Launching a suite of simulations with Job_FLUXNET_validation script

Job_FLUXNET_validation helps at running a suite of simulations ORCHIDEE over several Fluxnet sites. Typically, we can configure the length of each type of simulations (initialisation, full orchidee, teststomate, forcesoil, final) and the number of times we iterate on (full orchidee, teststomate, forcesoil).
In addition, for each FLUXNET site, the user can re-specify any "paremeter" he want (the main parameter to define being VEG_MAX).

Where is Job_FLUXNET_validation located ?

Job_FLUXNET_validation is under modipsl/config/ORCHIDEE_OL/FLUXNET dir.

What does FLUXNET dir contain ?

• config.card : information on Job Name, Tag Name, Dates and Restart.
• fluxnet.card configures the list of FLUXNET sites (type and associated parameters)
• PARAM/orchidee.def, the parameter file of ORCHIDEE
• atlas_FLUXNET.cfg (used for the post-treatment)
• The script "install"
• The scripts fluxnet.ksh and post_FLUXNET
• run.card.init

How to install Job_FLUXNET_validation ?

• If not done yet, first type under "util" dir :

  my_prompt>> ./ins_job 
  

  It will create Job_Sp (where Sp is the Job Name specified in config.card)
• Then, to create Job_FLUXNET_validation and Job_Post_FLUXNET (used for the post-treatment), under "FLUXNET" dir type

  my_prompt>> ./install
  

How to configure the Job_FLUXNET_validation script

In order to configure the script, you need to fill the fluxnet.card file.

Standard parameters to be filled into fluxnet.card

• FluxnetPath specifies the location where are stored the meteorological input files for each FLUXNET site.
• NbSitesParam specifies the number of parameters to modify per PFT for each site
• NameSitesParam specifies the name of the parameters to modify per PFT for each site (as it appears in the .def files)
• CompSitesParam specifies the name of the component for each parameter described in NameSitesParam (either, SECHIBA, STOMATE, or DRIVER)
• Sites is a list of parameter values fill for each FLUXNET sites. The four first parameters are Name (used as site Id), Forcing file (files stored being Fluxnetpath being of the type "Forcing file".nc), Initial Year, Number of years in forcing file. The following parameters are those defined by NameSitesParam.
• Initial step: set to a positive value either "duree_nostomate" (initialisation without stomate component), "duree_inistomate" (initialisation with stomate component) or "duree_offlineini" (initialisation with teststomate)
• Loop over ORCHIDEE runs:
  • n_iter, the whole job is restarted n_iter times
  • duree_sechiba, orchidee with sechiba (and stomate if ok_stomate=y below)
  • duree_stomate, length of teststomate runs
  • duree_carbonsol, length of forcesoil runs
• Final step: specify the length of the final run with the parameter "duree_final"
• Under the [UserChoices] section, the user specifies the main configurations of ORCHIDEE
  • To activate/desactivate stomate => ok_stomate=y/n
  • To activate/desactivate photosynhesis calculation => ok_co2=y/n
  • To activate/desactivate the new hydrology scheme (deRosnay) => ok_newhydrol=y/n
• Under the [SubJobParams] section, the user can specify any parameter to be modified in sechiba.def, stomate.def or driver.def

Optional parameters of fluxnet.card

IMPOSE_SOILT, a new flag of ORCHIDEE

Previously, when the flag IMPOSE_VEG was activated (set to TRUE, as it is required for running ORCHIDEE on Fluxent sites), the clay_fraction was automatically read into the .def file. Because on Fluxnet sites, the texture is not necessary known, there is now the possibility to read the clay_fraction from the SOIL map even when IMPOSE_VEG is set to TRUE. The configuration is now the standard one when IMPOSE_VEG=TRUE. To read the clay fraction from .def, you now need to set the new flag IMPOSE_SOILT to TRUE. Here below is an example of a fluxnet.card for sites over which we know the texture.

[FLUXNET]
#**** Information on the sites to be treated *************************
#  Number of parameters to modify for each site
NbSitesParam= 2
#  Name of the parameters to modify for on each site
NameSitesParam= ( SECHIBA_VEGMAX , CLAY_FRACTION)
#  Name of the component for each parameter described in NameSitesParam (either, SECHIBA, STOMATE, or DRIVER)
CompSitesParam= ( SECHIBA , SECHIBA )

# Sites descriptions
# 4 first parameters are Name, Forcing file, Initial Year, Number of years in forcing file
# following parameters are NameSitesParam
Sites= ( NL-Loo, NL-Loo.nc,  1996, 11, \
     0,   0,   0, 0.8,   0,   0,   0,   0,   0, 0.2,   0,   0,   0 , \
     0.2 )
\
       ( DE-Hai, DE-Hai.nc,  2000,  7, \
     0,   0,   0,   0,   0, 0.8,   0,   0,   0, 0.2,   0,   0,   0 , \
     0.4 )

[UserChoices]
sechiba_IMPOSE_SOILT = y

Option CONSERVE into fluxnet.card

If you want to keep the history files of all simulations ran by the Job_FLUXNET_Validation script, set to yes (CONSERVE=y) the flag CONSERVE, else set it to no (CONSERVE=n).

How to use it ?

my_prompt>> ksh
my_prompt>> nohup ./Job_FLUXNET_validation > out_Job 2>&1 &

Requirement

On Obelix, you need to have a passphrase for connecting to obelix when launching automatically new jobs.
Type, first

my_prompt>> ssh-keygen -t rsa -N ""

Then,

my_prompt>> cp id_rsa.pub authorized_keys

or, if the file "authorized_keys" already exists:

my_prompt>> cat id_rsa.pub >> authorized_keys