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user/flavoni/libIGCM_v4.0a (diff) – NEMO

Changes between Version 18 and Version 19 of user/flavoni/libIGCM_v4.0a


Ignore:
Timestamp:
2017-08-18T20:34:32+02:00 (7 years ago)
Author:
nicolasmartin
Comment:

--

Legend:

Unmodified
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  • user/flavoni/libIGCM_v4.0a

    v18 v19  
    11[[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)]] 
    22 
    3 = '''Using libIGCM library with ORCA2_LIM3_PISCES with nemo_v3_4_0_alpha (= dev_merge_2016) January 2017''' = 
    4 == Purposes == 
    5   Through LibIGCM give an example of 50 years run of ORCA2_LIM3_PISCES configuration, with : 
     3= '''Using libIGCM library with ORCA2_LIM3_PISCES with nemo_v3_4_0_alpha (= dev_merge_2016) January 2017''' 
    64 
    7  * Climatological and Interannual  (years from 1948 to 2009) forcing files COREII 
    8  * outputs: 
    9    * ocean:  1D 5D 1M 1Y 
    10    * ice:  1M 
    11    * biology: 1D 1M 1Y 
     5Last edition: '''[[Wikinfo(changed_ts)]]''' by '''[[Wikinfo(changed_by)]]''' 
    126 
    13  * RESTARTS every year 
    14  * on Idris ADA machine 
     7== Purposes 
     8 
     9Through LibIGCM give an example of 50 years run of ORCA2_LIM3_PISCES configuration, with : 
     10 
     11* Climatological and Interannual  (years from 1948 to 2009) forcing files COREII 
     12* outputs: 
     13  * ocean:  1D 5D 1M 1Y 
     14  * ice:  1M 
     15  * biology: 1D 1M 1Y 
     16* RESTARTS every year 
     17* on Idris ADA machine 
    1518 
    1619Official documentation of Libigcm is : 
     20 https://forge.ipsl.jussieu.fr/igcmg_doc/wiki/Doc 
    1721 
    18   https://forge.ipsl.jussieu.fr/igcmg_doc/wiki/Doc 
     22== Quick start guide 
    1923 
    20 == 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/] == 
    21  * Create and go into working directory : 
     24[source:/branches/2015/nemo_v3_6_STABLE/NEMOGCM] 
    2225 
    23 {{{ 
    24  cd $WORKDIR  ;  mkdir test_O2L3PIS_50years_merge2016 ; cd  test_O2L3PIS_50years_merge2016 
     26* Create and go into working directory : 
     27{{{#!sh 
     28cd $WORKDIR  ;  mkdir test_O2L3PIS_50years_merge2016 ; cd  test_O2L3PIS_50years_merge2016 
    2529}}} 
    26  * Define the following alias to use SVN : 
    2730 
    28 {{{ 
    29  alias svn_ano='svn co http://forge.ipsl.jussieu.fr/igcmg/svn/modipsl/trunk modipsl' 
     31* Define the following alias to use SVN : 
     32{{{#!sh 
     33alias svn_ano='svn co http://forge.ipsl.jussieu.fr/igcmg/svn/modipsl/trunk modipsl' 
    3034}}} 
    31  * Extract modipsl (modipsl with LibIGCM) 
    3235 
    33 {{{ 
    34  svn_ano 
     36* Extract modipsl (modipsl with LibIGCM) 
     37{{{#!sh 
     38svn_ano 
    3539}}} 
    36  * Change mod.def:  the model "NEMO_v5":   
    37 {{{ 
     40 
     41* Change mod.def:  the model "NEMO_v5":   
     42{{{#!sh 
    3843cd modipsl/util  
    3944vi mod.def 
    4045}}} 
    41  
    4246 edit mod.def file at ''NEMO_v5'' configuration: 
    4347 change the original with these lines:  
    … …  
    5357}}} 
    5458 
    55  
    5659* Extract the model "NEMO_v5":  
    57  
    5860{{{ 
    5961cd modipsl/util    
    60  ./model NEMO_v5 
     62./model NEMO_v5 
    6163}}} 
    6264 
    63   
    64  * To compile and run NEMO is needed to download and compile xios: 
     65* To compile and run NEMO is needed to download and compile xios: 
     66  * Download XIOS ('''branch 1.0 revision 703''')\\ 
     67    (The documentation of xios is available [//ioserver/wiki/documentation here]) 
     68  * Compile XIOS (on ADA machine): 
     69{{{#!sh 
     70cd $WORKDIR     
     71svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-1.0 XIOS -r 703 
     72cd XIOS 
     73./make_xios --avail 
     74./make_xios --arch X64_ADA --full --prod --job 8 
     75}}} 
    6576 
    66  * Download XIOS ('''branch 1.0 revision 703''') 
     77* Compile ORCA2_LIM3_PISCES configuration  (Using ./makenemo -h to see help ( to see list of compilers available, to see options,...)) 
     78{{{#!sh 
     79cd ../modeles/NEMOGCM/CONFIG 
     80./makenemo -n ORCA2_LIM3_PISCES -m X64_ADA  -j8  
     81#-j8 compile with 8 proc for compilation phase 
     82#-j0 option create only configuration directory but does not compile it  
     83}}} 
    6784 
    68   (The documentation of xios is available here: http://forge.ipsl.jussieu.fr/ioserver/wiki/documentation ) 
    69  
    70  * Compile XIOS (on ADA machine): 
    71  
    72 {{{ 
    73  cd $WORKDIR     
    74  svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-1.0 XIOS -r 703 
    75  cd XIOS 
    76 }}} 
    77 {{{ 
    78  ./make_xios --avail 
    79  ./make_xios --arch X64_ADA --full --prod --job 8 
    80  
    81 }}} 
    82  * Compile ORCA2_LIM3_PISCES configuration  (Using ./makenemo -h to see help ( to see list of compilers availables, to see options,...)) 
    83  
    84 {{{ 
    85 cd ../modeles/NEMOGCM/CONFIG 
    86  ./makenemo -n ORCA2_LIM3_PISCES -m X64_ADA  -j8  
    87  
    88 -j8 compile with 8 proc for compilation phase 
    89 -j0 option create only configuration directory but does not compile it  
    90  
    91 }}} 
    92  * Copy executable nemo.exe (and xios_server.exe if needed in detached mode) in modipsl : 
    93  
    94 {{{ 
     85* Copy executable nemo.exe (and xios_server.exe if needed in detached mode) in modipsl : 
     86{{{#!sh 
    9587cd ../../../bin 
    9688ln -s ../modeles/NEMOGCM/CONFIG/ORCA2_LIM3_PISCES/BLD/bin/nemo.exe nemo.exe 
    97 (ln -s $WORKDIR/XIOS/bin/xios_server.exe xios_server.exe)  
    98  
     89ln -s $WORKDIR/XIOS/bin/xios_server.exe xios_server.exe 
    9990}}} 
    100   '''                            NOTA: YOU CAN WANT TO USE MORE THAN ONE EXECUTABLE'''                            : so you can do, for example, 
    101 {{{ 
     91  '''NOTA: YOU CAN WANT TO USE MORE THAN ONE EXECUTABLE''': so you can do, for example, 
     92{{{#!sh 
    10293ln -s ../modeles/NEMOGCM/CONFIG/ORCA2_LIM3_PISCES/BLD/bin/nemo.exe nemo_orca2_lim3_pisces.exe 
    10394ln -s ../modeles/NEMOGCM/CONFIG/ORCA2_LIM2_PISCES/BLD/bin/nemo.exe nemo_orca2_lim2_pisces.exe 
     95}}} 
     96  JUST BE CAREFUL to use '''SAME''' executable '''name''' in config.card 
    10497 
    105 }}} 
    106   JUST BECAREFUL to use '''                            SAME'''                             executable '''                            name'''                             in config.card 
    107  
    108  * This is the structure of config in modipsl: 
    109  
     98* This is the structure of config in modipsl: 
    11099{{{ 
    111100 modipsl/config/NEMO_v6/ 
    … …  
    120109                                               opa9.card 
    121110}}} 
    122  * To create submission directory you have to copy config.card file in config/NEMO-v6 directory: 
    123111 
    124 {{{ 
    125  cd ../config/NEMO_v6 
    126  cp EXPERIMENTS/ORCA2_LIM3_PISCES/clim/config.card .  
     112* To create submission directory you have to copy config.card file in config/NEMO-v6 directory: 
     113{{{#!sh 
     114cd ../config/NEMO_v6 
     115cp EXPERIMENTS/ORCA2_LIM3_PISCES/clim/config.card .  
    127116}}} 
    128  * Editing at this point '''modipsl/config/NEMO_v6/config.card'''   (according to iodef.xml file)   see detailed page for more informations: [https://forge.ipsl.jussieu.fr/nemo/wiki/libIGCM_nemo_v_3_6/config.card_description page description of config.card] 
    129117 
     118* Editing at this point '''modipsl/config/NEMO_v6/config.card''' (according to iodef.xml file)\\ 
     119  See detailed page for more informations: [wiki:libIGCM_nemo_v_3_6/config.card_description page description of config.card] 
    130120 
    131 '''IMPORTANT NOTE''' : in config.card BE CAREFUL TO THESE LINES:  [[BR]] 
     121'''IMPORTANT NOTE''' : in config.card BE CAREFUL TO THESE LINES:\\ 
    132122Parameters Files   
    133123 
    134124in '''opa.card''' 
    135  
    136 List= [[BR]] 
    137 || (${MODIPSL}/modeles/NEMOGCM/CONFIG/SHARED/namelist_ref,               || namelist_ref ), \      || 
    138 || (${SUBMIT_DIR}/PARAM/v4_0_alpha/namelist_${RESOL_OCE}${EXPTYPE}_cfg,  || namelist_cfg ), \      || 
    139 || (${SUBMIT_DIR}/PARAM/v4_0_alpha/iodef.xml,                            || iodef.xml    ), \      || 
    140 || (${SUBMIT_DIR}/PARAM/v4_0_alpha/domain_def.xml,                       || domain_def.xml), \     || 
    141 || (${SUBMIT_DIR}/PARAM/v4_0_alpha/field_def.xml,                        || field_def.xml )        || 
    142              
     125{{{#!sh 
     126List= (${MODIPSL}/modeles/NEMOGCM/CONFIG/SHARED/namelist_ref             , namelist_ref       ), \ 
     127      (${SUBMIT_DIR}/PARAM/v4_0_alpha/namelist_${RESOL_OCE}${EXPTYPE}_cfg, namelist_cfg       ), \ 
     128      (${SUBMIT_DIR}/PARAM/v4_0_alpha/iodef.xml                          , iodef.xml          ), \ 
     129      (${SUBMIT_DIR}/PARAM/v4_0_alpha/domain_def.xml                     , domain_def.xml     ), \ 
     130      (${SUBMIT_DIR}/PARAM/v4_0_alpha/field_def.xml                      , field_def.xml      ) 
     131}}} 
     132      
    143133in '''lim3.card''' 
    144  
    145 || (${SUBMIT_DIR}/PARAM/v4_0_alpha/namelist_lim3_ref, || namelist_ice_ref),   \ || 
    146 || (${SUBMIT_DIR}/PARAM/v4_0_alpha/namelist_lim3_cfg, || namelist_ice_cfg)     || 
     134{{{#!sh 
     135      (${SUBMIT_DIR}/PARAM/v4_0_alpha/namelist_lim3_ref                  , namelist_ice_ref   ), \ 
     136      (${SUBMIT_DIR}/PARAM/v4_0_alpha/namelist_lim3_cfg                  , namelist_ice_cfg   ) 
     137}}} 
    147138 
    148139in '''pisces.card'''  
    149  
    150 || (${SUBMIT_DIR}/PARAM/v4_0_alpha/namelist_top_ref,                 || namelist_top_ref),    \ || 
    151 || (${SUBMIT_DIR}/PARAM/v4_0_alpha/namelist_top_${RESOL_OCE}_cfg,    || namelist_top_cfg),    \ || 
    152 || (${SUBMIT_DIR}/PARAM/v4_0_alpha/namelist_pisces_ref,              || namelist_pisces_ref), \ || 
    153 || (${SUBMIT_DIR}/PARAM/v4_0_alpha/namelist_pisces_${RESOL_OCE}_cfg, || namelist_pisces_cfg)    || 
    154  
    155           
    156  
     140{{{#!sh 
     141      (${SUBMIT_DIR}/PARAM/v4_0_alpha/namelist_top_ref                   , namelist_top_ref   ), \ 
     142      (${SUBMIT_DIR}/PARAM/v4_0_alpha/namelist_top_${RESOL_OCE}_cfg      , namelist_top_cfg   ), \ 
     143      (${SUBMIT_DIR}/PARAM/v4_0_alpha/namelist_pisces_ref                , namelist_pisces_ref), \ 
     144      (${SUBMIT_DIR}/PARAM/v4_0_alpha/namelist_pisces_${RESOL_OCE}_cfg   , namelist_pisces_cfg) 
     145}}} 
    157146here you're coping iodef.xml,field_def.xml and domain_def.xml for '''XIOS1'''  
    158147 
    159 {{{ 
    160  vi config.card   
    161  # Modify  AT LEAST JobName=eOR2L3P 
    162  
     148{{{#!sh 
     149vi config.card   
     150# Modify  AT LEAST JobName=eOR2L3P 
    163151}}} 
    164152 
    165  * Create Job :  (using ins_job in modsipl/lib IGCM directory) 
     153* Create Job :  (using ins_job in modsipl/lib IGCM directory) 
    166154 
    167 {{{ 
     155{{{#!sh 
    168156../../libIGCM/ins_job 
    169  
    170  ls modipsl/config/NEMO_v6 
     157ls modipsl/config/NEMO_v6 
    171158        GENERAL 
    172159        EXPERIMENTS 
    173160        eOR2L3P  #new submission directory, config card is now HERE 
     161}}} 
    174162 
    175 }}} 
    176  * '''LOOK AT all parameters of the Job you've created ''': 
     163* '''LOOK AT all parameters of the Job you've created ''': 
    177164 
    178165'''NOTE''' : VERY VERY IMPORTANT: increase size of memory:  
    … …  
    183170 
    184171* 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''' 
    185  
    186 {{{ 
     172{{{#!sh 
    187173cd eOR2L3P 
    188174vi Job_eOR2L3P 
    189175 # @ wall_clock_limit = 2:00:00 
    190176}}} 
    191  * Submit Job : 
    192177 
    193 {{{ 
     178* Submit Job : 
     179{{{#!sh 
    194180llsubmit Job_eOR2L3P 
    195181}}} 
    196182If you want to switch from climatological to interannual see [https://forge.ipsl.jussieu.fr/nemo/wiki/libIGCM_nemo_v_3_6/config.card_description page description of config.card] 
    197  
    198   Simona Flavoni last update: [[Timestamp]]