Changes between Version 41 and Version 42 of DevelopmentActivities/ORCHIDEE-CNP/howtoFLUXNET

Timestamp:

2016-08-11T03:40:44+02:00 (8 years ago)

Author:

dgoll

Comment:

--

DevelopmentActivities/ORCHIDEE-CNP/howtoFLUXNET

@@ -308 +308 @@
 3. modify fluxnet.card following [http://forge.ipsl.jussieu.fr/orchidee/wiki/Scripts/FluxnetValidation]
 
+
+== 1.5 create job ==
+{{{
+../../../libIGCM/ins_job
+}}}
+
+== 1.6 adjust job  ==
+
+'''on obelix'''
+Change the queue to longp to increase the wallclock time (the default queue mediump is too short for this setting and you will exceed wall clock time).
+'''WARNING:''' In case you have set level_hist=10 (fluxnet.card) you need to take the extra long queue:
+{{{
+#PBS -q longp
+}}}
+
+
+If you want to debug on obelix: set the variable RUN_DIR_PATH to disk with enough space (the default path is not accessible for the user)
+{{{
+# for example on scratch01
+RUN_DIR_PATH=/home/scratch01/dgoll/RUN_DIR
+}}}
+ACHTUNG: On curie, do not set RUN_DIR_PATH in the Job_*. If you do, the configuration will crash. You find the default path to the RUN_DIR_PATH in the section "3.2.8 check simulations".
+
+
+== 1.7 start simulations ==
+{{{
+ksh
+nohup ./Job_ENSEMBLE fluxnet > out_Job 2>&1 &
+}}}
+
+== 1.8 check simulations ==
+to see the decomposition of the spatial domain among the processors check in the run dir "Load_balance_orchidee.dat"
+'''on curie'''
+The RUN_DIR is in 
+{{{
+/ccc/scratch/cont003/dsm/<userid>/RUN_DIR
+}}}
+
+to check the status of the job; type
+{{{
+ccc_mstat -u <userid>
+}}}
+to delete a job; type
+{{{
+ccc_mdel <jobid>
+}}}
+=== 1.8.1 what to do when a simulation crash ===
+You cannot use clean_month and clean_year. You should remove the sites that crashed from the IGCM_OUT path
+and rerun the same experiment with a fluxnet.card containing only the sites which crashed.
+
+
+== 1.9 post processing ==
+ensure the Jobname and the path to the reference simulation is set in fluxnet.card; in case there is no reference set it to NONE
+{{{
+# History file of former ORCHIDEE runs (Reference) to compare with the current simulations
+reference_base_path=/home/scratch01/dgoll/IGCM_OUT/OL2/DEVT/ensemble
+reference_config=DSG04EnsCN
+}}}
+start the skript
+{{{
+ksh
+nohup ./Job_Post_FLUXNET fluxnet > out_Post 2>&1 &
+}}}
+you will find the graphics in the experiment folder in the IGCM_OUT path. There is a pdf in the folder starting with "fluxnet_taylor_diff".
+
+
+== OPTIONAL FEATURES ==
+=== specify the name of the exectuable of orchidee ===
+If you want to use different version of the orchidee_ol which you store in modipsl/bin you have to do the following:
+add the following line to the [Executable] section in ../SPINUP/config.card
+{{{
+OOL=(orchidee_ol, orchidee_ol)
+}}}
+add the following line to Job_ENSEMBLE; make sure it is exactly at this spot (before # Give path for ...):
+{{{
+IGCM_card_WriteOption ${New_SUBMIT_DIR}/config.card Executable OOL ${config_Executable_OOL}
+
+# Give path for all skeleton SubJob scripts to SPINUP directory
+IGCM_card_WriteOption ${New_SUBMIT_DIR}/COMP/spinup.card UserChoices SubJobPath ${Skeleton_Path}
+}}}
+At the moment I cannot figure out how to set the variable ${config_Executable_OOL} according to the config.card; thus I hardcode the name in Job_ENSEMBLE for the moment:
+{{{
+IGCM_card_WriteOption ${New_SUBMIT_DIR}/config.card Executable OOL "(my_orchidee_ol, orchidee_ol)"
+}}}
+PROBLEM: although my_orchidee_ol is not present in modipsl/bin a orchidee_ol is present in the RUN_DIR.
+
+=== output for the spinup simulations === 
 In case you want to check if the spinup works well, increase output level of the spinup simulations & prevent libIGCM from removing these files.
 The files can be found in the respective site folders in the experiment folder.
@@ -327 +414 @@
 }}}
 You find the files in the folder "JobName"STOI in the IGCM_OUT path for the STOI simulation. Exchange "STOI" with "ORC-1", "FIN" etc for the simulations you want to check.
-
-== 1.5 create job ==
-{{{
-../../../libIGCM/ins_job
-}}}
-
-== 1.6 adjust job  ==
-
-'''on obelix'''
-Change the queue to longp to increase the wallclock time (the default queue mediump is too short for this setting and you will exceed wall clock time).
-'''WARNING:''' In case you have set level_hist=10 (fluxnet.card) you need to take the extra long queue:
-{{{
-#PBS -q longp
-}}}
-
-
-If you want to debug on obelix: set the variable RUN_DIR_PATH to disk with enough space (the default path is not accessible for the user)
-{{{
-# for example on scratch01
-RUN_DIR_PATH=/home/scratch01/dgoll/RUN_DIR
-}}}
-ACHTUNG: On curie, do not set RUN_DIR_PATH in the Job_*. If you do, the configuration will crash. You find the default path to the RUN_DIR_PATH in the section "3.2.8 check simulations".
-
-
-== 1.7 start simulations ==
-{{{
-ksh
-nohup ./Job_ENSEMBLE fluxnet > out_Job 2>&1 &
-}}}
-
-== 1.8 check simulations ==
-to see the decomposition of the spatial domain among the processors check in the run dir "Load_balance_orchidee.dat"
-'''on curie'''
-The RUN_DIR is in 
-{{{
-/ccc/scratch/cont003/dsm/<userid>/RUN_DIR
-}}}
-
-to check the status of the job; type
-{{{
-ccc_mstat -u <userid>
-}}}
-to delete a job; type
-{{{
-ccc_mdel <jobid>
-}}}
-=== 1.8.1 what to do when a simulation crash ===
-You cannot use clean_month and clean_year. You should remove the sites that crashed from the IGCM_OUT path
-and rerun the same experiment with a fluxnet.card containing only the sites which crashed.
-
-
-== 1.9 post processing ==
-ensure the Jobname and the path to the reference simulation is set in fluxnet.card; in case there is no reference set it to NONE
-{{{
-# History file of former ORCHIDEE runs (Reference) to compare with the current simulations
-reference_base_path=/home/scratch01/dgoll/IGCM_OUT/OL2/DEVT/ensemble
-reference_config=DSG04EnsCN
-}}}
-start the skript
-{{{
-ksh
-nohup ./Job_Post_FLUXNET fluxnet > out_Post 2>&1 &
-}}}
-you will find the graphics in the experiment folder in the IGCM_OUT path. There is a pdf in the folder starting with "fluxnet_taylor_diff".
-
-
-== OPTIONAL FEATURES ==
-=== specify the name of the exectuable of orchidee ===
-If you want to use different version of the orchidee_ol which you store in modipsl/bin you have to do the following:
-add the following line to the [Executable] section in ../SPINUP/config.card
-{{{
-OOL=(orchidee_ol, orchidee_ol)
-}}}
-add the following line to Job_ENSEMBLE; make sure it is exactly at this spot (before # Give path for ...):
-{{{
-IGCM_card_WriteOption ${New_SUBMIT_DIR}/config.card Executable OOL ${config_Executable_OOL}
-
-# Give path for all skeleton SubJob scripts to SPINUP directory
-IGCM_card_WriteOption ${New_SUBMIT_DIR}/COMP/spinup.card UserChoices SubJobPath ${Skeleton_Path}
-}}}
-At the moment I cannot figure out how to set the variable ${config_Executable_OOL} according to the config.card; thus I hardcode the name in Job_ENSEMBLE for the moment:
-{{{
-IGCM_card_WriteOption ${New_SUBMIT_DIR}/config.card Executable OOL "(my_orchidee_ol, orchidee_ol)"
-}}}
-PROBLEM: although my_orchidee_ol is not present in modipsl/bin a orchidee_ol is present in the RUN_DIR.
-