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
  • There is a folder called components with shell and python scripts necessary for the work-flow management

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

How to simulate

  1. Creation of a new folder from where launch the experiment [ExperimentName] 
$ mkdir [ExperimentName]
cd [ExperimentName]
  1. copy the OR4L files to this folder 
$ cp /share/tools/work-flows/OR4L/hydra/EXPERIMENTparameters.txt ./
$ cp /share/tools/work-flows/OR4L/hydra/run_experiment.pbs ./
$ cp /share/tools/work-flows/OR4L/hydra/run_OR.pbs ./
  1. Edit the configuration/set-up of the simulation of the experiment 
$ vim EXPERIMENTparameters.txt
  1. Launch the simulation of the experiment 
$ qsub run_experiment.pbs

When it is running one would have (runnig ORCHIDEE job or_[SimName] `R', and exp_[SimName] in hold `H'): 

$ qstat -u $USER

hydra: 
                                                                         Req'd  Req'd   Elap
Job ID               Username Queue    Jobname          SessID NDS   TSK Memory Time  S Time
-------------------- -------- -------- ---------------- ------ ----- --- ------ ----- - -----
397.hydra            lluis.fi larga    or_oF-OKstomate_  27567     1  16   20gb 168:0 R   -- 
398.hydra            lluis.fi larga    exp_oF-OKstomate    --      1   1    2gb 168:0 H   --

In case of crash of the simulation, after fixing the issue, go to [runHOME]/[ExpName]/[SimName] and re-launch the experiment (after the first run the scratch is switched automatically to `false') 

$ qsub run_experiment.pbs

Checking the experiment

Once the experiment runs, one needs to look on (following name of the variables from EXPERIMENTparameters.txt

  • [runHOME]/[ExpName]/[SimName]: Will content the copies of the templates run.def, *.xml and a file chunk_attemps.inf which counts how many times a chunk has been attempted to be run (if it reached 4 times, the OPR4L is stopped)
  • [runHOME]/[ExpName]/[SimName]/run: actual folder where the computing nodes run the model. In a folder called orout there is a folder for each chunk with the standard output of the model
  • [runHOME]/[ExpName]/[SimName]/run/orout/[YYYYi][MMi][DDi][HHi][MIi][SSi]-[YYYYf][MMf][DDf][HHf][MIf][SSf]: folder with the standard output and all the required files to run a given chunk. The content of all this folder is compressed and kept in [storageHOME]/[ExpName]/[SimName]/config_[YYYYi][MMi][DDi][HHi][MIi][SSi]-[YYYYf][MMf][DDf][HHf][MIf][SSf].tar.gz
  • [storageHOME]/[ExpName]/[SimName] (in [storageHOST]): output of the already ran chunks as [YYYYi][MMi][DDi][HHi][MIi][SSi]-[YYYYf][MMf][DDf][HHf][MIf][SSf] for a chunk from [YYYYi]/[MMi]/[DDi] [HHi]:[MIi]:[SSi] to [YYYYf]/[MMf]/[DDf] [HHf]:[MIf]:[SSf]

When something went wrong

If there has been any problem check the last chunk (in orout/[PERIODchunk]) to try to understand what happens and where the problem comes from:

  • out_orchidee_[nnnn]: These are the files which content the standard output while running the model. One file for each process. If the problem was something related to model execution and it has been prepared for the error, a correct message must appear. (look first for the largest files... 
$ ls -lrS out_orchidee_*
  • run_or.log: These are the files which content the standard output of the model. Search for `segmentation faults' in form of (it might differ): 
forrtl: error (63): output conversion error, unit -5, file Internal Formatted Write
Image              PC                Routine            Line        Source
orchidee_ol        00000000032B736A  Unknown               Unknown  Unknown
orchidee_ol        00000000032B5EE5  Unknown               Unknown  Unknown
orchidee_ol        0000000003265966  Unknown               Unknown  Unknown
orchidee_ol        0000000003226EB5  Unknown               Unknown  Unknown
orchidee_ol        0000000003226671  Unknown               Unknown  Unknown
orchidee_ol        000000000324BC3C  Unknown               Unknown  Unknown
orchidee_ol        0000000003249C94  Unknown               Unknown  Unknown
orchidee_ol        00000000021B75FB  routing_mp_routin        3212  routing.f90
orchidee_ol        000000000217970D  routing_mp_routin        2690  routing.f90
orchidee_ol        00000000020915AE  routing_mp_routin         475  routing.f90
orchidee_ol        0000000000988860  sechiba_mp_sechib         491  sechiba.f90
orchidee_ol        00000000005E5A45  intersurf_mp_inte         374  intersurf.f90
orchidee_ol        00000000004DFB82  MAIN__                   1250  dim2_driver.f90
orchidee_ol        00000000004184DC  Unknown               Unknown  Unknown
libc.so.6          000000319021ECDD  Unknown               Unknown  Unknown
orchidee_ol        00000000004183D9  Unknown               Unknown  Unknown
  • on [runHOME]/[ExpName]/[SimName], check the output of the PBS jobs. Which are called:
    • exp_oF-[SimName].o[nnnn]: output of the run_experiment.pbs
    • or_oF-[SimName].o[nnnn]: output of the run_OR.pbs
  • Check [runHOME]/[ExpName]/[SimName]/run/used_run.def which holds all the parameters (even the default ones) used in the simulation

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

Name of the experiment 

# Experiment name
ExpName = DiPolo

Name of the simulation. Here is understood that a given experiment could have the model configured with different set-ups (here identified with a different name of simulation) 

# Simulation name
SimName = OKstomate_CRUNCEP_spinup

Which binary of python 2.x to be used 

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

Should this simulation be run from the beginning or not. If it is set to `true', it will remove all the pre-existing content of the folder [ExpName]/[SimName] in the running and in the storage spaces. Be careful. In case of `false' simulation will continue from the last successful ran chunk (checking the restart files). 

# Start from the beginning (keeping folder structure)
scratch = false

Period of the simulation of the simulation (In this example from 1958 Jan 1st to 2015 Dec 31) 

# Experiment starting date
exp_start_date = 19580101000000
# Experiment ending date
exp_end_date = 20150101000000

Length of the chunks (here and in all ORCHIDEE runs maximum to 1-year!!) 

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

Selection of the machines and users to each machine where the different requirement files are located and the output should be placed.

  • NOTE: this will only work if one set-up the .ssh public/private keys in each involved USER/HOST.
  • NOTE 2: All the forcings, compiled code, ... are already at hydra at the common space called share
  • NOTE 3: From the computing nodes, one can not access to the /share folder and to any of the CIMA's storage machines: skogul, freyja, ... For that reason, one need to use these system of [USER]@[HOST] accounts. *.pbs scripts uses a series of wrappers of the standard functions: cp, ln, ls, mv, .... which manage them `from' and `to' different pairs of [USER]@[HOST]. NOTE: this will only work if public keys have been set-up (see more details in llaves_ssh) 
# Hosts
#   list of different hosts and specific user
#     [USER]@[HOST]
#   NOTE: this will only work if public keys have been set-up
##
# Host with compiled code, namelist templates
codeHOST=lluis.fita@hydra
# forcing Host with forcings (atmospherics and morphologicals)
forcingHOST=lluis.fita@hydra
# output Host with storage of output (including restarts)
outHOST=lluis.fita@hydra

Templates of the configuration of ORCHIDEE: run.def, *.xml files. NOTE: only run.def will be changed according to the content of EXPERIMENTparameters.txt like period of the chunk, atmospheric forcing, differences of the set-up, ... (located in the [codeHOST] 

# Folder with the `run.def' and `xml' of the experiment
domainHOME = /home/lluis.fita/salidas/estudios/dominios/DiPolo/daily

Folder where the ORCHIDEE model will run in the computing nodes (on top of that there will be two more folders [ExpName]/[SimName]). ORCHIDEE will run at the folder [ExpName]/[SimName]/run 

# Running folder
runHOME = /home/lluis.fita/estudios/DiPolo/sims

Folder with the compiled version of the model (located at [codeHOST]) 

# Folder with the compiled source of ORCHIDEE
orHOME = /share/modipsl/bin/

Folder to storage all the output of the model (history files, restarts and compressed file with content of the configuration and the standard output of the given run). The content of the folder will be organized by chunks (located at [storageHOST]) 

# Storage folder of the output
storageHOME = /home/lluis.fita/salidas/estudios/DiPolo/sims/output

Wether modules should be load (not used for hydra) 

# Modules to load ('None' for any)
modulesLOAD = None

Which kind of simulation will be run (at this time only prepared for 'offline') 

# Simulation kind
#  'offline': Realistic off-line run, with initial conditions at each change of year
#  'periodic': Realistic off-line run, with the same initial conditions for each year
kindSIM = offline

Names of the files used to check that the chunk has properly ran 

# 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

Extensions of the files which content the configuration of the model 

# Extensions of the files with the configuration of the model
configEXTS = def:xml

To continue from a previous chunk one needs to use the `restart' files. But they need to be renamed, because otherwise they will be re-written. Here one specifies the original name of the file [origFile] and the name to be used to avoid the re-writting [destFile]. It uses a complex bash script which even can deal with the change of dates according to the period of the chunk (':' list of [origFile]@[destFile]). They will located at the [storageHOST] 

# restart file names
# ':' list of [tmplrstfilen|[NNNNN1]?[val1]#[...[NNNNNn]?[valn]]@[tmpllinkname]|[NNNNN1]?[val1]#[...[NNNNNn]?[valn]]
#    [tmplrstfilen]: template name of the restart file (if necessary with [NNNNN] variables to be substituted)
#      [NNNNN]: section of the file name to be automatically substituted
#        `[YYYY]': year in 4 digits
#        `[YY]': year in 2 digits
#        `[MM]': month in 2 digits
#        `[DD]': day in 2 digits
#        `[HH]': hour in 2 digits
#        `[SS]': second in 2 digits
#        `[JJJ]': julian day in 3 digits
#      [val]: value to use (which is systematically defined in `run_OR.pbs')
#        `%Y%': year in 4 digits
#        `%y%': year in 2 digits
#        `%m%': month in 2 digits
#        `%d%': day in 2 digits
#        `%h%': hour in 2 digits
#        `%s%': second in 2 digits
#        `%j%': julian day in 3 digits
#    [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

Folder with the forcing data (located at [forcingHOST]). 

# Folder with the input morphological forcing data
indataHOME = /share/ORCHIDEE/data/IGCM/SRF

Files to be used as morphological forcings (It uses the same complex bash script as in the restarts) 

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

Folder with the atmospheric forcing data (located at [forcingHOST]). 

# Folder which contents the atmospheric data to force the model (here an example for CRU-NCEP v5.4 half degree at <code>hydra</code>)
iniatmosHOME = /share/ORCHIDEE/data/IGCM/SRF/METEO/CRU-NCEP/v5.4/halfdeg

Files to be used as atmospheric forcings (It uses the same complex bash script as in the restarts). Files must be located at [forcingHOST]. In this example a CRU-NCEP file which is called cruncep_halfdeg_[YYYY].nc (where [YYYY] is for a year in four digits). It is said to change the [YYYY] by %Y% which will be the year of the chunk with four digits (C-like) 

# ':' list of [atmosfilen]|[NNNNN1]?[val1]:[...[NNNNNn]?[valn]]@[tpmllinkname]|[NNNNN1]?[val1]#[...[NNNNNn]?[valn]]
#    [filenTMPL]: template of the atmospheric data file name with [NNNN] variables to be substitued
#    [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

Name of the files with the set-up of the model 

## configuration files (':' separated list)
ORdef = run.def
ORxml = context_orchidee.xml:field_def_orchidee.xml:file_def_orchidee.xml:iodef.xml

Here on can change values on the template run.def. It will change the values of the provided parameters with a new value. If the given parameter is not in the template of the run.def it will be automatically added. 

## def,xml changes ([fileA]@[parm1]:[val1];...;[parmN]:[valN]|...|[fileZ]@....)
nlparametres = run.def@STOMATE_OK_STOMATE:y;STOMATE_OK_CO2:y

Name of ORCHIDEE's executable (to be localized at [orHOME] folder from [codeHOST]) 

# Name of the exectuable
nameEXEC=orchidee_ol

':' separated list of netCDF file names from ORCHIDEE's output which do not need to be kept 

# netCDF Files which will not be kept anywhere
NokeptfileNAMES=''

':' separated list of headers of netCDF file names from ORCHIDEE's output which need to be kept (NOTE: if one of these files does not exist, system will stop!) 

# Headers of netCDF files need to be kept
HkeptfileNAMES=sechiba_history:stomate_history:sechiba_history_4dim:sechiba_history_alma

':' separated list of headers of restarts netCDF file names from ORCHIDEE's output which need to be kept 

# Headers of netCDF restart files need to be kept
HrstfileNAMES=sechiba_rest_out:stomate_rest_out

ORCHIDEE off-line can not run with the parallel-netCDF. For that reason, output files are written for each computing node. At the end of the simulation they need to be concatenated with the tool flio_rbld (Already compiled in hydra). This is done automatically at the end of the simulation. (to be found at [codeHOST]) 

# Extras. rebuild program folder
binREBUILD = /share/modipsl_IOIPSLtools/bin

Parallel configuration of the run. NOTE: ORCHIDEE off-line can not be run using sharing memory 

# ORCHIDEE parallel run configuration
## Number of nodes
Nnodes = 1
## Number of mpi procs
Nmpiprocs = 16
## Number of shared memory threads ('None' for no openMP threads)
Nopenthreads = None
## Memory size of shared memory threads
SIZEopenthreads = 200M

Generic definitions 

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