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Using libIGCM library with ORCA2_LIM

Purposes:

• Document the using of libIGCM for NEMO, in configuration ORCA2_LIM

Quick start guide:

• Define the following alias to use SVN :
  

   alias svn_ano='svn co http://forge.ipsl.jussieu.fr/igcmg/svn/modipsl/trunk modipsl'
  

• Create and go into working directory :
  

   mkdir TRY ; cd TRY
  

• Extract modipsl :
  

   svn_ano 
  

• Extract NEMO :
  

   cd modipsl/util 
   ./model NEMO_IGCM 
  

• Choosing ORCA2_LIM configuration :
  

   cd ../modeles/UTIL
   ./fait_config ORCA2_LIM
  

• Install the makefiles :
  

   cd ../../util 
   ./ins_make
  

• Compile :
  

   cd ../config/ORCA2_LIM 
   gmake
  

• Submit Job :
  

   ( Editing at this point modipsl/config/ORCA2_LIM/IGCM00/config.card )
  
   ../../util/ins_job
   cd IGCM00 
   qsub Job_NL1  
  

Set up a simulation:

• First of all see official documentation

​http://forge.ipsl.jussieu.fr/libigcm/wiki/

• All parameters in config.card file

In modipsl/config/ORCA2_LIM/IGCM00/config.card file you can set all parameters to manage your experience:

How to manage restart files ( in the same simulation )

in config.card you have to set duration of your experience and setting PeriodLenght parameter, so you create restart files.

( for example : if you have and experience of 10 years and a PeriodLenght of 1 year, you will have 10 restart files )

#-- Début et fin de Job
#-- "YYYY-MM-DD"
DateBegin?=2001-01-01
DateEnd?=2010-12-31
#============================
#-- 1Y, 1M, 5D, 1D
PeriodLength?=1Y

Note : If you want to use restart data from another simulation ( already run not in this moment ) you have to manage "Restarts" part of config.card

#================
#D-- Restarts -
[Restarts]

How to manage write output frequency

in config.card you have to set WriteFrequency of your experience

( for example : if you want output files every 1 month you have to put for Ocean

#===================
#D-- OCE -
[OCE]
WriteFrequency?="1M"

and if you want output files every 1 month you have to put for ICE

#===================
#D-- ICE -
[ICE]
WriteFrequency?="1M"

)

How to manage calendar type

in config.card you have to set CalendarType like 360d or leap or noleap

( for example : if you want 360 days you have to be careful of

DateEnd?=2010-12-30

because every month has 30 days

If you put for example DateEnd?=2005-12-31, you will have another run, of duration like your PeriodLenght )

How to manage rdt ( i.e. timestep )

in COMP/nemo.driver you have to change parameter : ORCA_NPDT_JOUR=15

( 15 corresponds to 86400s/5760s; it does mean that in one day you have 15 iterations; and it does mean that timestep is 5760)

How control all parameters in modipsl/config/ORCA2_LIM/IGCM00/PARAM/namelist

libIGCM change namelist's values but not in namelist's file, so it is possible to control all changes of namelist's parameters looking at :

{OUTPUT_DIR}/IGCM_OUT/ORCA2_LIM/N360d_5d/OCE/Debug/!JobName_date_date_ocean.output

How to activate Monitoring

in config.card file

#D- If you want to produce time series, this flag determines #D- frequency of post-processing submission TimeSeriesFrequency?=NONE

you have to put you experience lenght. If you do an experience during 10 years you have to put:

TimeSeriesFrequency?=10Y

How to activate Atlas

in config.card file

#D- If you want to produce seasonal average, this flag determines #D- the period of this average SeasonalFrequency?=NONE

you have to put you experience lenght. If you do an experience during 10 years you have to put:

SeasonalFrequency?=10Y

How to manage frequency of post processing

( Note: in this moment is not possible to have atlas and monitoring of frequency different from 1M, if we want this we've to see it with Patrick Brockman!! )

in COMP/nemo.card you have to change in [OutputFiles?] chapter:

Post_1M_grid_T (U,V,W)

and you have to change [Post_1M_grid_T(U,V,W)] chapter.

and in in COMP/lim2.card you have to change in [OutputFiles?] chapiter:

List= (${PREFIX_NWRITE}_${DATE_OPA}_icemod.nc, ${R_OUT_ICE_NWRITE}/${PREFIX}_${WF1}_icemod.nc, Post_1M_icemod)

and you have to change [Post_1M_icemod] chapter.

• How to make a parallel run

first of all add a cpp key:

​http://www.nemo-ocean.eu/index.php//Using-NEMO/User-Guides/Advanced/How-to-add-modify-new-modules-or-new-cpp-keys

and then see: ​http://www.nemo-ocean.eu/index.php//Using-NEMO/User-Guides/Advanced/How-to-set-up-one-simulation#eztoc1210_5

• How to have mail of end of Job, sur ccrt's machines

on mercure: in Job_Name: #PBS -M name@mail

on platine: In Job_Name: #BSUB -u name@mail

• How to activate particular key cpp

(if not for example we have this error:

WARNING : IGCM_sys_Put_Out xxx_trends.nc DOES NOT EXIST
WARNING : IGCM_sys_Put_Out xxx_diagap.nc DOES NOT EXIST
WARNING : IGCM_sys_Put_Out output.abort.nc DOES NOT EXIST )

Run only post processing:

• If you have already run a job and you need only to run post processing

you have to move Script_Output.xxx

in Job_Name you have to change:

#PBS -l cputim_job=4:00:00 # Limite temps
DRYRUN=3

List of possible errors in modipsl/config/ORCA2_LIM/IGCM00/Script_Output_JobName :

• Error : TERM = (vt100) ${HOME:-.}/.profile: .bashrc: not found
• Error : ksh: D-----------------------------------==: not found

it can depends on .profile file.

To solve it

.profile file it can be like:

«# .profile (idris)
# Fichier d environnement a charger sur la frontale TX7 unix LINUX
# Vous pouvez mettre a jour le fichier .profile_tx
if [ `hostname!` = "brodie" -a -f $HOME/.profile_tx ]; then
. $HOME/.profile_tx
# Fichier d environnement a charger sur les noeuds SX8 unix SUPER-UX
# Vous pouvez mettre a jour le fichier .profile_sx
elif [ `hostname!` != "brodie" -a -f $HOME/.profile_sx ]; then
. $HOME/.profile_sx
else
echo
fi »

• Error : cat: cannot open ........./modipsl/config/ORCA2_LIM/IGCM00/../.resol :

it is due to modipsl/libIGCM/AA_job file.

To solve it

change in this way:

#-- Resolution FLAG for oasis input
#RESOL=$(cat ${SUBMIT_DIR}/../.resol)
RESOL=ORCA2

NOTE: Be careful because this is ok for ORCA2, but if we use ORCA0.5 ore ORCA0.25 is NOT TRUE!!!!'''

go in modipsl/config/ORCA2_LIM/IGCM00 directory

cancel run.card.init and Job_Name files

and then do an ins_job again.

(does not still fixed in libIGCM_v1_2)

• Error : Input files and BC for NEMO DO NOT EXIST (i.e. sst_data.nc, sss_data.nc, geothermal_heating.nc, bathy_level.nc, etc...)

IGCM_sys_Get, ERROR : regular file ...../OCE/ORCA2_LIM/bathy_level.nc DOES NOT EXIST .

To solve it

In this moment we've still to download on gaya.idris.fr:~/!reee512/NEMO/ORCA2_LIM_nemo_v3.tar file, and to untar it into the directory:

${R_BC}/OCE/ORCA2_LIM

and where ${R_BC} is a variable that can be changed in modipsl/config/ORCA2_LIM/IGCM00/config.card file.

• Error : IGCM_debug_Exit : IGCM_config_Initialize Error PeriodState : Fatal

To solve it

change line in modipsl/config/ORCA2_LIM/IGCM00/run.card

PeriodState=Fatal
in
PeriodState=

or rm modipsl/config/ORCA2_LIM/IGCM00/run.card

• ls: ERROR: Cannot access stack: No such file or directory

in Script_Outputxxx:

( is it a problem with filemane? )

IGCM_sys_Put_Out : out_nemo /dmnfs13/cont003/flavoni/IGCM_OUT/ORCA2_LIM/N365d_5d/Out/N365d_5d_20030101_20031231_out_nemo
IGCM_sys_MkdirArchive : /dmnfs13/cont003/flavoni/IGCM_OUT/ORCA2_LIM/N365d_5d/Out
IGCM_sys_Chmod : 444 out_nemo
--Debug1--> OCE
--Debug1--> ICE
Files that will be deleted before next period-run :
ls: ERROR: Cannot access stack: No such file or directory
-r--r--r-- N365d_5d_00016425_restart.nc
-r--r--r-- N365d_5d_00016425_restart_ice.nc

(no ok still with libIGCM_v1_2)

List of possible remarks and suggestions :

• be careful at group (for example for a gensi one)

if we use a common account on CCRT we have to be sure that everygroup can have access to it, this is important for chmod 444, do another test!!!!!!

• Every time that we change modipsl/config/ORCA2_LIM/IGCM00/config.card

we have to cancel modipsl/config/ORCA2_LIM/IGCM00/run.card.init

cancel modipsl/config/ORCA2_LIM/IGCM00/Job_Name

and run ./modipsl/util/ns_job script

• To perform a second simulation after a run with PeriodState=Fatal

cancel modipsl/config/ORCA2_LIM/IGCM00/stack_error, modipsl/config/ORCA2_LIM/IGCM00/Script_Output_JobName

but do not cancel modipsl/config/ORCA2_LIM/IGCM00/run.card.init file, if not run.card file is not re-created.

( File run.card.init is created with ins_job script )

• Does it exists a caption file for run.card.init options?

Or Is there a reference file?
In to run.card.init file who can we undesrtand syntax of? :

TimeSeriesRunning=n
TimeSeriesCompleted=

SeasonalRunning=n

• test tags/libIGCM_v1_2

Is it still true?: To use libIGCM trunk version it is necessary to add in config.card in POST Session:

RebuildFromArchive=NONE

• Change in nemo.card or in nemo.driver variable: ORCA_NPDT_JOUR and OPA_NPDT_JOURS

Done :

• run on CCRT machines ( mercure )

Tests for Calendar Type, Output frequency and Restarts:

Simulation environment

#- Repository informations
#-
#-S- 1 cvs anonymous@cvs.ipsl.jussieu.fr:/home/ioipsl/CVSROOT
#-S- 2 cvs sechiba@cvs.ipsl.jussieu.fr:/home/ssipsl/CVSREP
#-S- 3 cvs lmdzbrowse@cvs.lmd.jussieu.fr:/home/cvsroot
#-S- 4 cvs opa@cvs.ipsl.jussieu.fr:/home/opalod/CVSROOT
#-S- 5 cvs nemo@cvs.ipsl.jussieu.fr:/home/opalod/NEMOCVSROOT
#-S- 6 cvs inca@cvs.ipsl.jussieu.fr:/home/incaipsl/CVSROOT
#-S- 7 svn --username nemo_user http://forge.ipsl.jussieu.fr/nemo/svn
#-S- 8 svn http://forge.ipsl.jussieu.fr/igcmg/svn
#-S- 9 svn http://forge.ipsl.jussieu.fr/inca/svn
#-S- 10 svn http://forge.ipsl.jussieu.fr/libigcm/svn

#-H- NEMO_IGCM NEMO
#-H- NEMO_IGCM OPA
#-H- NEMO_IGCM LIM
#-H- NEMO_IGCM TOP
#-H- NEMO_IGCM IOIPSL/src - svn - tag v2_1_4
#-H- NEMO_IGCM libIGCM - svn -
#-H- NEMO_IGCM NEMO sources and configurations - svn - trunk
#-M- NEMO_IGCM opatlod@locean-ipsl.upmc.fr
#-C- NEMO_IGCM IOIPSL/tags/v2_1_4/src HEAD 8 IOIPSL/src modeles
#-C- NEMO_IGCM trunk/libIGCM 47 10 libIGCM .
#-C- NEMO_IGCM tags/nemo_v3_1_beta/NEMO HEAD 7 . modeles
#-C- NEMO_IGCM tags/nemo_v3_1_beta/UTIL HEAD 7 . modeles
#-C- NEMO_IGCM tags/nemo_v3_1_beta/CONFIG/GYRE_LOBSTER HEAD 7 GYRE_LOBSTER config
#-C- NEMO_IGCM tags/nemo_v3_1_beta/CONFIG/ORCA2_LIM HEAD 7 ORCA2_LIM config
#-C- NEMO_IGCM branches/libIGCM/ORCA2_LIM/IGCM00 HEAD 7 IGCM00 config/ORCA2_LIM

Simulation duration = 5 year

PeriodLength = 1Y

timestep: rdt = 5760 equivalent to ORCA_NPDT_JOUR = 15

		Output Frequency	Output Frequency	Output Frequency
		5d	1M	1Y
Calendar Type	360d	ok	ok	ok
Calendar Type	365d	ok	ko	ok
Calendar Type	leap	ok	ko	to do

ko = there are only 11 output ( point how NEMO do averadge for every month )

NOTE: control in:

• why in /dmnfs13/cont003/flavoni/IGCM_OUT/ORCA2_LIM/N360d_1m/OCE/Debug/*_ocean.output

Namelist namrun

job number no = 0

is EVER = 0????

N365d_1m_20011231_restart.nc

Control if file name is correct!!!! (my job is N365d_1m)

To do list :

• simulation=100Y ( ongoing with tags/libIGCM_v1_2 )
  periodlenght=10y
  and sortiee=1Y
  

• monitoring : ongoing on mercure/brodie for experience=10Y, PeriodLenght=1Y, WriteFrequency=1M

• atlas : ongoing on mercure/brodie for experience=10Y, PeriodLenght=1Y, WriteFrequency=1M

NOTE: changed COMP/nemo.card and set OutputFiles? and Post_xX_grid_T[U,V,W], where xX=WriteFrequency
NOTE: changed COMP/lim2.card and set OutputFiles? and Post_xX_grid_T[U,V,W], where xX=WriteFrequency

• test mpi

NOTE files to change (or changed) for NEMO :

• for 360d CalendarType? changed:

config/ORCA2_LIM/IGCM00/COMP/nemo.driver
and modipsl/modeles/NEMO/WORK/domain.F90

• modipsl/modeles/UTIL/fait_AA_make

difference with the old one:

in #- Compilation options ---

Committed: shade 10000 (for mercure)

• modipsl/libIGCM/AA_job

difference with the old one:
#RESOL=$(cat ${SUBMIT_DIR}/../.resol)
RESOL=ORCA2

• modipsl/modeles/NEMO/WORK/domain.F90

difference with the old one:

in line 171

WRITE(numout,*) ' leap year calendar (0/1/30) nleapy = ', nleapy

• modipsl/config/ORCA2_LIM/IGCM00/COMP/nemo.driver

difference with the old one:

added nleapy variable that corresponds to nbisex on opa.driver

# nleapy leap year calendar (0/1) (30 for 360d)

PAT_NLEAPY=$( supergrep nleapy ${SUBMIT_DIR}/PARAM/namelist )

in lines 141-151

case ${config_UserChoices_CalendarType} in

leap !|!| Gregorian)
ORCA_NLEAPY=1;;
noleap)
ORCA_NLEAPY=0;;
360d)
ORCA_NLEAPY=30;;

esac

in line 158

-e "s%${PAT_NLEAPY}% nleapy=${ORCA_NLEAPY}%" \

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