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user/flavoni/libIGCM_v4.0a – NEMO

Version 18 (modified by flavoni, 7 years ago) (diff)


TOC(heading=Using libIGCM library to run 50 years of ORCA2_LIM3_PISCES nemo_v4_0_alpha, depth=2, libIGCM_nemo_v_4_0_alpha/config.card_description)?

Using libIGCM library with ORCA2_LIM3_PISCES with nemo_v3_4_0_alpha (= dev_merge_2016) January 2017


Through LibIGCM give an example of 50 years run of ORCA2_LIM3_PISCES configuration, with :

  • Climatological and Interannual (years from 1948 to 2009) forcing files COREII
  • outputs:
    • ocean: 1D 5D 1M 1Y
    • ice: 1M
    • biology: 1D 1M 1Y
  • RESTARTS every year
  • on Idris ADA machine

Official documentation of Libigcm is :

Quick start guide :

  • Create and go into working directory :
 cd $WORKDIR  ;  mkdir test_O2L3PIS_50years_merge2016 ; cd  test_O2L3PIS_50years_merge2016
  • Define the following alias to use SVN :
 alias svn_ano='svn co modipsl'
  • Extract modipsl (modipsl with LibIGCM)
  • Change mod.def: the model "NEMO_v5":
    cd modipsl/util 
    vi mod.def

edit mod.def file at NEMO_v5 configuration: change the original with these lines:

#---- NEMO  configurations

#-H- NEMO_v5  NEMOGCM  in forced mode   dev_merge_2016  Compilation using FCM
#-H- NEMO_v5  libIGCM tag libIGCM_v2.8.2
#-M- NEMO_v5
#-C- NEMO_v5  tags/libIGCM_v2.8.2                                  HEAD  10 libIGCM               .
#-C- NEMO_v5  branches/2016/dev_merge_2016/NEMOGCM                                       HEAD  7  .                       modeles
#-C- NEMO_v5  CONFIG/UNIFORM/v6/NEMO_v6                                                  HEAD  8  NEMO_v6                 config
  • Extract the model "NEMO_v5":
cd modipsl/util   
 ./model NEMO_v5

  • To compile and run NEMO is needed to download and compile xios:
  • Download XIOS (branch 1.0 revision 703)

(The documentation of xios is available here: )

  • Compile XIOS (on ADA machine):
 cd $WORKDIR    
 svn co XIOS -r 703
 cd XIOS
 ./make_xios --avail
 ./make_xios --arch X64_ADA --full --prod --job 8

  • Compile ORCA2_LIM3_PISCES configuration (Using ./makenemo -h to see help ( to see list of compilers availables, to see options,...))
cd ../modeles/NEMOGCM/CONFIG
 ./makenemo -n ORCA2_LIM3_PISCES -m X64_ADA  -j8 

-j8 compile with 8 proc for compilation phase
-j0 option create only configuration directory but does not compile it 

  • Copy executable nemo.exe (and xios_server.exe if needed in detached mode) in modipsl :
cd ../../../bin
ln -s ../modeles/NEMOGCM/CONFIG/ORCA2_LIM3_PISCES/BLD/bin/nemo.exe nemo.exe
(ln -s $WORKDIR/XIOS/bin/xios_server.exe xios_server.exe) 

NOTA: YOU CAN WANT TO USE MORE THAN ONE EXECUTABLE : so you can do, for example,

ln -s ../modeles/NEMOGCM/CONFIG/ORCA2_LIM3_PISCES/BLD/bin/nemo.exe nemo_orca2_lim3_pisces.exe
ln -s ../modeles/NEMOGCM/CONFIG/ORCA2_LIM2_PISCES/BLD/bin/nemo.exe nemo_orca2_lim2_pisces.exe

JUST BECAREFUL to use SAME executable name in config.card

  • This is the structure of config in modipsl:
  • To create submission directory you have to copy config.card file in config/NEMO-v6 directory:
 cd ../config/NEMO_v6
 cp EXPERIMENTS/ORCA2_LIM3_PISCES/clim/config.card . 
  • Editing at this point modipsl/config/NEMO_v6/config.card (according to iodef.xml file) see detailed page for more informations: page description of config.card

Parameters Files

in opa.card


(${MODIPSL}/modeles/NEMOGCM/CONFIG/SHARED/namelist_ref, namelist_ref ), \
(${SUBMIT_DIR}/PARAM/v4_0_alpha/namelist_${RESOL_OCE}${EXPTYPE}_cfg, namelist_cfg ), \
(${SUBMIT_DIR}/PARAM/v4_0_alpha/iodef.xml, iodef.xml ), \
(${SUBMIT_DIR}/PARAM/v4_0_alpha/domain_def.xml, domain_def.xml), \
(${SUBMIT_DIR}/PARAM/v4_0_alpha/field_def.xml, field_def.xml )

in lim3.card

(${SUBMIT_DIR}/PARAM/v4_0_alpha/namelist_lim3_ref, namelist_ice_ref), \
(${SUBMIT_DIR}/PARAM/v4_0_alpha/namelist_lim3_cfg, namelist_ice_cfg)

in pisces.card

(${SUBMIT_DIR}/PARAM/v4_0_alpha/namelist_top_ref, namelist_top_ref), \
(${SUBMIT_DIR}/PARAM/v4_0_alpha/namelist_top_${RESOL_OCE}_cfg, namelist_top_cfg), \
(${SUBMIT_DIR}/PARAM/v4_0_alpha/namelist_pisces_ref, namelist_pisces_ref), \
(${SUBMIT_DIR}/PARAM/v4_0_alpha/namelist_pisces_${RESOL_OCE}_cfg,  namelist_pisces_cfg)

here you're coping iodef.xml,field_def.xml and domain_def.xml for XIOS1

 vi config.card  
 # Modify  AT LEAST JobName=eOR2L3P

  • Create Job : (using ins_job in modsipl/lib IGCM directory)

 ls modipsl/config/NEMO_v6
        eOR2L3P  #new submission directory, config card is now HERE

  • LOOK AT all parameters of the Job you've created :

NOTE : VERY VERY IMPORTANT: increase size of memory:

  • by default on ada is 3.5Gb ==> increase it to 5Gb (maximum is 20,... but 20 s really not necessary; for more information "news class" command on ada:

# @ as_limit = 5gb

  • by default is 1 hour (@ wall_clock_limit = 1:00:00), but for ORCA2-LIM3-PISCES is about ???? 1:45 on 32 cpus for 1 year ==>increas it to @ wall_clock_limit = 1:30:00
cd eOR2L3P
vi Job_eOR2L3P
 # @ wall_clock_limit = 2:00:00
  • Submit Job :
llsubmit Job_eOR2L3P

If you want to switch from climatological to interannual see page description of config.card

Simona Flavoni last update: Timestamp?