ecearth3/sources/tm5mp/rc/not-ported/pycasso-tm5-convert-meteo.rc

! ######################################################################
! ###
! ### TM5
! ###
! ### Template settings for standard run.
! ###
! ### VARIABLE EXPANSION IN RC FILE
! ### ------------------------------
! ###   The variables '${..}' in this file are expanded on reading.
! ###
! ###   Special variables are (read 'S' as '$'):
! ###     S{pid}       : evalutates to the process id of the calling script
! ###     S{script}    : "          "  "   name       "  "   "       "
! ###
! ###   Convention : variables 'my.*' are NOT read by the scripts or
! ###   the program, but only used to fill settings in this file or
! ###   the expert settings.
! ###
! ###   In post/preprocessing settings, <...> keys are expanded by the
! ###      underlying python script. Eg: <output.dir> <rcfile> <bindir>
! ###
! ###   Finally, there is the %{...} keys, similar to '${..}' but
! ###      expanded only at the end of the run in the "rs" file. See
! ###      post-processing settings, where this is used.
! ###
! ###
! ### QUICKSTART
! ### -----------------------------
! ###   Take the following steps for a first experience.
! ### 
! ###   1. Ensure that the setup script is linked:
! ### 
! ###        TM5>  ln  -s  base/trunk/bin/pycasso_setup_tm5  setup_tm5
! ###  
! ###   2. Obtain a copy of this file to edit:
! ### 
! ###        TM5>  cp  base/trunk/rc/pycasso-tm5.rc  pycasso-tm5.rc
! ###  
! ###   3. Select an approriate file with machine specific settings to be included;
! ###      if your system is not supported yet, use:
! ### 
! ###        my.machine.rc        :  pycasso-machine-template.rc
! ###  
! ###   4. The scripts will try to install, compile, and run ia TM5 code in 
! ###      the following directory structure (adopted from Carbon-Tracker):
! ### 
! ###        <basedir>/<project>/build/
! ###                           /run/
! ###                           /output/
! ###                           ...
! ###      Edit the rcfile and fill a proper base directory name:
! ### 
! ###          my.basedir   :  /scratch/yourname/run-TM5
! ### 
! ###   5. Try to install and compile a code, use '-v' for verbose mode:
! ### 
! ###        TM5>   ./setup_tm5  pycasso-tm5.rc  -v
! ### 
! ###   The first runs will probably fail due to incorrect settings.
! ###   Some hints on where to change them:
! ### 
! ###     o library paths and flags   :  pycasso-machine-*.rc
! ### 
! ###     o compiler flags            :  pycasso-machine-*.rc
! ###        (or the 'pycasso-compiler-*.rc' included from there)
! ### 
! ###   If the code is compiled correctly, also also try to submit it:
! ### 
! ###        TM5>   ./setup_tm5  pycasso-tm5.rc  -v  -s
! ### 
! ###   This will start the run in foreground.
! ### 
! ###   The first runs will probably fail due to missing input files.
! ###   See the settings in this file, and eventually the definition
! ###   of some common input paths in the machine.rc :
! ###            my.data.dir          : /data/TM5/input
! ###            my.meteo.dir         : /data/TM5/METEO
! ### 
! ###   Use the '-h' flag for info on how to submit to a queue.
! ###   Ensure that correct queue settings are specfified in the machine.rc.
! ### 
! ######################################################################
!
! ------------------------------------------------
! run description
! ------------------------------------------------
!
! Project Name : a convenient variable, you can use for whatever need
! you may have in defining your keys. Here it is only used to define
! the project top directory, under which build/run/output/archive/
! restart/save... directories are set): 
my.project      :  meteo-nc

! Id : short description for this run. It is used to name default
! standard output, but can be used anywhere else you want.
! ~ to convert glb100x100 meteo:
runid           :  glb100x100
! ~ to convert coarsened meteo:
!runid           :  coarsened

! benchmark settings ?
run.benchmark   :  T


! ----------------------------------------
! build and run directories
! ----------------------------------------
! The code is build and compiled in :
! 
!   <my.project.dir>/build/
!
! It is suggested (but you do not have to) to start my.run.dir with
! ${my.project.dir}, so you end up with the following tree :
! 
!   <my.project.dir>/build
!                   /<rundir>
!                   
! Output/restart/save/archive directories -see below- can also be
! set below ${my.project.dir} :
!
!   <my.project.dir> / build
!                    / <rundir>
!                    / <output.dir>
!                    / <savedir>
!                    / <restart.write.dir>
!                    
! Following these suggestions, the ${my.project.dir} fully becomes a
! project top directory, and not just the parent of the build dir.
! 
! Note that
!  (1) the 'my.scratch' variable (defined in machine.rc) is available
!  (2) you can always define and use intermediate key. For example,
!      my.basedir: 

! base directory for build/run/etc : choose an appropriate run
! directory on a scratch disk, or use ${my.scratch} 
my.basedir          :  ${SCRATCH}/run-TM5

! project directory:
my.project.dir      :  ${my.basedir}/${my.project}

! run directory:
my.run.dir          :  ${my.project.dir}/run


! ----------------------------------------
! build (See expert rcfile for more settings)
! ----------------------------------------

! basename for executable, runtime rcfile, logfiles, etc:
my.basename                   :  tm5-${my.project}-${runid}

! keys to select compiler flags; see compiler.*.rc for all values:
!my.build.configure.flags      :  optim-none check-all
my.build.configure.flags      :  optim-fast


! ----------------------------------------
! Start run automatically (True|False) ?
! ----------------------------------------

! Forced to 'True' by the '--submit' option to 'setup_tm5'. The job is
! started in the background, foreground or managed by a job scheduler,
! according to ${submit.to}, defined in pycasso-tm5-expert.rc. But
! this can also be overwritten at the command line.
submit.auto                   :  False


! ----------------------------------------
! User specified queue options.
! Only used for submission of a job to a queue system.
! ----------------------------------------

! Account is to specify scheduler (eg loadleveller) account. 
! Leave empty for default account associated to your user name.
my.queue.account              : nlchekli

! Run with high memory load ?
! Value of this queue is used in machine.rc to specfiy destination 
! queue or other settings. Supported values:
!    normal large huge absurd
! For ecmwf/c1a, 'large' means twice the default amount of consumable
! memory, 'huge' three times, and 'absurd' four times.
! Note that this is per MPI task.
! A pure OpenMP run (meteo100x100 production) therefore needs an
! 'absurd' memory load.
! Full chemistry run with 2-4 MPI tasks needs 'large' .
! Leave empty to not have any memory specific options.
my.queue.memoryload           :


! ----------------------------------------
! machine specific stuff (compiler name & flags, lib paths, ... )
! ----------------------------------------

!my.machine.rc       :  pycasso-machine-template.rc
my.machine.rc       :  pycasso-machine-ecmwf-ecgate.rc
!my.machine.rc       :  pycasso-machine-ecmwf-c1a.rc
!my.machine.rc       :  pycasso-machine-jrc-clust7.rc

! include settings:
#include base/${my.branch}/rc/${my.machine.rc}

! ----------------------------------------
! expert settings
! ----------------------------------------

! include expert settings to build source code
#include base/${my.branch}/rc/pycasso-tm5-expert.rc

!================================================================
!   GRIDS & LEVELS
 
! ----------------------------------------
! vertical layers
! ----------------------------------------

! Met fields levels depend on the meteo class (od/ei) and year.
! But number of model levels is set here.
! Choose between: all (default), tropo25, tropo34, ml40 
#if "${runid}" == "glb100x100"
my.levs                     :  all
#elif "${runid}" == "coarsened"
my.levs                     :  tropo25
#else
#error could not set my.levs for runid ${runid}
#endif

! source codes with level definition:
#if "${my.levs}" == "all"
my.levs.sources    :  proj/levels/${my.eclevs}/${my.branch}
#else
my.levs.sources    :  proj/levels/${my.eclevs}/${my.branch} \
                      proj/levels/${my.eclevs}/${my.levs}/${my.branch}
#endif


! ----------------------------------------
! horizontal grid (leave region name empty to not use them)
! ----------------------------------------

!~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#if "${runid}" == "glb100x100"
!~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

! regions name
my.region1                  :  glb100x100
my.region2                  :  
my.region3                  :  
my.region4                  :  
my.region5                  :  

! grid names for meteo input (allows on the flight regridding):
my.region1m                 :  ${my.region1}
my.region2m                 :  
my.region3m                 :  
my.region4m                 :  
my.region5m                 :  

!~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#elif "${runid}" == "coarsened"
!~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

! regions name
my.region1                  :  glb600x400
my.region2                  :  eur300x200
my.region3                  :  eux100x100
my.region4                  :  nam300x200
my.region5                  :  nam100x100

! grid names for meteo input (allows on the flight regridding):
my.region1m                 :  ${my.region1}
my.region2m                 :  ${my.region2}
my.region3m                 :  ${my.region3}
my.region4m                 :  ${my.region4}
my.region5m                 :  ${my.region5}

! parent regions for zoom
region.${my.region2}.parent :  ${my.region1}
region.${my.region3}.parent :  ${my.region2}
region.${my.region4}.parent :  ${my.region1}
region.${my.region5}.parent :  ${my.region4}

!~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#else
#error could not set my.levs for runid ${runid}
#endif
!~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

!=====================================================================!
! SOURCE CODE
!
! The source code is collected from a number of different directories.
! A base code for the model could be found in the directory:
!
!    base/${my.branch}/src
!
! where the 'my.branch' variable is set to 'trunk', or 'release/X.X'
! for a standard release, or 'branch/<your-branch>' for development
! versions. 
! The files in this directory are coppied to the build directory.
!
! Then, modifications to the base source could be copied from project
! directories. These could replace files from the base code.
! Common used projects:
!
!  o level selection of 34 layers out of 91 for tropospheric studies;
!    base is 25 out of 60 :
!
!      proj/levels/${my.eclevs}/<branch>
!      proj/levels/${my.eclevs}/tropo34/<branch>
!
!  o do not only run, but write something out too:
!
!      proj/user_output/trunk
!
! The base and project directories to be used should be specified 
! as a space seperated list to 'my.source.dirs' .
!
! NOTES:
!
!   *** USE THE '-n' OPTION IF YOU CHANGED THE PROJECT LIST ! ***
!   The files from the new project directories are probably older than
!   the current object files, and there 'make' will not recompile.
!   With the '-n' option a complete new build will be created.
! 

! Which branch to use ? 
!----------------------

! This key defines the branch of the TM5 "base" model. It sets the
! path to sources (here) but also to several other rc files (machine,
! expert, compiler, region,...).
! It can also be used to define other src directories (see
! pycasso-tm5_chembase.rc for example). 
! Possible values : trunk, "a branch", or a release [must be higher
! than 3.0]
!my.branch : release/4.0

my.branch           :  trunk

! which code directories ?
my.source.dirs      :  base/${my.branch} \
                       ${my.levs.sources} \
		       proj/chem/one/${my.branch}


!=====================================================================!
!  FLAGS
!  These are C-preprocessors that you can set here.
!  
!  You must define 3 sets of flags in the following keys:
!  
!      my.df.define  --> for scientific data format lib (for output & restart)
!      my.tmm.define --> for meteo reading (format) & processing
!      my.tm5.define --> everythnig else for tm5 model (processes, output, emiss,...)
!      
!=====================================================================!

! ----------------------------------------
! ~~ Data Format (DF)
! ----------------------------------------
!    To specify the scientific data libraries to use (via MDF module)
!
!  with_hdf4               : HDF
!  with_hdf5               : HDF5
!  with_hdf5_par           : HDF5 with parallel features
!  with_netcdf             : NetCDF
!  with_netcdf4            : NetCDF with NetCDF-4 features, requires 'with_hdf5'
!  with_netcdf4_par        : NetCDF with NetCDF-4 and parallel features, requires 'with_hdf5_par'
!
!! ~ only hdf4:
!my.df.define        :  with_hdf4
!
! ~ hdf4 and netcdf4 (used for restart files and cf output):
#if "${par.mpi}" in ["T","True"] :
my.df.define        :  with_hdf4 with_hdf5_par with_netcdf4_par
#else
my.df.define        :  with_hdf4 with_hdf5 with_netcdf4
#endif


! ----------------------------------------
! ~~ meteo (tmm module)
! ----------------------------------------
!
! ~~ meteo input 
! 
!  with_tmm_tmpp              : support TMPP HDF files
!  with_tmm_tm5               : support TM5 HDF or NetCDF files
!  with_tmm_ecmwf             : support ECMWF grib files for TMPP or TM5
!  with_tmm_ncep              : support NCEP cdc and gfs files
!  with_tmm_msc               : support data from Meteo Service Canada
! 
!  with_udunits               : UniData Units library, used for TM5 meteo in NetCDF
!
! ~~ meteo production
!
!  with_tmm_convec_raw        : compute convec from p, T, Q, etc
!  with_tmm_convec_ec         : compute convec from ecmwf convective fields
!  with_tmm_convec_ec_gg      : compute convec from ecmwf convective fields
!                                   on original gaussian grid
!
! macro's for meteo input:
#if "${my.meteo.format}" == "tm5-nc"
my.tmm.define       :  with_tmm_tm5 with_udunits
#else
my.tmm.define       :  with_tmm_tm5
#endif

! ----------------------------------------
! ~~ Other TM5 flags
! ----------------------------------------
!
! ~~ advection
!
!  slopes                  : use slopes advection
!  secmom                  : use second moments advection; requires 'slopes'
!
! ~~ convection levels:
!
!  without_lmax_conv      : convective fields not on limited number of layers
!
! ~~ to skip some processes:
!
!  without_advection
!  without_boundary
!  without_convection
!  without_diffusion
!  without_dry_deposition
!  without_wet_deposition
!  without_chemistry
!  without_photolysis
!  without_emission
!  without_sedimentation      (sedimentation requires emis and dry depos)
!
! ~~ coupling
!
!  with_prism
!  oasis3 
!  oasis4
!  with_tendencies
!  with_feedback
!
! ~~ user output
!
!  with_cf_output           : to use CF compliant netCDF output in
!                             user_output routines.
!  with_retro_output        : 
!
! ~~ miscellaneous
!
!  with_budgets             : to produce budget output files
!
! ~~ special libraries:
!
!  with_lapack              : to use LAPACK lib for linar algebra,
!                             and speed up convection
!
! ~~ Chemistry flags
!
!    with_cariolle	    : to use Cariolle parameterization of
!                             stratospheric O3
!    with_gems_emis	    : to use GEMS emissions instead of default EDGAR
!    with_GFED_8day	    : to use GFED2-8days BB emissions when
!                             using GEMS (requires with_gems_emis)
!    without_nmhc_gfed	    : to not use VOC from GFED2
!    with_m7		    : to use m7 aerosols model
!    with_optics	    : m7 flag - 
!    with_pm		    : m7 flag - 
!    with_online_bvoc	    : to use MEGAN for biogenic emissions
!    with_online_nox	    : 
!    with_ch4_emis	    : to switch on CH4 emissions
!    without_o3_nudging	    : to switch off O3 nudging
!
!=====================================================================!
!            YOU SHOULD ***NOT*** USE ANY OF THOSE :                  !
!=====================================================================!
!    with_barrier	    : ???	       	       	       	      !
!    with_budget	    : should be with_budgets  	       	      !
!    with_go		    : use GO module instead   	       	      !
!    with_mpi		    : use MPI instead: #ifdef MPI      	      !
!    with_okdebug	    : use okdebug flag below, available thru  !
!                             the dims module:	       	       	      !
!                              		       	       	       	      !
!                                   use dims, only : okdebug   	      !
!                                   ...	       	       	       	      !
!                                   if (okdebug) ...   	       	      !
!                                   	       	       	       	      !
!    with_openmp	    : use _OPENMP instead in your code	      !
!    without_wetdeposition  : should be without_wet_deposition        !
!    with_restart	    : deprecated                              !
!=====================================================================!

my.tm5.define       :  slopes 


! ----------------------------------------
! parallel
! ----------------------------------------
! compile with MPI library (T|F) ?
par.mpi               :  F

! number of mpi tasks:
! (used by scripts to launch job; source code gets npes from mpi routines)
par.ntask             :  4

! enable openmp ?
par.openmp            :  F

! threads per task:
par.nthread           :  1


! ----------------------------------------
! times
! ----------------------------------------
! A run from start to end is break into a series of chunk jobs. The
! length of each chunk is set by 'jobstep.length'.
!
! start and end time in "yyyy-mm-dd hh:mn:ss" format:
timerange.start       :  2008-01-01 00:00:00
timerange.end         :  2008-01-04 00:00:00
!
! break run after: 'n' days, or 'inf' (never), or a 'month'
!jobstep.length        :  1
jobstep.length        :  inf
!
! Forecast mode (F|T) ?
! If true, then specify the 'zero' forecast day yyyy-mm-dd
! (otherwise, comment or leave empty)
! NOTE: in forecast mode, start and final time should
!   not differ more than 10 days from fcday0
time.fc               :  F
time.fc.day0          :  


! ---------------------------------------------------------
! job chain
! ---------------------------------------------------------
! number of job step in chain;
! this is used to setup the next job in the chain,
! thus initialize to zero:
jobstep          :   0

! time range of this step;
! ==> filled automatically by submit scripts!
jobstep.timerange.start    :  ${timerange.start}
jobstep.timerange.end      :  ${timerange.end}

! output directory for restart
! ==> filled automatically by submit scripts!
prev.output.dir   :  


! ---------------------------------------------------------
! model timestep
! ---------------------------------------------------------
! time steps are set such that at least every 'ntimestep' seconds
! is the end of a dynamic time step:
!   10800  =  every 3   hour
!    5400  =  every 1.5 hour
!    3600  =  every 1   hour
!    1800  =  every 0.5 hour
time.ntimestep  : 1800

! maximum dynamic timestep (sec):
time.ndyn_max   : 1800


! ----------------------------------------
! processes
! ----------------------------------------
! to switch certain processes off, use the 'without_' defined above
!
! advection:
#if "${runid}" == "glb100x100" :
proces.advection.reduced      : T
#elif "${runid}" == "coarsened" :
proces.advection.reduced      : F
#else
#error reduced flag not set for runid ${runid}
#endif

! to become OBSOLETE -- uncomment if you are still using the grid project 
!!#if len("${regions}") == 0 :
!! file with reduced grid definition:
!proces.advection.RedGrid      : ${my.data.dir}/RedGrid
!#endif

! wet removal (applied in convec and sources_sinks)
proces.wet_removal.cp_scale   :  0.5


! ----------------------------------------
! compute global budgets ?
! ----------------------------------------
apply.budget.global           :  T


! ----------------------------------------
! initial fields
! ----------------------------------------
!
! Start options:
!  1  coldstart with initial fields set to 0
!  2  coldstart with initial fields computed
!       in sr trace1 in sources_sinks...
!  30 save file specified here with start.30.<region-name>
!  31 initial rm read from save file, no slopes, convert grids
!  33 restart file
!  4  coldstart with initial
!       fields read from model output stored
!       in mixing ratio (no slopes).
!  5  coldstart with initial
!       fields read from an mmix output file 
!       in mixing ratio (no slopes, missing field set to zero)
!  9  user defined in module 'user_input'
!
istart  : 2

!! For istart=30, specify save files with nonstandard names:
!start.30.glb600x400       :  /data/old-save-files/save.hdfglb6x4
!start.30.eur300x200       :  /data/old-save-files/save.hdfeur3x2
!start.30.eur100x100       :  /data/old-save-files/save.hdfeur1x1

! For initial istart=31, specify where the save files should be found;
! optionally, specify a TM4 save file to overwrite fields if possible:
!start.31.glb300x200       :  ${my.datadir}/save/tm5save-aero-tropo25-glb6x4.hdf
!start.31.glb300x200.TM4   :  ${my.datadir}/save/TM4-ml31-save_20051101_glb3x2.hdf

!! For initial istart=4, specify where the save files should be found:
!start.4.glb600x400        :  ${my.datadir}/save/savetm5m_glb6x4.hdf
!start.4.eur300x200        :  ${my.datadir}/save/savetm5m_eur3x2.hdf
!start.4.eur100x100        :  ${my.datadir}/save/savetm5m_eur1x1.hdf


! ----------------------------------------
! save files
! ----------------------------------------

! New save files are writen to the output directory.

! THIS IS NOT DONE ANYMORE:
! After the model run is finished, the job script will link 
! the save files to this special directory:
! SO THE FOLLOWING HAS BEEN MADE OBSOLETE IN PYCASSO:
!savedir                       : ${my.project.dir}/tm5_save


!~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
! OBSOLETE -- TO BE DELETED
! ensure creation of directory
! add 'save' to the 'install.tasks' list :
!save.install.dir              :  ${savedir}
!
! save files should be copied from output directory 
! to the save file directory;
! add 'save' to the 'store.tasks' list :
!save.store.from               :  <output.dir>
!save.store.files              :  save_*.hdf
!save.store.arch               :  ${savedir}
!
! NOTE : save.cmd has been retired too....
!~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

! ----------------------------------------
! restart files
! ----------------------------------------
!
! Write and read restart files (T|F) ? If empty, read as F. Does not
! apply to initial conditions (see "initial fields" above).
! Recommendation: set to T so subsequent jobs use restart files.
! Set to F for subsequent jobs to use "save files" instead.
! 
! Ensure to link with the NetCDF4 library by defining the macro's:
!   with_netcdf4 with_hdf5            # serial run
!   with_netcdf4_par with_hdf5_par    # MPI parallel run
!
restart.write                 :  T

! write extra restart files (T|F) ?
! write at specified hour (00,12,..) plus every dhour (24,06,...)
restart.write.extra           :  F
restart.write.extra.hour      :  00
restart.write.extra.dhour     :  24

! where to write restart files:
restart.write.dir             :  ${my.project.dir}/restart

! ensure creation of directory;
! the key 'restart' should remain included in the 'install.tasks' list:
restart.install.dir           :  ${restart.write.dir}

! *

! where to search for restart files for istart=33 :
restart.read.dir              :  ${restart.write.dir}


! ----------------------------------------
! meteo settings
! ----------------------------------------
! Time ranges of different meteo archives:
! 
! * od L60   1999-10-12 00:00:00    2006-02-01 00:00:00
! * od L91   2005-10-01 00:00:00    now
! * ei       1989-01-01 00:00:00    now
!
! Operational Data (od) or ERA Interim (ei) ?
my.meteo.class      :  ei

! o TMPP produced meteo:
!include base/${my.branch}/rc/pycasso-meteo.tmpp.rc

! o TM5 produced meteo:
!
! what kind of meteo archive ?
!my.meteo.resol      :  glb100x100    ! original archive with all ECMWF layers and 1.00x1.00 grid
my.meteo.resol      :  coarsened    ! data already regridded to ${my.levs} and regions resolution
!
! file format: "tm5-nc" for netcdf, "tm5-hdf" for good old hdf:
!my.meteo.format     :  tm5-hdf
my.meteo.format     :  tm5-nc

! ~ load meteo settings:
!#include base/${my.branch}/rc/pycasso-meteo-tm5.rc

! ~ load meteo settings to convert from hdf to netcdf; also:
!   - add "tmm.output" to "install.tasks" to create output directory;
!   - add call to "tm5-tmm-store" script to "output.user.scripts"
!     to have the new files stored in the archive;
!   - use a timestep of 1800 sec to avoid errors about problematic intervals;
!   - select single dummy tracer "proj/chem/one/" to speedup
#include base/${my.branch}/rc/pycasso-meteo-tm5-convert-hdf-to-nc.rc

! switch: call meteo setup script (T|F) ?
!my.tmm.setup.apply   :  F
my.tmm.setup.apply   :  T


! ----------------------------------------
! coupling
! ----------------------------------------

!include base/trunk/rc/prism.settings.rc


! ----------------------------------------
! input
! ----------------------------------------
! location of standard input files:
inputdir    : ${my.data.dir}/input/glb1x1

! OBSOLETE -- add input.sc to input.user.scripts below
! ! run the 'input.sc' script (T|F) ?
! input.link  :  F

! locations of input files:
!include base/${my.branch}/rc/input.base.rc

! for TIPP input:
!include base/${my.branch}/rc/tipp.settings.rc

! for chemistry versions:
!include base/${my.branch}/rc/chem.input.rc


! ----------------------------------------
! standard output
! ----------------------------------------
!
! The 'outputmode' determines what is done with standard output.
!   SCREEN     : not redirected, but written to screen;
!                in case of background or submitted jobs, 
!                it is therefore added to 'jb.<pid>.out' in launch dir.
!   DEFAULT    : redirected to default output file '${runid}.out' in run dir
!   <filename> : your favorite file name
!
!outputmode  :  benchmark.out

! print debug info (T|F) ?
okdebug     :  F

!
! message formatting
!

! print messages from all processors (T|F) ?
! default is root only
go.print.all        :  F

! print processor id prompt (T|F) ?
! default is only if npes>1
go.print.prompt.pe  :  T

! print label at begin and end of every routine ?
go.print.trace      :  F

! print messages to file (T|F) ?
! provide first part of file name, full names will be:
!    <rundir>/<base>.0        (proces 0)
!             <base>.1        (proces 1)
!                    :
go.print.file       :  F
go.print.file.base  :  ctm.tm5


!=====================================================================!
! output
!=====================================================================!

! ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
! Default Output Directory
! ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
output.dir                    :  ${output.dir.base}

! ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
! Alternative Output Directory
! ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
! The tm5 setup_rcfile can overwrite the default output.dir with a
! runtime-dependent value, defined as a series of subdirectories in a
! top dir. For an example, to get: 
! 
!      top-output-dir/sub1/sub2
!      
! you would set those keys:
! 
!      output.dir.base         : top-output-dir
!      output.dir.extensions   : sub1 sub2
!
! The dependence on runtime is done by using <> keys (they are
! recognized by the python script), or any rc keys from this file,
! in the extensions. Are available:  
! 
!   <jobstep>     : to use the jobstep number  
!   <timerange>   : for the timerange as yyyymmdd_hhmnss__yyyymmdd_hhmnss
!
! This alternative output.dir is ignored if "extensions" is empty 
output.dir.base               :  ${my.project.dir}/output
output.dir.extensions         :  


! ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
! Output Sub-Directory (who uses that?)
! ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
! A set of subdir can be created below "output.dir". Use "types" to
! list their keynames, and for each of these keynames, give the subdir
! name, and a flag to switch on/off creation. Example, for two subdir:
!
!  output.types       : sub1 sub2
!  sub1.output        : T
!  sub1.output.subdir : name1
!  sub2.output        : T
!  sub2.output.subdir : name2

output.types        :


! OBSOLETE -- all instances of outputdir should be
! replaced with output.dir
! for backwards compatibility ...
! outputdir                :  ${output.dir}


! ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
! write grid definition(s) to netcdf files
! ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

settings.output          : T


! ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
! station output
! ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

output.station             :  F

!!inputdir.station           :  ${datadir}/stationfiles/
!inputdir.station           :  ${my.data.dir}/output/ground/
!
!input.station.filename     :  station_test.list
!input.station.filename2    : 
!
!input.station.fileformat   :  1
!
!station.speclist           :  TEST1 TEST2 TEST3 TEST4 TEST5
!
!output.station.filename    :  station.hdf


! ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
! flight tracks
! ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

output.flight        :  F


! ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
! mixing ratio's
! ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

output.mix           :  F
output.mix.dhour     :  6


! ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
! mean mixing ratio's
! ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

output.mmix              : F


! ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
! timing
! ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

! write timing profiles ?
timing.output           : F

! optionally define a subdir of output.dir :
timing.output.subdir    :


! ---------------------------------------------------------
! Pre-processing I - Installation of input files ("install" keys)
! ---------------------------------------------------------
!
! Specify space seperated list with install tasks:
!
!    install.tasks                 :  obs diffusion
!
! For each task, an number of specific settings should be defined in
! one rc file.
!
! To have a number of files copied from an archive into a local directory,
! specify a space seperated list with file names:
!
!    <task>.install.files           :  krep.dat zooi.tar morezooi.tar
!    <task>.install.dir             :  /local/data/
!    <task>.install.arch            :  ecfs:/tmx/TM/data
!
! If a file ends with '.tar' it is unpacked automatically.
!
! The archive description should be understandible by the 'gss' scripts:
!
!      /archive/data/
!      ecfs:/tmx/TM/data        # ECMWF tape archive when running on ECMWF computer
!      ec:ecfs[tmx]:TM/data     # idem from a remote computer using EcAccess tools
!      mos:/fa/ks/TM/data       # KNMI tape archive
!
! If an alternative file is available in case of a primary file is
! missing, use the 'optional' list instead of next to the 'files' list:
!
!    <task>.install.optional        :  eventually.tar
!
! On some systems only a temporary scratch disk is present at run time.
! The user should ensure that all input data is present on this local disk.
! A useful UNIX command for this is 'rsync', which syncronizes the content
! of a local directory with another directory. Use the following specification
! for a list of files or directories that need to be present in the 'dir'
! and should be synchronized with the version present in 'arch' :
! 
!    <task>.install.rsync          :  TMtree
!
! The installtion performs a time loop over the 'jobstep.timerange' ;
! the 'dir', 'arch', 'files', 'optional', and 'rsync' values could then include
! special keys '<yyyy>', '<mm>', or '<dd>'
! that are replaced by the year, month, and day values respectively:
!
!    <task>.install.files           :  zooi_<yyyy><mm>.tar
!

! Default install tasks:
!  o machine specific installation only
!  o create destination of restart files
!install.tasks                 :  ${my.install.tasks} restart
install.tasks                 :  ${my.install.tasks} restart tmm.output

! ---------------------------------------------------------
! Pre-processing II - User scripts to setup run ("install" keys)
! ---------------------------------------------------------
!
! Provide a ';' seperated list with script commands to be exectuted:
!
!    input.user.scripts           :  mypath/myscript ; important.sc
!
! The path should be either absolute or relative to the run directory.
! For scripts in the 'bin' subdirectories of the source, use <bindir>:
!
!    input.user.scripts           :  <bindir>/input.sc
!
! Arguments/options can use <rcfile>, which is replaced by
! the name of the runtime rcfile. For example, to install meteo files
! for all days of the run:
!
!    input.user.scripts           :  <bindir>/tm5-tmm-setup -v <rcfile>
! 
input.user.scripts          :  <bindir>/tm5-tmm-setup <rcfile>

!! for the old, input.sc :
!input.user.scripts          :  <bindir>/input.sc <rcfile>

! ---------------------------------------------------------
! Post-processing I - Archiving output files ("store" keys)
! ---------------------------------------------------------
!
! Settings to store output files in archive.
!
! Specify space seperated list with store tasks:
!
!    store.tasks           :  task1 task2
!
! For each task, an number of task specific settings is defined in the
! rest of this file; some values are initialized below using a dummy
! task 'default' :  
!
!    ! from where ? leave empty for run directory, use '<output.dir>' for output directory:
!    <task>.store.from           :  <output.dir>
!
!    ! copy some extra files to output subdirectory for storage:
!    <task>.store.copy           :  station-list.txt
!    <task>.store.copy.to        :  STATION/
!
!    ! name(s) of target file(s) for storage;
!    ! if only one file is specified with extension '.tar' 
!    ! then an archive file is created. Default is a *.tar defined by
!    ! sources.store.files in pycasso-tm5-expert.rc file.
!    <task>.store.files          :  all.tar
!
!    ! if a tarfile has to be created, specify which files to archive
!    ! through a filter: 
!    <task>.store.tarfilter      :  STATION/*.hdf STATION/*.txt
!
!    ! zip files before archiving ? empty, or a zipper command (gzip, bzip2, compress, ...) :
!    default.zipper              :  gzip
!
!    ! archive into one or more destinations (space seperated list):
!    default.store.arch          :  ecfs:/xxx/MAIN_ARCHIVE/
!    <task>.store.arch           :  ecfs:/xxx/SPECIAL_OUTPUT/  /extra/backup/archive/
!
!    ! If the 'arch' does not contain any ':' characters it is assumed to be
!    ! a local directory. In this case, a 'cp' command is used to archive
!    ! the files rather than the 'gss' script, and the files might therefore
!    ! include filters:
!    <task>.store.files          :  save*.hdf
!    <task>.store.arch           :  ${SCRATCH}/savefiles/
!
!    ! store in archive even if already present ?
!    ! by default probably True, but might not be necessary for some precomputed data:
!    default.store.renew         :  True
!    correlations.store.renew    :  False
!
!    ! extra shell command to be called at the end of the task;
!    ! for example to cleanup or do other important stuff:
!    <task>.store.extra.command  :  rm -f STATION/*.hdf STATION/*.txt
!
! Storage might be subject to a special condition, e.g. end of iteration in a 4D-var run.
! Specifiy a condition line that could be evaluated by python.
! If not specified, the default condition is True .
! Keys '%{..}' in the condition line are expanded with the values in the restart file
! if present; this file is written by the main program and has the same name as
! the rcfile but with extension '.rs' instead of '.rc' .
! Note the '%' instead of '$', otherwise the line is evaluated too early!
! 
!     store.condition    :  %{m1qn3.finished} == 1
!

! only store for some condition ?
store.condition               :  True

! space seperated list with store tasks:
store.tasks                   :  sources

! zipper: empty, or a zipper command (gzip, bzip2, compress, ...) :
! HERE: hdf files already have internal compression, so do not waste time on this ...
default.store.zipper          :  

! default archive location(s):
default.store.arch            :  ${my.project.dir}/ARCHIVE

! renew files ?
default.store.renew           :  True


! ---------------------------------------------------------
! Post-processing II - Touch files
! ---------------------------------------------------------
! To avoid that output files are removed from scratch 
! during long, long runs.
! Enable this flag to touch recursively the access time 
! of all files in 'output.dir' .
! ---------------------------------------------------------

! touch files to prevent removal (True|False) ?
output.touch                  :  False


! ---------------------------------------------------------
! Post-processing III - User scripts
! ---------------------------------------------------------
! For more elaborate post-processing, you can write your own
! script. Then add the full command (including options and arguments)
! to the output.user.script key, so it will automatically be executed: 
!
!    output.user.scripts           :  <bindir>/myscript <rcfile>
!
! More than one command can be specified: use ';' to separate them.
! The path should be either absolute or relative to the run directory.
! For scripts in any of the 'bin' subdirectories of the source, use
! <bindir>. Arguments/options can use <rcfile>, which is replaced by
! the name of the runtime rcfile.
!
! Conditional call is possible. Just specifiy a condition line
! that can be evaluated with python eval() function. 
! Set with the `output.user.scripts.condition` key, 
! and default to True if not set or empty.
! The same condition apply to all listed scripts.
! ---------------------------------------------------------

! condition line:
output.user.scripts.condition :  True

! list with scripts to be called:
output.user.scripts           :  <bindir>/tm5-tmm-store <rcfile>


! -- Will output.sc become obsolete, and superseded by the "store"
! keys above?? -- 
! Anyway, if one of the user script is the existing output.sc, you
! must specify the correct arguments:
! 
! output.sc <rcfile> <output.dir> ${my.project.dir}/build/src
!
! and: one or more destination directories (gss descriptions),
! if all files must be first compressed using gzip (T|F), and
! if outpudir is cleaned after storing is completed (T|F).
!output.store.destdirs    :  ecfs:/nl5/TM5/output
!output.store.compress    :  T
!output.store.clean       :  T


! ---------------------------------------------------------
! DIADEM postprocessing
! ---------------------------------------------------------

!
! To run the postprocessor, uncomment the include line and start:
!
!    ./tools/diadem/py/diadem  <thisfile.rc>
!

! include settings:
!#include tools/diadem/rc/diadem.rc