The s2m command¶
Basic usage of s2m is the following:
s2m research -b begin_date -e end_date -f forcing [-o path_output] [-n namelist] [-g] [-G] [-s surfex_exe_directory]
On HPC (vortex run), more options are required and a basic use is as follows:
s2m research -b begin_date -e end_date -m model -f forcing -r region [-o output_xpid] [-n namelist] [-s surfex_exe_directory] [--walltime=h:mm:ss]
Full documentation is available with s2m research --help and is reported below:
s2m command help:
usage: s2m research [-h] -b DATEDEB -e DATEFIN [-o DIROUTPUT] [-f FORCING]
[-n NAMELIST] [-G] [-g] [-x DATESPINUP] [-a THRESHOLD]
[-r REGION] [-L MINLEVEL] [-U MAXLEVEL] [-c ASPECTS]
[-l SLOPES] [-E] [--addmask] [-s EXESURFEX] [-w WORKDIR]
[--geotype {unstructured,grid}]
[--veg {namelist,ecoclimap}] [--hydro HYDRO]
[--hydrovar HYDROVAR] [--uenv UENV] [-m MODEL]
[-p PREP_XPID] [--obsxpid OBSXPID] [--nnodes NNODES]
[--ntasks NTASKS] [--walltime WALLTIME] [--writesx]
[--save-pro {none,cache,archive,multi}]
[--postprocess POSTPROCESS_EXE] [--drhook]
[--task {surfex,surfex_dailyprep,escroc,escroc_scores,croco,croco_perturb,reforecast,debug,refill,interpol}]
[--escroc ESCROC] [--croco {openloop,synth,real}]
[--conf CONF] [--synthmember SYNTHMEMBER]
[--nforcing NFORCING] [--nmembers NMEMBERS]
[--startmember STARTMEMBER] [--sensor SENSOR]
[--interpol_blocks {meteo,pro,meteo,pro,pro,meteo}]
The command to be used for research tasks to launch SAFRAN-SURFEX-Crocus or
EDELWEISS simulations. s2m simulations need ground temperature to be
initialized. If initial conditions are not known (PREP file not available for
the starting date), then an init_TG.nc file is expected to be found in the
prep directory. It must contain an initial ground temperature variable called
TG with dimension (Number_of_points). The init_TG.nc file can be generated
using -G or -g options (see their description). Otherwise, the command will
crash.
options:
-h, --help show this help message and exit
Main arguments:
-b DATEDEB, --begin DATEDEB
Date of the beginning of the simulation. (default:
None)
-e DATEFIN, --end DATEFIN
Date of the end of the simulation (default: None)
-o DIROUTPUT, --output DIROUTPUT
Name of the output directory (default: output)
-f FORCING, --forcing FORCING
Standard use : Path of the forcing file or of the
directory with the forcing files. Vortex use : xpid or
xpid@login of forcing data (default: None)
-n NAMELIST, --namelist NAMELIST
Path of the mother namelist (default: /home/viallonl/o
pt/snowtools/snowtools/DATA/OPTIONS_V8.1_NEW_OUTPUTS_N
C.nam)
Initialization set up:
-G Generate a ground initialization file by computing a
climatological average of air temperature on the
provided period. With this option, the simulation is
not run, the user can use -g instead to combine the
ground temperature initialization and running the
simulation. (default: False)
-g Combines -G option and run the simulation aftterwards.
(default: False)
-x DATESPINUP, --spinupdate DATESPINUP
Date of validity of the spinup file (default: None)
-a THRESHOLD, --august_threshold THRESHOLD
Limit the snow water equivalent each 1st August to the
provided value in kg/m2 (default: -999)
Forcing pre-processing:
-r REGION, --region REGION, --geometry REGION
The geometry to use for SURFEX simulation. This option
is also used for pre-processing of the FORCING file by
extracting data or interpolating forcing files into a
new geometry Standard use: - If region is a single
massif number or a list of massif numbers separated by
comas or a generic name for a group of massifs,
extract the corresponding massifs. - If region is a
netcdf file describing the target geometry,
interpolate SAFRAN fields on this geometry. The netcdf
file describing the geometry must contain the
massif_number and ZS variables. It can be 1d
(Number_of_points) or 2d (y, x) in Lambert93 or 2d
(latitude, longitude). 1d files can optionnally
provide aspect and slope. These variables will be
computed by the software for 2d files. Note that you
need to compile the fortran interpolator to use this
extended option. Vortex use: - region must be a well-
defined geometry either in vortex either
in.vortexrc/geometries.ini - In case of a geometry
change, the syntax is -r
geometry_in:geometry_out:GRID.nc where GRID.nc is the
netcdf file describing the target geometry. Both
geometry_in and geometry_out must be defined either in
vortex either in.vortexrc/geometries.ini (default:
None)
-L MINLEVEL, --lowest MINLEVEL
Eliminate elevations lower than this level in FORCING
files (in meters) (default: None)
-U MAXLEVEL, --upper MAXLEVEL
Eliminate elevations above this level in FORCING files
(in meters) (default: None)
-c ASPECTS, --classes_aspect ASPECTS
Specify the number of aspect classes to extract or
generate. Default: 8 -c 8 : N, NE, E, SE, S, SW, W, NW
-c 4 : N, E, S, W -c 2 : N, S -c 135 : specify only 1
aspect in ° if multiple of 45° (default: None)
-l SLOPES, --list_slopes SLOPES
Extract a reduced number of slope angles in FORCING
files, or generate a larger number of slope angles for
a flat FORCING file (default: None)
-E, --extractforcing Only extract meteorological forcing (default: False)
--addmask Apply shadows on solar radiation from surrounding
masks (default: False)
Optional path definitions:
-s EXESURFEX, --surfexexec EXESURFEX
Specify the directory where to find SURFEX binaries.
(Must contains PGD, PREP, OFFLINE) If None, EXESURFEX
environment variable is used. (default: None)
-w WORKDIR, --workdir WORKDIR
Name of the running directory (workdir) (default:
None)
Other arguments:
--geotype {unstructured,grid}
Type of simulation geometry: grids must be defined in
namelist while namelists are automatically updated for
unstructured geometries according to the forcing file.
(default: unstructured)
--veg {namelist,ecoclimap}
When vegetation is extracted from ECOCLIMAP database,
the corresponding files are downloaded in the working
directory. Default is namelist when
--geotype=unstructured. Default is eoclimap when
--geotype=grid. (default: None)
--hydro HYDRO Netcdf file of areas describing the repartition of S2M
units for a listhydrological basins. If provided,
hydrological diagnostics are provided in a dedicated
output file for the variables listed by --hydrovar
(default: None)
--hydrovar HYDROVAR List of FORCING or PRO diagnostics separated by coma
that should be spatially aggregated at the scale of
hydrological basins. The basins are described in the
file provided with the --hydro option (default: None)
--uenv UENV In cases when additionnal input files are necessary,
use this option to define the absolute path of the
repository where those files are stored.This option
works for both Vortex/HPC and local executions.In a
Vortex execution, it is also possible (and advised) to
provide a an existing uenv using the followong syntax
: '--uenv=uenv:{uenv_name}@{username}'. (default:
None)
Vortex options (available only on Meteo-France supercomputers):
-m MODEL, --model MODEL
Meteorological forcing format: s2m for ready-to-use
s2m-generated FORCING and safran for raw SAFRAN files.
(default: None)
-p PREP_XPID, --prep_xpid PREP_XPID
xpid in wich are the PREP files to be used (default:
None)
--obsxpid OBSXPID xpid of the obs you want to assimilate (default: None)
--nnodes NNODES Total number of nodes requested by the s2m command
(can be split between several jobs or not). Take care,
this is not the number of nodes per job if several
jobs !!! (default: 1)
--ntasks NTASKS Number of tasks (and procs) per node. (default: None)
--walltime WALLTIME specify your job walltime (format hh:mm:ss) (default:
None)
--writesx Optionnaly transfer the PRO files towards sxcen
(default: False)
--save-pro {none,cache,archive,multi}
Wheteher and where to save PRO_ output files. multi is
the default and store both in cache and in archive.
Use none not to save the PRO_ files at all. (default:
multi)
--postprocess POSTPROCESS_EXE
Postprocessing of PRO file. Provide executable path
(absolute) and its options as a single string. Will be
executed after aSURFEX execution in the working
directory. If you want anythingto be saved, please
write in commonly used files (PRO, DIAG, CUMUL).Please
ensure yourself that your algorithm is correctly
parallelized. (default: None)
--drhook Profiling MPI task with DRHOOK (default: False)
--task {surfex,surfex_dailyprep,escroc,escroc_scores,croco,croco_perturb,reforecast,debug,refill,interpol}
The task, if not the default one. (default: surfex)
--escroc ESCROC ESCROC subensemble in case --task=escroc (default: E2)
--croco {openloop,synth,real}
assimilation mode in case --task=croco (default:
openloop)
--conf CONF configuration file in case --task=croco (default:
None)
--synthmember SYNTHMEMBER
synthetic member if --croco=synth (default: 1)
--nforcing NFORCING Number of members of forcing files in Croco task only
(default: 1)
--nmembers NMEMBERS Total number of executions of the binary or script
associatedwith the main algocomponent of the task.
(default: None)
--startmember STARTMEMBER
Number of first member (default: None)
--sensor SENSOR specify the sensor name of the obs you want to
assimilate (default: MODIS)
--interpol_blocks {meteo,pro,meteo,pro,pro,meteo}
List of blocks to interpol --task=interpol (default: )