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user/flavoni/libIGCM – NEMO
wiki:user/flavoni/libIGCM

Version 131 (modified by flavoni, 15 years ago) (diff)

--

ParentLinkage(=)?

Using libIGCM(v1_1) library with ORCA2_LIM

A - Purposes:


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



B - 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'
 alias svn_libigcm='svn co http://forge.ipsl.jussieu.fr/libigcm/svn/tags/libIGCM_v1_1 libIGCM'
 alias svn_nemoligcm='svn co http://forge.ipsl.jussieu.fr/nemo/svn/branches/libIGCM/ORCA2_LIM/IGCM00 IGCM00'
  • Create and go into working directory :
 mkdir TRY ; cd TRY
  • Extract modipsl :
 svn_ano 
  • Extract NEMO :
 cd modipsl/util 
 ./model NEMO 

  • Extract libigcm :
 cd ../ 
 svn_libigcm

  • Extract card for NEMO for libIGCM :
 cd config/ORCA2_LIM 
 svn_nemoligcm
  • 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  



C - List of possible errors :


C.1 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 your .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=

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_1)

  • 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

  • Error : compiling

For compiling problem on mercure and platine use new mod.def, fldread.F90, fait_AA_make, BB_make



D - List of possible remarks and suggestions


  • 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 il created with ins_job script )

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

In to run.card.init file who can we undesrtand syntax of? :

TimeSeriesRunning=n
TimeSeriesCompleted=

SeasonalRunning=n

Is there a reference file?

  • test with trunk/libIGCM

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

RebuildFromArchive=false

NOTE: We wait for http://forge.ipsl.jussieu.fr/libigcm/browser/tags version 2 to do changes in config.card:

http://forge.ipsl.jussieu.fr/nemo/svn/branches/libIGCM/ORCA2_LIM/IGCM00/

  • Change in nemo.card or in nemo.driver variable: ORCA_NPDT_JOUR and OPA_NPDT_JOURS
  • Have informations about mailing system for good jobs, on ccrt and idris



E - To do list


  • In config.card if CalendarType=360d ==>

Every month has 30 days, so you have to put DateEnd?=2005-12-30

If not, for example DateEnd?=2005-12-31, you will have another run, during like your PeriodLenght

  • run on CCRT machines

(errors: config.card,

in Job_NL1.e

libIGCM/libIGCM_debug/libIGCM_debug.ksh: line 59: set: +A: invalid option

# Declare a stack of functions calls

# insert last argument of the Stack set +A IGCM_debug_Stack ${NULL_STR} set +A IGCM_debug_StackArgs ${NULL_STR} IGCM_debug_LenStack=0

)

  • solve "test argument expected problem"
  • test mpi
  • test for Calendar Type, Output frequency and Restarts:

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 ongoing ongoing to do
Calendar Type 365d to do to do to do
Calendar Type leap to do to do to do



F - Remember: files to change for NEMO


  • TO CHANGE nemo.driver for 360d Calendar Type!!!!!!!!!

  • fait_AA_make

difference with the old one:

in #- Compilation options ---

echo '#-Q- sx8mercure F_O = -f2003 nocbind -size_t64 -dw -Wf\"-A dbl4\" -sx8 -C vopt -Wf"-P nh" -Wf',-pvctl noassume loopcnt=10000 -L transform' -I $(MODDIR) -I $(MODDIR)/oce -I $(NCDF_INC)'

( old version:

echo '#-Q- sx8mercure F_O = -f2003 nocbind noopt_ieee -size_t64 -dw -Wf\"-A dbl4\" -sx6 -C vopt -Wf"-P nh" -Wf',-pvctl noassume loopcnt=10000 -L transform' -I $(MODDIR) -I $(MODDIR)/oce -I $(NCDF_INC)'

)

  • BB_make
  • AA_job

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

  • fldread.F90

difference with the old one:

in line 74

INTEGER jf, ji, jj ! dummy indices

in line 94-99:

DO jj = 1, jpj

DO ji = 1, jpi

sd(jf)%fdta(ji,jj,1) = sd(jf)%fdta(ji,jj,2)

END DO

END DO

in lines 164-169:

sd(jf)%fnow(:,:) = ztintb * sd(jf)%fdta(:,:,1) + ztinta * sd(jf)%fdta(:,:,2)
DO jj = 1, jpj

DO ji = 1, jpi

sd(jf)%fnow(ji,jj) = ztintb * sd(jf)%fdta(ji,jj,1) + ztinta * sd(jf)%fdta(ji,jj,2)

END DO

END DO

in lines 172-181:

sd(jf)%fnow(:,:) = sd(jf)%fdta(:,:,2) ! piecewise constant field
DO jj = 1, jpj

DO ji = 1, jpi

sd(jf)%fnow(ji,jj) = sd(jf)%fdta(ji,jj,2) ! piecewise constant field

END DO

END DO

  • mod.def

difference with the old one:

#-S- 10 svn co -r 47 http://forge.ipsl.jussieu.fr/libigcm/svn
#-H- NEMO_IGCM IOIPSL/src - svn - tag v2_1_4
#-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

( note: NEMO_IGCM branches/libIGCM/ORCA2_LIM/IGCM00 has to be the last one command, if not it is impossible to download in ORCA2_LIM directory; because it does not exists yet)

( old version:

#-S- 10 svn http://forge.ipsl.jussieu.fr/libigcm/svn
#-H- NEMO_IGCM IOIPSL/src - svn - tag v2_1_6
#-C- NEMO_IGCM IOIPSL/tags/v2_1_6/src HEAD 8 IOIPSL/src modeles
#-C- NEMO_IGCM tags/libIGCM_v1_1 HEAD 10 libIGCM .
#-C- NEMO_IGCM branches/libIGCM/ORCA2_LIM/IGCM00 HEAD 7 IGCM00 config/ORCA2_LIM
#-C- NEMO_IGCM trunk/NEMO HEAD 7 . modeles
#-C- NEMO_IGCM trunk/UTIL HEAD 7 . modeles
#-C- NEMO_IGCM trunk/NVTK HEAD 7 . config
#-C- NEMO_IGCM trunk/CONFIG/GYRE_LOBSTER HEAD 7 GYRE_LOBSTER config
#-C- NEMO_IGCM trunk/CONFIG/ORCA2_LIM HEAD 7 ORCA2_LIM config

)



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