Changes between Version 22 and Version 23 of Doc/Setup


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Timestamp:
09/24/15 16:33:49 (9 years ago)
Author:
sdipsl
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  • Doc/Setup

    v22 v23  
    2222 
    2323 
    24 Each of these subdirectories may contain a reference experiment (e.g. '''clim''' and '''amip''' for LMDZOR, NMHC_AER, AER and GES for LMDZORINCA, '''piControl''', '''historical''' and cie for IPSLCM5_v5) and the file ''config.card'' which will be your simulation's initial setup.  
     24Each of these subdirectories may contain a reference experiment (e.g. '''clim''' and '''amip''' for LMDZOR, NMHC_AER, AER and GES for LMDZORINCA, '''piControl''', '''historical''' and cie for IPSLCM5_v5) and the file ''config.card'' which will be your simulation's initial setup. 
    2525 
    2626Before preparing the working directory you must know which kind of simulation you want to perform. Then, you must copy the ''config.card'' file at the same level as the main ''Makefile''.  
    … …  
    3434[[Image(wiki:DocEsetup:creation_exp_v5.jpg, 50%)]]  
    3535 
    36 The header of ''config.card'' contains the '''!JobName''' field for which you must specify your simulation's  name. Then run the '''`ins_job`''' script that will in first time ask you, if you are working on TGCC, your id group, and then create a directory for your experiment. If you are working on IDRIS it will directly create a directory for your experiment.  
     36The header of ''config.card'' contains the '''!JobName''' field for which you must specify your simulation's name. Then run the '''`ins_job`''' script that will in first time ask you, if you are working on TGCC, your id group, and then create a directory for your experiment. If you are working on IDRIS it will directly create a directory for your experiment.  
    3737[[BR]] In the previous example, a simulation called ''DIADEME'' is created: 
    3838{{{ 
    … …  
    4242ls  
    4343  AA_Make Makefile EXPERIMENTS GENERAL config.card 
    44 vi config.card    # Change JobName=DIADEME 
     44vi config.card      # Change JobName=DIADEME 
     45                    # Change [Executable] section to specify your executionType. see config.card description 
    4546../../util/ins_job  # Check and complet job's header 
    4647ls  
    4748  AA_Make Makefile EXPERIMENTS GENERAL DIADEME 
    4849}}} 
    49 The ''config.card'' file is deleted and a directory called DIADEME is created.  
    50  
     50A directory called ''DIADEME'' is created and the config.card file is moved in. 
    5151 
    5252---- 
    … …  
    8383[[BR]] [[BR]] 
    8484 
    85 Example 1: The output directory for the following case will be IGCM_OUT/LMDZOR/TEST/REINE/DIADEME 
     85'''Example 1: The output directory for the following case will be IGCM_OUT/LMDZOR/TEST/REINE/DIADEME''' 
    8686{{{ 
    8787#!sh  
    … …  
    9494 
    9595 
    96 Example 2: without !ExperimentName and !SpaceName 
     96'''Example 2: without !ExperimentName and !SpaceName''' 
    9797{{{ 
    9898#!sh  
    … …  
    106106 
    107107[[NoteBox(note,if !SpaceName=TEST all output will be store on scratchdir (on curie) or workdir (on ada), 600px)]] 
     108 
    108109#### !PeriodLength #### 
    109 The parameter !PeriodLength allows you to determine the continuous length of a simulation period for your configuration, i.e. the frequency at which restart files are created. '''The maximum !PeriodLength for any LMDZ model is 1M'''.  
    110  
    111  
    112 ### The [Restarts] section ### 
    113 The Restarts section allow to start from an existing simulation. This simulation can be found at the archive machine or at local scratch- or workdir. Activate by setting '''!OverRule=y'''. All components (e.g. ATM, SRF, etc) will then use the same simulation as restart state.   
    114  
    115 {{{ 
    116 #!sh  
    117 [Restarts] 
    118 OverRule=y 
    119 RestartDate=1999-12-31                                  # Last day of the experience used as restart for all components 
    120 RestartJobName=EXP00                                    # Define restart simulation name for all components 
    121 RestartPath=${ARCHIVE}/IGCM_OUT/IPSLCM5A/DEVT/pdControl # Path Server Group Login 
    122 }}} 
    123  
    124 The root path for the '''!RestartPath''' depend on the computing center. They are: 
    125 {{{ 
    126 #!sh  
    127 ${ARCHIVE}                           # The storage machine of the computing center 
    128                                      # (CCCSTOREDIR or ERGON). This space can contain   
    129                                      # tar of restarts or  
    130                                      # usual restarts files 
    131 /ccc/store/cont003/dsm/login         # TGCC 
    132 /u/rech/ces/login                    # IDRIS 
    133  
    134 ${SCRATCHDIR}                        # The large TGCC workspace (no backup)  
    135  
    136 /ccc/scratch/cont003/dsm/login       # This kind of space can contain  
    137                                      # usual restarts files 
    138  
    139 ${WORKDIR}                           # The large IDRIS workspace (no backup) 
    140                                      
    141 /workgpfs/rech/ces/login             # This kind of space can contain  
    142                                      # usual restarts files 
    143 }}} 
    144  
    145 [[NoteBox(note, libIGCM manages the difference in treatment between a path pointing to restart files that are directly accessible (without pack) and a path pointing to restart files that are in tar format (after pack). The management is made according to the path you provided. ,600px)]] 
    146  
    147   
    148 ### The [ATM], ..., sections of the model components ### 
    149  
    150 This section for each of the model components allows you to:  
    151  * '''define the output frequency'''; 
    152  * '''define whether this component is installed''' which will only be considered if you specified '''!OverRule=n''' in the [Restarts] section. 
    153  
    154 The possible settings for the '''!RestartPath''' options are the same as for the [Restarts] section. 
    155  
    156 The possible settings for the '''!WriteFrequency''' options are: 
    157  * 1M    (monthly) 
    158  * 5D    (5-day) 
    159  * 1D    (daily) 
    160  * HF    (6-hour high frequency) 
    161  * HF3h  (real-time 3-hour frequency - specific to LMDZ) 
    162  * HF3hm (3-hour averaged high frequency - specific to LMDZ) 
    163  * STN   (instantaneous output only for the CFMIP stations - specific to LMDZ). 
    164  
    165  
    166 {{{ 
    167 #!sh  
    168 [ATM] 
    169 WriteFrequency="1M 1D"                                  # Activate the writing frequency of this component 
    170 Restart=y                                               # If config_Restarts_OverRule == 'n' next 4 params are read 
    171 RestartDate=1999-12-31                                  # Last day of the experience used as restart for this component if Restart=y 
    172 RestartJobName=piControl25                              # Define restart simulation name for this component 
    173 RestartPath=${ARCHIVE}/IGCM_OUT/IPSLCM5A/PROD/piControl # Path Server Group Login 
    174 }}} 
    175  
    176  
    177 '''!WriteFrequency specific to the model components'''[[BR]] 
    178  
    179  * '''LMDZ''' : ([ATM]) Each of the frequencies settings 1M, 1D, HF, HF3h, HF3hm, and STN correspond to a given output file. For example, if you specify ''1M'', a histmth.nc file will be created. If you want to change the output frequency in the histmth file you must change the corresponding lmdz parameter file. See [wiki:DocImodelBlmdz here]. 
    180  
    181  * '''ORCHIDEE'''  
    182    * '''[SRF]''' : The first frequency corresponds to the output frequency for the sechiba_history.nc file. The available frequencies are: xY, xM, 5D, 1D and xs, where x is an integer and s means seconds. This file is required. If you add HF, a second sechiba_out_2.nc file will be written with the 3H frequency.  
    183    * '''[SBG]''' : Only one frequency (xY, xM, 5D, 1D or xs) can be specified. It applies to the stomate_history.nc file. The stomate_history_ipcc.nc file always contains daily outputs.  
    184  
    185  * '''INCA''' : the section !WriteFrequency does not work. Click [wiki:DocImodelDinca here] to learn more about how to change the writing frequency. 
     110The parameter !PeriodLength allows you to determine the continuous length of a simulation period for your configuration, i.e. the frequency at which restart files are created. '''Using v5 configuration having the LMDz model the maximum !PeriodLength for is 1M'''.  
    186111 
    187112### The section [Executable] ### 
    … …  
    197122Note : (",") indicates that this component has no executable. It is defined in a library linked to another executable (e.g. Orchidee in LMDZOR or Inca in LMDZINCA).  
    198123 
    199 '''Example for an hybrid MPI/OpenMP simulation with LMDZ''' : Atmosphere on 32 MPI process and 4 OMP threads per process. 
     124'''Example for an MPMD MPI execution with NEMO and XIOS''' : Ocean on 127 MPI process and IO Server on 1 MPI process. 
    200125{{{ 
    201126#!sh 
    202127[Executable] 
    203128#D- For each component, Real name of executable, Name of executable in RUN_DIR directory, Number of MPI process, Number of OpenMP threads 
    204 ATM= (gcm.e, lmdz.x, 32MPI, 4OMP) 
    205 SRF= ("" ,"" ) 
    206 SBG= ("" ,"" ) 
    207 }}} 
    208  
    209 '''Example for coupled configuration on curie''' : Atmosphere on 27 MPI process and 4 OMP threads per process, Ocean on 19 MPI process, IO Server on 1 MPI process. 
     129OCE= (opa, opa.xx, 127MPI) 
     130ICE= ("" ,"" ) 
     131MBG= ("" ,"" ) 
     132IOS= (xios_server.exe, xios.x, 1MPI) 
     133}}} 
     134 
     135'''Example for an MPMD hybrid MPI/OpenMP execution with IPSLCM coupled configuration''' : Atmosphere on 27 MPI process and 4 OMP threads per process, Ocean on 19 MPI process, IO Server on 1 MPI process. 
    210136{{{ 
    211137#!sh 
    … …  
    221147IOS= (xios_server.exe, xios.x, 1MPI) 
    222148}}} 
     149 
     150'''Another example for an MPMD hybrid MPI/OpenMP execution with LMDZ and XIOS''' : Atmosphere on 47 MPI process, 8 OMP threads per processand and IO server on 1 MPI process. 
     151{{{ 
     152#!sh 
     153[Executable] 
     154#D- For each component, Real name of executable, Name of executable in RUN_DIR directory, Number of MPI process, Number of OpenMP threads 
     155ATM= (gcm.e, lmdz.x, 47MPI, 8OMP) 
     156SRF= ("" ,"" ) 
     157SBG= ("" ,"" ) 
     158IOS= (xios_server.exe, xios.x, 1MPI) 
     159}}} 
     160 
     161'''Example for an SPMD hybrid MPI/OpenMP simulation with LMDZ''' : Atmosphere on 32 MPI process and 4 OMP threads per process. 
     162{{{ 
     163#!sh 
     164[Executable] 
     165#D- For each component, Real name of executable, Name of executable in RUN_DIR directory, Number of MPI process, Number of OpenMP threads 
     166ATM= (gcm.e, lmdz.x, 32MPI, 4OMP) 
     167SRF= ("" ,"" ) 
     168SBG= ("" ,"" ) 
     169}}} 
     170 
     171### The [Restarts] section ### 
     172The Restarts section allow to start from an existing simulation. This simulation can be found at the archive machine or at local scratch- or workdir. Activate by setting '''!OverRule=y'''. All components (e.g. ATM, SRF, etc) will then use the same simulation as restart state.   
     173 
     174{{{ 
     175#!sh  
     176[Restarts] 
     177OverRule=y 
     178RestartDate=1999-12-31                                  # Last day of the experience used as restart for all components 
     179RestartJobName=EXP00                                    # Define restart simulation name for all components 
     180RestartPath=${ARCHIVE}/IGCM_OUT/IPSLCM5A/DEVT/pdControl # Path Server Group Login 
     181}}} 
     182 
     183The root path for the '''!RestartPath''' depend on the computing center. They are: 
     184{{{ 
     185#!sh  
     186${ARCHIVE}                           # The storage machine of the computing center 
     187                                     # (CCCSTOREDIR or ERGON). This space can contain   
     188                                     # tar of restarts or  
     189                                     # usual restarts files 
     190/ccc/store/cont003/dsm/login         # TGCC 
     191/u/rech/ces/login                    # IDRIS 
     192 
     193${SCRATCHDIR}                        # The large TGCC workspace (no backup)  
     194 
     195/ccc/scratch/cont003/dsm/login       # This kind of space can contain  
     196                                     # usual restarts files 
     197 
     198${WORKDIR}                           # The large IDRIS workspace (no backup) 
     199                                     
     200/workgpfs/rech/ces/login             # This kind of space can contain  
     201                                     # usual restarts files 
     202}}} 
     203 
     204[[NoteBox(note, libIGCM manages the difference in treatment between a path pointing to restart files that are directly accessible (without pack) and a path pointing to restart files that are in tar format (after pack). The management is made according to the path you provided. ,600px)]] 
     205 
     206  
     207### The [ATM], ..., sections of the model components ### 
     208 
     209This section for each of the model components allows you to:  
     210 * '''define the output frequency'''; 
     211 * '''define whether this component is installed''' which will only be considered if you specified '''!OverRule=n''' in the [Restarts] section. 
     212 
     213The possible settings for the '''!RestartPath''' options are the same as for the [Restarts] section. 
     214 
     215The possible settings for the '''!WriteFrequency''' options are: 
     216 * 1M    (monthly) 
     217 * 5D    (5-day) 
     218 * 1D    (daily) 
     219 * HF    (6-hour high frequency) 
     220 * HF3h  (real-time 3-hour frequency - specific to LMDZ) 
     221 * HF3hm (3-hour averaged high frequency - specific to LMDZ) 
     222 * STN   (instantaneous output only for the CFMIP stations - specific to LMDZ). 
     223 
     224 
     225{{{ 
     226#!sh  
     227[ATM] 
     228WriteFrequency="1M 1D"                                  # Activate the writing frequency of this component 
     229Restart=y                                               # If config_Restarts_OverRule == 'n' next 4 params are read 
     230RestartDate=1999-12-31                                  # Last day of the experience used as restart for this component if Restart=y 
     231RestartJobName=piControl25                              # Define restart simulation name for this component 
     232RestartPath=${ARCHIVE}/IGCM_OUT/IPSLCM5A/PROD/piControl # Path Server Group Login 
     233}}} 
     234 
     235 
     236'''!WriteFrequency specific to the model components'''[[BR]] 
     237 
     238 * '''LMDZ''' : ([ATM]) Each of the frequencies settings 1M, 1D, HF, HF3h, HF3hm, and STN correspond to a given output file. For example, if you specify ''1M'', a histmth.nc file will be created. If you want to change the output frequency in the histmth file you must change the corresponding lmdz parameter file. See [wiki:DocImodelBlmdz here]. 
     239 
     240 * '''ORCHIDEE'''  
     241   * '''[SRF]''' : The first frequency corresponds to the output frequency for the sechiba_history.nc file. The available frequencies are: xY, xM, 5D, 1D and xs, where x is an integer and s means seconds. This file is required. If you add HF, a second sechiba_out_2.nc file will be written with the 3H frequency.  
     242   * '''[SBG]''' : Only one frequency (xY, xM, 5D, 1D or xs) can be specified. It applies to the stomate_history.nc file. The stomate_history_ipcc.nc file always contains daily outputs.  
     243 
     244 * '''INCA''' : the section !WriteFrequency does not work. Click [wiki:DocImodelDinca here] to learn more about how to change the writing frequency. 
    223245 
    224246### The [Post] section ###