Skilled (#3) - NEMO v4 DOMAINcfg tool (#94) - Message List

NEMO v4 DOMAINcfg tool
 unsolved

Hi there

Been trying to use the domain cfg tool, but without success. I am new to nemo v4. The MPI also fails. I attached the ocean.output and part of the name list below. If anyone has Ideas, please let me know. Thank you in advance.

Here is the output from my ocean.output file. please excuse the length of text:

    CNRS - NERC - Met OFFICE - MERCATOR-ocean - INGV - CMCC
                        NEMO team
             Ocean General Circulation Model
                   version 3.7  (2015)
  mynode : mpi initialisation
  ~~~~~~
     Namelist nammpp
        mpi send type          cn_mpi_send = I
        size exported buffer   nn_buffer   =            0  bytes
        jpni, jpnj and jpnij will be calculated automatically
        avoid use of mpi_allgather at the north fold  ln_nnogather =  F
             Immediate non-blocking send (isend)
AAAAAAAA
 nemo_ctl: Control prints & Benchmark
 ~~~~~~~
    Namelist namctl
       run control (for debugging)     ln_ctl     =  F
       level of print                  nn_print   =            0
       Start i indice for SUM control  nn_ictls   =            0
       End i indice for SUM control    nn_ictle   =            0
       Start j indice for SUM control  nn_jctls   =            0
       End j indice for SUM control    nn_jctle   =            0
       number of proc. following i     nn_isplt   =            1
       number of proc. following j     nn_jsplt   =            1
       benchmark parameter (0/1)       nn_bench   =            0
       timing activated    (0/1)       nn_timing  =            0
 namcfg  : configuration initialization through namelist read
 ~~~~~~~
    Namelist namcfg
       vertical scale factors =T: e3.=dk[depth]       ln_e3_dep =  T
                              =F: old definition
       configuration name                               cp_cfg  = orca
       configuration zoom name                          cp_cfz  = no zoom
       configuration resolution                         jp_cfg  =            4
       1st lateral dimension ( >= jpiglo )              jpidta  =           20
       2nd    "         "    ( >= jpjglo )              jpjdta  =           20
       3nd    "         "                               jpkdta  =           10
       1st dimension of global domain in i              jpiglo  =           20
       2nd    -                  -    in j              jpjglo  =           20
       left bottom i index of the zoom (in data domain) jpizoom =            1
       left bottom j index of the zoom (in data domain) jpizoom =            1
       lateral cond. type (between 0 and 6)             jperio  =            0
       use file attribute if exists as i/p j-start ln_use_jattr =  F
 mpp_init : Message Passing MPI
 ~~~~~~~~
  mpp_init: defines mpp subdomains
  ~~~~~~  ----------------------
 iresti=           1  irestj=           2
 jpni=           1  jpnj=           2
  sum ilcit(i,1)=   20.000000000000000       jpiglo=          20
  sum ilcit(1,j)=   20.000000000000000       jpjglo=          20
     ****************
     *              *
   2 *   20  x 11   *
     *          1   *
     *              *
     ****************
     *              *
   1 *   20  x 11   *
     *          0   *
     *              *
     ****************
             1
  nproc  =            0
  nowe   =           -1  noea   =             1
  nono   =            1  noso   =            -1
  nbondi =            2
  nbondj =           -1
  npolj  =            0
  nperio =            0
  nlci   =           20
  nlcj   =           11
  nimpp  =            1
  njmpp  =            1
  nreci  =            2  npse   =            0
  nrecj  =            2  npsw   =           -2
  jpreci =            1  npne   =            2
  jprecj =            1  npnw   =            0
 mpp_init_ioipsl :   iloc  =           20          11
 ~~~~~~~~~~~~~~~     iabsf =            1           1
                     ihals =            0           0
                     ihale =            0           1
  phy_cst : initialization of ocean parameters and constants
  ~~~~~~~
        Domain info
           dimension of model
                  Local domain      Global domain       Data domain
               jpi     :      20   jpiglo  :      20   jpidta  :      20
               jpj     :      11   jpjglo  :      20   jpjdta  :      20
               jpk     :      10   jpk     :      10   jpkdta  :      10
               jpij    :          220
           mpp local domain info (mpp)
              jpni    :            1    jpreci  :            1
              jpnj    :            2    jprecj  :            1
              jpnij   :            2
           lateral domain boundary condition type : jperio  =            0
        Constants
           mathematical constant                 rpi =    3.1415926535897931
           day                                rday   =    86400.000000000000       s
           sideral year                       rsiyea =    31558149.010110732       s
           sideral day                        rsiday =    86164.099655911836       s
           omega                              omega  =    7.2921150830460618E-005  s^-1
           nb of months per year               raamo =    12.000000000000000       months
           nb of hours per day                 rjjhh =    24.000000000000000       hours
           nb of minutes per hour              rhhmm =    60.000000000000000       mn
           nb of seconds per minute            rmmss =    60.000000000000000       s
           earth radius                         ra   =    6371229.0000000000       m
           gravity                              grav =    9.8066499999999994       m/s^2
           triple point of temperature      rtt      =    273.16000000000003       K
           freezing point of water          rt0      =    273.14999999999998       K
           melting point of snow            rt0_snow =    273.14999999999998       K
           melting point of ice             rt0_ice  =    273.05000000000001       K
           reference density and heat capacity now defined in eosbn2.f90
           thermal conductivity of the snow          =   0.22000000000000000       J/s/m/K
           thermal conductivity of the ice           =    2.0343960000000001       J/s/m/K
           fresh ice specific heat                   =    2093.0000000000000       J/kg/K
           latent heat of fusion of fresh ice / snow =    333700.00000000000       J/kg
           density times specific heat for snow      =    690690.00000000000       J/m^3/K
           density times specific heat for ice       =    1883700.0000000000       J/m^3/K
           volumetric latent heat fusion of sea ice  =    300330000.00000000       J/m
           latent heat of sublimation of snow        =    2800000.0000000000       J/kg
           volumetric latent heat fusion of snow     =    110121000.00000000       J/m^3
           density of sea ice                        =    900.00000000000000       kg/m^3
           density of snow                           =    330.00000000000000       kg/m^3
           emissivity of snow or ice                 =   0.96999999999999997
           salinity of ice                           =    6.0000000000000000       psu
           salinity of sea                           =    34.700000000000003       psu
           latent heat of evaporation (water)        =    2500000.0000000000       J/m^3
           correction factor for solar radiation     =   0.90000000000000002
           von Karman constant                       =   0.40000000000000002
           Stefan-Boltzmann constant                 =    5.6699999999999998E-008  J/s/m^2/K^4
           conversion: degre ==> radian          rad =    1.7453292519943295E-002
           smallest real computer value       rsmall =    1.1102230246251565E-016
 eos_init : equation of state
 ~~~~~~~~
    Namelist nameos : Chosen the Equation Of Seawater (EOS)
       TEOS-10 : rho=F(Conservative Temperature, Absolute  Salinity, depth)   ln_TEOS10 =  T
       EOS-80  : rho=F(Potential    Temperature, Practical Salinity, depth)   ln_EOS80  =  F
       S-EOS   : rho=F(Conservative Temperature, Absolute  Salinity, depth)   ln_SEOS   =  F
           use of TEOS-10 equation of state (cons. temp. and abs. salinity)
              model uses Conservative Temperature
              Important: model must be initialized with CT and SA fields
           volumic mass of reference           rau0  =    1026.0000000000000       kg/m^3
           1. / rau0                        r1_rau0  =    9.7465886939571145E-004  m^3/kg
           ocean specific heat                 rcp   =    3991.8679571196299       J/Kelvin
           rau0 * rcp                       rau0_rcp =    4095656.5240047402
           1. / ( rau0 * rcp )           r1_rau0_rcp =    2.4416109948160356E-007
 dom_cfg : set the ocean configuration
 ~~~~~~~
    ocean model configuration used :   cp_cfg = orca                                                                                                                                                                                                                                                             jp_cfg =            4
    global domain lateral boundaries
       jperio= 0, closed
 dom_glo : domain: data / local
 ~~~~~~~
           data input domain    : jpidta =           20  jpjdta =           20  jpkdta =           10
           global or zoom domain: jpiglo =           20  jpjglo =           20  jpk    =           10
           local domain         : jpi    =           20  jpj    =           11  jpk    =           10
           south-west indices    jpizoom =            1  jpjzoom =            1
           zoom flags :
              lzoom   =  F  (T = zoom, F = global )
              lzoom_e =  F  (T = forced closed east  boundary)
              lzoom_w =  F  (T = forced closed west  boundary)
              lzoom_s =  F  (T = forced closed South boundary)
              lzoom_n =  F  (T = forced closed North boundary)
 dom_init : domain initialization
 ~~~~~~~~
 dom_nam  : domain initialization through namelist read
 ~~~~~~~
    Namelist namrun
       job number                      nn_no      =            0
       experiment name for output      cn_exp     = domaincfg
       file prefix restart input       cn_ocerst_in= restart
       restart input directory         cn_ocerst_indir= .
       file prefix restart output      cn_ocerst_out= restart
       restart output directory        cn_ocerst_outdir= .
       restart logical                 ln_rstart  =  F
       start with forward time step    nn_euler   =            1
       control of time step            nn_rstctl  =            1
       number of the first time step   nn_it000   =            1
       number of the last time step    nn_itend   =           75
       initial calendar date aammjj    nn_date0   =        10101
       initial time of day in hhmm     nn_time0   =            0
       leap year calendar (0/1)        nn_leapy   =            0
       initial state output            nn_istate  =            0
       frequency of restart file       nn_stock   =           75
       frequency of output file        nn_write   =            1
       mask land points                ln_mskland =  F
       additional CF standard metadata ln_cfmeta  =  F
       overwrite an existing file      ln_clobber =  T
       NetCDF chunksize (bytes)        nn_chunksz =            0
       IS coupling at the restart step ln_iscpl   =  F
 ===>>> : W A R N I N G
         ===============
  ln_rstart =.FALSE., nn_euler is forced to 0
    The IOIPSL calendar is "noleap", i.e. no leap year
    Namelist namdom : space & time domain
       flag read/compute bathymetry      nn_bathy     =            0
       Depth (if =0 bathy=jpkm1)         rn_bathy     =    4500.0000000000000
       min depth of the ocean    (>0) or    rn_hmin   =   -3.0000000000000000
       min number of ocean level (<0)
       treshold to open the isf cavity   rn_isfhmin   =    1.0000000000000000       (m)
       minimum thickness of partial      rn_e3zps_min =    20.000000000000000       (m)
          step level                     rn_e3zps_rat =   0.10000000000000001
       create mesh/mask file(s)          nn_msh       =            1
            = 0   no file created
            = 1   mesh_mask
            = 2   mesh and mask
            = 3   mesh_hgr, msh_zgr and mask
       ocean time step                       rn_rdt    =    360.00000000000000
       asselin time filter parameter         rn_atfp   =   0.10000000000000001
       suppression of closed seas (=0)       nn_closea =            0
       online coarsening of dynamical fields ln_crs    =  F
       type of horizontal mesh jphgr_msh           =            1
       longitude of first raw and column T-point ppglam0 =    0.0000000000000000
       latitude  of first raw and column T-point ppgphi0 =   -60.000000000000000
       zonal      grid-spacing (degrees) ppe1_deg        =   0.25000000000000000
       meridional grid-spacing (degrees) ppe2_deg        =   0.25000000000000000
       zonal      grid-spacing (degrees) ppe1_m          =    10.000000000000000
       meridional grid-spacing (degrees) ppe2_m          =    10.000000000000000
       ORCA r4, r2 and r05 coefficients  ppsur           =   -1033.1942952833849
                                         ppa0            =    100.83253696641530
                                         ppa1            =    100.36159186018899
                                         ppkth           =    17.285203724197910
                                         ppacr           =    5.0000000000000000
       Minimum vertical spacing ppdzmin                  =    1.0000000000000000
       Maximum depth pphmax                              =    7000.0000000000000
       Use double tanf function for vertical coordinates ldbletanh =  F
       Double tanh function parameters ppa2              =    999999.00000000000
                                       ppkth2            =    999999.00000000000
                                       ppacr2            =    999999.00000000000
 dom_clo : closed seas
 ~~~~~~~
 dom_hgr : define the horizontal mesh from ithe following par_oce parameters
 ~~~~~~~      type of horizontal mesh           jphgr_msh =            1
              position of the first row and     ppglam0  =    0.0000000000000000
              column grid-point (degrees)       ppgphi0  =   -60.000000000000000
              zonal      grid-spacing (degrees) ppe1_deg =   0.25000000000000000
              meridional grid-spacing (degrees) ppe2_deg =   0.25000000000000000
              zonal      grid-spacing (meters)  ppe1_m   =    10.000000000000000
              meridional grid-spacing (meters)  ppe2_m   =    10.000000000000000
           geographical mesh on the sphere with regular grid-spacing
           given by ppe1_deg and ppe2_deg
 dom_zgr : vertical coordinate
 ~~~~~~~
    Namelist namzgr : set vertical coordinate
       z-coordinate - full steps      ln_zco    =  T
       z-coordinate - partial steps   ln_zps    =  F
       s- or hybrid z-s-coordinate    ln_sco    =  F
       ice shelf cavities             ln_isfcav =  F
       linear free surface            ln_linssh =  F
     zgr_z   : Reference vertical z-coordinates
     ~~~~~~~
            Value of coefficients for vertical mesh:
                  zsur =   -1033.1942952833849
                  za0  =    100.83253696641530
                  za1  =    100.36159186018899

namelist:

!-----------------------------------------------------------------------
&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
   !                       !
   cp_cfg      =  "orca"   !  name of the configuration
   jp_cfg      =       4   !  resolution of the configuration
   jpidta      =     20   !  1st lateral dimension ( >= jpi )
   jpjdta      =     20   !  2nd    "         "    ( >= jpj )
   jpkdta      =      10   !  number of levels      ( >= jpk )
   jpiglo      =     20   !  1st dimension of global domain --> i =jpidta
   jpjglo      =     20   !  2nd    -                  -    --> j  =jpjdta
   jpizoom     =       1   !  left bottom (i,j) indices of the zoom
   jpjzoom     =       1   !  in data domain indices
   jperio      =       0   !  lateral cond. type (between 0 and 6)
/
!-----------------------------------------------------------------------
&namzgr        !   vertical coordinate
!-----------------------------------------------------------------------
   ln_zps      = .false.    !  z-coordinate - partial steps
   ln_linssh   = .false.    !  linear free surface
   ln_sco      = .false.
   ln_zco      = .true.
/
!-----------------------------------------------------------------------
&namzgr_sco    !   s-coordinate or hybrid z-s-coordinate
!-----------------------------------------------------------------------
   ln_s_sh94   = .false.   !  Song & Haidvogel 1994 hybrid S-sigma   (T)|
   ln_s_sf12   = .true.    !  Siddorn & Furner 2012 hybrid S-z-sigma (T)| if both are false the !NEMO tanh stretching is applied
   ln_sigcrit  = .true.    !  use sigma coordinates below critical depth (T) or Z coordinates !!(F) for Siddorn & Furner stretch
!                           !  stretching coefficients for all functions
   rn_hc       =   50.0    !  critical depth for transition to stretched coordinates
/
!-----------------------------------------------------------------------
&namdom        !   space and time domain (bathymetry, mesh, timestep)
!-----------------------------------------------------------------------
   nn_bathy    =    0      !  compute (=0) or read (=1) the bathymetry file
   rn_bathy    =    4500.     !  value of the bathymetry. if (=0) bottom flat at jpkm1
   rn_rdt      = 360.     !  time step for the dynamics (and tracer if nn_acc=0)
   jphgr_msh   =      1               !  type of horizontal mesh
   ppglam0     =  0.0             !  longitude of first raw and column T-point (jphgr_msh = 1)
   ppgphi0     =  -60.0             ! latitude  of first raw and column T-point (jphgr_msh = 1)
   ppe1_deg    =  0.25               !  zonal      grid-spacing (degrees)
   ppe2_deg    =  0.25               !  meridional grid-spacing (degrees)
   ppe1_m      =  10.0               !  zonal      grid-spacing (degrees)
   ppe2_m      =  10.0               !  meridional grid-spacing (degrees)
   ppsur       =   -1033.194295283385    !  ORCA r4, r2 and r05 coefficients
   ppa0        =     100.8325369664153   ! (default coefficients)
   ppa1        =     100.3615918601890   !
   ppkth       =      17.28520372419791  !
   ppacr       =       5.0               !
   ppdzmin     =  1.0               !  Minimum vertical spacing
   pphmax      =  7000.0               !  Maximum depth
   ldbletanh   =  .FALSE.                !  Use/do not use double tanf function for vertical
   ppa2        =  999999.0              !  Double tanh function parameters
   ppkth2      =  999999.0              !
   ppacr2      =  999999.0              !
/

mpi run output:

mpirun -v ./make_domain_cfg.exe
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
Backtrace for this error:
#0  0x7f924caadcd1 in ???
#1  0x7f924caacea5 in ???
#2  0x7f924c77820f in ???
#3  0x7f924c7f114c in ???
#4  0x560a28a76a40 in ???
#5  0x560a28995d4c in ???
#6  0x560a289cbec1 in ???
#7  0x560a28948af9 in ???
#8  0x560a28920d5e in ???
#9  0x560a2892322d in ???
#10  0x560a2891fb2e in ???
#11  0x7f924c7590b2 in ???
#12  0x560a2891fb6d in ???
#13  0xffffffffffffffff in ???
--------------------------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------

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