TOC(user/flavoni/libIGCM_v3.6*, heading=Using libIGCM library with ORCA2_LIM nemo_v3_6, depth=2 )?

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 :

igcmgdoc:wiki/Doc

Quick start guide source:/NEMO/releases/release-3.6/NEMOGCM​

• Create and go into working directory :

 cd $WORKDIR  ;  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: shaco: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: xios: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 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 -j 8

-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
(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/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 modipsl/config/NEMO_v6/GENERAL/PARAM/namelist_ORCA1clim(ia)_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/lib IGCM directory)

../../IGCM/IGCM/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 about 1:45 on 221 cpus for 1 year

cd eOR1L3P
vi Job_eOR1L3P
 # @ wall_clock_limit = 2:00:00

• Submit Job :

llsubmit Job_eOR1L3P

* 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

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