Version 123 (modified by flavoni, 15 years ago) (diff) |
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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 | 365d | to do | to do | to do |
Calendar Type | 360d | 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, jpjDO 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, jpjDO 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
)
Simona Flavoni last update: Timestamp?
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