[[TOC(heading=Using libIGCM library with ORCA2_LIM nemo_v3_6,  depth=2, libIGCM/setupsimupage, libIGCM/change_BC,  libIGCM/postprocessingpage, libIGCM/postalreadyrunpage,  libIGCM_nemo_v_3_4/parallelpage_3_4, libIGCM/common_account,  libIGCM/suggestpage, libIGCM/appendixpage )]]

= '''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 :[https://forge.ipsl.jussieu.fr/nemo/browser/branches/2015/nemo_v3_6_STABLE/NEMOGCM 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
}}}
  [[BR]]     ** verify NEMOGCM revision in '''     modipsl/util/mod.def '''     file:  (fixed revision of NEMO: '''     5618'''     )

  #-H- NEMO_v6  NEMOGCM for CMIP6 exercise [[BR]]    #-H- NEMO_v6  libIGCM tag libIGCM_v2.6[[BR]]    #-M- NEMO_v6  Christian.Ethe@ipsl.jussieu.fr[[BR]]    #-C- NEMO_v6  tags/libIGCM_v2.7                                                                      HEAD  10     libIGCM                        .   [[BR]]    #-C- NEMO_v6  '''    branches/2015/nemo_v3_6_STABLE/NEMOGCM'''                                '''    5618'''        7           .                       modeles[[BR]]    #-C- NEMO_v6  trunk/ORCA1_LIM3_PISCES                                                                HEAD  17             .              modeles/NEMOGCM/CONFIG[[BR]]    #-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 -r 703
 ./make_xios --arch X64_ADA

 (./make_xios -h for help) 

}}}
 * 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) 

}}}
 * Create submission directory:

  modipsl       |   config|      NEMO_v6| ---------------------------------------------[[BR]]|                    |                                   |GENERAL                                     EXPERIMENTS[[BR]]
[[BR]]
{{{
 cd modipsl/config/NEMO_v6
 cp EXPERIMENTS/ORCA1_LIM3_PISCES/clim/config.card . 
}}}
 * Editing at this point modipsl/config/NEMO_v6/EXPERIMENTS/ORCA1_LIM3_PISCES/clim/'''config.card   (according to iodef.xml file)'''

{{{
 vi modipsl/config/NEMO_v6/EXPERIMENTS/ORCA1_LIM3_PISCES/clim/config.card  
 # Modify  AT LEAST JobName=EXP00

}}}
  '''                NOTE : for ada ( idris ) machine'''                                                 starting from revision 2021 of trunk of  libigcm it is possible to add in [Post] section of config.card options [[BR]]                                               [Post] [[BR]]                                               SpaceName                                                =PROD   (to have IGCM_OUT on gaya)[[BR]]                                                PackFrequency                                                =10Y  (to have pack option; i.e. only one tar file)

 * Editing at this point modipsl/config/NEMO_v6/EXPERIMENTS/ORCA1_LIM3_PISCES/clim/COMP/'''xios.card'''
 * Editing at this point modipsl/config/NEMO_v6/EXPERIMENTS/ORCA1_LIM3_PISCES/clim/COMP/'''opa9.card'''
 * Editing at this point modipsl/config/NEMO_v6/EXPERIMENTS/ORCA1_LIM3_PISCES/clim/COMP/'''lim3.card'''
 * Editing at this point modipsl/config/NEMO_v6/EXPERIMENTS/ORCA1_LIM3_PISCES/clim/COMP/'''pisces.card'''

 * Create Job :

{{{
cd ../../     (back into modipsl directory) 
}}}
{{{
./util/ins_job

ls modipsl/config/NEMO_v6
	GENERAL
        EXPERIMENTS
        EXP00  #new submission directory, config card is now HERE

}}}
***#### OLD VERSION

see : [https://forge.ipsl.jussieu.fr/nemo/wiki/libIGCM/setupsimupage setupsimupage]

 * Submit Job : [[BR]]
{{{
cd ../     (back into modipsl directory) 
}}}
{{{
./util/ins_job
 cd ../config/ORCA2_LIM/IGCM00 
 llsubmit Job_Name
}}}

And also see useful remarks: [https://forge.ipsl.jussieu.fr/nemo/wiki/libIGCM/suggestpage suggestpage]

If you want to switch from climatological to interannual see: [https://forge.ipsl.jussieu.fr/nemo/wiki/libIGCM/change_BC change_BC]

  Simona Flavoni last update: [[Timestamp]]