MODULE filter_mod

DART project logo

Jump to DART Documentation Main Index
version information for this file:
$Id: filter_mod.html 12166 2017-12-01 23:29:08Z nancy@ucar.edu $

NAMELIST / MODULES / FILES / ERRORS / PLANS / TERMS OF USE

Overview

Main module for driving ensemble filter assimilations. Used by filter.f90, perfect_model_obs.f90, model_mod_check.f90, and a variety of test programs. See the filter description for a general description of filter capabilities and controls.

filter_mod is a Fortran 90 module, and provides a large number of options for controlling execution behavior and parameter configuration that are driven from its namelist. See the namelist section below for more details. The number of assimilation steps to be done is controlled by the input observation sequence and by the time-stepping capabilities of the model being used in the assimilation.

See the DART web site for more documentation, including a discussion of the capabilities of the assimilation system, a diagram of the entire execution cycle, the options and features.

[top]

NAMELIST

This namelist is read from the file input.nml. Namelists start with an ampersand '&' and terminate with a slash '/'. Character strings that contain a '/' must be enclosed in quotes to prevent them from prematurely terminating the namelist.

&filter_nml
   single_file_in               = .false.,
   input_state_files            = '',
   input_state_file_list        = '',
   init_time_days               = 0,
   init_time_seconds            = 0,
   perturb_from_single_instance = .false.,
   perturbation_amplitude       = 0.2,

   stages_to_write              = 'output'

   single_file_out              = .false.,
   output_state_files           = '',
   output_state_file_list       = '',
   output_interval              = 1,
   output_members               = .true.,
   num_output_state_members     = 0,
   output_mean                  = .true.,
   output_sd                    = .true.,
   write_all_stages_at_end      = .false.,

   ens_size                     = 20,
   num_groups                   = 1,
   distributed_state            = .true.,

   async                        = 0,
   adv_ens_command              = "./advance_model.csh",
   tasks_per_model_advance      = 1,

   obs_sequence_in_name         = "obs_seq.out",
   obs_sequence_out_name        = "obs_seq.final",
   num_output_obs_members       = 0,
   first_obs_days               = -1,
   first_obs_seconds            = -1,
   last_obs_days                = -1,
   last_obs_seconds             = -1,
   obs_window_days              = -1,
   obs_window_seconds           = -1,

   inf_flavor                   = 0,                       0,
   inf_initial_from_restart     = .false.,                 .false.,
   inf_sd_initial_from_restart  = .false.,                 .false.,
   inf_deterministic            = .true.,                  .true.,
   inf_initial                  = 1.0,                     1.0,
   inf_sd_initial               = 0.0,                     0.0,
   inf_damping                  = 1.0,                     1.0,
   inf_lower_bound              = 1.0,                     1.0,
   inf_upper_bound              = 1000000.0,               1000000.0,
   inf_sd_lower_bound           = 0.0,                     0.0,

   trace_execution              = .false.,
   output_timestamps            = .false.,
   output_forward_op_errors     = .false.,
   write_obs_every_cycle        = .false.,
   silence                      = .false.,
 /


Particular options to be aware of are: async, ens_size, cutoff (localization radius), inflation flavor, outlier_threshold, restart filenames (including inflation), obs_sequence_in_name, horiz_dist_only, binary or ascii controls for observation sequence file formats. Some of these important items are located in other namelists, but all are in the same input.nml file.

The inflation control variables are all dimensioned 2, the first value controls the prior inflation and the second controls the posterior inflation.


Item Type Description
single_file_in logical True means all ensemble members are read from a single NetCDF file. False means each member is in a separate file. NOT SUPPORTED as of March, 2017 only multiple files can be used.
input_state_files character(len=256) dimension(MAXFILES) A list of the NetCDF files to open to read the state vectors. Models using multiple domains must put the domain and ensemble numbers in the file names. The order and format of those is to be determined. NOT SUPPORTED as of March, 2017.
input_state_file_list character(len=256) dimension(MAXFILES) A list of files, one per domain. Each file must be a text file containing the names of the NetCDF files to open, one per ensemble member, one per line.
init_time_days integer If negative, don't use. If non-negative, override the initial days read from state data restart files.
init_time_seconds integer If negative don't use. If non-negative, override the initial seconds read from state data restart files.
perturb_from_single_instance logical False means start from an ensemble-sized set of restart files. True means perturb a single state vector from one restart file. This may be done by model_mod, if model_mod provides subroutine pert_model_copies.
perturbation_amplitude real(r8) Standard deviation for the gaussian noise added when generating perturbed ensemble members. Ignored if perturb_from_single_instance = .false. or the perturbed ensemble is created in model_mod.
Random noise values drawn from a gaussian distribution with this standard deviation will be added to the data in a single initial ensemble member to generate the rest of the members.
This option is more frequently used in the low order models and less frequently used in large models. This is in part due to the different scales of real geophysical variable values, and the resulting inconsistencies between related field values. A more successful initial condition generation strategy is to generate climatological distributions from long model runs which have internally consistent structures and values and then use observations with a 'spin-up' period of assimilation to shape the initial states into a set of members with enough spread and which match the current set of observations.
stages_to_write character(len=10) dimension(4) Controls diagnostic and restart output. Valid values are 'input', 'preassim', 'postassim', 'output', and 'null'.
single_file_out logical True means all ensemble members are written to a single NetCDF file. False means each member is output in a separate file. NOT SUPPORTED as of March, 2017 - only multiple files can be used.
output_state_files character(len=256) dimension(MAXFILES) A list of the NetCDF files to open for writing updated state vectors. Models using multiple domains must put the domain and ensemble numbers in the file names. The order and format of those is to be determined. NOT SUPPORTED as of March, 2017.
output_state_file_list character(len=256) dimension(MAXFILES) A list of files, one per domain. Each file must be a text file containing the names of the NetCDF files to open, one per ensemble member, one per line.
output_interval integer Output state and observation diagnostics every 'N'th assimilation time, N is output_interval.
output_members logical True means output the ensemble members in any stage that is enabled.
num_output_state_members integer Number of ensemble members to be included in the state diagnostic output for stages 'preassim' and 'postassim'. output_members must be TRUE.
output_mean logical True means output the ensemble mean in any stage that is enabled.
output_sd logical True means output the ensemble standard deviation (spread) in any stage that is enabled.
write_all_stages_at_end logical For most cases this should be .false. and data will be output as it is generated for the 'preassim', 'postassim' diagnostics, and then restart data will be output at the end. However, if I/O time dominates the runtime, setting this to .true. will store the data and it can all be written in parallel at the end of the execution. This will require slightly more memory at runtime, but can lower the cost of the job significantly in some cases.
ens_size integer Size of ensemble.
num_groups integer Number of groups for hierarchical filter. It should evenly divide ens_size.
distributed_state logical True means the ensemble data is distributed across all tasks as it is read in, so a single task never has to have enough memory to store the data for an ensemble member. Large models should always set this to .true., while for small models it may be faster to set this to .false. This is different from &assim_tools_mod :: distributed_mean .
async integer Controls method for advancing model:
  • 0 is subroutine call
  • 2 is shell command
  • 4 is mpi-job script
Ignored if filter is not controlling the model advance, e.g. in CESM assimilations.
adv_ens_command character(len=256) Command sent to shell if async is 2.
tasks_per_model_advance integer Number of tasks to assign to each ensemble member advance.
obs_sequence_in_name character(len=256) File name from which to read an observation sequence.
obs_sequence_out_name character(len=256) File name to which to write output observation sequence.
num_output_obs_members integer Number of ensemble members to be included in the output observation sequence file.
first_obs_days integer If negative, don't use. If non-negative, ignore all observations before this time.
first_obs_seconds integer If negative, don't use. If non-negative, ignore all observations before this time.
last_obs_days integer If negative, don't use. If non-negative, ignore all observations after this time.
last_obs_seconds integer If negative, don't use. If non-negative, ignore all observations after this time.
obs_window_days integer Assimilation window days; defaults to model timestep size.
obs_window_seconds integer Assimilation window seconds; defaults to model timestep size.
All variables named inf_* are arrays of length 2.
The first element controls the prior inflation, the second element controls the posterior inflation. See filter.html for a discussion of inflation and effective strategies for using it.
inf_flavor integer array dimension(2) Inflation flavor for [prior, posterior]
  • 0 = none
  • 2 = spatially-varying state space
  • 3 = spatially-fixed state space
  • 4 = Relaxation To Prior Spread (Posterior inflation only)
(See inf_sd_initial below for how to set the time evolution options.)
inf_initial_from_restart logical array dimension(2) If true, get initial mean values for inflation from restart file. If false, use the corresponding namelist value inf_initial.
inf_sd_initial_from_restart logical array dimension(2) If true, get initial standard deviation values for inflation from restart file. If false, use the corresponding namelist value inf_sd_initial.
inf_deterministic logical array dimension(2) True means deterministic inflation, false means stochastic.
inf_initial real(r8) dimension(2) Initial value of inflation if not read from restart file.
inf_sd_initial real(r8) dimension(2) Initial value of inflation standard deviation if not read from restart file. If ≤ 0, do not update the inflation values, so they are time-constant. If positive, the inflation values will adapt through time, so they are time-varying.
inf_damping real(r8) dimension(2) Damping factor for inflation mean values. The difference between the current inflation value and 1.0 is multiplied by this factor before the next assimilation cycle. The value should be between 0.0 and 1.0. Setting a value of 0.0 is full damping, which in fact turns all inflation off by fixing the inflation value at 1.0. A value of 1.0 turns inflation damping off leaving the original inflation value unchanged.
inf_lower_bound real(r8) dimension(2) Lower bound for inflation value.
inf_upper_bound real(r8) dimension(2) Upper bound for inflation value.
inf_sd_lower_bound real(r8) dimension(2) Lower bound for inflation standard deviation. If using a negative value for sd_initial this should also be negative to preserve the setting. The inflation standard deviation is a non-increasing quantity, so the sd value will eventually reach and keep this lower bound.
trace_execution logical True means output very detailed messages about what routines are being called in the main filter loop. Useful if a job hangs or otherwise doesn't execute as expected.
output_timestamps logical True means write timing information to the log before and after the model advance and the observation assimilation phases.
output_forward_op_errors logical True means output errors from forward observation operators. This is the 'istatus' error return code from the model_interpolate routine. An ascii text file prior_forward_op_errors and/or post_forward_op_errors will be created in the current directory. For each ensemble member which returns a non-zero return code, a line will be written to this file. Each line will have three values listed: the observation number, the ensemble member number, and the istatus return code. Be cautious when turning this option on. The number of lines in this file can be up to the number of observations times the number of ensemble members times the number of assimilation cycles performed. This option is generally most useful when run with a small observation sequence file and a small number of ensemble members to diagnose forward operator problems.
write_obs_every_cycle logical For debug use; this option can significantly slow the execution of filter. True means to write the entire output observation sequence diagnostic file each time through the main filter loop even though only observations with times up to and including the current model time will have been assimilated. Unassimilated observations have the value -888888.0 (the DART "missing value"). If filter crashes before finishing it may help to see the forward operator values of observations that have been assimilated so far.
silence logical True means output almost no runtime messages. Not recommended for general use, but can speed long runs of the lower order models if the execution time becomes dominated by the volume of output.


[top]

MODULES USED

types_mod
obs_sequence_mod
obs_def_mod
obs_def_utilities_mod
time_manager_mod
utilities_mod
assim_model_mod
assim_tools_mod
obs_model_mod
ensemble_manager_mod
adaptive_inflate_mod
mpi_utilities_mod
smoother_mod
random_seq_mod
state_vector_io_mod
io_filenames_mod
forward_operator_mod
quality_control_mod

[top]

FILES

See the filter overview for the list of files.

[top]

ERROR CODES and CONDITIONS

RoutineMessageComment
filter_main ens_size in namelist is ###: Must be > 1 Ensemble size must be at least 2.
filter_main inf_flavor= ### Must be 0, 2, 3. Observation Inflation is no longer supported (i.e flavor 1).
filter_main Posterior observation space inflation (type 1) not supported. Posterior observation space inflation doesn't work.
filter_main Number of processes > model size. Number of processes can't exceed model size for now.
filter_generate_copy_meta_data output metadata in filter needs state ensemble size < 10000, not ###. Only up to 10000 ensemble members with state output for now.
filter_generate_copy_meta_data output metadata in filter needs obs ensemble size < 10000, not ###. Only up to 10000 ensemble members with obs space output for now.
filter_setup_obs_sequence input obs_seq file has ### qc fields; must be < 2. Only 0 or 1 qc fields in input obs sequence for now.
get_obs_copy_index Did not find observation copy with metadata observation. Only 0 or 1 qc fields in input obs sequence for now.

KNOWN BUGS

none

[top]

FUTURE PLANS

Many. New assimilation algorithms, support for new observation types, support for additional models, better performance on higher numbers of MPI tasks... The list is long. Send email to dart@ucar.edu if you are interested in additional functionality in DART.

[top]

Terms of Use

DART software - Copyright UCAR. This open source software is provided by UCAR, "as is", without charge, subject to all terms of use at http://www.image.ucar.edu/DAReS/DART/DART_download

Contact: DART core group
Revision: $Revision: 12166 $
Source: $URL: https://svn-dares-dart.cgd.ucar.edu/DART/releases/Manhattan/assimilation_code/modules/assimilation/filter_mod.html $
Change Date: $Date: 2017-12-01 16:29:08 -0700 (Fri, 01 Dec 2017) $
Change History: try "svn log" or "svn diff"