CrocO technical doc¶

Data assimilation of snow observations with CrocO¶

Implementation of a Particle Filter to assimilate spatialized snow observations within SURFEX platform
Development of vortex task to perform the assimilation sequence on beaufix-hendrix, launched through a s2m (snowtools) command.
User documentation : see CrocO user doc

Publication:
Cluzet et al., CrocO : a Particle Filter to assimilate snowpack observations in a spatialised framework (in prep)

Git projects :

Surfex_Git2, branch cen_dev
Vortex, branch cen_assim
snowtools_git, branch cen_assim

Main developments¶

Spatialized PF algorithms developped into SURFEX/SODA in global, k-localized and r-localized configurations
Use of ESCROC ensemblist version of Crocus (Lafaysse et al. 2017) and perturbed meteorological forcings (Charrois et al., 2016)
Use of Vortex (cen_assim branch) /snowtools_git to launch the assimilation sequence on beaufix and store data on hendrix (similarly as described in Run a SURFEX-Crocus experiment with vortex)

Developer name¶

Bertrand Cluzet

Date of start of development¶

January 2018

Commit number before the development¶

Surfex_Git2 : b469f610
Vortex : 4ab65aa3

Current status¶

Surfex_Git2: Phased in SURFEX V8.1 branch cen_dev, tag CrocO_v1.0
Vortex : Phased with recent (late october 2018 (commit 87922088)) cen_assim branch, tag CrocO_v1.0
snowtools_git : commit 53e2e16, cen_assim branch, tag CrocO_v1.0

Key technical points (SURFEX)¶

new diag variable SPECMOD to represent sow reflectance in MODIS bands, sampled from SPEC_ALB
writing of this diag variable into PREP file (mandatory for soda assimilation)
new dimension in PRO file : MODIS_bands
in SODA, use of a SURFEX_LIST (vector of SURFEX_TYPE) to store all members (PREP files) before the assimilation mix
mixing of PREP is done "manually" in PUT_ALL_VAR_PF.F90. Some fields (..._ISBA) are not mixed at the moment (no need for us.)
Need to actualize this routine after any change in the SURFEX types and variable names and for new prognostic/cumulated variables
LFIX_OUTPUT (see below)
reading of obs. in NETCDF.
computing Snow Cover Fraction from SWE in PREP : implementation of a depletion curve (Zaitchik et al., 2009, De Lannoy et al., 2012)

Evaluated against SURFEX test database ?¶

No, in progress.

New test added in the database¶

No, in progress

Changes in namelist¶

&NAM_ASSIM

LASSIM = .TRUE.                       ! Activate Surfex data assimilation  
LCROCO = .TRUE.                       ! Activate CrocO
CASSIM_ISBA = 'PF   '                 ! Particle Filter activation in SODA  (/!\ don't forget the '   ' ) 
CPF_CROCUS = 'GLOBAL' (default)       ! select the PF algo to perform ('GLOBAL', 'RLOCAL', 'KLOCAL')
NLOC_PF = 0 (default)                 ! set the maximal number of obs (>0) to select in the 'RLOCAL' and 'KLOCAL' algo.
NEFF_PF = 1                           ! set the targer effective sample size for the PF with inflation.
NPRINTLEV=1,                          ! verbosity
LEXTRAP_SEA=.FALSE.,                  !  |
LEXTRAP_WATER=.FALSE.,                !  |  Prevent SODA 
LEXTRAP_NATURE=.FALSE.,               !  |  from being too fancy
LWATERTG2=.TRUE.,                     !  |

&NAM_OBS

  
NOBSTYPE = 8                 ! number of different obs. variables (up to 9)
CFILE_FORMAT_OBS="NC    "    ! daily obs. files on NETCDF file format (/!\ don't forget the '    ' ) 
COBS_M = 'B1','B2','B3','B4','B5','B6','B7','SCF'             ! Names of MODIS bands and Snow cover fraction variables in observation file. (/!\ same length as NOBSTYPE), other possible values : 'DEP', 'R51', R52', 'R53', 'R54'
NNCO = 1,1,1,1,1,1,1,1       ! select which variables to assimilate among COBS_M (/!\ same length as NOBSTYPE)
XERROBS_M = 0.00071, 0.00046, 0.00056, 0.00056, 0.002, 0.0015, 0.00078, 0.05 ! default obs.error *variances* for MODIS bands (charrois PhD manuscript pp 104.,140.), last one is a percentage of value for SCF.
XERROBS_FACTOR_M = 1,1,1,1,1,1,1,1 ! If necessary multiply the prescribed errors by some factors

&NAM_VAR

NVAR=8                     ! number of different model assimilation variables (up to 9)
CVAR_M='PB1','PB2','PB3','PB4','PB5','PB6','PB7','PSB' ! model variables (7 MODIS spectral bands + bulk SWE), other possible values : 'DEP', 'R51', 'R52', 'R53', 'R54'
NNCV = 1,1,1,1,1,1,1,1   ! select which variables to assimilate among CVAR_M
XTAUSCF ! value for the tau parameter of the depletion curve used to retrieve model SCF from bulk SWE (default=4)
XCEILSCF ! value for the ceil SWE of the depletion curve (default=20mm)

&NAM_ENS

NENS = 1         ! number of ensemble members (overwritten by snowtools_git argument --nmembers)

&NAM_DIAG_ISBAN

LSPECMOD = .TRUE.  ! activation of MODIS spectral bands output in PREP, mandatory for assimilation
LPROBANDS = .TRUE. ! mandatory too for MODIS assimilation

&NAM_DIAG_SURFN

LRAD_BUDGET = .TRUE.

&NAM_WRITE_DIAG_SURFn

LRESETCUMUL = .TRUE.
LSNOWDIMNC = .TRUE. ! mandatory + activate layer/bands dimensions in PRO
CSELECT = 'SPECMOD' ! add MODIS bands to PRO file

&NAM_IO_OFFLINE

LFIX_OUTPUT = .TRUE. !(default : .FALSE.) : force hours of output in PRO at 00h+n*timestep instead of timestart+ n*timestep (/!\ possible edge effects on cumulated diags)

local testing of SODA¶

SODA is the executable performing the assimilation. Provided a set of background PREP files and an observation, it produces a set of analyzed PREP files.
It is possible to test the performance of this algorithm locally, (without the use of vortex, snowtoools_git etc.)
For that, simply execute SODA in a repertory where all files are given (Namelist, PGD, PREP files, observations, etc.)
For more details, ask for support.

Other required changes¶

Namelist¶

Computing of snow reflectance in MODIS bands requires impurities handling options, see Explicit representation of impurities

Forcing files¶

only yearly files are handled at the moment
see Explicit representation of impurities about adding impurities deposition fluxes to the forcings

Spinup files¶

mandatory
/!\ V8.0 files are not compatible with V8.1, but it is possible to upgrade it (ask for support).

New files¶

Assimilation configuration file¶

mandatory
named s2m_<region_id>.ini
- region_id is the safran id of the region (for ex. 12 for Grandes-Rousses)
- region_name is the safran name of the region (for ex. grandes_rousses for Grandes-Rousses)
write down your data assimilation dates (see attached example)
some additional information on the experiment are appended to it during the run. It is then archived (see below)
For twin experiments and traceability : With ESCROC E1* ensemble, you can prescribe the members you'd like to run, otherwise they will be randomly drawn (and written down in the configuration file)
ex : membersId = 505, 402, 705

Observation files¶

daily files named obs_<your_sensor>_<region_name>_yyyymmddhh.nc
ex : obs_MODIS_grandes_rousses_20341231.nc
NETCDF format(see attached example)

same geometry as PREP/PGD
variables must be double
variables _FillValue must be set to 1.e+20.

for synthetical observations, <your_sensor> is free to define.

Particle Filter sample files¶

Output from the assimilation sequence.
One file per assimilation date, named PART_YYYYMMDDHH.txt (see attached example, distributed assim with 187pts and 3 members)
FORMAT : (DISTRIBUTED assimilation, assimilation per grid point): one line per grid point, then for each line, ids of the replicated members on the corresponding point, separated by spaces
(SEMI-DISTRIBUTED assimilation, global assimilation) : only one line, ids of the replicated members, separated by spaces

Simulation framework¶

Simulations are performed on beaufix-hendrix through an s2m command (see added options below).
Vortex requires a strict file storing and naming. The following lines are detailing it.

Forcing files¶

stored in a vortex path on hendrix :
<yourhome>/vortex/safran/<region_id>/<xpid_forcing>/mbxxxx/meteo/
- xpid_forcing is a user-defined name (usually the name of the experiment that generated the forcings), given to s2m via -f option (see below)

Spinup files¶

named PGD_<region_name>.nc and PREP_<starting_date>.nc
stored in a vortex path on hendrix (xxx is "pgd" and "prep" respectively):
<yourhome>/vortex/s2m/<region_id>/spinup/<xxx>/

Namelist¶

Stored on beaufix home.

Assimilation Configuration file¶

Stored on beaufix home.

Observation files¶

stored in a vortex path on hendrix :
<yourhome>/vortex/s2m/<region_id>/obs/<your_sensor>/
for synthetical observations : do the same.

Simulation outputs storing¶

If the simulation has succeded :

all files are deleted from beaufix
PREP and PRO files are stored on hendrix :
<your_home>/vortex/s2m/<region_id>/<xpid>/<mbxxxx>/<xxx>
- xpid is specified through s2m -o option, see below
- xxx is bg, an or pro for backgroud PREP, analysis PREP and PRO files respectively
Assimilation configuration file (useful for twin experiments and traceability) is stored in <your_home>/vortex/s2m/<region_id>/conf/
Base namelist is also stored in <your_home>/vortex/s2m/<region_id>/conf/ (name namelist.surfex.foo)
PF sample files are stored in <your_home>/vortex/s2m/<region_id>/workSODA/ (name PART_YYYYMMDDHH.txt.foo)
For post-processing and dev, PREP files and the configuration file can also be fetched to sxcen (in /cnrm/cen/users/NO_SAVE/...), which has no backup and limited space (see the options below)

New s2m options/modifications¶

- w option is useless
- o xpid : output repertory on hendrix
--escroc E1Tartes or E1noTartes : Escroc big ensembles with Tartes only (1944 members) or no Tartes (the rest). nmembers will be randomly drawn from this ensemble between each assimilation date
--croco your_path_to_assimilation_configuration_file : activate CrocO and give the path to your conf file.
--nforcing : numbers of different forcings to use
- f xpid_forcing: xpid for your forcing files on hendrix
--openloop : activate openloop sequence (no assimilation but output at each assimilation date)
--synth mbid : assimilation of synthetic data. Remove and replace the <mbid> member (synthetic truth)
--real : assimilation of real data
--walltime : estimate for execution time on beaufix
--writesx yourpath_to_NO_SAVE_on_sxcen.cnrm: fetch output data directly to a vortex path on sxcen NO_SAVE (/cnrm/cen/users/NO_SAVE/***id***/vortex/)
--sensor your_sensor: specify the name of the sensor used to generate the observations (default :MODIS), or of your synthetical obs.

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Project

General

Profile

snowtools_git

Wiki

CrocO technical doc¶

Data assimilation of snow observations with CrocO¶

Main developments¶

Developer name¶

Date of start of development¶

Commit number before the development¶

Current status¶

Key technical points (SURFEX)¶

Evaluated against SURFEX test database ?¶

New test added in the database¶

Changes in namelist¶

local testing of SODA¶

Other required changes¶

Namelist¶

Forcing files¶

Spinup files¶

New files¶

Assimilation configuration file¶

Observation files¶

Particle Filter sample files¶

Simulation framework¶

Forcing files¶

Spinup files¶

Namelist¶

Assimilation Configuration file¶

Observation files¶

Simulation outputs storing¶

New s2m options/modifications¶