Changes between Version 9 and Version 10 of Doc/CheckDebug


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Timestamp:
09/22/14 14:57:48 (6 years ago)
Author:
ncarenton
Comment:

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  • Doc/CheckDebug

    v9 v10  
    274274}}} 
    275275 
    276 ## Start or restart post processing jobs ## 
    277 Please look at the next paragraph. 
    278  
    279 # Start or restart post processing jobs # 
    280  
    281 You can run post processing jobs once the main job is finished (for example if the post processing job was deactivated in [#Lespost-traitementsdansconfig.card config.card] or if you encountered a [#Debug bug]). 
    282  
    283 On TGCC, the machine used for post processing is the same as the computing machine. On IDRIS, the machine to be used for post-processing is adapp (since July 2013) with same file system available : $WORKDIR, $HOME, ... . You can :  
    284   1. work directly in the experiment directory (which looks like `PATH_MODIPSL/config/IPSLCM5A/ST11/`). Possible option but not recommended.  
    285   1. work in a dedicated directory located in the experiment directory (e.g. `PATH_MODIPSL/config/IPSLCM5A/ST11/POST_REDO`). Best choice.  
    286   1. work in a dedicated directory which is independent of the experiment directory (e.g. `$WORKDIR/POST_REDO`). 
    287  
    288 For the last two options you must first: 
    289   * If your post processing directory is a subdirectory located in the experiment directory, copy (or make a link `ln -s`) the files and directories `config.card` `POST`, `COMP` and run.card if you want to post process only part of the simulation 
    290   * If your post processing directory is an independant directory : 
    291     * create a dedicated directory (for all simulations) ; 
    292     * transfer libIGCM and run ins_job (for all simulations) ; 
    293     * create a directory for the simulation to analyze (i.e. for each simulation) : 
    294 {{{ 
    295 #!sh 
    296 cd $PATH_MODIPSL/config/IPSLCM5A/ST11 
    297 mkdir -p POST_REDO 
    298 cd POST_REDO/ 
    299 cp -pr ../COMP  .  
    300 cp -pr ../POST  . 
    301 cp -pr ../config.card  . 
    302 cp -pr ../run.card . 
    303 }}} 
    304  
    305  
    306 [[NoteBox(warn, Before submitting a post processing job at TGCC (`rebuild_fromWorkdir.job`\, `pack_debug.job`\, `pack_output.job`\, `pack_restart.job`\, `monitoring.job`\, `create_ts.job`\, `create_se.job`) you must make sure that the submission group in present in the job header (#MSUB -A genxxxx). If it isn't\, add it., 600px)]] 
    307 ## Restart REBUILD ## 
    308  
    309  * Copy the `rebuild_fromWorkdir.job` file to the experiment directory or to the dedicated directory; 
    310  
    311  * Edit it: 
    312 {{{ 
    313 #!sh 
    314 StandAlone=true 
    315  
    316 libIGCM=                    # Points to the libIGCM directory of the experiment  
    317  
    318 PeriodDateBegin=            # beginning date of the last serie to be "rebuilded"  
    319  
    320 NbRebuildDir=               # Number of directories in the series to be "rebuilded"  
    321                             # until the PeriodDateBegin  
    322  
    323  
    324 REBUILD_DIR=                # Path for the backup of files waiting to be reconstructed  
    325                             # (looking like $SCRATCHDIR/IGCM_OUT/.../JobName/REBUILD or $SCRATCHDIR/TagName/JobName/REBUILD  for version older than libIGCM_v2.0 
    326                             # if RebuildFromArchive=NONE)  
    327  
    328 MASTER=${MASTER:=curie|ada} # Select the computing machine : MASTER=curie for example 
    329 }}} 
    330  
    331  
    332  * Submit the job: 
    333 {{{ 
    334 #!sh 
    335 ccc_msub rebuild_fromWorkdir.job                # TGCC 
    336  
    337 llsubmit rebuild_fromWorkdir.job                # IDRIS 
    338 }}} 
    339  
    340  
    341 [[NoteBox(note, The rebuild job submits `pack_output.job` automatically., 600px)]] 
    342 ## Restart Pack_output ## 
    343  
    344  The pack_output (e.g. in case it was not submitted by the rebuild job): 
    345  
    346   * Copy the `libIGCM/pack_output.job` file to the experiment directory or to the dedicated directory; 
    347   * Edit it :  
    348 {{{ 
    349 #!sh 
    350 libIGCM=${libIGCM:=::modipsl::/libIGCM}         # path of the libIGCM library 
    351  
    352 MASTER=${MASTER:=curie|ada}                     # machine on which you work 
    353  
    354 DateBegin=${DateBegin:=20000101}                # start date of the period to be packed 
    355    
    356 DateEnd=${DateEnd:=20691231}                    # end date of the period to be packed 
    357    
    358 PeriodPack=${PeriodPack:=10Y}                   # pack frequency 
    359 }}} 
    360   * Submit the job: 
    361 {{{ 
    362 #!sh 
    363 ccc_msub pack_output.job                        # TGCC 
    364  
    365 llsubmit pack_output.job                        # IDRIS 
    366 }}} 
    367  
    368 [[NoteBox(note, `create_ts.job` and `create_se.job` are submitted automatically., 600px)]] 
    369  
    370 ## Restart Pack_restart or Pack_debug ## 
    371  
    372    * Copy the libIGCM/pack_debug.job and libIGCM/pack_restart.job files to the experiment directory or to the dedicated directory; 
    373    * Edit them :  
    374 {{{ 
    375 #!sh 
    376 libIGCM=${libIGCM:=::modipsl::/libIGCM}         # path of the libIGCM library 
    377  
    378 MASTER=${MASTER:=curie|ada}                     # machine on which you work 
    379  
    380 DateBegin=${DateBegin:=20000101}                # start date of the period to be packed 
    381    
    382 DateEnd=${DateEnd:=20691231}                    # end date of the period to be packed 
    383    
    384 PeriodPack=${PeriodPack:=10Y}                   # pack frequency 
    385 }}} 
    386    * Submit the two jobs:  
    387 {{{ 
    388 #!sh 
    389 ccc_msub pack_debug.job ; ccc_msub pack_restart.job      # TGCC 
    390  
    391 llsubmit pack_debug.job ; llsubmit pack_restart.job      # IDRIS 
    392 }}} 
    393  
    394  
    395  
    396 ## Restart the Time series ## 
    397  
    398 [[NoteBox(tip, In case you haven't done it yet\, retrieve `config.card` `COMP` `POST` and eventually `run.card` (post process only part of the simulation) in the `POST_REDO/` directory., 600px)]] 
    399  
    400 There are two ways: 
    401  
    402 ### !TimeSeries_checker.job - Recommended method ### 
    403  
    404    * Copy the `libIGCM/TimeSeries_Checker.job` file to the experiment directory or to the dedicated directory; 
    405    * Edit it: 
    406 {{{ 
    407 #!sh 
    408 libIGCM=${libIGCM:=...MYEXP/modipsl/libIGCM}    # Path of the libIGCM library 
    409  
    410 SpaceName=${SpaceName:=DEVT}                  
    411  
    412 ExperimentName=${ExperimentName:=pdControl} 
    413  
    414 JobName=${JobName:=MYEXP} 
    415  
    416 CARD_DIR=${CARD_DIR:=${CURRENT_DIR}}            # Path of the experiment directory  
    417                                                 # (including CURRENT_DIR if you copied  
    418                                                 # TimeSeries_Checker.job properly)  
    419  
    420 export BRIDGE_MSUB_PROJECT=gen2211              # number of your genci project 
    421  
    422 }}} 
    423    * Run the !TimeSeries_Checker.job in interactive mode. It will call the missing create_ts jobs : 
    424 {{{ 
    425 #!sh 
    426 ./TimeSeries_Checker.job 
    427 }}} 
    428      or alternatively, in ksh : 
    429 {{{ 
    430 #!sh 
    431 ./TimeSeries_Checker.job 2>&1 | tee TSC_OUT     # Create log file 
    432  
    433 grep Batch TSC_OUT                              # find all the submitted jobs 
    434 }}} 
    435  
    436  
    437 ### Restart create_ts.job ### 
    438  
    439    * Copy the `libIGCM/create_ts.job` file to the experiment directory or to the dedicated directory; 
    440    * Edit it: 
    441 {{{ 
    442 #!sh 
    443 StandAlone=true 
    444  
    445 libIGCM=                                        # Path of the libIGCM library 
    446  
    447 PeriodDateEnd                                   # end date of the time series to be created 
    448  
    449 CompletedFlag                                   # end date of the existing time series  
    450  
    451 TsTask=2D                                       # select 2D or 3D 
    452  
    453 RebuildFrequency=true 
    454 }}} 
    455    * Run the job:  
    456 {{{ 
    457 #!sh 
    458 ccc_msub create_ts.job                          # TGCC 
    459  
    460 llsubmit create_ts.job                          # IDRIS 
    461 }}} 
    462  
    463 [[NoteBox(note, If your time series (TS) are 2D and 3D you must run the create_ts jobs twice and change the !TsTask variable accordingly., 600px)]] 
    464  
    465 ## Restarting the seasonal mean calculations ## 
    466  
    467 [[NoteBox(tip, Transfer `config.card`\, `COMP`\, `POST`\, and `run.card` (post process part of the simulation only) in the `POST_REDO/` directory if you have not done so yet., 600px)]] 
    468  
    469 There are two methods:  
    470  
    471 ### SE_Checker.job (recommended method) ### 
    472  
    473  * Copy the `libIGCM/SE_Checker.job` file to the experiment directory or to the dedicated directory; 
    474  * Edit it ; 
    475  * Run `SE_checker.job` in interactive mode. This will call the create_se jobs:  
    476 {{{ 
    477 #!sh 
    478 ./SE_Checker.job 
    479 }}}  
    480    or alternatively, in ksh :  
    481 {{{ 
    482 #!sh 
    483 # Create logfile: 
    484 ./SE_Checker.job 2>&1 | tee SE_OUT 
    485 # Find all started jobs : 
    486 grep Batch SE_OUT 
    487 }}} 
    488   
    489 ### Restart create_se.job ### 
    490  
    491  * Copy the `libIGCM/create_se.job` file to the experiment directory or to the dedicated directory; 
    492  * Edit it: 
    493 {{{ 
    494 #!sh 
    495 StandAlone=true 
    496  
    497 libIGCM=                                        # path of the libIGCM library 
    498  
    499 PeriodDateEnd=                                  # end date of the decade to be processed 
    500 }}} 
    501  * Submit the job:  
    502 {{{ 
    503 #!sh 
    504 ccc_msub create_se.job                          # TGCC 
    505  
    506 llsubmit create_se.job                          # IDRIS 
    507 }}} 
    508