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; revision 7554)

Purposes

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 :

​https://forge.ipsl.jussieu.fr/igcmg_doc/wiki/Doc

Quick start guide :http://www.nemo-ocean.eu/Using-NEMO/Configurations/

• 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 http://forge.ipsl.jussieu.fr/igcmg/svn/modipsl/trunk modipsl'

• Extract modipsl (modipsl with LibIGCM)

 svn_ano

• Change mod.def: the model "NEMO_v5":

  cd modipsl/util 
  vi mod.def
  

revision 7554.

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  simona.flavoni@locean.upmc.fr
#-C- NEMO_v5  tags/libIGCM_v2.8.2                                  HEAD  10 libIGCM               .
#-C- NEMO_v5  branches/2016/dev_merge_2016/NEMOGCM                                       7553  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

Verify NEMOGCM revision in modipsl/util/mod.def file: (fixed revision for dev_merge_2016 : 7554 )

• 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: ​http://forge.ipsl.jussieu.fr/ioserver/wiki/documentation )

• Compile XIOS (on ADA machine):

 cd $WORKDIR    
 svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-1.0 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:

 modipsl/config/NEMO_v6/
	            GENERAL
                    EXPERIMENTS/
                         ORCA2_LIM3_PISCES/
                                         clim/
                                           config.card
                                           COMP/
                                               lim3.card
                                               pisces.card
                                               opa9.card

• 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

IMPORTANT NOTE : in config.card BE CAREFUL TO THESE LINES:

[ParametersFiles?]
List= (${MODIPSL}/modeles/NEMOGCM/CONFIG/SHARED/namelist_ref , namelist_ref ), \

(${SUBMIT_DIR}/PARAM/field_def_nemo-opa.xml , field_def_nemo-opa.xml ), \
(${MODIPSL}/modeles/NEMOGCM/CONFIG/ORCA1_LIM3_PISCES/EXP00/domain_def_nemo.xml , domain_def_nemo.xml ), \
(${SUBMIT_DIR}/PARAM/namelist_${RESOL_OCE}_cfg , namelist_cfg ), \
(${MODIPSL}/modeles/NEMOGCM/CONFIG/ORCA1_LIM3_PISCES/EXP00/context_nemo.xml , context_nemo.xml ), \
(${SUBMIT_DIR}/PARAM/file_def_nemo-opa.xml , file_def_nemo-opa.xml )

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)

../../libIGCM/ins_job

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

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

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

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?