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

Version 128 (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


  • 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
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


  • 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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