[Dart-users] IMPORTANT rma_trunk updates

[Jonathan Hendricks]

Dear DART users,

This e-mail is important for current rma_trunk users. Please disregard if
you are using Lanai or the trunk.


In preparation for releasing the new version of DART we’ve made
modifications to the code which have some highly visible user changes. Our
apologies in advance for the disruption this will cause.   If you’ve been
using the alpha version of the branches/rma_trunk code (or any of its
variants), after the next update you will need to make changes to your
input.nml namelist and to your scripts for filename convention changes.

Our intent is to reduce the number of namelist options and the interaction
between different selections.  We also hope that using more fixed filenames
will simplify the scripting needed to cycle a model with DART.

Before you update, you should know this version also has some
restrictions.  It will NOT do multiple assimilation cycles in a single run
of filter, and it will not support reading/writing multiple ensemble
members from a single file.  Both these restrictions will be lifted in
future updates to the code before the release.

And finally, remember that our subversion repository has moved to a new
location :


https://svn-dares-dart.cgd.ucar.edu/DART/branches/rma_trunk/


and the original server has been removed from service.  To convert existing
checked out copies please reference :


https://www.image.ucar.edu/~thoar/svn_primer.html#converting


Contact us at dart at ucar.edu for help in migrating any code changes from
your checked-out version to a new version based on the new server.


Specific namelist changes include:

1. ) Earlier versions of the RMA branch code supported both direct NetCDF
reads/writes and the original binary/ascii DART format restart files.  As
of the next update DART format files are no longer supported.  All I/O is
NetCDF only.  If your model does not use NetCDF you will still need a
model_to_dart and dart_to_model converter; otherwise all DART programs read
the model’s NetCDF files directly.  The namelist options related to
selecting direct netcdf I/O have been removed.

2. ) Diagnostic and state space data (such as inflation, mean and sd
information) that were previously stored in {Prior,Posterior}_Diag.nc are
now broken up into multiple files and have fixed filenames. This decreases
the IO time for diagnostic output and reduces the number of namelist
options.

3. ) There is no longer support for observation space inflation (i.e.
inf_flavor = 1).  Contact us at dart at ucar.edu if you have an interest in
using this option.


Changes to the filter_nml are :

   -

   restart_in_file_name -- has been replaced with input_restart_file_list
   which is a text file which contains a list of NetCDF input restart files.
   For multiple domains such as WRF you can specify files for each domain.
   This is the same for restart_out_file_name.
   -

   restart_out_file_name -- has been replaced with output_restart_file_list
   -

   inf_in_file_name -- REMOVED, now have fixed names of the form
   input_{prior,posterior}inf_{mean,sd}.nc
   -

   inf_out_file_name -- REMOVED, now have fixed names of the form
   output_{prior,posterior}inf_{mean,sd}.nc.
   -

   inf_diag_filename -- REMOVED
   -

   inf_output_restart -- REMOVED, inflation restarts will be written out if
   inflation is turned on
   -

   output_inflation -- REMOVED, inflation files written only if inf_flavor
   > 1.
   -

   stages_to_write -- There is more control over what state data to write.
   Options are at stages *'input', 'preassim', postassim', 'output'*.
   Stages preassim and postassim will output state data originally contained
   within the copies of Prior_Diag.nc and Posterior_Diag.nc.  See
   README_rma_updates.txt for details on the filename conventions. For
   example, running filter with prior inflation enabled with stage ‘preassim’
   enabled will produce files with names:
   -

        preassim_member_####.nc
      -

        preassim_{mean,sd}.nc
      -

        preassim_priorinf_{mean,sd}.nc
      -

   write_all_stages_at_end -- important for large models - all output file
   I/O is deferred until the end of filter, but will use more memory to store
   the data.  More detailed info is in RMA_rma_updates.txt
   -

   output_restart_mean -- renamed output_mean
   -

   output_restart -- renamed output_restarts
   -

   direct_netcdf_{read,write} -- REMOVED, always true
   -

   restart_list_file -- renamed input_restart_file_list
   -

   single_restart_file_in -- renamed single_file_in
   -

   single_restart_file_out -- renamed single_file_out
   -

   add_domain_extension -- REMOVED
   -

   use_restart_list -- REMOVED
   -

   overwrite_state_input -- REMOVED, equivalent functionality can be set
   with single_restart_file_in = single_restart_file_out



Changes to the perfect_model_obs_nml are :

   -

   restart_in_filename -- renamed restart_in_file_names takes a NetCDF
   file. For multiple domains you can specify a list.
   -

   direct_netcdf_{read,write} -- REMOVED, always true


Changes to the state_space_diag_nml are :

   -

   single_file -- REMOVED, diagnostic files are now controlled in filter_nml
   with stages_to_write
   -

   make_diagnostic_files -- REMOVED, no longer produce original
   Prior_Diag.nc and Posterior_Diag.nc. These files are controlled with
   stages_to_write
   -

   netCDF_large_file_support -- REMOVED, always true


Changes to the state_vector_io_nml are :

   -

   write_binary_restart_files -- REMOVED


Changes to the ensemble_manager_nml are :

   -

   flag_unneeded_transposes -- REMOVED


Changes to the integrate_model_nml are :

   -

   advance_restart_format -- REMOVED, only supporting NetCDF format.


A more detailed summary of namelist and filename changes can be found in
README_rma_updates.txt.   See models/cam-fv/scripts_cesm1_5/assimilate.csh
for an example of how to handle the new filename conventions.

Subsequent updates will add back the options for single file input and
output for filter, and cycling multiple model advances and assimilation
cycles inside a single run of filter.  We believe these missing features
should not affect most of the current users of the RMA versions, but please
contact us at dart at ucar.edu if you need either or both of these features,
and tell us which model you are using.

Please contact us if you want help in updating your namelist or to report
any problems.

Regards,
DART Team
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