Version 54 (modified by flavoni, 5 years ago) (diff)

Using libIGCM library with ORCA2_LIM nemo_v3_6

    Error: Page libIGCM_nemo_v_3_6/config.card_description does not exist

Using libIGCM library with ORCA2_LIM for nemo_v3_6

Purposes

Through libIGCM give an example of run of configuration ORCA1_LIM3_PISCES 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 :
 mkdir TP-NEMO-libIGCM ; cd TP-NEMO-libIGCM
  • 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
  • Extract the model "NEMO_v6":
cd modipsl/util    **
 ./model NEMO_v6

verify NEMOGCM revision in modipsl/util/mod.def file: (fixed revision of NEMO: 5618 )

#-H- NEMO_v6 NEMOGCM for CMIP6 exercise
#-H- NEMO_v6 libIGCM tag libIGCM_v2.6
#-M- NEMO_v6 Christian.Ethe@…
#-C- NEMO_v6 tags/libIGCM_v2.7 HEAD 10 libIGCM .
#-C- NEMO_v6 branches/2015/nemo_v3_6_STABLE/NEMOGCM 5618 7 . modeles
#-C- NEMO_v6 trunk/ORCA1_LIM3_PISCES HEAD 17 . modeles/NEMOGCM/CONFIG
#-C- NEMO_v6 CONFIG/UNIFORM/v6/NEMO_v6 HEAD 8 NEMO_v6 config

(The OFFICIAL repository for the CONFIG ORCA1_LIM3_PISCES is the web site shaconemo: https://forge.ipsl.jussieu.fr/shaconemo/wiki/README_ORCA1_LIM3_PISCES )

NOTA BENE : ORA1_LIM3_PISCES configuration is by default (in libIGCM) run with xios_server en detached mode —> so you need 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
 ./make_xios --arch X64_ADA

 (./make_xios -h for help) 

  • Edit NEMOGCM/CONFIG/cfg.txt file, and add the following line:
ORCA1_LIM3_PISCES OPA_SRC LIM_SRC_3 NST_SRC TOP_SRC
  • Compile ORCA1_LIM3_PISCES configuration (Using ./makenemo -h to see help ( to see list of compilers availables, to see options,…))
cd ../modeles/NEMOGCM/CONFIG
 ./makenemo -n ORCA1_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/ORCA1_LIM3_PISCES/BLD/bin/nemo.exe nemo.exe
(cp $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/ORCA1_LIM3_PISCES/BLD/bin/nemo.exe nemo_orca1_lim3_pisces.exe
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/
                         ORCA1_LIM3_PISCES/
                                         clim/
                                           config.card
                                           COMP/
                                               xios.card
                                               lim3.card
                                               pisces.card
                                               opa9.card
                                         ia/
                                           config.card 
                                           COMP/
                                               xios.card
                                               lim3.card
                                               pisces.card
                                               opa9.card
                         ORCA2_LIM2_PISCES/
                                         clim/
                                           config.card
                                           COMP/
                                               lim2.card
                                               pisces.card
                                               opa9.card                                         
                                        
                         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 modipsl/config/NEMO_v6
 cp EXPERIMENTS/ORCA1_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
 vi config.card  
 # Modify  AT LEAST JobName=eOR1L3P

  • BE CAREFUL at this point: VERIFY in namelist_ORCA1_cfg that you domain decomposition is:
    • jpni = 17
    • jpnij = 221
    • jpnj = 13

if not NEMO makes itself its decomposition like 221 * 1 and THIS DOES NOT WORK (your ocean.output will end with : "dta_tsd: deallocte T & S arrays as they are only use to initialize the run" WITHOUT ERROR MESSAGE

  • Create Job : (using ins_job in modsipl/libIGCM directory)
../../libIGCM/ins_job

 ls modipsl/config/NEMO_v6
	GENERAL
        EXPERIMENTS
        eOR1L3P  #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 ORCA1-LIM3-PISCES is 1:45 for 1 year

vi eOR1L3P/Job_eOR1L3P
 # @ wall_clock_limit = 1:45:00
  • Submit Job :
cd ../     (back into modipsl directory)

./util/ins_job  

cd ../config/ORCA2_LIM/IGCM00   

llsubmit Job_Name 

* SPECIAL INFORMATIONS FOR RUN ORCA2-LIM3-PISCES *

ORCA2-LIM3-PISCES does not exists between reference configurations in v3_6_STABLE NEMOGCM/CONFIGURATION so you've to:

  • Create configuration ORCA2_LIM3_PISCES without compile it (with -j0):
./makenemo -n ORCA2_LIM3_PISCES -r ORCA2_LIM_PISCES -j0
  • Edit cfg.txt file by changing ORCA2_LIM3_PISCES definition :
vi cfg.txt 
ORCA2_LIM3_PISCES OPA_SRC '''LIM_SRC_3''' NST_SRC TOP_SRC
  • Clean the configuration ORCA2_LIM3_PISCES just created :
./makenemo -n ORCA2_LIM3_PISCES clean
  • Change cpp keys:
vi ORCA2_LIM3_PISCES/cpp_ORCA2_LIM3_PISCES.fcm 
bld::tool::fppkeys key_trabbl '''key_lim3''' key_dynspg_flt key_diaeiv key_ldfslp key_traldf_c2d key_traldf_eiv key_dynldf_c3d key_zdftke key_zdfddm key_zdftmx key_top key_pisces key_iomput key_mpp_mpi
  • And finally compile the ORCA2_LIM3_PISCES configuration :
./makenemo -n ORCA2_LIM3_PISCES -j 8 -m X64_ADA

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

Simona Flavoni last update: Timestamp?