Lake_jersey test case error at first time steps

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briskbamboo
Posts: 20
Joined: Thu Aug 20, 2020 1:24 pm
Location: University of Tsukuba

Lake_jersey test case error at first time steps

#1 Unread post by briskbamboo »

Dear

I am new to roms and trying to run testcases, I compiled lake_jersey and try to run romsM then it gave me this error. As some other topic recommended that with NaN error at first time steps may related to ana_ and input script but I still do not know where to fix. I have already checked the matching of Masking land/ocean between lake_jersey_grd_a.nc and lake_jersey_ini_a.nc and found no problems.

Code: Select all

 NL ROMS/TOMS: started time-stepping: (Grid: 01 TimeSteps: 000000000001 - 000000001440)

 Node   #    2 CPU:       0.064
 Node   #    1 CPU:       0.064

 TIME-STEP YYYY-MM-DD hh:mm:ss.ss  KINETIC_ENRG   POTEN_ENRG    TOTAL_ENRG    NET_VOLUME
                     C => (i,j,k)       Cu            Cv            Cw         Max Speed

         0 0001-01-01 00:00:00.00           NaN           NaN           NaN           NaN
                       (000,00,0)  0.000000E+00  0.000000E+00  0.000000E+00  0.000000E+00
 Found Error: 01   Line: 313      Source: ROMS/Nonlinear/main3d.F
 Found Error: 01   Line: 300      Source: ROMS/Drivers/nl_ocean.h
Thanks for reading
Best

jcwarner
Posts: 1172
Joined: Wed Dec 31, 2003 6:16 pm
Location: USGS, USA

Re: Lake_jersey test case error at first time steps

#2 Unread post by jcwarner »

can you look through the entire stdout and see if there are any nans above that? maybe there is something wrong with the forcings??

briskbamboo
Posts: 20
Joined: Thu Aug 20, 2020 1:24 pm
Location: University of Tsukuba

Re: Lake_jersey test case error at first time steps

#3 Unread post by briskbamboo »

Thank you jcwarner.
I compiled the romM with default setting of Forward in Lake_jersey folder, then try using my own grid and ini condition (attached .nc files
lake_jersey_ini_a.nc
(1.94 MiB) Downloaded 222 times
lake_jersey_grd_a.nc
(1.21 MiB) Downloaded 207 times
). run the default .in file in the folder then Roms gave me this stdout:

Code: Select all

--------------------------------------------------------------------------------
 Model Input Parameters:  ROMS/TOMS version 3.9  
                          Tuesday - August 25, 2020 -  8:38:30 AM
--------------------------------------------------------------------------------

 Lake Jersey nesting test case with top-right refined grid

 Operating system  : Linux
 CPU/hardware      : x86_64
 Compiler system   : gfortran
 Compiler command  : /usr/bin/mpif90
 Compiler flags    : -frepack-arrays -O3 -ffast-math -
 OCN Communicator  : 0,  PET size = 3

 Input Script      : roms_lake_jersey.in

 SVN Root URL     : https://www.myroms.org/svn/src/trunk
 SVN Revision     : 1037

 Local Root       : /home/bangdt/200820/trunk
 Header Dir       : /home/bangdt/200820/test/lake_jersey/Forward
 Header file      : lake_jersey.h
 Analytical Dir   : /home/bangdt/200820/test/lake_jersey/Forward

 Resolution, Grid 01: 100x80x8,  Parallel Nodes: 3,  Tiling: 1x3


 Physical Parameters, Grid: 01
 =============================

       1440  ntimes            Number of timesteps for 3-D equations.
    120.000  dt                Timestep size (s) for 3-D equations.
         30  ndtfast           Number of timesteps for 2-D equations between
                                 each 3D timestep.
          1  ERstr             Starting ensemble/perturbation run number.
          1  ERend             Ending ensemble/perturbation run number.
          0  nrrec             Number of restart records to read from disk.
          T  LcycleRST         Switch to recycle time-records in restart file.
         60  nRST              Number of timesteps between the writing of data
                                 into restart fields.
          1  ninfo             Number of timesteps between print of information
                                 to standard output.
          T  ldefout           Switch to create a new output NetCDF file(s).
         15  nHIS              Number of timesteps between the writing fields
                                 into history file.
          0  nQCK              Number of timesteps between the writing fields
                                 into quicksave file.
          1  ntsAVG            Starting timestep for the accumulation of output
                                 time-averaged data.
        720  nAVG              Number of timesteps between the writing of
                                 time-averaged data into averages file.
          F  LuvSponge         Turning OFF sponge on horizontal momentum.
          F  LtracerSponge(01) Turning OFF sponge on tracer 01: temp
          F  LtracerSponge(02) Turning OFF sponge on tracer 02: salt
 5.0000E-06  Akt_bak(01)       Background vertical mixing coefficient (m2/s)
                                 for tracer 01: temp
 5.0000E-06  Akt_bak(02)       Background vertical mixing coefficient (m2/s)
                                 for tracer 02: salt
 5.0000E-05  Akv_bak           Background vertical mixing coefficient (m2/s)
                                 for momentum.
 5.0000E-06  Akk_bak           Background vertical mixing coefficient (m2/s)
                                 for turbulent energy.
 5.0000E-06  Akp_bak           Background vertical mixing coefficient (m2/s)
                                 for turbulent generic statistical field.
      0.000  gls_p             GLS stability exponent.
      1.000  gls_m             GLS turbulent kinetic energy exponent.
      1.000  gls_n             GLS turbulent length scale exponent.
 5.0000E-06  gls_Kmin          GLS minimum value of turbulent kinetic energy.
 5.0000E-06  gls_Pmin          GLS minimum value of dissipation.
 5.5440E-01  gls_cmu0          GLS stability coefficient.
 9.0000E-01  gls_c1            GLS shear production coefficient.
 5.2000E-01  gls_c2            GLS dissipation coefficient.
 2.5000E+00  gls_c3m           GLS stable buoyancy production coefficient.
 1.0000E+00  gls_c3p           GLS unstable buoyancy production coefficient.
 1.9600E+00  gls_sigk          GLS constant Schmidt number for TKE.
 1.9600E+00  gls_sigp          GLS constant Schmidt number for PSI.
   1400.000  charnok_alpha     Charnok factor for Zos calculation.
      0.500  zos_hsig_alpha    Factor for Zos calculation using Hsig(Awave).
      0.250  sz_alpha          Factor for Wave dissipation surface tke flux .
    100.000  crgban_cw         Factor for Craig/Banner surface tke flux.
 3.0000E-04  rdrg              Linear bottom drag coefficient (m/s).
 3.0000E-03  rdrg2             Quadratic bottom drag coefficient.
 1.5000E-02  Zob               Bottom roughness (m).
 2.0000E-02  Zos               Surface roughness (m).
          2  Vtransform        S-coordinate transformation equation.
          4  Vstretching       S-coordinate stretching function.
 1.0000E+00  theta_s           S-coordinate surface control parameter.
 1.0000E+00  theta_b           S-coordinate bottom  control parameter.
     10.000  Tcline            S-coordinate surface/bottom layer width (m) used
                                 in vertical coordinate stretching.
   1025.000  rho0              Mean density (kg/m3) for Boussinesq approximation.
      0.000  dstart            Time-stamp assigned to model initialization (days).
       0.00  time_ref          Reference time for units attribute (yyyymmdd.dd)
 0.0000E+00  Tnudg(01)         Nudging/relaxation time scale (days)
                                 for tracer 01: temp
 0.0000E+00  Tnudg(02)         Nudging/relaxation time scale (days)
                                 for tracer 02: salt
 0.0000E+00  Znudg             Nudging/relaxation time scale (days)
                                 for free-surface.
 0.0000E+00  M2nudg            Nudging/relaxation time scale (days)
                                 for 2D momentum.
 0.0000E+00  M3nudg            Nudging/relaxation time scale (days)
                                 for 3D momentum.
 0.0000E+00  obcfac            Factor between passive and active
                                 open boundary conditions.
          F  VolCons(1)        NLM western  edge boundary volume conservation.
          F  VolCons(2)        NLM southern edge boundary volume conservation.
          F  VolCons(3)        NLM eastern  edge boundary volume conservation.
          F  VolCons(4)        NLM northern edge boundary volume conservation.
     10.000  T0                Background potential temperature (C) constant.
     30.000  S0                Background salinity (PSU) constant.
      1.000  gamma2            Slipperiness variable: free-slip (1.0) or 
                                                      no-slip (-1.0).
          F  LuvSrc            Turning OFF momentum point Sources/Sinks.
          F  LwSrc             Turning OFF volume influx point Sources/Sinks.
          F  LtracerSrc(01)    Turning OFF point Sources/Sinks on tracer 01: temp
          F  LtracerSrc(02)    Turning OFF point Sources/Sinks on tracer 02: salt
          F  LsshCLM           Turning OFF processing of SSH climatology.
          F  Lm2CLM            Turning OFF processing of 2D momentum climatology.
          F  Lm3CLM            Turning OFF processing of 3D momentum climatology.
          F  LtracerCLM(01)    Turning OFF processing of climatology tracer 01: temp
          F  LtracerCLM(02)    Turning OFF processing of climatology tracer 02: salt
          F  LnudgeM2CLM       Turning OFF nudging of 2D momentum climatology.
          F  LnudgeM3CLM       Turning OFF nudging of 3D momentum climatology.
          F  LnudgeTCLM(01)    Turning OFF nudging of climatology tracer 01: temp
          F  LnudgeTCLM(02)    Turning OFF nudging of climatology tracer 02: salt

          T  Hout(idFsur)      Write out free-surface.
          T  Hout(idUbar)      Write out 2D U-momentum component.
          T  Hout(idVbar)      Write out 2D V-momentum component.
          T  Hout(idUvel)      Write out 3D U-momentum component.
          T  Hout(idVvel)      Write out 3D V-momentum component.
          T  Hout(idWvel)      Write out W-momentum component.
          T  Hout(idOvel)      Write out omega vertical velocity.
          T  Hout(idTvar)      Write out tracer 01: temp
          T  Hout(idTvar)      Write out tracer 02: salt

          T  Aout(idFsur)      Write out averaged free-surface.
          T  Aout(idUbar)      Write out averaged 2D U-momentum component.
          T  Aout(idVbar)      Write out averaged 2D V-momentum component.
          T  Aout(idUvel)      Write out averaged 3D U-momentum component.
          T  Aout(idVvel)      Write out averaged 3D V-momentum component.
          T  Aout(idWvel)      Write out averaged W-momentum component.
          T  Aout(idOvel)      Write out averaged omega vertical velocity.
          T  Aout(idTvar)      Write out averaged tracer 01: temp
          T  Aout(idTvar)      Write out averaged tracer 02: salt

 Output/Input Files:

               Output Restart File:  lake_jersey_rst.nc
               Output History File:  lake_jersey_his.nc
              Output Averages File:  lake_jersey_avg.nc
                   Input Grid File:  ../Data/lake_jersey_grd_a.nc
      Input Nonlinear Initial File:  ../Data/lake_jersey_ini_a.nc
  ROMS I/O variables Metadata File:  /home/bangdt/200820/trunk/ROMS/External/varinfo.dat


 Sediment Parameters, Grid: 01
 =============================


 Size     Sd50        Csed        Srho        Wsed        Erate       poros
 Class    (mm)       (kg/m3)     (kg/m3)     (mm/s)     (kg/m2/s)    (nondim)

   1    1.0000E-02  0.0000E+00  2.6500E+03  1.0000E-01  5.0000E-05  0.0000E+00
   2    6.0000E-02  0.0000E+00  2.6500E+03  1.0000E-01  5.0000E-05  0.0000E+00
   3    1.0000E+00  0.0000E+00  2.6500E+03  1.0000E+00  1.0000E-05  5.0000E-01

         tau_ce      tau_cd      nl_tnu2     nl_tnu4     Akt_bak      Tnudg
         (N/m2)      (N/m2)      (m2/s)      (m4/s)       (m2/s)      (day)

   1    5.0000E-02  1.0000E-02  0.0000E+00  0.0000E+00  5.0000E-06  0.0000E+00
   2    5.0000E-02  1.0000E-02  0.0000E+00  0.0000E+00  5.0000E-06  0.0000E+00
   3    7.0000E-02  2.0000E-02  0.0000E+00  0.0000E+00  5.0000E-06  0.0000E+00

         morph_fac
         (nondim)

   1    1.0000E+00
   2    1.0000E+00
   3    1.0000E+00

 New bed layer formed when deposition exceeds  0.10000E-01 (m).
 Two first layers are combined when 2nd layer smaller than  0.00000E+00 (m).
 Rate coefficient for bed load transport =  0.50000E-01

          F  LtracerSponge(03Turning OFF sponge on tracer 03: mud_01
          F  LtracerSponge(04Turning OFF sponge on tracer 04: mud_02
          F  LtracerSponge(05Turning OFF sponge on tracer 05: sand_01
          F  LtracerSrc(03)  Turning OFF point sources/Sink on tracer 03: mud_01
          F  LtracerSrc(04)  Turning OFF point sources/Sink on tracer 04: mud_02
          F  LtracerSrc(05)  Turning OFF point sources/Sink on tracer 05: sand_01
          F  LtracerCLM(03)  Turning OFF processing of climatology tracer 03: mud_01
          F  LtracerCLM(04)  Turning OFF processing of climatology tracer 04: mud_02
          F  LtracerCLM(05)  Turning OFF processing of climatology tracer 05: sand_01
          F  LnudgeTCLM(03)  Turning OFF nudging of climatology tracer 03: mud_01
          F  LnudgeTCLM(04)  Turning OFF nudging of climatology tracer 04: mud_02
          F  LnudgeTCLM(05)  Turning OFF nudging of climatology tracer 05: sand_01

          T  Hout(idTvar)   Write out sediment01: mud_01
          T  Hout(idTvar)   Write out sediment02: mud_02
          T  Hout(idTvar)   Write out sediment03: sand_01
          T  Hout(idfrac)   Write out bed fraction, sediment 01: mudfrac_01
          T  Hout(idfrac)   Write out bed fraction, sediment 02: mudfrac_02
          T  Hout(idfrac)   Write out bed fraction, sediment 03: sandfrac_01
          T  Hout(idfrac)   Write out mass, sediment 01: mudmass_01
          T  Hout(idfrac)   Write out mass, sediment 02: mudmass_02
          T  Hout(idfrac)   Write out mass, sediment 03: sandmass_01
          T  Hout(idUbld)   Write out bed load at U-points, sediment 01: bedload_Umud_01
          T  Hout(idVbld)   Write out bed load at V-points, sediment 01: bedload_Vmud_01
          T  Hout(idUbld)   Write out bed load at U-points, sediment 02: bedload_Umud_02
          T  Hout(idVbld)   Write out bed load at V-points, sediment 02: bedload_Vmud_02
          T  Hout(idUbld)   Write out bed load at U-points, sediment 03: bedload_Usand_01
          T  Hout(idVbld)   Write out bed load at V-points, sediment 03: bedload_Vsand_01
          T  Hout(idSbed)   Write out BED property 01: bed_thickness
          T  Hout(idSbed)   Write out BED property 02: bed_age
          T  Hout(idSbed)   Write out BED property 03: bed_porosity
          T  Hout(idBott)   Write out BOTTOM property 01: grain_diameter
          T  Hout(idBott)   Write out BOTTOM property 02: grain_density
          T  Hout(idBott)   Write out BOTTOM property 03: settling_vel
          T  Hout(idBott)   Write out BOTTOM property 04: erosion_stress
          T  Hout(idBott)   Write out BOTTOM property 05: ripple_length
          T  Hout(idBott)   Write out BOTTOM property 06: ripple_height
          T  Hout(idBott)   Write out BOTTOM property 07: bed_wave_amp
          T  Hout(idBott)   Write out BOTTOM property 08: Zo_def
 Node #    1 (pid=   18540) is active.
 Node #    2 (pid=   18541) is active.
          T  Hout(idBott)   Write out BOTTOM property 09: Zo_app

          T  Aout(idTvar)   Write out averaged sediment01: mud_01
          T  Aout(idTvar)   Write out averaged sediment02: mud_02
          T  Aout(idTvar)   Write out averaged sediment03: sand_01
          T  Aout(idUbld)   Write out U-bedload, sediment 01: bedload_Umud_01
          T  Aout(idVbld)   Write out V-bedload, sediment 01: bedload_Vmud_01
          T  Aout(idUbld)   Write out U-bedload, sediment 02: bedload_Umud_02
          T  Aout(idVbld)   Write out V-bedload, sediment 02: bedload_Vmud_02
          T  Aout(idUbld)   Write out U-bedload, sediment 03: bedload_Usand_01
          T  Aout(idVbld)   Write out V-bedload, sediment 03: bedload_Vsand_01

 Tile partition information for Grid 01:  100x80x8  tiling: 1x3

     tile     Istr     Iend     Jstr     Jend     Npts

        0        1      100        1       27    21600
        1        1      100       28       54    21600
        2        1      100       55       80    20800

 Tile minimum and maximum fractional coordinates for Grid 01:
   (interior points only)

     tile     Xmin     Xmax     Ymin     Ymax     grid

        0     0.50   100.50     0.50    27.50  RHO-points
        1     0.50   100.50    27.50    54.50  RHO-points
        2     0.50   100.50    54.50    80.50  RHO-points

        0     1.00   100.00     0.50    27.50    U-points
        1     1.00   100.00    27.50    54.50    U-points
        2     1.00   100.00    54.50    80.50    U-points

        0     0.50   100.50     1.00    27.50    V-points
        1     0.50   100.50    27.50    54.50    V-points
        2     0.50   100.50    54.50    80.00    V-points

 Maximum halo size in XI and ETA directions:

               HaloSizeI(1) =     333
               HaloSizeJ(1) =     123
                TileSide(1) =     105
                TileSize(1) =    3675


 Tracer Advection Scheme: NLM
 ========================

 Variable               Grid  Horizontal         Vertical
 ---------              ----  ------------       ------------

 temp                     1   Upstream3          Centered4

 salt                     1   Upstream3          Centered4

 mud_01                   1   HSIMT              HSIMT

 mud_02                   1   HSIMT              HSIMT

 sand_01                  1   HSIMT              HSIMT

 Akima4     Fourth-order Akima advection
 Centered2  Second-order centered differences advection
 Centered4  Fourth-order centered differences advection
 HSIMT      Third High-order Spatial Inteporlation at Middle Time Advection with TVD limiter
 MPDATA     Multidimensional Positive Definite Advection Algorithm, recursive method
 Splines    Conservative Parabolic Splines Reconstruction Advection (only vertical; not recommended)
 Split_U3   Split third-order Upstream Advection
 Upstream3  Third-order Upstream-biased Advection (only horizontal)


 Lateral Boundary Conditions: NLM
 ============================

 Variable               Grid  West Edge    South Edge   East Edge    North Edge
 ---------              ----  ----------   ----------   ----------   ----------

 zeta                     1   Closed       Closed       Closed       Closed

 ubar                     1   Closed       Closed       Closed       Closed

 vbar                     1   Closed       Closed       Closed       Closed

 u                        1   Closed       Closed       Closed       Closed

 v                        1   Closed       Closed       Closed       Closed

 temp                     1   Closed       Closed       Closed       Closed

 salt                     1   Closed       Closed       Closed       Closed

 mud_01                   1   Closed       Closed       Closed       Closed

 mud_02                   1   Closed       Closed       Closed       Closed

 sand_01                  1   Closed       Closed       Closed       Closed

 tke                      1   Closed       Closed       Closed       Closed

 Activated C-preprocessing Options:

 LAKE_JERSEY             Lake Jersey nesting test case with top-right refined grid
 ANA_BPFLUX              Analytical bottom passive tracers fluxes
 ANA_BSFLUX              Analytical kinematic bottom salinity flux
 ANA_BTFLUX              Analytical kinematic bottom temperature flux
 ANA_SEDIMENT            Analytical sediment initial conditions
 ANA_SMFLUX              Analytical kinematic surface momentum flux
 ANA_SPFLUX              Analytical surface passive tracer fluxes
 ANA_SSFLUX              Analytical kinematic surface salinity flux
 ANA_STFLUX              Analytical kinematic surface temperature flux
 ANA_WWAVE               Analytical wind induced waves
 ASSUMED_SHAPE           Using assumed-shape arrays
 AVERAGES                Writing out time-averaged nonlinear model fields
 BEDLOAD_SOULSBY         Activate bed load sediment transport Soulsby formula
 !BOUNDARY_ALLGATHER     Using mpi_allreduce in mp_boundary routine
 !COLLECT_ALL...         Using mpi_isend/mpi_recv in mp_collect routine
 DJ_GRADPS               Parabolic Splines density Jacobian (Shchepetkin, 2002)
 DOUBLE_PRECISION        Double precision arithmetic numerical kernel.
 GLS_MIXING              Generic Length-Scale turbulence closure
 MASKING                 Land/Sea masking
 MPI                     MPI distributed-memory configuration
 NONLINEAR               Nonlinear Model
 NONLIN_EOS              Nonlinear Equation of State for seawater
 N2S2_HORAVG             Horizontal smoothing of buoyancy and shear
 OUT_DOUBLE              Double precision output fields in NetCDF files
 POWER_LAW               Power-law shape time-averaging barotropic filter
 PROFILE                 Time profiling activated
 K_GSCHEME               Third-order upstream advection of TKE fields
 REDUCE_ALLREDUCE        Using mpi_allreduce in mp_reduce routine
 !RST_SINGLE             Double precision fields in restart NetCDF file
 SALINITY                Using salinity
 SEDIMENT                Cohesive and noncohesive sediments
 SUSPLOAD                Activate suspended sediment transport
 SOLVE3D                 Solving 3D Primitive Equations
 SSW_BBL                 Styles and Glenn Bottom Boundary Layer - modified
 SSW_CALC_UB             Internal computation of bottom orbital velocity
 SSW_CALC_ZNOT           Internal computation of bottom roughness
 UV_ADV                  Advection of momentum
 UV_COR                  Coriolis term
 UV_U3HADVECTION         Third-order upstream horizontal advection of 3D momentum
 UV_C4VADVECTION         Fourth-order centered vertical advection of momentum
 VAR_RHO_2D              Variable density barotropic mode

 Process Information:

 Node #    0 (pid=   18539) is active.

 INITIAL: Configuring and initializing forward nonlinear model ...
 *******

    GET_GRID    - bathymetry at RHO-points: h
                   (Grid = 01, File: ../Data/lake_jersey_grd_a.nc)
                   (Min = -1.77282174E+03 Max =  4.25088269E+03)
    GET_GRID    - Coriolis parameter at RHO-points: f
                   (Grid = 01, File: ../Data/lake_jersey_grd_a.nc)
                   (Min =  0.00000000E+00 Max =  0.00000000E+00)
    GET_GRID    - reciprocal XI-grid spacing: pm
                   (Grid = 01, File: ../Data/lake_jersey_grd_a.nc)
                   (Min =  1.92864618E-04 Max =  1.92864618E-04)
    GET_GRID    - reciprocal ETA-grid spacing: pn
                   (Grid = 01, File: ../Data/lake_jersey_grd_a.nc)
                   (Min =  9.65484794E-05 Max =  9.65484794E-05)
    GET_GRID    - x-location of RHO-points: x-rho
                   (Grid = 01, File: ../Data/lake_jersey_grd_a.nc)
                   (Min =  1.12348007E+07 Max =  1.17584841E+07)
    GET_GRID    - x-location of U-points: x_u
                   (Grid = 01, File: ../Data/lake_jersey_grd_a.nc)
                   (Min =  1.12373931E+07 Max =  1.17558916E+07)
    GET_GRID    - x-location of V-points: x_v
                   (Grid = 01, File: ../Data/lake_jersey_grd_a.nc)
                   (Min =  1.12348007E+07 Max =  1.17584841E+07)
    GET_GRID    - x-location of PSI-points: x_psi
                   (Grid = 01, File: ../Data/lake_jersey_grd_a.nc)
                   (Min =  1.12373931E+07 Max =  1.17558916E+07)
    GET_GRID    - y-location of RHO-points: y_rho
                   (Grid = 01, File: ../Data/lake_jersey_grd_a.nc)
                   (Min =  1.74528726E+06 Max =  2.58424402E+06)
    GET_GRID    - y-location of U-points: y_u
                   (Grid = 01, File: ../Data/lake_jersey_grd_a.nc)
                   (Min =  1.74528726E+06 Max =  2.58424402E+06)
    GET_GRID    - y-location of V-points: y_v
                   (Grid = 01, File: ../Data/lake_jersey_grd_a.nc)
                   (Min =  1.75046600E+06 Max =  2.57906528E+06)
    GET_GRID    - y-location of PSI-points: y-psi
                   (Grid = 01, File: ../Data/lake_jersey_grd_a.nc)
                   (Min =  1.75046600E+06 Max =  2.57906528E+06)
    GET_GRID    - mask on RHO-points: mask_rho
                   (Grid = 01, File: ../Data/lake_jersey_grd_a.nc)
                   (Min =  0.00000000E+00 Max =  1.00000000E+00)
    GET_GRID    - mask on U-points: mask_u
                   (Grid = 01, File: ../Data/lake_jersey_grd_a.nc)
                   (Min =  0.00000000E+00 Max =  1.00000000E+00)
    GET_GRID    - mask on V-points: mask_v
                   (Grid = 01, File: ../Data/lake_jersey_grd_a.nc)
                   (Min =  0.00000000E+00 Max =  1.00000000E+00)
    GET_GRID    - mask on PSI-points: mask_psi
                   (Grid = 01, File: ../Data/lake_jersey_grd_a.nc)
                   (Min =  0.00000000E+00 Max =  1.00000000E+00)

 Vertical S-coordinate System, Grid 01:

 level   S-coord     Cs-curve   Z   at hmin       at hc    half way     at hmax

     8   0.0000000   0.0000000        0.000       0.000       0.000       0.000
     7  -0.1250000  -0.0226239       39.079      -0.738     -29.047     -97.193
     6  -0.2500000  -0.0889092      156.000      -1.695    -111.759    -379.550
     5  -0.3750000  -0.1942304      342.518      -2.846    -242.451    -827.454
     4  -0.5000000  -0.3313167      585.669      -4.157    -412.185   -1410.071
     3  -0.6250000  -0.4908874      868.907      -5.579    -609.555   -2088.043
     2  -0.7500000  -0.6624894     1173.596      -7.062    -821.713   -2817.038
     1  -0.8750000  -0.8354715     1480.744      -8.552   -1035.567   -3551.886
     0  -1.0000000  -1.0000000     1772.822     -10.000   -1239.030   -4250.883

 Time Splitting Weights for Grid 01:    ndtfast =  30    nfast =  42
 ==================================

    Primary            Secondary            Accumulated to Current Step

  1-0.0008094437383769 0.0333333333333333-0.0008094437383769 0.0333333333333333
  2-0.0014053566728197 0.0333603147912792-0.0022148004111966 0.0666936481246126
  3-0.0017877524645903 0.0334071600137066-0.0040025528757869 0.1001008081383191
  4-0.0019566842408176 0.0334667517625262-0.0059592371166046 0.1335675599008453
  5-0.0019122901320372 0.0335319745705535-0.0078715272486418 0.1670995344713988
  6-0.0016548570247459 0.0335957175749547-0.0095263842733877 0.2006952520463536
  7-0.0011849025289723 0.0336508794757796-0.0107112868023600 0.2343461315221331
  8-0.0005032751608631 0.0336903762267453-0.0112145619632232 0.2680365077488784
  9 0.0003887272597151 0.0337071520654408-0.0108258347035081 0.3017436598143192
 10 0.0014892209965583 0.0336941944901169-0.0093366137069498 0.3354378543044362
 11 0.0027955815694920 0.0336445537902317-0.0065410321374578 0.3690824080946679
 12 0.0043042707117221 0.0335513677379153-0.0022367614257357 0.4026337758325831
 13 0.0060106451121704 0.0334078920475245 0.0037738836864347 0.4360416678801076
 14 0.0079087469427945 0.0332075372104522 0.0116826306292293 0.4692492050905598
 15 0.0099910761708920 0.0329439123123590 0.0216737068001212 0.5021931174029188
 16 0.0122483446563884 0.0326108764399960 0.0339220514565096 0.5348039938429148
 17 0.0146692120341107 0.0322025982847830 0.0485912634906203 0.5670065921276978
 18 0.0172400033810439 0.0317136245503127 0.0658312668716642 0.5987202166780105
 19 0.0199444086685725 0.0311389577709445 0.0857756755402367 0.6298591744489550
 20 0.0227631639997064 0.0304741441486588 0.1085388395399431 0.6603333185976138
 21 0.0256737146312910 0.0297153720153352 0.1342125541712341 0.6900486906129490
 22 0.0286498597812016 0.0288595815276255 0.1628624139524357 0.7189082721405746
 23 0.0316613792205220 0.0279045862015855 0.1945237931729577 0.7468128583421600
 24 0.0346736416507075 0.0268492068942347 0.2291974348236651 0.7736620652363948
 25 0.0376471948657328 0.0256934188392112 0.2668446296893979 0.7993554840756060
 26 0.0405373376992232 0.0244385123436867 0.3073819673886211 0.8237939964192927
 27 0.0432936737565711 0.0230872677537126 0.3506756411451922 0.8468812641730054
 28 0.0458596469320356 0.0216441452951603 0.3965352880772278 0.8685254094681656
 29 0.0481720587108284 0.0201154903974257 0.4447073467880562 0.8886408998655914
 30 0.0501605672561820 0.0185097551070648 0.4948679140442381 0.9071506549726561
 31 0.0517471682814030 0.0168377361985254 0.5466150823256412 0.9239883911711815
 32 0.0528456577069106 0.0151128305891453 0.5994607400325517 0.9391012217603267
 33 0.0533610761022577 0.0133513086655816 0.6528218161348094 0.9524525304259084
 34 0.0531891349131379 0.0115726061288397 0.7060109510479473 0.9640251365547481
 35 0.0522156244733761 0.0097996349650684 0.7582265755213234 0.9738247715198165
 36 0.0503158038019031 0.0080591141492892 0.8085423793232265 0.9818838856691057
 37 0.0473537721847153 0.0063819206892258 0.8558961515079418 0.9882658063583315
 38 0.0431818225418188 0.0048034616164019 0.8990779740497606 0.9930692679747335
 39 0.0376397765791564 0.0033640675316746 0.9367177506289170 0.9964333355064081
 40 0.0305543017255206 0.0021094083123694 0.9672720523544377 0.9985427438187775
 41 0.0217382098544505 0.0010909315881854 0.9890102622088881 0.9996336754069629
 42 0.0109897377911119 0.0003663245930371 1.0000000000000000 1.0000000000000000

 ndtfast, nfast =   30  42   nfast/ndtfast =  1.40000

 Centers of gravity and integrals (values must be 1, 1, approx 1/2, 1, 1):

    1.000000000000 1.047601458608 0.523800729304 1.000000000000 1.000000000000

 Power filter parameters, Fgamma, gamma =  0.28400   0.18933

 Metrics information for Grid 01:
 ===============================

 Minimum X-grid spacing, DXmin =  5.18498422E+00 km    Water points =  5.18498422E+00 km
 Maximum X-grid spacing, DXmax =  5.18498422E+00 km    Water points =  5.18498422E+00 km
 Minimum Y-grid spacing, DYmin =  1.03574909E+01 km    Water points =  1.03574909E+01 km
 Maximum Y-grid spacing, DYmax =  1.03574909E+01 km    Water points =  1.03574909E+01 km
 Minimum Z-grid spacing, DZmin = -3.07148846E+02 m     Water points = -5.80559302E+00 m
 Maximum Z-grid spacing, DZmax =  7.34847624E+02 m     Water points =  7.34847624E+02 m

 Minimum barotropic Courant Number =  1.14531898E-03
 Maximum barotropic Courant Number =  1.76175818E-01
 Maximum Coriolis   Courant Number =  0.00000000E+00


 NLM: GET_STATE - Reading state initial conditions,                       0001-01-01 00:00:00.00
                   (Grid 01, t = 0.0000, File: lake_jersey_ini_a.nc, Rec=0001, Index=1)
                - free-surface
                   (Min =  0.00000000E+00 Max =  0.00000000E+00)
                - vertically integrated u-momentum component
                   (Min =  0.00000000E+00 Max =  0.00000000E+00)
                - vertically integrated v-momentum component
                   (Min =  0.00000000E+00 Max =  0.00000000E+00)
                - u-momentum component
                   (Min =  0.00000000E+00 Max =  0.00000000E+00)
                - v-momentum component
                   (Min =  0.00000000E+00 Max =  0.00000000E+00)
                - potential temperature
                   (Min =  1.05902901E+01 Max =  1.94097099E+01)
                - salinity
                   (Min =  3.32000313E+01 Max =  3.67999992E+01)

 Basin information for Grid 01:

 Maximum grid stiffness ratios:  rx0 =   1.219780E+02 (Beckmann and Haidvogel)
                                 rx1 =   2.067214E+01 (Haney)

 Initial domain volumes:  TotVolume =  1.6543354048E+14 m3
                         MinCellVol = -3.1178024141E+08 m3
                         MaxCellVol =  3.6654217247E+10 m3
                            Max/Min = -1.1756427245E+02


 NL ROMS/TOMS: started time-stepping: (Grid: 01 TimeSteps: 000000000001 - 000000001440)

 Node   #    1 CPU:       0.061

 TIME-STEP YYYY-MM-DD hh:mm:ss.ss  KINETIC_ENRG   POTEN_ENRG    TOTAL_ENRG    NET_VOLUME
                     C => (i,j,k)       Cu            Cv            Cw         Max Speed

         0 0001-01-01 00:00:00.00           NaN           NaN           NaN           NaN
                       (000,00,0)  0.000000E+00  0.000000E+00  0.000000E+00  0.000000E+00
 Found Error: 01   Line: 313      Source: ROMS/Nonlinear/main3d.F
 Found Error: 01   Line: 300      Source: ROMS/Drivers/nl_ocean.h

Elapsed wall CPU time for each process (seconds):

 Node   #    0 CPU:       0.059
 Total:                   0.180
 Average:                 0.060
 Minimum:                 0.059
 Maximum:                 0.061

 Nonlinear model elapsed CPU time profile, Grid: 01

  Allocation and array initialization ..............         0.049  (27.2253 %)
  Ocean state initialization .......................         0.011  ( 5.8664 %)
  Reading of input data ............................         0.000  ( 0.0277 %)
  Processing of input data .........................         0.003  ( 1.4475 %)
  Computation of global information integrals ......         0.003  ( 1.6577 %)
  2D/3D coupling, vertical metrics .................         0.006  ( 3.5699 %)
  Omega vertical velocity ..........................         0.001  ( 0.5080 %)
  Equation of state for seawater ...................         0.009  ( 4.7390 %)
                                              Total:         0.081   45.0414 %

  Unique kernel(s) regions profiled ................         0.081   45.0414 %
  Residual, non-profiled code ......................         0.099   54.9586 %


 All percentages are with respect to total time =            0.180


 MPI communications profile, Grid: 01

  Message Passage: 2D halo exchanges ...............         0.007  ( 3.6758 %)
  Message Passage: 3D halo exchanges ...............         0.006  ( 3.4523 %)
  Message Passage: 4D halo exchanges ...............         0.002  ( 1.3643 %)
  Message Passage: data broadcast ..................         0.039  (21.7060 %)
  Message Passage: data reduction ..................         0.001  ( 0.8058 %)
  Message Passage: data scattering..................         0.018  ( 9.7802 %)
  Message Passage: point data gathering ............         0.000  ( 0.0372 %)
  Message Passage: synchronization barrier .........         0.001  ( 0.3644 %)
                                              Total:         0.074   41.1859 %

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

 Dynamic and Automatic memory (MB) usage for Grid 01:  100x80x8  tiling: 1x3

     tile          Dynamic        Automatic            USAGE      MPI-Buffers

        0            16.11             2.47            18.58             1.17
        1            17.09             2.47            19.55             1.17
        2            16.11             2.39            18.50             1.17

    TOTAL            49.31             7.32            56.63             3.50

<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

 ROMS/TOMS - Output NetCDF summary for Grid 01:

 Analytical header files used:

     ROMS/Functionals/ana_btflux.h
     /home/bangdt/200820/test/lake_jersey/Forward/ana_sediment.h
     /home/bangdt/200820/test/lake_jersey/Forward/ana_smflux.h
     /home/bangdt/200820/test/lake_jersey/Forward/ana_stflux.h
     /home/bangdt/200820/test/lake_jersey/Forward/ana_wwave.h
 Found Error: 01   Line: 357      Source: ROMS/Utility/close_io.F

 ROMS/TOMS - Blows up ................ exit_flag: 1

 Node   #    2 CPU:       0.060
ERROR STOP 
ERROR STOP 
ERROR STOP 
-------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

  Process name: [[39142,1],2]
  Exit code:    1
--------------------------------------------------------------------------

User avatar
wilkin
Posts: 875
Joined: Mon Apr 28, 2003 5:44 pm
Location: Rutgers University
Contact:

Re: Lake_jersey test case error at first time steps

#4 Unread post by wilkin »

Code: Select all

 Minimum Z-grid spacing, DZmin = -3.07148846E+02 m     Water points = -5.80559302E+00 m
 Maximum Z-grid spacing, DZmax =  7.34847624E+02 m     Water points =  7.34847624E+02 m

 
You have negative vertical grid spacing. Check your bathymetry and initial zeta.
John Wilkin: DMCS Rutgers University
71 Dudley Rd, New Brunswick, NJ 08901-8521, USA. ph: 609-630-0559 jwilkin@rutgers.edu

briskbamboo
Posts: 20
Joined: Thu Aug 20, 2020 1:24 pm
Location: University of Tsukuba

Re: Lake_jersey test case error at first time steps

#5 Unread post by briskbamboo »

Thanks to wilkin

I corrected as your recommended then the model pass that error. After 137 steps it blowup again. This time it blowedup when the boundary flow reached to an Island in the mìddle of the grid. I checked that Island, it has 1.e37 in h which is strange because I changed it to 10 m depth in h, and the hraw from topo base map is just about -130 m. I guest may be it changed due to ana_ setting when the model started but still cant find how to fix.

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