Troubles in running FABM-GOTM

[geo-hy]

Hello everyone,
I get into a trouble with running the model. The error is:

$ ./gotm gotm_generic.yaml 
 ------------------------------------------------------------------------
 GOTM started on 2024/06/21 at 19:36:04
 ------------------------------------------------------------------------
    initialize_gotm
 ------------------------------------------------------------------------
        Reading configuration from: gotm_generic.yaml
 FATAL ERROR: The configuration in gotm_generic.yaml does not have a version key and is therefore not compatible with this version of GOTM.
    Please update your configuration by running <GOTMDIR>/scripts/python/update_setup.py.
STOP 1

The model was installed in Centos. The installed version is:

 ------------------------------------------------------------------------
 GOTM:    v6.0.0-158-g6ea1665f (master branch)
 Config:             7
 TEOS-10  3.5
 YAML:    0.1.0 (unknown branch)
 flexout: 0.1.0 (unknown branch)
 FABM:    v2.0.1-4-g1a653ed8 (tags/v2.0.2~18 branch)
 NetCDF:  4.8.0 of Oct 10 2022 15:48:52 $
 ------------------------------------------------------------------------
 Compiler: GNU 8.5.0

I have no idea about modfying the update_setup.py or overcome this problem.
Thank you for your help.

[bolding]

Hi

This is actually a GOTM question on the FABM site .....

Newer versions of GOTM check for a version number in the configuration file to be sure that the yaml file is compatabile with the executable.

Where did you get the gotm_generic.yaml file from? Anyway from the error message it is clear that the file you provided does not provide such a version information.

If you have compiled from the most previous source code from the Github site you should be aware that it is under development and might not work as excpected. I might be better to use the stable version.

Karsten

[geo-hy]

The gotm_generic.yaml is a entrainment case of the GOTM package from github. This is the context in .yaml:

title: shear-driven entrainment            # simulation title used in output [default=GOTM simulation]
location:
   name: equator                           # station name used in output [default=GOTM site]
   latitude: 0.0                           # latitude [degrees North; min=-90.0; max=90.0; default=0.0]
   longitude: 0.0                          # longitude [degrees East; min=-360.0; max=360.0; default=0.0]
   depth: 50.0                             # water depth [m; min=0.0; default=100.0]
time:
   start: 2005-01-01 00:00:00              # start date and time [yyyy-mm-dd HH:MM:SS; default=2017-01-01 00:00:00]
   stop: 2005-01-02 00:00:00               # stop date and time [yyyy-mm-dd HH:MM:SS; default=2018-01-01 00:00:00]
   dt: 60.0                                # time step for integration [s; min=0.0; default=3600.0]
grid:
   nlev: 100                               # number of layers [min=1; default=100]
   method: 0                               # layer thicknesses [0=equal by default with optional zooming, 1=prescribed relative fractions, 2=prescribed thicknesses; default=0]
   ddu: 0.0                                # surface zooming [dimensionless; min=0.0; default=0.0]
   ddl: 0.0                                # bottom zooming [dimensionless; min=0.0; default=0.0]
   file:                                   # file with custom grid [default=]
temperature:                               # temperature profile used for initialization and optionally relaxation
   method: 1                               # method [0=off, 1=analytical, 2=from file; default=0]
   file:                                   # path to file with series of profiles [default=]
   column: 1                               # index of column to read from [default=1]
   analytical:
      method: 3                            # type of analytical initial temperature profile [1=constant, 2=two layers, 3=from salinity and buoyancy frequency; default=1]
      z_t1: 30.0                           # upper layer thickness [m; min=0.0; default=0.0]
      t_1: 20.0                            # upper layer temperature [Celsius; min=0.0; max=40.0; default=0.0]
      z_t2: 40.0                           # lower layer thickness [m; min=0.0; default=0.0]
      t_2: 15.0                            # lower layer temperature [Celsius; min=0.0; max=40.0; default=0.0]
      obs_NN: 1.00000000E-04               # constant buoyancy frequency [s^-2; min=0.0; default=0.0]
   relax:                                  # relax model temperature to observed/prescribed value
      tau: 1.00000000E+15                  # time scale for interior layer [s; min=0.0; default=1.00000000E+15]
salinity:                                  # salinity profile used for initialization and optionally relaxation
   method: 1                               # method [0=off, 1=analytical, 2=from file; default=0]
   file:                                   # path to file with series of profiles [default=]
   column: 1                               # index of column to read from [default=1]
   analytical:
      method: 1                            # type of analytical initial salinity profile [1=constant, 2=two layers, 3=from temperature and buoyancy frequency; default=1]
      z_s1: 30.0                           # upper layer thickness [m; min=0.0; default=0.0]
      s_1: 20.0                            # upper layer salinity [psu; min=0.0; max=40.0; default=0.0]
      z_s2: 40.0                           # lower layer thickness [m; min=0.0; default=0.0]
      s_2: 15.0                            # lower layer salinity [psu; min=0.0; max=40.0; default=0.0]
      obs_NN: 2.56000000E-04               # constant buoyancy frequency [s^-2; min=0.0; default=0.0]
   relax:                                  # relax model salinity to observed/prescribed value
      tau: 1.00000000E+15                  # time scale for interior layer [s; min=0.0; default=1.00000000E+15]
surface:
   fluxes:                                 # heat and momentum fluxes
      method: 0                            # method to calculate fluxes from meteorology [0=use prescribed fluxes, 1=Kondo (1975), 2=Fairall et al. (1996); default=0]
      heat:                                # prescribed total heat flux (sensible, latent and net back-radiation)
         method: 0                         # method [0=constant, 2=from file; default=0]
         constant_value: 0.0               # value to use throughout the simulation [W/m^2; default=0.0]
         file:                             # path to file with time series [default=]
         column: 1                         # index of column to read from [default=1]
      tx:                                  # prescribed momentum flux in West-East direction
         method: 0                         # method [0=constant, 2=from file; default=0]
         constant_value: 1.02700000E-01    # value to use throughout the simulation [Pa; default=0.0]
         file:                             # path to file with time series [default=]
         column: 1                         # index of column to read from [default=1]
      ty:                                  # prescribed momentum flux in South-North direction
         method: 0                         # method [0=constant, 2=from file; default=0]
         constant_value: 0.0               # value to use throughout the simulation [Pa; default=0.0]
         file:                             # path to file with time series [default=]
         column: 1                         # index of column to read from [default=1]
   meteo:
      u10:                                 # wind speed in West-East direction @ 10 m
         method: 2                         # method [0=constant, 2=from file; default=0]
         constant_value: 0.0               # value to use throughout the simulation [m/s; default=0.0]
         file:                             # path to file with time series [default=]
         column: 1                         # index of column to read from [default=1]
      v10:                                 # wind speed in South-North direction @ 10 m
         method: 2                         # method [0=constant, 2=from file; default=0]
         constant_value: 0.0               # value to use throughout the simulation [m/s; default=0.0]
         file:                             # path to file with time series [default=]
         column: 2                         # index of column to read from [default=1]
      airp:                                # air pressure
         method: 2                         # method [0=constant, 2=from file; default=0]
         constant_value: 0.0               # value to use throughout the simulation [Pa; default=0.0]
         file:                             # path to file with time series [default=]
         column: 3                         # index of column to read from [default=1]
         scale_factor: 100.0               # scale factor to be applied to values read from file [default=1.0]
      airt:                                # air temperature @ 2 m
         method: 2                         # method [0=constant, 2=from file; default=0]
         constant_value: 0.0               # value to use throughout the simulation [Celsius or K; default=0.0]
         file:                             # path to file with time series [default=]
         column: 4                         # index of column to read from [default=1]
      hum:                                 # humidity @ 2 m
         method: 2                         # method [0=constant, 2=from file; default=0]
         constant_value: 0.0               # value to use throughout the simulation [default=0.0]
         file:                             # path to file with time series [default=]
         column: 5                         # index of column to read from [default=1]
         type: 1                           # humidity metric [1=relative humidity (%), 2=wet-bulb temperature, 3=dew point temperature, 4=specific humidity (kg/kg); default=1]
      cloud:                               # cloud cover
         method: 2                         # method [0=constant, 2=from file; default=0]
         constant_value: 0.0               # value to use throughout the simulation [fraction; min=0.0; max=1.0; default=0.0]
         file:                             # path to file with time series [default=]
         column: 6                         # index of column to read from [default=1]
      swr:                                 # shortwave radiation
         method: 0                         # method [0=constant, 2=from file, 3=from time, location and cloud cover; default=0]
         constant_value: 0.0               # value to use throughout the simulation [W/m^2; min=0.0; default=0.0]
         file:                             # path to file with time series [default=]
         column: 1                         # index of column to read from [default=1]
      precip:                              # precipitation
         method: 0                         # method [0=constant, 2=from file; default=0]
         constant_value: 0.0               # value to use throughout the simulation [m/s; default=0.0]
         file:                             # path to file with time series [default=]
         column: 1                         # index of column to read from [default=1]
         flux_impact: false                # include effect on fluxes of sensible heat and momentum [default=false]
      calc_evaporation: false              # calculate evaporation from meteorological conditions [default=false]
      ssuv_method: 0                       # wind treatment [0=use absolute wind speed, 1=use wind speed relative to current velocity; default=1]
   longwave_radiation:                     # net longwave radiation
      method: 1                            # method [0=from file, 1=Clark, 2=Hastenrath, 3=Bignami, 4=Berliand, 5=Josey-1, 6=Josey-2; default=1]
      file:                                # path to file with time series [default=]
      column: 1                            # index of column to read from [default=1]
   albedo:
      method: 0                            # method to compute albedo [0=constant, 1=Payne (1972), 2=Cogley (1979); default=1]
      constant_value: 0.0                  # constant value to use throughout the simulation [fraction; min=0.0; max=1.0; default=0.0]
   roughness:
      charnock: false                      # use Charnock (1955) roughness adaptation [default=false]
      charnock_val: 1400.0                 # empirical constant for roughness adaptation [dimensionless; min=0.0; default=1400.0]
      z0s_min: 0.02                        # hydrodynamic roughness (minimum value if Charnock adaptation is used) [m; min=0.0; default=0.02]
bottom:
   h0b: 0.05                               # physical bottom roughness [m; min=0.0; default=0.05]
light_extinction:
   method: 1                               # water type [1=Jerlov type I, 2=Jerlov type 1 (upper 50 m), 3=Jerlov type IA, 4=Jerlov type IB, 5=Jerlov type II, 6=Jerlov type III, 7=custom; default=1]
   A:                                      # non-visible fraction of shortwave radiation
      method: 0                            # method [0=constant, 2=from file; default=0]
      constant_value: 0.7                  # value to use throughout the simulation [fraction; min=0.0; max=1.0; default=0.7]
      file:                                # path to file with time series [default=]
      column: 1                            # index of column to read from [default=1]
   g1:                                     # e-folding depth of non-visible shortwave radiation
      method: 0                            # method [0=constant, 2=from file; default=0]
      constant_value: 0.4                  # value to use throughout the simulation [m; min=0.0; default=0.4]
      file:                                # path to file with time series [default=]
      column: 1                            # index of column to read from [default=1]
   g2:                                     # e-folding depth of visible shortwave radiation
      method: 0                            # method [0=constant, 2=from file; default=0]
      constant_value: 8.0                  # value to use throughout the simulation [m; min=0.0; default=8.0]
      file:                                # path to file with time series [default=]
      column: 1                            # index of column to read from [default=1]
turbulence:
   turb_method: 3                          # turbulence closure [0=convective adjustment, 2=first-order, 3=second-order, 100=cvmix; default=3]
   tke_method: 2                           # turbulent kinetic energy equation [1=algebraic length scale equation, 2=differential equation for tke (k-epsilon style), 3=differential equation for q^2/2 (Mellor-Yamada style); default=2]
   len_scale_method: 10                    # dissipative length scale [1=parabolic, 2=triangular, 3=Xing and Davies (1995), 4=Robert and Ouellet (1987), 5=Blackadar (two boundaries) (1962), 6=Bougeault and Andre (1986), 7=Eifler and Schrimpf (ISPRAMIX) (1992), 8=dynamic dissipation rate equation, 9=dynamic Mellor-Yamada q^2 l-equation, 10=generic length scale (GLS); default=8]
   stab_method: 1                          # stability functions [1=constant, 2=Munk and Anderson (1954), 3=Schumann and Gerz (1995), 4=Eifler and Schrimpf (1992); default=1]
   turb_param:
      cm0_fix: 5.47700000E-01              # value of cm0 [dimensionless; min=0.0; default=5.47700000E-01]
      Prandtl0_fix: 0.74                   # turbulent Prandtl-number [dimensionless; min=0.0; default=0.74]
      cw: 100.0                            # constant of the wave-breaking model [dimensionless; min=0.0; default=100.0]
      compute_kappa: true                  # compute von Karman constant from model parameters [default=false]
      kappa: 0.4                           # von Karman constant [dimensionless; min=0.0; default=0.4]
      compute_c3: true                     # compute c3 (E3 for Mellor-Yamada) from steady-state Richardson number [default=true]
      Ri_st: 0.25                          # desired steady-state Richardson number [dimensionless; min=0.0; default=0.25]
      length_lim: false                    # apply Galperin et al. (1988) length scale limitation [default=true]
      galp: 0.53                           # coefficient for length scale limitation [dimensionless; min=0.0; default=0.27]
      const_num: 5.00000000E-04            # constant eddy diffusivity [m^2/s; min=0.0; default=5.00000000E-04]
      const_nuh: 5.00000000E-04            # constant heat diffusivity [m^2/s; min=0.0; default=5.00000000E-04]
      k_min: 1.00000000E-10                # minimum turbulent kinetic energy [m^2/s^2; min=0.0; default=1.00000000E-10]
      eps_min: 1.00000000E-14              # minimum dissipation rate [m^2/s^3; min=0.0; default=1.00000000E-12]
      kb_min: 1.00000000E-10               # minimum buoyancy variance [m^2/s^4; min=0.0; default=1.00000000E-10]
      epsb_min: 1.00000000E-14             # minimum buoyancy variance destruction rate [m^2/s^5; min=0.0; default=1.00000000E-14]
   generic:                                # generic length scale (GLS) model
      gen_m: 1.0                           # exponent for k [dimensionless; default=1.5]
      gen_n: -0.67                         # exponent for l [dimensionless; default=-1.0]
      cpsi1: 1.0                           # empirical coefficient cpsi1 in psi equation [dimensionless; default=1.44]
      cpsi2: 1.22                          # empirical coefficient cpsi2 in psi equation [dimensionless; default=1.92]
      sig_kpsi: 0.8                        # Schmidt number for TKE diffusivity [dimensionless; default=1.0]
      sig_psi: 1.07                        # Schmidt number for psi diffusivity [dimensionless; default=1.3]
   scnd:                                   # second-order model
      cc1: 5.0                             # cc1 [dimensionless; default=3.6]
      cc3: 1.968                           # cc3 [dimensionless; default=1.2]
      cc4: 1.136                           # cc4 [dimensionless; default=1.2]
      cc6: 0.4                             # cc6 [dimensionless; default=0.3]
      ct1: 5.95                            # ct1 [dimensionless; default=3.28]
      ct2: 0.6                             # ct2 [dimensionless; default=0.4]
      ct3: 1.0                             # ct3 [dimensionless; default=0.4]
      ct5: 3.33300000E-01                  # ct5 [dimensionless; default=0.4]
      ctt: 0.72                            # ctt [dimensionless; default=0.8]
mimic_3d:                                  # effects of horizontal gradients
   ext_pressure:                           # external pressure
      mode: 0                              # formulation [0=horizontal gradient in surface elevation, 1=horizontal velocities at given height above bed, 2=vertically averaged horizontal velocities; default=0]
      dpdx:                                # pressure in West-East direction
         method: 0                         # method [0=constant, 1=from tidal constituents, 2=from file; default=0]
         constant_value: 0.0               # value to use throughout the simulation [default=0.0]
         file:                             # path to file with time series [default=]
         column: 1                         # index of column to read from [default=1]
         AmpM: 0.0                         # amplitude of 1st harmonic [dimensionless; default=0.0]
         PhaseM: 0.0                       # phase of 1st harmonic [s; default=0.0]
         AmpS: 0.0                         # amplitude of 2nd harmonic [dimensionless; default=0.0]
         PhaseS: 0.0                       # phase of 2nd harmonic [s; default=0.0]
      dpdy:                                # pressure in South-North direction
         method: 0                         # method [0=constant, 1=from tidal constituents, 2=from file; default=0]
         constant_value: 0.0               # value to use throughout the simulation [default=0.0]
         file:                             # path to file with time series [default=]
         column: 1                         # index of column to read from [default=1]
         AmpM: 0.0                         # amplitude of 1st harmonic [dimensionless; default=0.0]
         PhaseM: 0.0                       # phase of 1st harmonic [s; default=0.0]
         AmpS: 0.0                         # amplitude of 2nd harmonic [dimensionless; default=0.0]
         PhaseS: 0.0                       # phase of 2nd harmonic [s; default=0.0]
      h:                                   # height above bed
         method: 0                         # method [0=constant, 2=from file; default=0]
         constant_value: 0.0               # value to use throughout the simulation [m; min=0.0; default=0.0]
         file:                             # path to file with time series [default=]
         column: 1                         # index of column to read from [default=1]
      PeriodM: 44714.0                     # period of 1st tidal harmonic (eg. M2-tide) [s; default=44714.0]
      PeriodS: 43200.0                     # period of 2nd tidal harmonic (eg. S2-tide) [s; default=43200.0]
   int_press:                              # internal pressure
      dtdx:                                # temperature gradient in West-East direction
         method: 0                         # method [0=off, 1=constant, 2=from file; default=0]
         constant_value: 0.0               # value to use throughout the simulation [Celsius/m; default=0.0]
         file:                             # path to file with series of profiles [default=]
         column: 1                         # index of column to read from [default=1]
      dtdy:                                # temperature gradient in South-North direction
         method: 0                         # method [0=off, 1=constant, 2=from file; default=0]
         constant_value: 0.0               # value to use throughout the simulation [Celsius/m; default=0.0]
         file:                             # path to file with series of profiles [default=]
         column: 1                         # index of column to read from [default=1]
      dsdx:                                # salinity gradient in West-East direction
         method: 0                         # method [0=off, 1=constant, 2=from file; default=0]
         constant_value: 0.0               # value to use throughout the simulation [psu/m; default=0.0]
         file:                             # path to file with series of profiles [default=]
         column: 1                         # index of column to read from [default=1]
      dsdy:                                # salinity gradient in South-North direction
         method: 0                         # method [0=off, 1=constant, 2=from file; default=0]
         constant_value: 0.0               # value to use throughout the simulation [psu/m; default=0.0]
         file:                             # path to file with series of profiles [default=]
         column: 1                         # index of column to read from [default=1]
      t_adv: false                         # horizontally advect temperature [default=false]
      s_adv: false                         # horizontally advect salinity [default=false]
   zeta:                                   # surface elevation
      method: 0                            # method [0=constant, 1=from tidal constituents, 2=from file; default=0]
      constant_value: 0.0                  # value to use throughout the simulation [m; default=0.0]
      file:                                # path to file with time series [default=]
      column: 1                            # index of column to read from [default=1]
      period_1: 44714.0                    # period of 1st harmonic (eg. M2-tide) [s; default=44714.0]
      amp_1: 1.0                           # amplitude of 1st harmonic [m; default=0.0]
      phase_1: 0.0                         # phase of 1st harmonic [s; default=0.0]
      period_2: 43200.0                    # period of 2nd harmonic (eg. S2-tide) [s; default=43200.0]
      amp_2: 0.5                           # amplitude of 2nd harmonic [m; default=0.0]
      phase_2: 0.0                         # phase of 2nd harmonic [s; default=0.0]
   w:                                      # vertical velocity
      max:                                 # maximum velocity
         method: 0                         # method [0=off, 1=constant, 2=from file; default=0]
         constant_value: 0.0               # value to use throughout the simulation [m/s; default=0.0]
         file:                             # path to file with time series [default=]
         column: 1                         # index of column to read from [default=1]
      height:                              # height of maximum velocity
         method: 1                         # method [1=constant, 2=from file; default=1]
         constant_value: 0.0               # value to use throughout the simulation [m; default=0.0]
         file:                             # path to file with time series [default=]
         column: 1                         # index of column to read from [default=1]
      adv_discr: 4                         # vertical advection scheme [1=first-order upstream, 3=third-order upstream-biased polynomial, 4=third-order TVD with Superbee limiter, 5=third-order TVD with MUSCL limiter, 6=third-order TVD with ULTIMATE QUICKEST limiter; default=6]
velocities:                                # observed/prescribed horizontal velocities
   u:                                      # velocity in West-East direction
      method: 0                            # method [0=off, 2=from file; default=0]
      file:                                # path to file with series of profiles [default=]
      column: 1                            # index of column to read from [default=1]
   v:                                      # velocity in South-North direction
      method: 0                            # method [0=off, 2=from file; default=0]
      file:                                # path to file with series of profiles [default=]
      column: 1                            # index of column to read from [default=1]
   relax:                                  # relax model velocities towards observed/prescribed value
      tau: 1.00000000E+15                  # time scale [s; min=0.0; default=1.00000000E+15]
      ramp: 1.00000000E+15                 # duration of initial relaxation period [s; min=0.0; default=1.00000000E+15]
o2:                                        # oxygen
   scale_factor: 31.25                     # scale factor to be applied to values read from file [default=1.0]
stokes_drift:                              # observed/prescribed Stokes drift
   us:                                     # Stokes drift in West-East direction
      method: 0                            # method [0=off, 2=from file, 3=exponential profile, 4=empirical theory-wave of Li et al., 2017; default=0]
      file:                                # path to file with series of profiles [default=]
      column: 1                            # index of column to read from [default=1]
   vs:                                     # Stokes drift in South-North direction
      method: 0                            # method [0=off, 2=from file, 3=exponential profile, 4=empirical theory-wave of Li et al., 2017; default=0]
      file:                                # path to file with series of profiles [default=]
      column: 1                            # index of column to read from [default=1]
   dusdz:                                  # Stokes drift shear in West-East direction
      method: 0                            # method [0=off, 2=from file, 3=compute from us; default=0]
      file:                                # path to file with series of profiles [default=]
      column: 1                            # index of column to read from [default=1]
   dvsdz:                                  # Stokes drift shear in South-North direction
      method: 0                            # method [0=off, 2=from file, 3=compute from vs; default=0]
      file:                                # path to file with series of profiles [default=]
      column: 1                            # index of column to read from [default=1]
   exponential:                            # exponential Stokes drift profile defined by surface value and decay depth
      us0:                                 # Surface Stokes drift in West-East direction
         method: 0                         # method [0=off, 1=constant, 2=from file; default=0]
         constant_value: 0.0               # value to use throughout the simulation [m/s; min=0.0; default=0.0]
         file:                             # path to file with time series [default=]
         column: 1                         # index of column to read from [default=1]
      vs0:                                 # Surface Stokes drift in South-North direction
         method: 0                         # method [0=off, 1=constant, 2=from file; default=0]
         constant_value: 0.0               # value to use throughout the simulation [m/s; min=0.0; default=0.0]
         file:                             # path to file with time series [default=]
         column: 1                         # index of column to read from [default=1]
      ds:                                  # Stokes drift decay depth
         method: 0                         # method [0=off, 1=constant, 2=from file; default=0]
         constant_value: 5.0               # value to use throughout the simulation [m; min=0.0; default=5.0]
         file:                             # path to file with time series [default=]
         column: 1                         # index of column to read from [default=1]
   empirical:                              # approximate Stokes drift from empirical wave spectrum following Li et al., 2017
      uwnd:                                # Surface wind for Stokes drift in West-East direction
         method: 0                         # method [0=off, 1=constant, 2=from file; default=0]
         constant_value: 0.0               # value to use throughout the simulation [m/s; min=0.0; default=0.0]
         file:                             # path to file with time series [default=]
         column: 1                         # index of column to read from [default=1]
      vwnd:                                # Surface wind for Stokes drift in South-North direction
         method: 0                         # method [0=off, 1=constant, 2=from file; default=0]
         constant_value: 0.0               # value to use throughout the simulation [m/s; min=0.0; default=0.0]
         file:                             # path to file with time series [default=]
         column: 1                         # index of column to read from [default=1]
buoyancy:
   NN_ini: 1.00000000E-04                  # initial value of NN (=buoyancy gradient) [s^-2; default=0.0]
eq_state:                                  # equation of state
   mode: 1                                 # formula [1=UNESCO, 2=Jackett et al. (2005); default=2]
   method: 2                               # implementation [1=full with in-situ temperature/density, 2=full with potential temperature/density, 3=linearized at T0,S0,p0, 4=linearized at T0,S0,p0,dtr0,dsr0; default=1]
   T0: 10.0                                # reference temperature [Celsius; min=-2.0; default=10.0]
   S0: 35.0                                # reference salinity [psu; min=0.0; default=35.0]
   p0: 0.0                                 # reference pressure [Pa; default=0.0]
   dtr0: -0.17                             # thermal expansion coefficient [kg/m^3/K; default=-0.17]
   dsr0: 0.78                              # saline expansion coefficient [kg/m^3/psu; default=0.78]
restart:
   load: false                             # initialize simulation with state stored in restart.nc [default=false]
output:
   entrainment:                            # path of output file, excluding extension
      format: netcdf                       # format [text, netcdf; default=netcdf]
      time_unit: dt                        # time unit [second, hour, day, month, year, dt=model time step; default=day]
      time_step: 60                        # number of time units between output [min=1; default=1]
      time_method: point                   # treatment of time dimension [point=instantaneous, mean, integrated; default=point]
      variables:
      - source: /*                         # variable name in model

So ... which stable version of GOTM is suggested? Or how to modify this file?

[bolding]

But you have used the most up to date source code - and a quite old version of the YAML file. It will not work.

Depending on what you want - you have to choose between stable or devel version.

Karsten

[geo-hy]

Thanks you for your reply, now i know the problems ... I see it is better for me to choose the devel version.
I updated the YAML-CPP(i am not sure if it is the same thing) to 0.8.0, but in fact, i didnt find any materials can help me update YAML in GOTM...
So, should i re-compile the GOTM-FABM for the newer version of YAML in cloud computer (CentOS7)?

Thank you so much for your help!

[bolding]

Code version and case versions must match - and it is up to you what you chose. The stable version is - stable - and the devel version might change and does not necessarily work all the time.

If you have cloned the cases from Github you can change to the devel branch.

Karsten