Changes between Version 16 and Version 17 of Documentation/UserGuide/FLUXNETValidation

Timestamp:

2019-12-12T09:29:53+01:00 (5 years ago)

Author:

mmcgrath

Comment:

Refining the instructions to work from a fresh svn install...not yet there

Documentation/UserGuide/FLUXNETValidation

@@ -69 +69 @@
 17) SPIN_OptionsStomate from ${}/COMP/spinup.driver sets the values of SPINUP_ANALYTIC, TimeSeriesVars3D and TimeSeriesVars2D in ${}/STOI/COMP/sechiba.card, as well as the values of FORCESOIL_STEP_PER_YEAR, STOMATE_FORCING_NAME, and STOMATE_CFORCING_NAME in ${}/STOI/PARAM/run.def.
 18) Execute the STOI run
+
+Sometimes, the scripts replace variables by values found in the various .card and .def files.  Othertimes, the variables are added onto the end.  This distinction is important if you get an error saying that a variable appears multiple times.
 
 == Practical steps  ==
@@ -215 +217 @@
 NINPUT_UPDATE=0Y
 NINPUT_SUFFIX_YEAR = n
+
+(remove the following lines, otherwise ORCHIDEE will not find a land point for any site outside of this window)
+LIMIT_WEST=8
+LIMIT_NORTH=48
+LIMIT_SOUTH=46
+LIMIT_EAST=10
+
 }}}
 
@@ -317 +326 @@
 (make sure the following are in run.def and not in orchidee.def)
 
+STOMATE_IMPOSE_CN = _AUTO_
 SECHIBA_restart_in = _AUTOBLOCKER_
 STOMATE_RESTART_FILEIN = _AUTOBLOCKER_
@@ -329 +339 @@
 STOMATE_OK_STOMATE = _AUTOBLOCKER_ 
 NINPUT_UPDATE = _AUTO_
+
+(now copy the files)
+cp PARAM/*def ../SPINUP/SUBJOB/OOL_SEC_STO/PARAM/
 }}}
 Notice that SPINUP_PERIOD and SPINUP_ANALYTIC had to be deleted from orchidee.def, but we already had them in run.def since we copied them from fluxnet.card.
 
 Note that we can not use the analytical spinup at the present.  In order to use the analytical spinup, we need to make sure CyclicBegin and CyclicEnd appear in the ${}/STOI/config.card, as ${}/STOI/COMP/stomate.card checks for these values.  I have not yet figured out how to do that.
+
+Some variables appear in fluxnet.card, but they are also special variables having an AUTO value in orchidee.def (that we moved to param.def).  Therefore, remove the following lines from FLUXNET/fluxnet.card and PARAM/run.def (if they exist).  We remove the _AUTO_ value of SPINUP_PERIOD since we attempt to calculate that in an automatic way using
+a different variable in Job_ENSEMBLE, as opposed to in SPINUP/COMP/spinup.driver.
+{{{
+NINPUT_UPDATE=0Y
+SPINUP_ANALYTIC=y
+SPINUP_PERIOD = _AUTO_
+XIOS_ORCHIDEE_OK=n
+
+(now copy the file)
+cp PARAM/run.def ../SPINUP/SUBJOB/OOL_SEC_STO/PARAM/
+}}}
 
 Launch the job (from the README file).
@@ -458 +483 @@
 which leads to libIGCM getting confused.  The solution is to replace "10Y" in the line above with "NONE".  You must then go into the config/ORCHIDEE_OL/SPINUP directory, remove the Job_JOBNAME file, and redo the ../../../libIGCM/ins_job command to create a new Job_JOBNAME file. 
 
+Another error:
+{{{
+IGCM_debug_Exit :  IGCM_comp_modifyDefFile : Error in run.def: Variable=STOMATE_HIST_DT is set 2 times
+}}}
+Either you added a variable to FLUXNET/PARAM/run.def and forgot to delete it from FLUXNET/PARAM/orchidee.def or FLUXNET/PARAM/orchidee_pft.def_28pft.1ac, OR the variable appears in FLUXNET/PARAM/*def and it gets added to the run.def by the ensemble (doesn't appear to be possible, even if there is a line written in the run.def indicating it happens...the script crashes if the option doesn't already exist) or spinup (SubJobParams in ${}/COMP/spinup.card or ${}/COMP/spinup.driver).
+
 == Cleaning ==
 If an ENSEMBLE run crashes, it can sometimes be difficult to clean up all the files so that you can easily relaunch the run after figuring out what went wrong.  In particular, each site creates a new directory, which can add up to a lot of directories.  It's possible that some of your runs overlap, too (i.e., they use the same base directory, but the current run only uses forested sites, while a different run used agricultural sites).  There may be a libIGCM tool that does this well, but if you aren't familiar with it, here is a short script that works.  Copy it to your submission directory (i.e., where you launch the ./Job_ENSEMBLE script), make it executable (e.g., chmod +x clean.sh), and launch it before re-launching the run (e.g., ./clean.sh).