]=[year, month, week, day, hour, minute, second]

chunk_length = 1@year

  1. Hosts
  2. list of different hosts and specific user
  3. [USER]@[HOST]
  4. NOTE: this will only work if public keys have been set-up
  5. Running host (including domain definition)
  6. runHOST=lluis.fita@hydra
  7. Host with compiled code, namelist templates

codeHOST=lluis.fita@hydra

  1. forcing Host with forcings (atmospherics and morphologicals)

forcingHOST=lluis.fita@hydra

  1. output Host with storage of output (including restarts)
  2. outHOST=lluis.fita@skogul

outHOST=lluis.fita@hydra

  1. Folder with the `run.def' and `xml' of the experiment

domainHOME = /home/lluis.fita/salidas/estudios/dominmios/DiPolo/daily

  1. Running folder

runHOME = /home/lluis.fita/estudios/DiPolo/sims

  1. Folder with the compiled source of ORCHIDEE

orHOME = /share/modipsl_dbg/bin/

  1. Storage folder of the output
  2. storageHOME = /datoslluis/estudios/DiPolo/sims/output

storageHOME = /home/lluis.fita/salidas/estudios/DiPolo/sims/output

  1. Modules to load ('None' for any)

modulesLOAD = None

  1. Simulation kind
  2. 'offline': Realistic off-line run, with initial conditions at each change of year
  3. 'periodic': Realistic off-line run, with the same initial conditions for each year

kindSIM = offline

  1. Model reference output names (to be used as checking file names)

nameLISTfile = run.def # namelist nameRSTfile = sechiba_rest_out.nc # restart file nameOUTfile = sechiba_history.nc # output file

  1. Extensions configuration of the model

configEXTS = def:xml

  1. restart file names
  2. ':' list of [tmplrstfilen|[NNNNN1]?[val1]#[...[NNNNNn]?[valn]]@[tmpllinkname]|[NNNNN1]?[val1]#[...[NNNNNn]?[valn]]
  3. [tmplrstfilen]: template name of the restart file (if necessary with [NNNNN] variables to be substituted)
  4. [NNNNN]: section of the file name to be automatically substituted
  5. `[YYYY]': year in 4 digits
  6. `[YY]': year in 2 digits
  7. `[MM]': month in 2 digits
  8. `[DD]': day in 2 digits
  9. `[HH]': hour in 2 digits
  10. `[SS]': second in 2 digits
  11. `[JJJ]': julian day in 3 digits
  12. [val]: value to use (which is systematically defined in `run_OR.pbs')
  13. `%Y%': year in 4 digits
  14. `%y%': year in 2 digits
  15. `%m%': month in 2 digits
  16. `%d%': day in 2 digits
  17. `%h%': hour in 2 digits
  18. `%s%': second in 2 digits
  19. `%j%': julian day in 3 digits
  20. [tmpllinkname]: template name of the link of the restart file (if necessary with [NNNNN] variables to be substituted)

rstFILES=sechiba_rest_out.nc@sechiba_rst.nc:stomate_rest_out.nc@stomate_rst.nc

  1. Folder with the input morphological forcing data

indataHOME = /share/ORCHIDEE/data/IGCM/SRF

  1. ':' separated list of [morphfilen]|[NNNNN1]?[val1]#[...[NNNNNn]?[valn]]@[tpmllinkname]|[NNNNN1]?[val1]#[...[NNNNNn]?[valn]]
  2. [morphfilen]: morphological forcing file (relative to ${indataHOME}) (if necessary with [NNNNN] variables to be substituted)
  3. [tmpllinkname]: template name of the link of the restart file (if necessary with [NNNNN] variables to be substituted)

indataFILES = albedo/alb_bg_modisopt_2D_ESA_v2.nc@alb_bg_modisopt_2D_ESA.nc:cartepente2d_15min.nc@cartepente2d_15min.nc:carteveg5km.nc@carteveg5km.nc:floodplains.nc@floodplains.nc:lai2D.nc@lai2D.nc:PFTMAPS/CMIP6/ESA-LUH2/historical/v1.2/withNoBio/13PFTmap_[YYYY]_ESA_LUH2v2h_withNoBio_v1.2.nc|YYYY?%Y%@PFTmap_025.nc:PFTmap_IPCC_1850.nc@PFTmap_IPCC.nc:reftemp.nc@reftemp.nc:soils_param.nc@soils_param.nc:soils_param_usda.nc@soils_param_usda.nc:soils_param_usdatop.nc@soils_param_usdatop.nc:routing.nc@routing.nc

  1. Folder which contents the atmospheric data to force the model

iniatmosHOME = /share/ORCHIDEE/data/IGCM/SRF/METEO/CRU-NCEP/v5.4/halfdeg

  1. ':' list of [atmosfilen]|[NNNNN1]?[val1]:[...[NNNNNn]?[valn]]@[tpmllinkname]|[NNNNN1]?[val1]#[...[NNNNNn]?[valn]]
  2. [filenTMPL]: template of the atmospheric data file name with [NNNN] variables to be substitued
  3. [tmpllinkname]: template name of the link of the restart file (if necessary with [NNNNN] variables to be substituted)

filenameTMPL = cruncep_halfdeg_[YYYY].nc|YYYY?%Y%@atmos_forcing.nc

    1. configuration files (':' separated list)

ORdef = run.def ORxml = context_orchidee.xml:field_def_orchidee.xml:file_def_orchidee.xml:iodef.xml

    1. def,xml changes ([fileA]@[parm1]:[val1];...;[parmN]:[valN]|...|[fileZ]@....)

nlparametres = run.def@STOMATE_OK_STOMATE:y;STOMATE_OK_CO2:y

  1. Name of the exectuable

nameEXEC=orchidee_ol

  1. netCDF Files which will not be kept anywhere

NokeptfileNAMES=

  1. Headers of netCDF files need to be kept

HkeptfileNAMES=sechiba_history:stomate_history:sechiba_history_4dim:sechiba_history_alma

  1. Headers of netCDF restart files need to be kept

HrstfileNAMES=sechiba_rest_out:stomate_rest_out

  1. Extras. rebuild program folder

binREBUILD = /share/modipsl_IOIPSLtools/bin

  1. ORCHIDEE parallel run configuration
    1. Number of nodes

Nnodes = 1

    1. Number of mpi procs

Nmpiprocs = 16

    1. Number of shared memory threads ('None' for no openMP threads)

Nopenthreads = None

    1. Memory size of shared memory threads

SIZEopenthreads = 200M

    1. Generic

errormsg=ERROR -- error -- ERROR -- error warnmsg=WARNING -- warning -- WARNING -- warning

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