This was tested for ORCHIDEE-CN-CAN (r5678 of ORCHIDEE and r5673 of ORCHIDEE_OL) on obelix.

First, look at Nicolas's page.

​http://forge.ipsl.jussieu.fr/orchidee/wiki/Scripts/FluxnetValidation

And then look at the README file in config/ORCHIDEE_OL/ENSEMBLE.

Be sure you have checked out both CN-CAN modeles/ORCHIDEE and config/ORCHIDEE_OL (Documentation/UserGuide/ORCHIDEEDOFOCOInstall).

Be sure that ioipsl_debug=.FALSE. in modeles/IOIPSL/src/errioipsl.f90. Otherwise, the output files become huge because of the high frequency writes combined with the debug information.

Start from a clean SVN ENSEMBLE install. Notice that ENSEMBLE/Job_ENSEMBLE is the main driver, and it should not be deleted! This is what I refer to when I say "Nicolas's FLUXNET scripts". It will create jobs based on SPINUP/SUBJOB/OOL_SEC_STO/.

I have found the following files are used. Care should be made to make sure that conflicting options are not specified in these files (assuming you are running analytical spinup, sechiba, and stomate):

ENSEMBLE/fluxnet.card
ENSEMBLE/PARAM/run.def
SPINUP/COMP/spinup.card
SPINUP/SUBJOBS/OOL_SEC_STO/COMP/sechiba.card
SPINUP/SUBJOBS/OOL_SEC_STO/COMP/stomate.card

I am uncertain what the priority is. All of the .card files add things onto the end of the run.def, and I believe fluxnet.card takes priority over the others in case of conflict.

I have noticed that the script will complain if a value is specified in fluxnet.card but not the run.def. It will not complain if a value is specified in run.def and not fluxnet.card. Check the [UserChoices?] and [SubJobParams?] sections of fluxnet.card. Many of the UserChoices? are already in SPINUP/COMP/spinup.card, and many of the SubJobParams? are in the run.def. It seems that the scripts make decisions based on what is in fluxnet.card, so this should typically take precedence.

Before we get to some specifics, let's create the jobs.

cd config/ORCHIDEE_OL/ENSEMBLE
vi config.card

Change the following lines (on obelix...on Irene, the ARCHIVE line should be fine):

JobName=FLUXNET
  ARCHIVE=/home/scratch01/$LOGIN

then create the job scripts

../../../libIGCM/ins_job

this creates Job_FLUXNET. Notice that this job will pull from the SPINUP directory as well. ins_job used to create Job files in every directory, but that functionally changed a while ago. Therefore, the following is now necessary (OOL_SEC_STO because we will run a job with sechiba and stomate).

cd ../SPINUP
../../../libIGCM/ins_job
cd SUBJOB/OOL_SEC_STO/
../../../../../libIGCM/ins_job
cd ../../../ENSEMBLE

Now edit the Job file. Notice that this is the Job file that is copied to all the subjobs when they run, so if you want them to run on a different queue (I use the long queue on obelix, as 500 years can take more than 12 hours), you should do that here. I also modify the run directory so I know where the jobs are running and can go to that directory easily if needed.

vi Job_FLUXNET
(change RUN_DIR_PATH=/home/scratch01/mmcgrath/RUN_DIR)
(change JobType=DEV if you are not sure this will work)
mkdir /home/scratch01/mmcgrath/RUN_DIR

Now change the options for the sites to run against.

vi fluxnet.card

Best to run a small test with a single site. If you are running with age classes (not recommended) or any number of PFTs other than the standard 13 in ORCHIDEE, you will need to change the following:

  NbPFTs= 13
  Groups= ( TEST )
  TEST =	   ( BR-Sa3 , BR-Sa3_2000-2003.nc , 2000 , 4 , 0,1,0,0,0,0,0,0,0,0,0,0,0 ) 

If you have 13 PFTs, you can add the above lines just as they are. COMMENT OUT ANY OTHER GROUPS LINES. Else, when you submit the job, you will launch a run over all of the sites in groups, and you have to cancel them one at a time.

The length of the spinup also matters. I use the following for the moment (in fluxnet.card, also in SPINUP/spinup.card)

n_iter=1
duree_inistomate=1
duree_sechiba=500
duree_final=1

All of the other duree values I set to 0. This launches a simulation over one loop of the forcing file, then 500 years (regardless of the length of the forcing file), and then one final loop for analysis.

The following directories are used in the runs (from what I can tell):

ENSEMBLE/PARAM/
SPINUP/COMP/
SPINUP/SUBJOBS/OOL_SEC_STO/COMP/

Therefore, we need to copy the CN-CAN run.def that we want to use (strongly advise 13 MTC with no age classes) to one of these directories. XXXXXX is the run.def file from whatever configuration directory you have that is currently working. Note that you also need to copy the COMP directory of one of the working CN-CAN directories (e.g., SPINUP_ANALYTIC_FG1, OOL_SEC_STO_FG1trans,OOL_SEC_STO_FG2to) to SPINUP/SUBJOBS/OOL_SEC_STO/COMP).

   cp ../OOL_SEC_STO_FG2/PARAM/run.def ../ENSEMBLE/PARAM/   (for the run.def...this one is not 13 MTCs, though)
   cp ../OOL_SEC_STO_FG2/COMP/* ../SPINUP/SUBJOBS/OOL_SEC_STO/COMP/

We need to make sure all of the following lines are commented out (or do not exist in the run.def), since the script will change the vegetation for each site by adding lines at the end of the run.def and if these lines are present they will override them:

SECHIBA_VEG__01=0.0769230769231
...
SECHIBA_VEGMAX__01=0.0769230769231
  ...

Make sure the following line is in the run.def.

IMPOSE_VEG=y

Also confirm that IMPOSE_VEG is not set in another of the files above. Another line that may be needed is:

ATM_CO2 =_AUTO_: DEFAULT = 350.

In some versions of the run.def, no DEFAULT value is given, but the .driver expects a default and will crash if it's not there.

The scripts expect some variables in SPINUP/SUBJOBS/OOL_SEC_STO/COMP/sechiba.card, and will crash if you don't have them. It tries to change them (perhaps based on fluxnet.card) and gives up if it doesn't find them in sechiba.card to change.

[UserChoices]
NEWHYDROL=y
ROUTING=n
LAIMAP=n
IMPOSE_VEG=y
LAND_USE=n
OKCO2=y
CO2varying=n

Something similar in SPINUP/SUBJOBS/OOL_SEC_STO/COMP/orchidee_ol.card

[UserChoices]
NORESTART=n
TIMELENGTH=y

If we turn off XIOS, we have a couple variables undeclared in IOIPSL, so it crashes. Instead, let's leave XIOS on and include the following hack for it to find the iodef.xml file. Note that you will have to change this path!

        (/home/orchidee03/mmcgrath/MYFOLDER/config/ORCHIDEE_OL/SPINUP_ANALYTIC_FG1/PARAM/iodef.xml, .)   ,\

And change the following "blocker" to "nonblocker" in SPINUP/SUBJOBS/OOL_SEC_STO/COMP/sechiba.driver, since we want to let fluxnet.card control options (since it makes choices of which directories to copy based on the contents of fluxnet.card, not the contents of run.def).

        IGCM_comp_modifyDefFile blocker run.def STOMATE_OK_STOMATE y
	IGCM_comp_modifyDefFile blocker run.def STOMATE_OK_STOMATE n

Launch the job (from the README file).

   ./Job_ENSEMBLE fluxnet > out.Job_ENSEMBLE

BE SURE TO CHECK THE USED RUN.DEFs. These can be found by changing to the RUN_DIR when the job is running. The scripts will add flags to the end of the run.def, and sometimes these may conflict with what you want to run.