Hello!
I’m trying to create a domain and mask files via DOMAINcfg tool. Coordinate mesh_mask is cut from the ORCA_R025 (min lat ~ 53 N) and I use GEBCO_2022 (min lat ~45 N) as a bathymetry data.
Input coordinates and bathymetry
namelist_cfg
!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
!! NEMO/OCE : Configuration namelist_cfg used to overwrite defaults value defined in namelist_ref
!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
!! NEMO/OCE : 1 - Domain & run manager (namrun, namcfg, namdom, namzgr, namzgr_sco )
!! 2 - diagnostics (namnc4)
!! 3 - miscellaneous (nammpp, namctl)
!!
!! namelist skeleton : egrep -E '(^/ *$|^! *$|^ *$|&nam.*|!---.*|!! .*|!!==.*|!!>>>.*)' namelist_ref > namelist_skl
!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
!-----------------------------------------------------------------------
&namrun ! parameters of the run
!-----------------------------------------------------------------------
cn_exp = "Arct_ORCA025" ! experience name
/
!-----------------------------------------------------------------------
&namdom ! space and time domain (bathymetry, mesh, timestep)
!-----------------------------------------------------------------------
ln_read_cfg = .false.
nn_bathy = 2 ! = 0 compute analyticaly
! = 1 read the bathymetry file
! = 2 compute from external bathymetry
! = 3 compute from parent (if "key_agrif")
nn_interp = 1 ! type of interpolation (nn_bathy =2)
cn_fcoord = 'arct_orca025_coord_v2.nc' ! external coordinates file (jphgr_msh = 0)
cn_topo = 'GEBCO_arct_2022.nc' ! external topo file (nn_bathy =2)
cn_bath = 'elevation' ! topo name in file (nn_bathy =2)
cn_lon = 'lon' ! lon name in file (nn_bathy =2)
cn_lat = 'lat' ! lat name in file (nn_bathy =2)
rn_scale = -1 ! multiplicative factor to account for possibly negative input bathymetry (agrif only)
rn_bathy = 0. ! value of the bathymetry. if (=0) bottom flat at jpkm1
nn_msh = 1 ! create (=1) a mesh file or not (=0)
jphgr_msh = 0 ! type of horizontal mesh
ppglam0 = 999999.0 ! longitude of first raw and column T-point (jphgr_msh = 1)
ppgphi0 = 999999.0 ! latitude of first raw and column T-point (jphgr_msh = 1)
ppe1_deg = 999999.0 ! zonal grid-spacing (degrees)
ppe2_deg = 999999.0 ! meridional grid-spacing (degrees)
ppe1_m = 999999.0 ! zonal grid-spacing (degrees)
ppe2_m = 999999.0 ! meridional grid-spacing (degrees)
ppsur = -4762.96143546300 ! ORCA r4, r2 and r05 coefficients
ppa0 = 255.58049070440 ! (default coefficients)
ppa1 = 245.58132232490 !
ppkth = 21.43336197938 !
ppacr = 3.0 !
ppdzmin = 999999. ! Minimum vertical spacing
pphmax = 999999. ! Maximum depth
ldbletanh = .FALSE. ! Use/do not use double tanf function for vertical coordinates
ppa2 = 999999. ! Double tanh function parameters
ppkth2 = 999999. !
ppacr2 = 999999. !
/
!-----------------------------------------------------------------------
&namcfg ! parameters of the configuration
!-----------------------------------------------------------------------
!
ln_e3_dep = .true. ! =T : e3=dk[depth] in discret sens.
! ! ===>>> will become the only possibility in v4.0
! ! =F : e3 analytical derivative of depth function
! ! only there for backward compatibility test with v3.6
! ! if ln_e3_dep = T
ln_dept_mid = .false. ! =T : set T points in the middle of cells
! !
cp_cfg = "orca" ! name of the configuration
jp_cfg = 025 ! resolution of the configuration
jpidta = 488 ! 1st lateral dimension ( >= jpi )
jpjdta = 422 ! 2nd " " ( >= jpj )
jpkdta = 31 ! number of levels ( >= jpk )
Ni0glo = 488 ! 1st dimension of global domain --> i =jpidta
Nj0glo = 422 ! 2nd - - --> j =jpjdta
jpkglo = 31
jperio = 4 ! lateral cond. type (between 0 and 6)
ln_use_jattr = .false. ! use (T) the file attribute: open_ocean_jstart, if present
! in netcdf input files, as the start j-row for reading
ln_domclo = .false. ! computation of closed sea masks (see namclo)
/
!-----------------------------------------------------------------------
&namzgr ! vertical coordinate (default: NO selection)
!-----------------------------------------------------------------------
!-----------------------------------------------------------------------
ln_zco = .false. ! z-coordinate - full steps
ln_zps = .true. ! z-coordinate - partial steps
ln_sco = .false. ! s- or hybrid z-s-coordinate
ln_isfcav = .false. ! ice shelf cavity (T: see namzgr_isf)
/
!-----------------------------------------------------------------------
&namzgr_isf ! isf cavity geometry definition
!-----------------------------------------------------------------------
/
!-----------------------------------------------------------------------
&namzgr_sco ! s-coordinate or hybrid z-s-coordinate (default F)
!-----------------------------------------------------------------------
/
!-----------------------------------------------------------------------
&namclo ! (closed sea : need ln_domclo = .true. in namcfg)
!-----------------------------------------------------------------------
/
!-----------------------------------------------------------------------
&namlbc ! lateral momentum boundary condition (default: NO selection)
!-----------------------------------------------------------------------
/
!-----------------------------------------------------------------------
&namagrif ! AGRIF zoom ("key_agrif")
!-----------------------------------------------------------------------
/
!-----------------------------------------------------------------------
&namnc4 ! netcdf4 chunking and compression settings ("key_netcdf4")
!-----------------------------------------------------------------------
/
But output files look crashed and ocean.output file has 1 error:
We solved error in ocean.output with usage of global GEBCO bathymetry.
But I still have the bad data at the last row of the domain. It looks like that the DOMAINcgf writes wrong coordinates in appropriate variables:
Last (-1) and second to last gphit rows
Last (-1) and second to last glamt rows
DOMAINcfg run ends with next MPICH message:
===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= PID 39159 RUNNING AT hm-vm-nemo
= EXIT CODE: 9
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Killed (signal 9)
This typically refers to a problem with your application.
Please see the FAQ page for debugging suggestions
Original coordinate mesh is ok:
Original last (-1) and second to last gphit rows
Original last (-1) and second to last glamt rows
Relevant DOMAINcfg namelist
!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
!! NEMO/OCE : Configuration namelist_cfg used to overwrite defaults value defined in namelist_ref
!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
!! NEMO/OCE : 1 - Domain & run manager (namrun, namcfg, namdom, namzgr, namzgr_sco )
!! 2 - diagnostics (namnc4)
!! 3 - miscellaneous (nammpp, namctl)
!!
!! namelist skeleton : egrep -E '(^/ *$|^! *$|^ *$|&nam.*|!---.*|!! .*|!!==.*|!!>>>.*)' namelist_ref > namelist_skl
!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
!-----------------------------------------------------------------------
&namrun ! parameters of the run
!-----------------------------------------------------------------------
cn_exp = "Arct_ORCA025" ! experience name
/
!-----------------------------------------------------------------------
&namdom ! space and time domain (bathymetry, mesh, timestep)
!-----------------------------------------------------------------------
ln_read_cfg = .false.
nn_bathy = 2 ! = 0 compute analyticaly
! = 1 read the bathymetry file
! = 2 compute from external bathymetry
! = 3 compute from parent (if "key_agrif")
nn_interp = 1 ! type of interpolation (nn_bathy =2)
cn_fcoord = 'arct_orca025_coord_v2.nc' ! external coordinates file (jphgr_msh = 0)
cn_topo = 'GEBCO_2022.nc' ! external topo file (nn_bathy =2)
cn_bath = 'elevation' ! topo name in file (nn_bathy =2)
cn_lon = 'lon' ! lon name in file (nn_bathy =2)
cn_lat = 'lat' ! lat name in file (nn_bathy =2)
rn_scale = -1 ! multiplicative factor to account for possibly negative input bathymetry (agrif only)
rn_bathy = 0. ! value of the bathymetry. if (=0) bottom flat at jpkm1
nn_msh = 1 ! create (=1) a mesh file or not (=0)
rn_hmin = 5. ! min depth of the ocean (>0) or min number of ocean level (<0)
rn_e3zps_min= 2. ! partial step thickness is set larger than the minimum of
rn_e3zps_rat= 0.1 ! rn_e3zps_min and rn_e3zps_rat*e3t, with 0<rn_e3zps_rat<1
jphgr_msh = 0 ! type of horizontal mesh
! ppglam0 = 999999.0 ! longitude of first raw and column T-point (jphgr_msh = 1)
! ppgphi0 = 999999.0 ! latitude of first raw and column T-point (jphgr_msh = 1)
! ppe1_deg = 999999.0 ! zonal grid-spacing (degrees)
! ppe2_deg = 999999.0 ! meridional grid-spacing (degrees)
! ppe1_m = 999999.0 ! zonal grid-spacing (degrees)
! ppe2_m = 999999.0 ! meridional grid-spacing (degrees)
ppsur = -4762.96143546300 ! ORCA r4, r2 and r05 coefficients
ppa0 = 255.58049070440 ! (default coefficients)
ppa1 = 245.58132232490 !
ppkth = 21.43336197938 !
ppacr = 3.0 !
ppdzmin = 2. ! Minimum vertical spacing
pphmax = 5000. ! Maximum depth
ldbletanh = .FALSE. ! Use/do not use double tanf function for vertical coordinates
! ppa2 = 999999. ! Double tanh function parameters
! ppkth2 = 999999. !
! ppacr2 = 999999. !
/
!-----------------------------------------------------------------------
&namcfg ! parameters of the configuration
!-----------------------------------------------------------------------
!
ln_e3_dep = .true. ! =T : e3=dk[depth] in discret sens.
! ! ===>>> will become the only possibility in v4.0
! ! =F : e3 analytical derivative of depth function
! ! only there for backward compatibility test with v3.6
! ! if ln_e3_dep = T
ln_dept_mid = .false. ! =T : set T points in the middle of cells
! !
cp_cfg = "orca" ! name of the configuration
jp_cfg = 025 ! resolution of the configuration
jpidta = 488 ! 1st lateral dimension ( >= jpi )
jpjdta = 418 ! 2nd " " ( >= jpj )
jpkdta = 31 ! number of levels ( >= jpk )
Ni0glo = 488 ! 1st dimension of global domain --> i =jpidta
Nj0glo = 418 ! 2nd - - --> j =jpjdta
jpkglo = 31
jperio = 4 ! lateral cond. type (between 0 and 6)
ln_use_jattr = .false. ! use (T) the file attribute: open_ocean_jstart, if present
! in netcdf input files, as the start j-row for reading
ln_domclo = .false. ! computation of closed sea masks (see namclo)
/
!-----------------------------------------------------------------------
&namzgr ! vertical coordinate (default: NO selection)
!-----------------------------------------------------------------------
!-----------------------------------------------------------------------
ln_zco = .false. ! z-coordinate - full steps
ln_zps = .true. ! z-coordinate - partial steps
ln_sco = .false. ! s- or hybrid z-s-coordinate
ln_isfcav = .false. ! ice shelf cavity (T: see namzgr_isf)
/
!-----------------------------------------------------------------------
&namzgr_isf ! isf cavity geometry definition
!-----------------------------------------------------------------------
/
!-----------------------------------------------------------------------
&namzgr_sco ! s-coordinate or hybrid z-s-coordinate (default F)
!-----------------------------------------------------------------------
/
!-----------------------------------------------------------------------
&namclo ! (closed sea : need ln_domclo = .true. in namcfg)
!-----------------------------------------------------------------------
/
!-----------------------------------------------------------------------
&namlbc ! lateral momentum boundary condition (default: NO selection)
!-----------------------------------------------------------------------
/
!-----------------------------------------------------------------------
&namagrif ! AGRIF zoom ("key_agrif")
!-----------------------------------------------------------------------
/
!-----------------------------------------------------------------------
&nammpp ! Massively Parallel Processing ("key_mpp_mpi")
!-----------------------------------------------------------------------
! ln_listonly = .false. ! do nothing else than listing the best domain decompositions (with land domains suppression)
! ! ! if T: the largest number of cores tested is defined by max(mppsize, jpni*jpnj)
/
!-----------------------------------------------------------------------
&namctl ! Control prints (default: OFF)
!-----------------------------------------------------------------------
sn_cfctl%l_runstat = .TRUE.
ln_timing = .true. ! timing by routine write out in timing.output file
/
!-----------------------------------------------------------------------
&namnc4 ! netcdf4 chunking and compression settings ("key_netcdf4")
!-----------------------------------------------------------------------
/
gphit, glamt are indeed more or less duplicated in extreme (masked) ghosts points (interpolation from parent is not possible there). This should not matter ?
Thanks for attention)
I guess this shouldn’t be a problem because all previous i-rows are calculated correctly at masked points. Is it possible to run the DOMAINcfg tool in debug mode?
