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 42 and Version 43 of user/flavoni/libIGCM/setupsimupage


Ignore:
Timestamp:
2013-03-11T11:34:31+01:00 (11 years ago)
Author:
flavoni
Comment:

--

Legend:

Unmodified
Added
Removed
Modified

  • user/flavoni/libIGCM/setupsimupage

    v42 v43  
    1 == '''Set up a simulation''' ==   
    2 [[BR]] 
     1== !'''Set up a simulation!''' ==   [[BR]] 
    32 
    43[[PageOutline]] 
    5     
    6     '''First of all see official documentation''' 
    74 
    8  http://forge.ipsl.jussieu.fr/libigcm/wiki/ 
     5  ''' First of all see official documentation''' 
    96 
    10  === Important files === 
    11   
    12  Important files to set up a simulation are:  [[BR]] 
    13  ORCA2_LIM/IGCM00/config.card  [[BR]] 
    14  ORCA2_LIM/IGCM00/PARAM/iodef.xml  [[BR]] 
    15  ORCA2_LIM/IGCM00/COMP/opa9.card  [[BR]] 
     7  http://forge.ipsl.jussieu.fr/igcmg/wiki/platform/documentation 
    168 
    17  === config.card === 
    18  ==== How to manage job name, start date, end date, and restart files ==== 
    19   
    20 Here you can find a description of some parts of config.card 
     9=== 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 
     12=== config.card === 
     13==== 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 
    2115 
    2216In ORCA2_LIM/IGCM00/'''config.card''' file  [[BR]] 
    23  you have to put a '''!JobName''' maximum of 8 characters [[BR]] 
    24  in !LongName you can put a comment that can remember to you all properties of the Job.[[BR]] 
    25   
    26  you have to set duration of your experience and setting '''!PeriodLength''' parameter, so you manage write output frequency of restart files. 
    2717 
    28  ( for example : if you have and experience of 10 years and a !PeriodLength of 1 year, you will have 10 restart files ) 
     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]] 
    2919 
    30  #-- Début et fin de Job [[BR]] 
    31  #-- "YYYY-MM-DD" [[BR]] 
    32  DateBegin=2001-01-01 [[BR]] 
    33  DateEnd=2010-12-31 [[BR]] 
    34  #============================ [[BR]] 
    35  #-- 1Y, 1M, 5D, 1D [[BR]] 
    36  PeriodLength=1Y [[BR]] 
     20  you have to set duration of your experience and setting ''' !PeriodLength '''  parameter, so you manage write output frequency of restart files. 
    3721 
    38  '''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 
     22  ( for example : if you have and experience of 10 years and a !PeriodLength  of 1 year, you will have 10 restart files ) 
    3923 
    40  ==== How to continue a simulation ==== 
    41   
    42  see french version : [http://forge.ipsl.jussieu.fr/libigcm/wiki/libIGCM/DocUtilisateur/FAQ#Commentcontinuerunesimulation here] 
    43   
    44  If you have finished a previous simulation and now you want to continue it you have to change : 
    45   
    46  in ORCA2_LIM/IGCM00/config.card you have to set : [[BR]] 
    47  new '''DateEnd'''[[BR]] 
    48    
    49   
    50  in ORCA2_LIM/IGCM00/run.card[[BR]] 
    51  '''PeriodDateEnd'''[[BR]] 
    52  '''PeriodState= OnQueue''' 
    53   
     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]] 
    5425 
    55  ==== How to manage calendar type ==== 
     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 
    5627 
    57  in ORCA2_LIM/IGCM00/config.card you have to set !CalendarType  like 360d or leap or noleap  
     28==== How to continue a simulation ==== 
     29  see french version : [http://forge.ipsl.jussieu.fr/libigcm/wiki/libIGCM/DocUtilisateur/FAQ#Commentcontinuerunesimulation here] 
    5830 
    59  # for '''360d''' :[[BR]]  
    60  you have to be careful at[[BR]] 
    61  DateEnd=2010-12-3'''0''' [[BR]] 
    62  because every month has 30 days[[BR]]  
     31  If you have finished a previous simulation and now you want to continue it you have to change : 
    6332 
    64  If you put for example DateEnd=2005-12-31, you will have another run, of duration like your !PeriodLength  
    65   
    66  # for '''noleap''' :  [[BR]] 
    67  '''How to manage rdt ( i.e. timestep )'''[[BR]] 
    68  in ORCA2_LIM/IGCM00/COMP/opa9.driver you have to change parameter : ORCA_NPDT_JOUR=15 [[BR]] 
    69  ( 15 corresponds to 86400s/5760s; it does mean that in one day you have 15 iterations; and it does mean that timestep is 5760) 
    70   
    71  ==== How to manage monoprocessor or multiprocessor run ==== 
     33  in ORCA2_LIM/IGCM00/config.card you have to set : [[BR]] new ''' DateEnd ''' [[BR]] 
    7234 
    73  From nemo '''version 3_3''' set up and compile a mono-processor run : 
     35  in ORCA2_LIM/IGCM00/run.card[[BR]] ''' PeriodDateEnd ''' [[BR]] ''' PeriodState = OnQueue ''' 
    7436 
    75  ./makenemo -m SX8_BRODIE -n ORCA2_LIM   
     37==== How to manage calendar type ==== 
     38  in ORCA2_LIM/IGCM00/config.card you have to set !CalendarType   like 360d or leap or noleap 
    7639 
    77  for multiprocessor run see : [[BR]] 
    78  [https://forge.ipsl.jussieu.fr/nemo/wiki/libIGCM_nemo_v_3_3/parallelpage_3_3 parallelpage for nemo version 3_3] [[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]] 
    7941 
    80  ( To understand more on  mono or multi proc run with nemo till version 3_2_2 see also : [[BR]] 
    81  [https://forge.ipsl.jussieu.fr/nemo/wiki/libIGCM/parallelpage parallelpage till nemo version 3_2_2] ) [[BR]] 
     42  If you put for example DateEnd =2005-12-31, you will have another run, of duration like your !PeriodLength 
    8243 
    83  #-- PBS Class (required ONLY on brodie mono/multi)  [[BR]] 
    84  JobClass=mono     [[BR]] 
    85  #JobClass=multi   [[BR]] 
    86  #============================   [[BR]] 
    87  #-- Total Number of Processors  [[BR]] 
    88  #JobNumProcTot=4  (put same number of processors choosen at compiling time, in this example is 4)               [[BR]] 
    89  JobNumProcTot=1                 [[BR]] 
    90  #============================   [[BR]] 
    91  #-- Run Options :               [[BR]] 
    92  #JobRunOptions='"-np "${BATCH_NUM_PROC_TOT}"'    [[BR]] 
    93  JobRunOptions=''          [[BR]] 
    94  #============================   [[BR]] 
     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) 
    9545 
    96  ==== How to set Init & Boundary condition's directory ==== 
     46==== How to manage monoprocessor or multiprocessor run ==== 
     47  From nemo ''' version 3_3'''  set up and compile a mono-processor run : 
    9748 
    98  By default R_BC is commented, it does mean that INIT & Boundary files are in common account of IPSL, at IDRIS or CCRT :   
    99   
    100  #R_BC=/u/rech/psl/rpsl035/IGCM/BC  [[BR]] 
    101  #R_BC=/dmnfs/cont003/p86ipsl/IGCM/BC  [[BR]] 
     49  ./makenemo -m SX8_BRODIE -n ORCA2_LIM 
    10250 
    103  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]] 
    104  with all initial files for nemo, and where you have to add your forcing files. [[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]] 
    10552 
    106  ==== How to restart from another run ==== 
     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]] 
    10754 
    108  In ORCA2_LIM/IGCM00/config.card :  
     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]]'' 
    10956 
    110  If you want to restart from restart file of experience core260i (corersponding at the Job_core260i) of the year 2007 you have to put:   
     57==== How to set Init & Boundary condition's directory ==== 
     58  By default R_BC is commented, it does mean that INIT & Boundary files are in common account of IPSL, at IDRIS or CCRT : 
    11159 
    112  #================ [[BR]] 
    113  #D-- Restarts - [[BR]] 
    114  [Restarts]  [[BR]] 
    115  #D- If you want a GENERAL RULE FOR RESTARTS, put this flag to 'y'  [[BR]] 
    116  OverRule=y   [[BR]] 
    117  #D- Last day of the experience used as restart  [[BR]] 
    118  RestartDate=2007-12-31  [[BR]] 
    119  #D- Define restart simulation name  [[BR]] 
    120  RestartJobName=core260i   [[BR]] 
    121  #D- Path Server Group Login    [[BR]] 
    122  RestartPath=${ARCHIVE}/IGCM_OUT/ORCA2_LIM2   [[BR]] 
    123   
    124  ==== How to have post treatement ==== 
     60  #R_BC=/u/rech/psl/rpsl035/IGCM/BC  [[BR]] #R_BC=/dmnfs/cont003/p86ipsl/IGCM/BC  [[BR]] 
    12561 
    126  if you want to activate post treatment with libigcm to have monitoring & ATLAS see :  
    127  [https://forge.ipsl.jussieu.fr/nemo/wiki/libIGCM/postprocessingpage postprocessingpage] 
    128   
     62  If you want to have you own directory you have to create a directory in wich you have to create OCE/ORCA2_LIM2 directory in which you have to put tar file : http://www.nemo-ocean.eu/Using-NEMO/Configurations/ORCA2_LIM  [[BR]] with all initial files for nemo, and where you have to add your forcing files. [[BR]] 
    12963 
    130  ==== How to manage write output frequency ==== 
     64==== How to restart from another run ==== 
     65  In ORCA2_LIM/IGCM00/config.card : 
    13166 
    132  in ORCA2_LIM/IGCM00/config.card you have to set !WriteFrequency of your experience  
    133   
    134  You can have multiple frequencies, you need to have a blank between every frequency, for example : [[BR]] 
     67  If you want to restart from restart file of experience core260i (corersponding at the Job_core260i) of the year 2007 you have to put: 
    13568 
    136  '''ocean''' output files every 1 year and 1 month : [[BR]]  
    137  #=================== [[BR]] 
    138  #D-- OCE - [[BR]] 
    139  [OCE] [[BR]] 
    140  WriteFrequency="1Y 1M" 
    141   
    142  and '''ice''' output files every 1 month : [[BR]] 
    143  #=================== [[BR]] 
    144  #D-- ICE - [[BR]] 
    145  [ICE] [[BR]] 
    146  WriteFrequency="1M" 
    147    
    148  These settings have to be coherents also with path in ORCA2_LIM/IGCM00/COMP/'''opa9.card''' in part :  [[BR]] 
    149  [OutputFiles]    [[BR]] 
    150  List=   (${PREFIX_WF'''1'''}_grid_T.nc,         ${R_OUT_OCE_WF'''1'''}/${PREFIX}_${WF'''1'''}_grid_T.nc,               NONE),\   [[BR]] 
    151   (${PREFIX_WF'''1'''}_grid_U.nc,         ${R_OUT_OCE_WF'''1'''}/${PREFIX}_${WF'''1'''}_grid_U.nc,               NONE),\    [[BR]] 
    152   (${PREFIX_WF'''1'''}_grid_V.nc,         ${R_OUT_OCE_WF'''1'''}/${PREFIX}_${WF'''1'''}_grid_V.nc,               NONE),\    [[BR]] 
    153   (${PREFIX_WF'''2'''}_grid_T.nc,         ${R_OUT_OCE_WF'''2'''}/${PREFIX}_${WF'''2'''}_grid_T.nc,               NONE),\    [[BR]] 
    154   (${PREFIX_WF'''2'''}_grid_U.nc,         ${R_OUT_OCE_WF'''2'''}/${PREFIX}_${WF'''2'''}_grid_U.nc,               NONE),\   [[BR]] 
    155   (${PREFIX_WF'''2'''}_grid_V.nc,         ${R_OUT_OCE_WF'''2'''}/${PREFIX}_${WF'''2'''}_grid_V.nc,               NONE),\   [[BR]] 
    156   
    157  You have to put number of frequencies that you put in part [OCE] of config.card (in this case you have 2 frequencies : 1Y 1M)      
     69  #================ [[BR]] #D-- Restarts - [[BR]] [Restarts]  [[BR]] #D- If you want a GENERAL RULE FOR RESTARTS, put this flag to 'y'  [[BR]] OverRule =y   [[BR]] #D- Last day of the experience used as restart  [[BR]] RestartDate =2007-12-31  [[BR]] #D- Define restart simulation name  [[BR]] RestartJobName =core260i   [[BR]] #D- Path Server Group Login    [[BR]] RestartPath =${ARCHIVE}/IGCM_OUT/ORCA2_LIM2   [[BR]] 
    15870 
    159  The same for ice : ORCA2_LIM/IGCM00/COMP/'''lim2.card'''   (in this example you have only WF1) 
     71==== How to have post treatement ==== 
     72  if you want to activate post treatment with libigcm to have monitoring & ATLAS see :  [https://forge.ipsl.jussieu.fr/nemo/wiki/libIGCM/postprocessingpage postprocessingpage] 
    16073 
    161  '''VERY IMPORTANT NOTE :''' these settings are to be coherents with the ones in iodef.xml see doc : ????? (to add link to seb?) [[BR]] 
    162  In iodef.xml you can choose variables that you want to have in output at every frequency 
    163   
    164  === How to manage Interannual or Climatological Runs === 
    165  ==== in ORCA2_LIM/IGCM00/COMP/'''opa9.card''' ==== 
     74==== How to manage write output frequency ==== 
     75  in ORCA2_LIM/IGCM00/config.card you have to set !WriteFrequency  of your experience 
    16676 
    167  You have to set  
     77  You can have multiple frequencies, you need to have a blank between every frequency, for example : [[BR]] 
    16878 
    169  # Interannual_Run '''y''' if you want to do interannual runs or '''n''' if you want to do climatological runs   
    170   
    171  # In [Interannual] section you have to fill List_jobsbc of file names like they appear in namelist.  [[BR]] 
    172  ( for example if you want to do interannual run using clio bulk core you can put :  [[BR]] 
    173   List_jobsbc=(flx, taux_1m, tauy_1m)  
    174  ) 
     79  ''' ocean'''  output files every 1 year and 1 month : [[BR]]   #=================== [[BR]] #D-- OCE - [[BR]] [OCE] [[BR]] WriteFrequency ="1Y 1M" 
    17580 
    176   
    177  === How to manage Interannual or Climatological Runs === 
    178  ==== in ORCA2_LIM/IGCM00/PARAM/'''namelist''' ==== 
    179   
    180  You have to set in "namsbc" part if you want to do climatological run and if you want to do an interpolation : [[BR]]  
    181  '''time interpol.''' (logical) and '''clim''' (T/F)   
     81  and ''' ice'''  output files every 1 month : [[BR]] #=================== [[BR]] #D-- ICE - [[BR]] [ICE] [[BR]] WriteFrequency ="1M" 
    18282 
    183  see : [https://forge.ipsl.jussieu.fr/nemo/wiki/libIGCM/change_BC change_BC] 
     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]] 
    18485 
    185  === How to have mail of end of Job, on ccrt's machines === 
     86  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) 
    18687 
    187  on mercure: in Job_Name: #PBS -M name@mail [[BR]] 
    188  on platine: In Job_Name: #BSUB -u name@mail  
     88  The same for ice : ORCA2_LIM/IGCM00/COMP/''' lim2.card'''    (in this example you have only WF1) 
    18989 
     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 
    19091 
    191  Simona Flavoni last update:  [[Timestamp]] 
     92=== How to manage Interannual or Climatological Runs === 
     93==== in ORCA2_LIM/IGCM00/COMP/'''opa9.card''' ==== 
     94  You have to set 
     95 
     96  # Interannual_Run ''' y'''  if you want to do interannual runs or ''' n'''  if you want to do climatological runs 
     97 
     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    List_jobsbc=(flx, taux_1m, tauy_1m) 
     100  ) 
     101 
     102=== How to manage Interannual or Climatological Runs === 
     103==== 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 
     106  see : [https://forge.ipsl.jussieu.fr/nemo/wiki/libIGCM/change_BC change_BC] 
     107 
     108=== 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 
     111  Simona Flavoni last update:  [[Timestamp]]