11. Running with interannual forcing#

11.1. Run after classical interannual pre-processing#

Before running you should prepare your interannual inputs files following the Interannual Preprocessing tutorial of croco_tools (https://croco-ocean.gitlabpages.inria.fr/croco_tools/ ) or croco_pytools (https://croco-ocean.gitlabpages.inria.fr/croco_pytools/ ) documentations.

To run a plurimonth simulation, we provide the following scripts in ~/croco/croco/SCRIPTS/Plurimonths_scripts:

run_croco_inter.bash: Plurimonth run with interannual forcing
run_croco.bash: Plurimonth run with climatological/cycling forcing. It is a simplified version of run_croco_inter.bash which is not described below.

These scripts:

get the grid, the forcing, the initial and the boundary files
run the model for 1 month
store the output files in a specific form: e.g. croco_avg_Y????M?.nc
replace the initial file by the restart file (croco_rst.nc) which has been generated at the end of the month
re-launch the model for next month

A dedicated namelist input file is also requested and provided ~/croco/croco/OCEAN/croco_inter.in

All these files are already copied to your configuration directory if you have used create_config.bash. Otherwise, copy them from the source directory to your configuration directory.

Edit run_croco_inter.bash: Paths should already be correct.

#
# Name used for the input files. For example croco_grd.nc
MODEL=croco

# Scratch directory where the model is run
SCRATCHDIR=`pwd`/SCRATCH

# Input directory where the croco_inter.in input file is located
INPUTDIR=`pwd`/CROCO_IN  # prod architecture
#INPUTDIR=`pwd`          # dev architecture

# AGRIF input file which defines the position of child grids
AGRIF_FILE=AGRIF_FixedGrids.in

# Directory where the croco input NetCDF files (croco_grd.nc, ...) are stored
MSSDIR=`pwd`/CROCO_FILES

# Directory where the croco output and restart NetCDF files (croco_his.nc, ...) are stored
MSSOUT=$SCRATCHDIR

# CROCO executable
CODFILE=croco

Warning

check INPUTDIR depending on the architecture you choosed (prod or dev architecture)

Number of MPI CPUs and command for running

# number of processors for MPI run
NBPROCS=4

# command for running the mode : ./ for sequential job, mpirun -np NBPROCS for mpi run
# WARNING: for mpi run command, it is needed to add a space at the end and take care about ./
RUNCMD='./'
#RUNCMD="mpirun -np $NBPROCS ./"
#RUNCMD="$MPI_LAUNCH ./"
#RUNCMD='srun ./'
#RUNCMD="mpiexec -np ${NBPROCS} ./"

Define environment variables for OPENMP

OMP_SCHEDULE=static
OMP_NUM_THREADS=2
OMP_DYNAMIC=false
OMP_NESTED=false
KMP_LIBRARY=throughput
KMP_STACKSIZE=2m
KMP_DUPLICATE_LIB_OK=TRUE

Type of forcings

# Define which type of inputs are used
#
BULK_FILES=1
FORCING_FILES=0
CLIMATOLOGY_FILES=0
BOUNDARY_FILES=1
RUNOFF_FILES=0
TIDE_FILES=0
ONLINE_FILES=0
ONLINEFREQ=4
ONLINEPATH="../DATA/CFSR_Benguela_LR" # we recommend using an absolute path

Names of forcings

# Atmospheric bulk file suffix (croco_blk_ATMOS_BULK_Y????M??.nc) - NOT USED IF ONLINE
ATMOS_BULK=ERA5
# Atmospheric forcing file suffix (croco_frc_ATMOS_FRC_Y????M??.nc) - NOT USED IF BULK or ONLINE
ATMOS_FRC=QSCAT
# Oceanic boundary and initial files suffix (croco_ini_OGCM_Y????M??.nc and croco_bry_OGCM_Y????M??.nc)
OGCM=SODA
# Runoff file sufix (croco_runoff_RUNOFF_Y????M??.nc)
RUNOFF=DAI
# Tide file suffix (croco_frc_TIDE_FRC.nc)
TIDE_FRC=tpxo7_croco

Time step settings

# Model time step [seconds]
DT=3600
# Number of barotropic time steps within one baroclinic time step [number], NDTFAST in croco.in
NFAST=60

Agrif nesting settings

# Number total of grid levels (1: No child grid)
NLEVEL=1
# AGRIF nesting refinement coefficient
AGRIF_REF=3

Dates settings (according to crocotools_param.m for Matlab tools or *.ini files for Python tools)

# Start and End year
NY_START=2005
NY_END=2005
# Start and End month
NM_START=1
NM_END=3
# Set month format at 1 or 2 digits (for input and output files): "%01d" = 1 digit/ "%02d" = 2 digit
MTH_FORMAT="%02d"
#  Time Schedule  -  TIME_SCHED=0 --> yearly files
#                    TIME_SCHED=1 --> monthly files
TIME_SCHED=1

# Number of year that are considered to be part of the spin-up (i.e. 365 days per year)
NY_SPIN=0

Outputs settings

# Output frequency [days] - case 1 : No USE_CALENDAR - DEFAULT
#   average
ND_AVG=3
#   history (if = -1 set equal to NUMTIMES, the end of each month/year)
ND_HIS=-1
#   restart (if = -1 set equal to NUMTIMES, the end of each month/year)
ND_RST=-1

# Output frequency [hours] - case 2 : USE_CALENDAR - USED ONLY IF USE_CALENDAR
#
USE_CALENDAR=1
#
#  average (in hours)
NHAVG_UC=$((24))
#  history (in hours, if = -1 set equal t NUMTIMES*DT/3600, the end of each month/year)
NHHIS_UC=-1
#  restart (in hours, if = -1 set equal to NUMTIMES*DT/3600, the end of each month/year)
NHRST_UC=-1

Restart settings

#  Restart file - RSTFLAG=0 --> No Restart
#                 RSTFLAG=1 --> Restart
RSTFLAG=0
#  Exact restart - EXACT_RST=0 --> Exact restart OFF
#                - EXACT_RST=1 --> Exact restart ON
EXACT_RST=0

Launch the simulation Copy the adequate job script

cp ~/croco/croco/SCRIPTS/example_job_run_croco_inter.pbs .

Check the MPI settings and launch the job

qsub example_job_run_croco_inter.pbs

Check at your outputs: You should have
```
croco_his_Y2000M1.nc
croco_his_Y2000M2.nc
croco_his_Y2000M3.nc
croco_avg_Y2000M1.nc
croco_avg_Y2000M2.nc
croco_avg_Y2000M3.nc
croco_rst.nc
```
Warning

If you have an error while you run did not BLOW UP, maybe it is because you have define LOGFILE in your cppdefs.h. For using run_croco_inter.in it should be undef.

11.2. Alternative method: online interpolation of atmospheric bulk forcing#

Instead of pre-processing your atmospheric bulk forcing, you can use online interpolation of atmospheric bulk forcing.

To do so:

Your atmospheric files need to be in a format readable by CROCO: At the moment the following forcing are implemented for online interpolation:
- In Matlab croco_tools :
  - CFSR data pre-formatted using the script Process_CFSR_files_for_CROCO.sh available in croco_tools
  - ERAI data pre-formatted using reformat_ECMWF.m (used in make_ECMWF.m in the croco_tools)
  - AROME data formatted in Meteo France framework
- In Python croco_pytools:
  - ERAI data pre-formatted using download_era5.py
Edit cppdefs.h In Surface forcing section
```
#  define ONLINE
#  ifdef ONLINE
#   undef  AROME
#   undef  ERA_ECMWF
#  endif
```
Note

for ONLINE interpolation, default is CFSR format. AROME and ERA_ECMWF are also available by defining the cpp-keys.
Re-compile the model First copy your old executable to keep it, then re-compile
```
cp croco croco.bck
./jobcomp > jobcomp.log.online
```

Link or copy the CFSR files to your DATA directory

mkdir DATA/CFSR_Benguela_LR/
#ln -s ~/DATA/METEOROLOGICAL_FORCINGS/CFSR/BENGUELA/CROCO_format/*2005*.nc DATA/CFSR_Benguela_LR/.
cp ~/DATA/METEOROLOGICAL_FORCINGS/CFSR/BENGUELA/CROCO_format/*2005*.nc DATA/CFSR_Benguela_LR/.

Check and eventually edit croco_inter.in last section

online:    byear  bmonth recordsperday byearend bmonthend / data path
           NYONLINE   NMONLINE      4             2011     3
          ../DATA/CFSR_Benguela_LR/

Re-run the model
```
qsub example_job_run_croco_inter.sh
```
Note

In case of errors while using ONLINE, it is probably associated to time issues: check the time in your CFSR input files, and check your time origin Yorig.

Running with interannual forcing

Contents

11. Running with interannual forcing#

11.1. Run after classical interannual pre-processing#

11.2. Alternative method: online interpolation of atmospheric bulk forcing#