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user/flavoni/libIGCM/setupsimupage (diff) – NEMO

Changes between Version 44 and Version 45 of user/flavoni/libIGCM/setupsimupage


Ignore:
Timestamp:
2013-03-11T12:34:09+01:00 (11 years ago)
Author:
flavoni
Comment:

--

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  • user/flavoni/libIGCM/setupsimupage

    v44 v45  
    1 == !'''Set up a simulation!''' ==   [[BR]] 
     1== Set up a simulation == 
     2 
    23 
    34[[PageOutline]] 
    45 
    5   '''  First of all see official documentation''' 
     6  '''   First of all see official documentation''' 
    67 
    78  http://forge.ipsl.jussieu.fr/igcmg/wiki/platform/documentation 
    89 
    910=== Important files === 
    10   Important files to set up a simulation are:  [[BR]]  ORCA2_LIM/IGCM00/config.card  [[BR]]  ORCA2_LIM/IGCM00/PARAM/iodef.xml  [[BR]]  ORCA2_LIM/IGCM00/COMP/opa9.card  [[BR]] 
     11  Important files to set up a simulation are:  [[BR]]   ORCA2_LIM/IGCM00/config.card  [[BR]]   ORCA2_LIM/IGCM00/PARAM/iodef.xml  [[BR]]   ORCA2_LIM/IGCM00/COMP/opa9.card  [[BR]] 
    1112 
    1213=== config.card === 
     
    1617In ORCA2_LIM/IGCM00/'''config.card''' file  [[BR]] 
    1718 
    18   you have to put a '''  !JobName  '''   maximum of 8 characters [[BR]]  in !LongName   you can put a comment that can remember to you all properties of the Job.[[BR]] 
     19  you have to put a '''   !JobName   '''    maximum of 8 characters [[BR]]   in !LongName    you can put a comment that can remember to you all properties of the Job.[[BR]] 
    1920 
    20   you have to set duration of your experience and setting '''  !PeriodLength  '''   parameter, so you manage write output frequency of restart files. 
     21  you have to set duration of your experience and setting '''   !PeriodLength   '''    parameter, so you manage write output frequency of restart files. 
    2122 
    22   ( for example : if you have and experience of 10 years and a !PeriodLength   of 1 year, you will have 10 restart files ) 
     23  ( for example : if you have and experience of 10 years and a !PeriodLength    of 1 year, you will have 10 restart files ) 
    2324 
    24   #-- Début et fin de Job [[BR]]  #-- "YYYY-MM-DD" [[BR]]  DateBegin  =2001-01-01 [[BR]]  DateEnd  =2010-12-31 [[BR]]  #============================ [[BR]]  #-- 1Y, 1M, 5D, 1D [[BR]]  PeriodLength  =1Y [[BR]] 
     25  #-- Début et fin de Job [[BR]]   #-- "YYYY-MM-DD" [[BR]]   DateBegin   =2001-01-01 [[BR]]   DateEnd   =2010-12-31 [[BR]]   #============================ [[BR]]   #-- 1Y, 1M, 5D, 1D [[BR]]   PeriodLength   =1Y [[BR]] 
    2526 
    26   '''  Note : '''   If you want to use restart data from another simulation ( already run not in this moment ) you have to manage "Restarts" part of config.card 
     27  '''   Note : '''    If you want to use restart data from another simulation ( already run not in this moment ) you have to manage "Restarts" part of config.card 
    2728 
    2829==== How to continue a simulation ==== 
    29   see french version : [http://forge.ipsl.jussieu.fr/igcmg/wiki/platform/documentation/simulation#Commentprolongerourelancerunesimulation here] 
     30  see french version : [http://forge.ipsl.jussieu.fr/igcmg/wiki/platform/documentation/simulation#Commentprolongerourelancerunesimulation here] 
    3031 
    3132  If you have finished a previous simulation and now you want to continue it you have to change : 
    3233 
    33   in ORCA2_LIM/IGCM00/config.card you have to set : [[BR]]  new '''  DateEnd  '''  [[BR]] 
     34  in ORCA2_LIM/IGCM00/config.card you have to set : [[BR]]   new '''   DateEnd   '''   [[BR]] 
    3435 
    35   in ORCA2_LIM/IGCM00/run.card[[BR]]  '''  PeriodDateEnd  '''  [[BR]]  '''  PeriodState  = OnQueue  ''' 
     36  in ORCA2_LIM/IGCM00/run.card[[BR]]   '''   PeriodDateEnd   '''   [[BR]]   '''   PeriodState   = OnQueue   ''' 
    3637 
    3738==== How to manage calendar type ==== 
    38   in ORCA2_LIM/IGCM00/config.card you have to set !CalendarType    like 360d or leap or noleap 
     39  in ORCA2_LIM/IGCM00/config.card you have to set !CalendarType     like 360d or leap or noleap 
    3940 
    40   # for '''  360d'''   :[[BR]]    you have to be careful at[[BR]]  DateEnd  =2010-12-3'''  0'''   [[BR]]  because every month has 30 days[[BR]] 
     41  # for '''   360d'''    :[[BR]]     you have to be careful at[[BR]]   DateEnd   =2010-12-3'''   0'''    [[BR]]   because every month has 30 days[[BR]] 
    4142 
    42   If you put for example DateEnd  =2005-12-31, you will have another run, of duration like your !PeriodLength 
     43  If you put for example DateEnd   =2005-12-31, you will have another run, of duration like your !PeriodLength 
    4344 
    44   # for '''  noleap'''   :  [[BR]]  '''  How to manage rdt ( i.e. timestep )'''  [[BR]]  in ORCA2_LIM/IGCM00/COMP/opa9.driver you have to change parameter : ORCA_NPDT_JOUR=15 [[BR]]  ( 15 corresponds to 86400s/5760s; it does mean that in one day you have 15 iterations; and it does mean that timestep is 5760) 
     45  # for '''   noleap'''    :  [[BR]]   '''   How to manage rdt ( i.e. timestep )'''   [[BR]]   in ORCA2_LIM/IGCM00/COMP/opa9.driver you have to change parameter : ORCA_NPDT_JOUR=15 [[BR]]   ( 15 corresponds to 86400s/5760s; it does mean that in one day you have 15 iterations; and it does mean that timestep is 5760) 
    4546 
    4647==== How to manage monoprocessor or multiprocessor run ==== 
    47   From nemo '''  version 3_3'''   set up and compile a mono-processor run : 
     48  From nemo '''   version 3_3'''    set up and compile a mono-processor run : 
    4849 
    4950  ./makenemo -m SX8_BRODIE -n ORCA2_LIM 
    5051 
    51   for multiprocessor run see : [[BR]]  [https://forge.ipsl.jussieu.fr/nemo/wiki/libIGCM_nemo_v_3_3/parallelpage_3_3 parallelpage for nemo version 3_3]   [[BR]] 
     52  for multiprocessor run see : [[BR]]   [https://forge.ipsl.jussieu.fr/nemo/wiki/libIGCM_nemo_v_3_3/parallelpage_3_3 parallelpage for nemo version 3_3]    [[BR]] 
    5253 
    53   ( To understand more on  mono or multi proc run with nemo till version 3_2_2 see also : [[BR]]  [https://forge.ipsl.jussieu.fr/nemo/wiki/libIGCM/parallelpage parallelpage till nemo version 3_2_2]   ) [[BR]] 
     54  ( To understand more on  mono or multi proc run with nemo till version 3_2_2 see also : [[BR]]   [https://forge.ipsl.jussieu.fr/nemo/wiki/libIGCM/parallelpage parallelpage till nemo version 3_2_2]    ) [[BR]] 
    5455 
    55   #-- PBS Class (required ONLY on brodie mono/multi)  [[BR]]  JobClass  =mono     [[BR]]  #JobClass  =multi   [[BR]]  #============================   [[BR]]  #-- Total Number of Processors  [[BR]]  #JobNumProcTot  =4  (put same number of processors choosen at compiling time, in this example is 4)               [[BR]]  JobNumProcTot  =1                 [[BR]]  #============================   [[BR]]  #-- Run Options :               [[BR]]  #JobRunOptions  ='"-np "${BATCH_NUM_PROC_TOT}"'    [[BR]]  JobRunOptions  =''            [[BR]]  #============================   [[BR]] '' 
     56  #-- PBS Class (required ONLY on brodie mono/multi)  [[BR]]   JobClass   =mono     [[BR]]   #JobClass   =multi   [[BR]]   #============================   [[BR]]   #-- Total Number of Processors  [[BR]]   #JobNumProcTot   =4  (put same number of processors choosen at compiling time, in this example is 4)               [[BR]]   JobNumProcTot   =1                 [[BR]]   #============================   [[BR]]   #-- Run Options :               [[BR]]   #JobRunOptions   ='"-np "${BATCH_NUM_PROC_TOT}"'    [[BR]]   JobRunOptions   =''             [[BR]]   #============================   [[BR]] '' 
    5657 
    5758==== How to set Init & Boundary condition's directory ==== 
    5859  By default R_BC is commented, it does mean that INIT & Boundary files are in common account of IPSL, at IDRIS or CCRT : 
    5960 
    60   #R_BC=/u/rech/psl/rpsl035/IGCM/BC  [[BR]]  #R_BC=/dmnfs/cont003/p86ipsl/IGCM/BC  [[BR]] 
     61  #R_BC=/u/rech/psl/rpsl035/IGCM/BC  [[BR]]   #R_BC=/dmnfs/cont003/p86ipsl/IGCM/BC  [[BR]] 
    6162 
    62   If you want to have you own directory you have to create a directory in wich you have to create OCE/ORCA2_LIM2 directory in which you have to put tar file : http://www.nemo-ocean.eu/Using-NEMO/Configurations/ORCA2_LIM   [[BR]]  with all initial files for nemo, and where you have to add your forcing files. [[BR]] 
     63  If you want to have you own directory you have to create a directory in wich you have to create OCE/ORCA2_LIM2 directory in which you have to put tar file : http://www.nemo-ocean.eu/Using-NEMO/Configurations/ORCA2_LIM    [[BR]]   with all initial files for nemo, and where you have to add your forcing files. [[BR]] 
    6364 
    6465==== How to restart from another run ==== 
     
    6768  If you want to restart from restart file of experience core260i (corersponding at the Job_core260i) of the year 2007 you have to put: 
    6869 
    69   #================ [[BR]]  #D-- Restarts - [[BR]]  [Restarts]  [[BR]]  #D- If you want a GENERAL RULE FOR RESTARTS, put this flag to 'y'  [[BR]]  OverRule  =y   [[BR]]  #D- Last day of the experience used as restart  [[BR]]  RestartDate  =2007-12-31  [[BR]]  #D- Define restart simulation name  [[BR]]  RestartJobName  =core260i   [[BR]]  #D- Path Server Group Login    [[BR]]  RestartPath  =${ARCHIVE}/IGCM_OUT/ORCA2_LIM2   [[BR]] 
     70  #================ [[BR]]   #D-- Restarts - [[BR]]   [Restarts]  [[BR]]   #D- If you want a GENERAL RULE FOR RESTARTS, put this flag to 'y'  [[BR]]   OverRule   =y   [[BR]]   #D- Last day of the experience used as restart  [[BR]]   RestartDate   =2007-12-31  [[BR]]   #D- Define restart simulation name  [[BR]]   RestartJobName   =core260i   [[BR]]   #D- Path Server Group Login    [[BR]]   RestartPath   =${ARCHIVE}/IGCM_OUT/ORCA2_LIM2   [[BR]] 
    7071 
    7172==== How to have post treatement ==== 
     
    7374 
    7475==== How to manage write output frequency ==== 
    75   in ORCA2_LIM/IGCM00/config.card you have to set !WriteFrequency   of your experience 
     76  in ORCA2_LIM/IGCM00/config.card you have to set !WriteFrequency    of your experience 
    7677 
    7778  You can have multiple frequencies, you need to have a blank between every frequency, for example : [[BR]] 
    7879 
    79   '''  ocean'''   output files every 1 year and 1 month : [[BR]]    #=================== [[BR]]  #D-- OCE - [[BR]]  [OCE] [[BR]]  WriteFrequency  ="1Y 1M" 
     80  '''   ocean'''    output files every 1 year and 1 month : [[BR]]     #=================== [[BR]]   #D-- OCE - [[BR]]   [OCE] [[BR]]   WriteFrequency   ="1Y 1M" 
    8081 
    81   and '''  ice'''   output files every 1 month : [[BR]]  #=================== [[BR]]  #D-- ICE - [[BR]]  [ICE] [[BR]]  WriteFrequency  ="1M" 
     82  and '''   ice'''    output files every 1 month : [[BR]]   #=================== [[BR]]   #D-- ICE - [[BR]]   [ICE] [[BR]]   WriteFrequency   ="1M" 
    8283 
    83   These settings have to be coherents also with path in ORCA2_LIM/IGCM00/COMP/'''  opa9.card'''   in part :  [[BR]]  [OutputFiles  ]    [[BR]]  List=   (${PREFIX_WF'''  1'''  }_grid_T.nc,         ${R_OUT_OCE_WF'''  1'''  }/${PREFIX}_${WF'''  1'''  }_grid_T.nc,               NONE),\   [[BR]] 
    84     (${PREFIX_WF'''  1'''  }_grid_U.nc,         ${R_OUT_OCE_WF'''  1'''  }/${PREFIX}_${WF'''  1'''  }_grid_U.nc,               NONE),\    [[BR]]  (${PREFIX_WF'''  1'''  }_grid_V.nc,         ${R_OUT_OCE_WF'''  1'''  }/${PREFIX}_${WF'''  1'''  }_grid_V.nc,               NONE),\    [[BR]]  (${PREFIX_WF'''  2'''  }_grid_T.nc,         ${R_OUT_OCE_WF'''  2'''  }/${PREFIX}_${WF'''  2'''  }_grid_T.nc,               NONE),\    [[BR]]  (${PREFIX_WF'''  2'''  }_grid_U.nc,         ${R_OUT_OCE_WF'''  2'''  }/${PREFIX}_${WF'''  2'''  }_grid_U.nc,               NONE),\   [[BR]]  (${PREFIX_WF'''  2'''  }_grid_V.nc,         ${R_OUT_OCE_WF'''  2'''  }/${PREFIX}_${WF'''  2'''  }_grid_V.nc,               NONE),\   [[BR]] 
     84  These settings have to be coherents also with path in ORCA2_LIM/IGCM00/COMP/'''   opa9.card'''    in part :  [[BR]]   OutputFiles     [[BR]]   List=   (${PREFIX_WF'''   1'''   }_grid_T.nc,         ${R_OUT_OCE_WF'''   1'''   }/${PREFIX}_${WF'''   1'''   }_grid_T.nc,               NONE),\   [[BR]] 
     85    (${PREFIX_WF'''   1'''   }_grid_U.nc,         ${R_OUT_OCE_WF'''   1'''   }/${PREFIX}_${WF'''   1'''   }_grid_U.nc,               NONE),\    [[BR]]   (${PREFIX_WF'''   1'''   }_grid_V.nc,         ${R_OUT_OCE_WF'''   1'''   }/${PREFIX}_${WF'''   1'''   }_grid_V.nc,               NONE),\    [[BR]]   (${PREFIX_WF'''   2'''   }_grid_T.nc,         ${R_OUT_OCE_WF'''   2'''   }/${PREFIX}_${WF'''   2'''   }_grid_T.nc,               NONE),\    [[BR]]   (${PREFIX_WF'''   2'''   }_grid_U.nc,         ${R_OUT_OCE_WF'''   2'''   }/${PREFIX}_${WF'''   2'''   }_grid_U.nc,               NONE),\   [[BR]]   (${PREFIX_WF'''   2'''   }_grid_V.nc,         ${R_OUT_OCE_WF'''   2'''   }/${PREFIX}_${WF'''   2'''   }_grid_V.nc,               NONE),\   [[BR]] 
    8586 
    8687  You have to put number of frequencies that you put in part [OCE] of config.card (in this case you have 2 frequencies : 1Y 1M) 
    8788 
    88   The same for ice : ORCA2_LIM/IGCM00/COMP/'''  lim2.card'''     (in this example you have only WF1) 
     89  The same for ice : ORCA2_LIM/IGCM00/COMP/'''   lim2.card'''      (in this example you have only WF1) 
    8990 
    90   '''  VERY IMPORTANT NOTE :'''   these settings are to be coherents with the ones in iodef.xml see doc : ????? (to add link to seb?) [[BR]]  In iodef.xml you can choose variables that you want to have in output at every frequency 
     91  '''   VERY IMPORTANT NOTE :'''    these settings are to be coherents with the ones in iodef.xml see doc : ????? (to add link to seb?) [[BR]]   In iodef.xml you can choose variables that you want to have in output at every frequency 
    9192 
    9293=== How to manage Interannual or Climatological Runs === 
     
    9495  You have to set 
    9596 
    96   # Interannual_Run '''  y'''   if you want to do interannual runs or '''  n'''   if you want to do climatological runs 
     97  # Interannual_Run '''   y'''    if you want to do interannual runs or '''   n'''    if you want to do climatological runs 
    9798 
    98   # In [Interannual] section you have to fill List_jobsbc of file names like they appear in namelist.  [[BR]]  ( for example if you want to do interannual run using clio bulk core you can put :  [[BR]] 
     99  # In [Interannual] section you have to fill List_jobsbc of file names like they appear in namelist.  [[BR]]   ( for example if you want to do interannual run using clio bulk core you can put :  [[BR]] 
    99100    List_jobsbc=(flx, taux_1m, tauy_1m) 
    100101  ) 
     
    102103=== How to manage Interannual or Climatological Runs === 
    103104==== in ORCA2_LIM/IGCM00/PARAM/'''namelist''' ==== 
    104   You have to set in "namsbc" part if you want to do climatological run and if you want to do an interpolation : [[BR]]    '''  time interpol.'''   (logical) and '''  clim'''   (T/F) 
     105  You have to set in "namsbc" part if you want to do climatological run and if you want to do an interpolation : [[BR]]     '''   time interpol.'''    (logical) and '''   clim'''    (T/F) 
    105106 
    106107  see : [https://forge.ipsl.jussieu.fr/nemo/wiki/libIGCM/change_BC change_BC] 
    107108 
    108109=== How to have mail of end of Job, on ccrt's machines === 
    109   on mercure: in Job_Name: #PBS -M name@mail [[BR]]  on platine: In Job_Name: #BSUB -u name@mail 
     110  on mercure: in Job_Name: #PBS -M name@mail [[BR]]   on platine: In Job_Name: #BSUB -u name@mail 
    110111 
    111112  Simona Flavoni last update:  [[Timestamp]]