Pre- and post-processing scripts

1.   version-dependent, that change with model versions (found in ${gemclim}/scripts/*) and
2.   version-invariant, that do not change (found in ${ARMNLIB}/scripts/Climat_*)
   

• a list of all scripts used by GEM/GEMCLIM,
• a list of all jobs created by these scripts and
• a diagram showing the calling sequence of scripts, jobs and models.

Calling sequences for the GEM/GEMCLIM models, scripts and jobs

Pre processing and model run

List of scripts in alphabetical order

Scripts starting with "Climat_" are only used when the model is running in climate mode. All other scripts are used in both climate and non-climate modes, unless noted otherwise.

Climat_archive_pilot

• Archives pilot information files. Usually one file per month; if the total volume is greater than 2GByte, a second, third, ... file will be created.
  

Climat_beta

• Calculates GJB's beta field.

Climat_check_rdiag

• Checks the r.diag version number (as defined by the ${RDIAG} environment variable) and compares it to ${minimal_rdiag_version} (the r.diag version that is needed to do specific calculations, i.e. rotate, during the post processing).

Climat_diag

• Takes care of the creation of global and zonal means, variances and covariances over time. Therefore it calls 'Climat_make_mean',  'Climat_make_zonaux' and 'Climat_make_covar'.

Climat_diag_phy

• Takes care of the creation of means and variances of 2-D variables from the physics.
• It sorts the variables in accumulators, non accumulators and multi level variables.
• To create the means and variances of the accumulators it calls 'Climat_surfacc_mean'.
• For the creation of the means and variances of the non accumulators and multi level variables it calls 'Climat_diag'.
• At the end it calls 'Climat_mv2cfs' to transfer the files in an archive.

Climat_eta2preshyb

• Sets all variables depending on the ${etaname} vertical configuration name.
  

Climat_get_grtyp

• Determines the grid type of a standard file.

Climat_lancer_diag

• Produces a full set of diagnostics, following WCRP and AMIP2 guidelines including:
  
  • Monthly means
    
  • Monthly zonal means
    
  • Time variances
    
  • Time covariances
    
  • zonal rms of  monthly means and variances
    
  • 0-D (global averages) and 2-D time series
    

Climat_launch_next_interval.sh

• Launches the next interval.

Climat_make_covar

• Calculates covariances over time supposing the time mean already exist.

Climat_make_gaussien

• Converts GEM-native Z-type grids into gaussian grids when ${gaussout} is set

Climat_make_mean

• Calculates means and variances over time.

Climat_make_zonaux

• Calculates zonal means and variances.
• If requires it also creates zonal plots as metacod-files.

Climat_mdpr_clean

Climat_multi_diag

• Creates inter- and intra-annual statistics from the relevant monthly means.

Climat_mv2cfs

• Archives files (using cmcarc) with the same prefix and transfers them to another machine.

Climat_post_processing

• Creates d2z_job, pilot_job (if required), rassemble_job and the post-processing- and diag_job (if required)
• Submits the post-processing_job which calls d2z-, pilot- and rassemble_job to ${dest_mach}
• Calls Climat_save_restarts at the end of a job interval (month or season)
  

Climat_prepare_job

• Calls Climat_var_test
  
• Creates 'outcfg.out' for first job
  
• Checks if ${startdate}, ${enddate}, and ${interval} are correct
  
• Calculates climatic date objective for first job
  
• Updates 'configexp.dot.cfg', 'gemclim_settings.nml', and 'outcfg.out'.
  
  • In 'configexp.dot.cfg': exp, step_total, lam_nest_exp
    
  • In 'gemclim_settings.nml': Mod_runstrt_S, Pil_jobstrt_S, Pil_jobend_S, Step_total, Step_rsti, Step_cleanup
    
  • In 'outcfg.out': steps
    
• Updates 'gemclim_settings.nml' according to ${etaname}
  
  • Creates hybrid levels: hyb
    
  • Sets pressure at model top: Pres_ptop
    
  • Creates radiation levels: RADNIVL
    
• Updates fularch
  
• Sets variables for next job
  
• Calculates 'anal_step' from 'save_anal' to save an analysis file
  
• Sets/Updates all 'Pil_' variables needed for LAM
  

Climat_rotate_vectors

• Rotates vectors fields in a file. Other fields are not touched. I.e. it transforms the wind in a rotated grid from x-,y-components into lat-,lon-components.

Climat_save_analysis

• Separates records needed for creation of an analysis file.
  
• Converts the variable name "GY" to "LG" and every IP1 level descriptors to the old style (1989) format.
  
• creates and submits anal_job.
  

Climat_save_listings

• Creates and submits save_listings_job
  

Climat_save_pilot

• Extracts nesting informations from the model output.
  
• Converts names and units.
  

Climat_save_restarts

• Creates and submits save_job
  

Climat_series_temporelles

• Extracts some of the time series required by the AMIP2 protocol. At this time, this means the following fields:
  P0, PN, T5 (1 sg), T9 (1 sg), AR, PR, UU (200+850 hPa, 1 sg), VV (200+850 hPa, 1 sg), GZ (500 hPa), TT (1 sg), HU (1 sg)

Climat_strip_phy

• Re-organizes the GEMDM dynamic (dm- and dp-) and physic (pm-) output files. At every sample time, multi-level physic variables on model levels are interpolated to the same pressure levels as are used for the dynamic output and written to a pr- file, along with the content of the dp- file. All other pm- and dm- (single-) model-level variables are written to a md- file. Note that all multi-level variables defined on ARBITRARY levels (eg. accounting for different surface types or soil levels) such as the surface albedo AL and the soil temperatures I0 are also written to the md- file.
  

Climat_surfacc_mean

• Creates temporal means and variances of 2D fields of accumulators.
• If required it also creates plots as metacod-files.

Climat_var_test

Climat_xfer

• Creates up to three jobs as needed:
  
  1. back_job:
     1. Saves analysis file from output
        
     2. Saves files for nesting information
        
  2. xfer_job:
     1. Does transfer of dm-, dp-, pm-files when post-processing is not done on ${mach}
        
  3. post_job:
     1. Moves dm-, dp-, pm-files when post-processing is done on ${mach}
        
     2. Launches Climat_post_processing
        
• Then these jobs get submitted, the first one directly, the others at the end of the previous job.
  i.e.: back_job gets submitted directly. When it finishes, back_job submits xfer_job, which itself submits post_job when it ends. Alternatively, if back_job is not needed, xfer_job gets submitted directly; or if xfer_job is not needed, back_job and post_job get concatenated and submitted directly...
  

Climat_xfer_pilot

• Creates and submits a job which transfers pilot information files from ${mach} to ${pil_mach} to ${lehost}.
  
• This created and submitted job then creates and submits a job which calls Climat_archive_pilot to ${pil_mach}.

Um_delam

• Takes care of the conversion from slab-files into standard files by calling delam.

Um_launch

• Takes care of the preparation of the environment by calling Um_preprep, Um_loadbin and Um_shipstuff.
• Creates the jobs to launch the entry and the model and then launches the entry job.
• In climate mode it also takes care of the preparation and checking of the "climate environment" by calling Climat_prepare_job.

Um_loadbin

• Compiles and loads the absolutes if necessary.
• Copies/Links them into $EXECDIR.

Um_maindriver.sh

• Launches the entry by calling Um_runent.sh resp. the model by calling Um_runent.sh.
• After the model has finished it also does some clean up in $REPRUN.

Um_preprep

• Creates the $EXECDIR.

Um_runent.sh

• It copies all files needed to run the model in the appropriate directory. These files are 'gemclim_settings.nml', the analysis file, the file with the geophysical fields, the climatology file and the model job created by Um_launch.
• It checks if the analysis file contains the right fields at the right time step.
• Then it launches the model entry absolute, main${MODEL}ntr_${ARCH}_${MODEL_VERSION}.Abs.
  
• When the model is run in LAM mode this absolute also creates the bm-files, the bitmap-files containing the nesting informations.
• In LAM climate mode it also:
  • Copies files needed by the entry from ${mach} to launching machine
    
  • Unpacks pilot information for the whole interval
    
  • Transfers the fully or partially interpolaterd pilot files to ${mach}

Um_runmod.sh

• It links a few files like model_settings, output_settings, imclima and imanclima.
• It creates the directory $REPRUN and if the model is not run in restart mode a subdirectory for each MPI processes.
• It then links other need files into the 00-00 process directory.
• Finally it launches the main model absolute, main${MODEL}dm_${ARCH}_${MODEL_VERSION}.Abs.
• After this absolute has finished the script cleans up the environment and moves the output files into $EXECDIR/output.

Um_shipstuff

• First it cleans up $EXECDIR of old, no longer needed files.
• Then it copies (ships) certain files for the actual job into $EXECDIR, eg. the configuration files, '${MODEL}_settings.nml' and 'outcfg.out' as well as *.sh, constantes, ozoclim* and irtab5_*.
• If the model is run in restart mode it retreives the restart files from the previous job.  In climate mode it will also  removes the previous job's bm-files (possibly carried on by the retreival process).
  

Um_xfer

• Tranfers the model output using Um_xfer_rsync to ${dest_mach} and if required the model listing.
• Submits a tailjob if required.

Um_xfer.sh

• In climate mode it moves the output-files from the process-directory into the output-directory
• It moves the output-files (again) in the directory 'last_step${endstep}'
• In non-climate mode it then creates and submits a job which does delamineur by calling Um_delam and starts the transfer of the ouput files by calling Um_xfer_prep.sh.
  
• In climate mode it calls Climat_xfer to start the climate post processing.
  

Um_xfer_cpac

Um_xfer_mach

• Checks if the two remote systems src_mach and dest_mach are available.

Um_xfer_mvf

Um_xfer_prep.sh

• This script takes care of the reassemblage of the output files from the different processors by calling d2z.
• It takes care of the time series files 'time_series.bin'.
• It assembles dynamics and physics output if required.
• It creates and submits a job to do the actual transfer. This last job calls Um_xfer.

Um_xfer_rsync

• Transfers directory contents from one machine to another using rsync.

d2z

• This script reassembles the output files from the different processors into one file.

delam

• This script converts files that were written slab-wise to ones that contain regular 2- and 3-D records.

List of jobs in alphabetical order

• Transfers analysis file from ${mach} to ${arch_mach}
  

• Transfers the diagnostics to ${arch_mach}
  

• Calls the Um_delam (only for version 3.1.2 and older)
  
• Calls Climat_save_analysis, if required
  
• Submits xfer_job, when post-processing is not done on ${mach} or when analysis and/or pilots information are produced
• Moves dm-, dp-, pm-files when post-processing is done on ${mach}, if  xfer_job is not called
• Calls Climat_post_processing, if xfer_job is not called
  

• Launches the next job of the model by calling typically Um_launch
  
• Calls Climat_save_restarts to start the archiving of the restart file, if required

• Does 'd2z' (converting partial-domain tile-specific #-type grids to full-domain Z-type grids)

• Calls Climat_lancer_diag
  
• Archives diagnostics created by Climat_lancer_diag
  
• Transfers diagnostics to ${arch_mach} or, if ${dest_mach} = ${mach}, creates and submits archfer_job
  
• Calls Climat_save_listings

• Exports several variables
• Creates ${EXECDIR} resp. the working directory for LAM-Climate mode
• Calls Um_maindriver.sh which than executes the entry model
• Calls soumet_la_job which than submits the model

• Calls Um_xfer to start the file transfer

• Exports several variables
• Calls Um_maindriver.sh which than executes the main model
• Calls the tailscript in non-climate mode resp. Climat_launch_next_interval.sh in climate mode
• Calls Um_xfer.sh to start the post-processing
• Takes care of cloning

• Transfers pilot files to ${pil_mach}
• Creates and submits job which calls Climat_archive_pilot

• Calls Climat_save_pilot

• Calls Climat_post_processing
  

• Calls d2z_job, pilot_job (if required), rassemble_job
• Submits diag_job at the end of an interval (if required)

• Re-organizes the multiple-variable individual-sample pr-files into a much smaller set of variable-specific files, each containing a large fraction of all samples.  These variable-specific files are then used by the latter diagnostic steps called by the parent script. Each cpu used here will produce one file per variable. The number of cpus this step will use is partly determined by the number of total model samples.

• Calls Um_xfer_prep.sh to prepare the file transfer
  

• Creates high- and coarse-resolution versions of output files if required
  
• calls Climat_strip_phy
  

• Transfers and archives all listings to ${list_mach}
  

• Archives most of the content of ${EXECDIR}on ${mach} as a restart backup
  
• Transfers archived restart to ${arch_mach}
  

• Submits the model job

• Does transfer of dm-, dp-, pm-files if post-processing is not done on ${mach}
  
• Submits post_job