New URL for NEMO forge!   http://forge.nemo-ocean.eu

Since March 2022 along with NEMO 4.2 release, the code development moved to a self-hosted GitLab.
This present forge is now archived and remained online for history.
user/flavoni/libIGCM/setupsimupage (diff) – NEMO

Changes between Version 43 and Version 44 of user/flavoni/libIGCM/setupsimupage


Ignore:
Timestamp:
2013-03-11T11:37:42+01:00 (11 years ago)
Author:
flavoni
Comment:

--

Legend:

Unmodified
Added
Removed
Modified

  • user/flavoni/libIGCM/setupsimupage

    v43 v44  
    33[[PageOutline]] 
    44 
    5   ''' First of all see official documentation''' 
     5  '''  First of all see official documentation''' 
    66 
    77  http://forge.ipsl.jussieu.fr/igcmg/wiki/platform/documentation 
    88 
    99=== 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]] 
     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]] 
    1111 
    1212=== config.card === 
    1313==== How to manage job name, start date, end date, and restart files ==== 
    14  Here you can find a description of some parts of config.card 
     14  Here you can find a description of some parts of config.card 
    1515 
    1616In ORCA2_LIM/IGCM00/'''config.card''' file  [[BR]] 
    1717 
    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]] 
     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]] 
    1919 
    20   you have to set duration of your experience and setting ''' !PeriodLength '''  parameter, so you manage write output frequency of restart files. 
     20  you have to set duration of your experience and setting '''  !PeriodLength  '''   parameter, so you manage write output frequency of restart files. 
    2121 
    22   ( for example : if you have and experience of 10 years and a !PeriodLength  of 1 year, you will have 10 restart files ) 
     22  ( for example : if you have and experience of 10 years and a !PeriodLength   of 1 year, you will have 10 restart files ) 
    2323 
    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]] 
     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]] 
    2525 
    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 
     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 
    2727 
    2828==== How to continue a simulation ==== 
    29   see french version : [http://forge.ipsl.jussieu.fr/libigcm/wiki/libIGCM/DocUtilisateur/FAQ#Commentcontinuerunesimulation here] 
     29  see french version : [http://forge.ipsl.jussieu.fr/igcmg/wiki/platform/documentation/simulation#Commentprolongerourelancerunesimulation here] 
    3030 
    3131  If you have finished a previous simulation and now you want to continue it you have to change : 
    3232 
    33   in ORCA2_LIM/IGCM00/config.card you have to set : [[BR]] new ''' DateEnd ''' [[BR]] 
     33  in ORCA2_LIM/IGCM00/config.card you have to set : [[BR]]  new '''  DateEnd  ''' [[BR]] 
    3434 
    35   in ORCA2_LIM/IGCM00/run.card[[BR]] ''' PeriodDateEnd ''' [[BR]] ''' PeriodState = OnQueue ''' 
     35  in ORCA2_LIM/IGCM00/run.card[[BR]]  '''  PeriodDateEnd  '''  [[BR]]  '''  PeriodState  = OnQueue ''' 
    3636 
    3737==== How to manage calendar type ==== 
    38   in ORCA2_LIM/IGCM00/config.card you have to set !CalendarType   like 360d or leap or noleap 
     38  in ORCA2_LIM/IGCM00/config.card you have to set !CalendarType    like 360d or leap or noleap 
    3939 
    40   # for ''' 360d'''  :[[BR]]   you have to be careful at[[BR]] DateEnd =2010-12-3''' 0'''  [[BR]] because every month has 30 days[[BR]] 
     40  # for '''  360d'''   :[[BR]]    you have to be careful at[[BR]]  DateEnd  =2010-12-3'''  0'''   [[BR]] because every month has 30 days[[BR]] 
    4141 
    42   If you put for example DateEnd =2005-12-31, you will have another run, of duration like your !PeriodLength 
     42  If you put for example DateEnd  =2005-12-31, you will have another run, of duration like your !PeriodLength 
    4343 
    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) 
     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) 
    4545 
    4646==== How to manage monoprocessor or multiprocessor run ==== 
    47   From nemo ''' version 3_3'''  set up and compile a mono-processor run : 
     47  From nemo '''  version 3_3'''   set up and compile a mono-processor run : 
    4848 
    4949  ./makenemo -m SX8_BRODIE -n ORCA2_LIM 
    5050 
    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]] 
     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]] 
    5252 
    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]] 
     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]] 
    5454 
    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 "${BATCH_NUM_PROC_TOT}"'    [[BR]] JobRunOptions =''           [[BR]] #============================   [[BR]]'' 
     55  #-- PBS Class (required ONLY on brodie mono/multi)  [[BR]]  JobClass  =mono     [[BR]]  #JobClass  =multi   [[BR]]  #============================   [[BR]]  #-- Total Number of Processors  [[BR]]  #JobNumProcTot  =4  (put same number of processors choosen at compiling time, in this example is 4)               [[BR]]  JobNumProcTot  =1                 [[BR]]  #============================   [[BR]]  #-- Run Options :               [[BR]]  #JobRunOptions  ='"-np "${BATCH_NUM_PROC_TOT}"'    [[BR]]  JobRunOptions  =''            [[BR]]  #============================   [[BR]] '' 
    5656 
    5757==== How to set Init & Boundary condition's directory ==== 
    5858  By default R_BC is commented, it does mean that INIT & Boundary files are in common account of IPSL, at IDRIS or CCRT : 
    5959 
    60   #R_BC=/u/rech/psl/rpsl035/IGCM/BC  [[BR]] #R_BC=/dmnfs/cont003/p86ipsl/IGCM/BC  [[BR]] 
     60  #R_BC=/u/rech/psl/rpsl035/IGCM/BC  [[BR]]  #R_BC=/dmnfs/cont003/p86ipsl/IGCM/BC  [[BR]] 
    6161 
    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]] 
     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]] 
    6363 
    6464==== How to restart from another run ==== 
    … …  
    6767  If you want to restart from restart file of experience core260i (corersponding at the Job_core260i) of the year 2007 you have to put: 
    6868 
    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 =${ARCHIVE}/IGCM_OUT/ORCA2_LIM2   [[BR]] 
     69  #================ [[BR]]  #D-- Restarts - [[BR]]  [Restarts]  [[BR]]  #D- If you want a GENERAL RULE FOR RESTARTS, put this flag to 'y'  [[BR]]  OverRule  =y   [[BR]]  #D- Last day of the experience used as restart  [[BR]]  RestartDate  =2007-12-31  [[BR]]  #D- Define restart simulation name  [[BR]]  RestartJobName  =core260i   [[BR]]  #D- Path Server Group Login    [[BR]]  RestartPath =${ARCHIVE}/IGCM_OUT/ORCA2_LIM2   [[BR]] 
    7070 
    7171==== How to have post treatement ==== 
    … …  
    7373 
    7474==== How to manage write output frequency ==== 
    75   in ORCA2_LIM/IGCM00/config.card you have to set !WriteFrequency  of your experience 
     75  in ORCA2_LIM/IGCM00/config.card you have to set !WriteFrequency   of your experience 
    7676 
    7777  You can have multiple frequencies, you need to have a blank between every frequency, for example : [[BR]] 
    7878 
    79   ''' ocean'''  output files every 1 year and 1 month : [[BR]]   #=================== [[BR]] #D-- OCE - [[BR]] [OCE] [[BR]] WriteFrequency ="1Y 1M" 
     79  '''  ocean'''   output files every 1 year and 1 month : [[BR]]    #=================== [[BR]]  #D-- OCE - [[BR]]  [OCE] [[BR]]  WriteFrequency ="1Y 1M" 
    8080 
    81   and ''' ice'''  output files every 1 month : [[BR]] #=================== [[BR]] #D-- ICE - [[BR]] [ICE] [[BR]] WriteFrequency ="1M" 
     81  and '''  ice'''   output files every 1 month : [[BR]]  #=================== [[BR]]  #D-- ICE - [[BR]]  [ICE] [[BR]]  WriteFrequency ="1M" 
    8282 
    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}_${WF''' 2''' }_grid_V.nc,               NONE),\   [[BR]] 
     83  These settings have to be coherents also with path in ORCA2_LIM/IGCM00/COMP/'''  opa9.card'''   in part :  [[BR]]  [OutputFiles  ]    [[BR]]  List=   (${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]] 
    8585 
    8686  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) 
    8787 
    88   The same for ice : ORCA2_LIM/IGCM00/COMP/''' lim2.card'''    (in this example you have only WF1) 
     88  The same for ice : ORCA2_LIM/IGCM00/COMP/'''  lim2.card'''     (in this example you have only WF1) 
    8989 
    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 
     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 
    9191 
    9292=== How to manage Interannual or Climatological Runs === 
    … …  
    9494  You have to set 
    9595 
    96   # Interannual_Run ''' y'''  if you want to do interannual runs or ''' n'''  if you want to do climatological runs 
     96  # Interannual_Run '''  y'''   if you want to do interannual runs or '''  n'''   if you want to do climatological runs 
    9797 
    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]] 
     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]] 
    9999    List_jobsbc=(flx, taux_1m, tauy_1m) 
    100100  ) 
    … …  
    102102=== How to manage Interannual or Climatological Runs === 
    103103==== 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) 
     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) 
    105105 
    106106  see : [https://forge.ipsl.jussieu.fr/nemo/wiki/libIGCM/change_BC change_BC] 
    107107 
    108108=== 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 
     109  on mercure: in Job_Name: #PBS -M name@mail [[BR]]  on platine: In Job_Name: #BSUB -u name@mail 
    110110 
    111111  Simona Flavoni last update:  [[Timestamp]]