Blow up problem

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IBH123
Posts: 9
Joined: Wed Feb 27, 2019 8:24 pm
Location: Stony Brook University

Blow up problem

#1 Unread post by IBH123 »

Hi:

Could I use some help from anyone on solving the following blow up problem?

I'm trying to forcing my model on three open boundaries. The model is at a relative shallow water region with the depth at around 4m, with the resolution of around 30m. I thought the blow up might be due the too small z-grid spacing, so I turned on the WET-DRY but it doesn't help much (if WET-DRY is off, it stops at the step of omega computation). I also tried to mask out all the places with the depth smaller than 0.2m but it still report a smallest z-grid spacing closer to zero.... Should I try even smaller time steps ? Smooth the bathymetry more ? Or there are some other obvious mistakes ?

Thank you very much

Code: Select all

 Tidal flow at OIB

 Operating system : Linux
 CPU/hardware     : x86_64
 Compiler system  : gfortran
 Compiler command : /gpfs/software/openmpi-3.0.0/bin/mpif90
 Compiler flags   : -frepack-arrays -g -fbounds-check -fbacktrace -fcheck=all -fsanitize=address -fsanitize=undefined -finit-real=nan -ffpe-trap=invalid,zero,overflow -
 MPI Communicator : 0  PET size = 1

 Input Script     : roms_oib.in

 SVN Root URL     : https://www.myroms.org/svn/src/trunk
 SVN Revision     : 1013

 Local Root       : /gpfs/projects/WilsonGroup/ROMS/trunk
 Header Dir       : /gpfs/projects/WilsonGroup/ROMS/OIB
 Header file      : roms_oib.h
 Analytical Dir   : /gpfs/projects/WilsonGroup/ROMS/OIB

 Resolution, Grid 01: 153x208x5,  Parallel Nodes: 1,  Tiling: 1x1


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

        200  ntimes            Number of timesteps for 3-D equations.
     27.940  dt                Timestep size (s) for 3-D equations.
        100  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.
        200  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).
          1  nHIS              Number of timesteps between the writing fields
                                 into history file.
          0  nQCK              Number of timesteps between the writing fields
                                 into quicksave file.
 1.0000E-03  nl_visc2          NLM Horizontal, harmonic mixing coefficient
                                 (m2/s) for momentum.
          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.
      3.000  gls_p             GLS stability exponent.
      1.500  gls_m             GLS turbulent kinetic energy exponent.
     -1.000  gls_n             GLS turbulent length scale exponent.
 7.6000E-06  gls_Kmin          GLS minimum value of turbulent kinetic energy.
 1.0000E-12  gls_Pmin          GLS minimum value of dissipation.
 5.4770E-01  gls_cmu0          GLS stability coefficient.
 1.4400E+00  gls_c1            GLS shear production coefficient.
 1.9200E+00  gls_c2            GLS dissipation coefficient.
-4.0000E-01  gls_c3m           GLS stable buoyancy production coefficient.
 1.0000E+00  gls_c3p           GLS unstable buoyancy production coefficient.
 1.0000E+00  gls_sigk          GLS constant Schmidt number for TKE.
 1.3000E+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).
 2.5000E-02  rdrg2             Quadratic bottom drag coefficient.
 1.5000E-02  Zob               Bottom roughness (m).
 5.0000E-01  Zos               Surface roughness (m).
 1.0000E-01  Dcrit             Minimum depth for wetting and drying (m).
          2  Vtransform        S-coordinate transformation equation.
          1  Vstretching       S-coordinate stretching function.
 0.0000E+00  theta_s           S-coordinate surface control parameter.
 0.0000E+00  theta_b           S-coordinate bottom  control parameter.
   1000.000  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.
          T  VolCons(1)        NLM western  edge boundary volume conservation.
          T  VolCons(2)        NLM southern edge boundary volume conservation.
          T  VolCons(3)        NLM eastern  edge boundary volume conservation.
          T  VolCons(4)        NLM northern edge boundary volume conservation.
     10.000  T0                Background potential temperature (C) constant.
     35.000  S0                Background salinity (PSU) constant.
   1027.000  R0                Background density (kg/m3) used in linear Equation
                                 of State.
 1.7000E-04  Tcoef             Thermal expansion coefficient (1/Celsius).
 7.6000E-04  Scoef             Saline contraction coefficient (1/PSU).
      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

 Output/Input Files:

               Output Restart File:  roms_rst.nc
               Output History File:  roms_his.nc
                   Input Grid File:  /gpfs/projects/WilsonGroup/ROMS/OIB/ROMS_Grid1_msk02.nc
      Input Nonlinear Initial File:  /gpfs/projects/WilsonGroup/ROMS/OIB/oib_ini.nc
               Input Boundary File:  /gpfs/projects/WilsonGroup/ROMS/OIB/oib_obc.nc
  ROMS I/O variables Metadata File:  /gpfs/projects/WilsonGroup/ROMS/OIB/varinfo.dat

 Tile partition information for Grid 01:  153x208x5  tiling: 1x1

     tile     Istr     Iend     Jstr     Jend     Npts

        0        1      153        1      208   159120

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

     tile     Xmin     Xmax     Ymin     Ymax     grid

        0     0.50   153.50     0.50   208.50  RHO-points

        0     1.00   153.00     0.50   208.50    U-points

        0     0.50   153.50     1.00   208.00    V-points

 Maximum halo size in XI and ETA directions:

               HaloSizeI(1) =     326
               HaloSizeJ(1) =     438
                TileSide(1) =     213
                TileSize(1) =   33441


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

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

 temp                     1   Upstream3          Centered4

 salt                     1   Upstream3          Centered4

 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   Chapman Imp  Chapman Imp  Chapman Imp  Closed

 ubar                     1   Flather      Flather      Flather      Closed

 vbar                     1   Flather      Flather      Flather      Closed

 u                        1   Radiation    Radiation    Radiation    Closed

 v                        1   Radiation    Radiation    Radiation    Closed

 temp                     1   Radiation    Radiation    Radiation    Closed

 salt                     1   Radiation    Radiation    Radiation    Closed

 tke                      1   Radiation    Radiation    Radiation    Closed

 Activated C-preprocessing Options:

 roms_oib                Tidal flow at OIB
 ANA_BSFLUX              Analytical kinematic bottom salinity flux
 ANA_BTFLUX              Analytical kinematic bottom temperature flux
 ANA_SMFLUX              Analytical kinematic surface momentum flux
 ANA_SSFLUX              Analytical kinematic surface salinity flux
 ANA_STFLUX              Analytical kinematic surface temperature flux
 ASSUMED_SHAPE           Using assumed-shape arrays
 !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
 LIMIT_BSTRESS           Limit bottom stress to maintain bottom velocity direction
 KANTHA_CLAYSON          Kantha and Clayson stability function formulation
 MASKING                 Land/Sea masking
 MIX_S_UV                Mixing of momentum along constant S-surfaces
 MPI                     MPI distributed-memory configuration
 NONLINEAR               Nonlinear Model
 !NONLIN_EOS             Linear Equation of State for seawater
 N2S2_HORAVG             Horizontal smoothing of buoyancy and shear
 POWER_LAW               Power-law shape time-averaging barotropic filter
 PROFILE                 Time profiling activated
 K_GSCHEME               Third-order upstream advection of TKE fields
 REDUCE_ALLGATHER        Using mpi_allgather in mp_reduce routine
 RI_SPLINES              Parabolic Spline Reconstruction for Richardson Number
 !RST_SINGLE             Double precision fields in restart NetCDF file
 SOLVE3D                 Solving 3D Primitive Equations
 SPLINES_VDIFF           Parabolic Spline Reconstruction for Vertical Diffusion
 SPLINES_VVISC           Parabolic Spline Reconstruction for Vertical Viscosity
 SPHERICAL               Spherical grid configuration
 UV_QDRAG                Quadratic bottom stress
 UV_VIS2                 Harmonic mixing of momentum
 VAR_RHO_2D              Variable density barotropic mode
 WET_DRY                 Wetting and drying activated

 Process Information:

 Node #    0 (pid=   30370) is active.

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

    GET_GRID    - angle between XI-axis and EAST: angler
                   (Grid = 01, File: /gpfs/projects/WilsonGroup/ROMS/OIB/ROMS_Grid1_msk02.nc)
                   (Min =  3.63290745E-01 Max =  4.03162787E-01)
    GET_GRID    - bathymetry at RHO-points: h
                   (Grid = 01, File: /gpfs/projects/WilsonGroup/ROMS/OIB/ROMS_Grid1_msk02.nc)
                   (Min =  0.00000000E+00 Max =  1.15236203E+01)
    GET_GRID    - Coriolis parameter at RHO-points: f
                   (Grid = 01, File: /gpfs/projects/WilsonGroup/ROMS/OIB/ROMS_Grid1_msk02.nc)
                   (Min =  9.51175864E-05 Max =  9.52489999E-05)
    GET_GRID    - reciprocal XI-grid spacing: pm
                   (Grid = 01, File: /gpfs/projects/WilsonGroup/ROMS/OIB/ROMS_Grid1_msk02.nc)
                   (Min =  3.34922159E-02 Max =  3.40657003E-02)
    GET_GRID    - reciprocal ETA-grid spacing: pn
                   (Grid = 01, File: /gpfs/projects/WilsonGroup/ROMS/OIB/ROMS_Grid1_msk02.nc)
                   (Min =  3.26098114E-02 Max =  3.35705449E-02)
    GET_GRID    - longitude of RHO-points: lon_rho
                   (Grid = 01, File: /gpfs/projects/WilsonGroup/ROMS/OIB/ROMS_Grid1_msk02.nc)
                   (Min = -7.29389253E+01 Max = -7.28611025E+01)
    GET_GRID    - longitude of U-points: lon_u
                   (Grid = 01, File: /gpfs/projects/WilsonGroup/ROMS/OIB/ROMS_Grid1_msk02.nc)
                   (Min = -7.29387624E+01 Max = -7.28612654E+01)
    GET_GRID    - longitude of V-points: lon_v
                   (Grid = 01, File: /gpfs/projects/WilsonGroup/ROMS/OIB/ROMS_Grid1_msk02.nc)
                   (Min = -7.29388592E+01 Max = -7.28611687E+01)
    GET_GRID    - longitude of PSI-points: lon_psi
                   (Grid = 01, File: /gpfs/projects/WilsonGroup/ROMS/OIB/ROMS_Grid1_msk02.nc)
                   (Min = -7.29386963E+01 Max = -7.28613316E+01)
    GET_GRID    - latitude of RHO-points lat_rho
                   (Grid = 01, File: /gpfs/projects/WilsonGroup/ROMS/OIB/ROMS_Grid1_msk02.nc)
                   (Min =  4.07080613E+01 Max =  4.07762032E+01)
    GET_GRID    - latitude of U-points: lat_u
                   (Grid = 01, File: /gpfs/projects/WilsonGroup/ROMS/OIB/ROMS_Grid1_msk02.nc)
                   (Min =  4.07081139E+01 Max =  4.07761563E+01)
    GET_GRID    - latitude of V-points: lat_v
                   (Grid = 01, File: /gpfs/projects/WilsonGroup/ROMS/OIB/ROMS_Grid1_msk02.nc)
                   (Min =  4.07081897E+01 Max =  4.07760790E+01)
    GET_GRID    - latitude of PSI-points lat_psi
                   (Grid = 01, File: /gpfs/projects/WilsonGroup/ROMS/OIB/ROMS_Grid1_msk02.nc)
                   (Min =  4.07082423E+01 Max =  4.07760321E+01)
    GET_GRID    - mask on RHO-points: mask_rho
                   (Grid = 01, File: /gpfs/projects/WilsonGroup/ROMS/OIB/ROMS_Grid1_msk02.nc)
                   (Min =  0.00000000E+00 Max =  1.15000000E+02)
    GET_GRID    - mask on U-points: mask_u
                   (Grid = 01, File: /gpfs/projects/WilsonGroup/ROMS/OIB/ROMS_Grid1_msk02.nc)
                   (Min =  0.00000000E+00 Max =  1.17000000E+02)
    GET_GRID    - mask on V-points: mask_v
                   (Grid = 01, File: /gpfs/projects/WilsonGroup/ROMS/OIB/ROMS_Grid1_msk02.nc)
                   (Min =  0.00000000E+00 Max =  1.18000000E+02)
    GET_GRID    - mask on PSI-points: mask_psi
                   (Grid = 01, File: /gpfs/projects/WilsonGroup/ROMS/OIB/ROMS_Grid1_msk02.nc)
                   (Min =  0.00000000E+00 Max =  1.15000000E+02)

 Vertical S-coordinate System, Grid 01:

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

     5   0.0000000   0.0000000        0.000       0.000       0.000       0.000
     4  -0.2000000  -0.2000000       -0.000      -2.305      -1.152      -2.305
     3  -0.4000000  -0.4000000       -0.000      -4.609      -2.305      -4.609
     2  -0.6000000  -0.6000000       -0.000      -6.914      -3.457      -6.914
     1  -0.8000000  -0.8000000       -0.000      -9.219      -4.609      -9.219
     0  -1.0000000  -1.0000000       -0.000     -11.524      -5.762     -11.524

 Time Splitting Weights for Grid 01:    ndtfast = 100    nfast = 136
 ==================================

    Primary            Secondary            Accumulated to Current Step

  1-0.0001594457047350 0.0100000000000000-0.0001594457047350 0.0100000000000000
  2-0.0003102043539850 0.0100015944570474-0.0004696500587199 0.0200015944570474
  3-0.0004522759527012 0.0100046965005872-0.0009219260114211 0.0300062909576346
  4-0.0005856605201383 0.0100092192601142-0.0015075865315594 0.0400155102177488
  5-0.0007103581063581 0.0100150758653156-0.0022179446379175 0.0500305860830644
  6-0.0008263688153356 0.0100221794463792-0.0030443134532531 0.0600527655294436
  7-0.0009336928346655 0.0100304431345325-0.0039780062879186 0.0700832086639761
  8-0.0010323304718712 0.0100397800628792-0.0050103367597898 0.0801229887268553
  9-0.0011222821973150 0.0100501033675979-0.0061326189571048 0.0901730920944532
 10-0.0012035486937100 0.0100613261895711-0.0073361676508149 0.1002344182840242
 11-0.0012761309122332 0.0100733616765082-0.0086122985630481 0.1103077799605324
 12-0.0013400301352409 0.0100861229856305-0.0099523286982890 0.1203939029461629
 13-0.0013952480455848 0.0100995232869829-0.0113475767438738 0.1304934262331457
 14-0.0014417868025304 0.0101134757674387-0.0127893635464042 0.1406069020005845
 15-0.0014796491242768 0.0101278936354640-0.0142690126706810 0.1507347956360485
 16-0.0015088383770778 0.0101426901267068-0.0157778510477588 0.1608774857627553
 17-0.0015293586709646 0.0101577785104776-0.0173072097187234 0.1710352642732329
 18-0.0015412149620705 0.0101730720971872-0.0188484246807939 0.1812083363704202
 19-0.0015444131615570 0.0101884842468079-0.0203928378423509 0.1913968206172281
 20-0.0015389602511410 0.0102039283784235-0.0219317980934918 0.2016007489956516
 21-0.0015248644052242 0.0102193179809349-0.0234566624987160 0.2118200669765865
 22-0.0015021351196239 0.0102345666249872-0.0249587976183399 0.2220546336015737
 23-0.0014707833469051 0.0102495879761834-0.0264295809652450 0.2323042215777571
 24-0.0014308216383147 0.0102642958096525-0.0278604026035597 0.2425685173874096
 25-0.0013822642923165 0.0102786040260356-0.0292426668958762 0.2528471214134452
 26-0.0013251275097287 0.0102924266689588-0.0305677944056049 0.2631395480824039
 27-0.0012594295554622 0.0103056779440561-0.0318272239610671 0.2734452260264600
 28-0.0011851909268611 0.0103182722396107-0.0330124148879281 0.2837634982660707
 29-0.0011024345286441 0.0103301241488793-0.0341148494165722 0.2940936224149500
 30-0.0010111858544481 0.0103411484941657-0.0351260352710203 0.3044347709091157
 31-0.0009114731749732 0.0103512603527102-0.0360375084459935 0.3147860312618259
 32-0.0008033277327288 0.0103603750844599-0.0368408361787224 0.3251464063462858
 33-0.0006867839433822 0.0103684083617872-0.0375276201221045 0.3355148147080730
 34-0.0005618796037077 0.0103752762012210-0.0380894997258122 0.3458900909092941
 35-0.0004286561061383 0.0103808949972581-0.0385181558319504 0.3562709859065522
 36-0.0002871586599182 0.0103851815583195-0.0388053144918686 0.3666561674648717
 37-0.0001374365188575 0.0103880531449187-0.0389427510107261 0.3770442206097904
 38 0.0000204567843123 0.0103894275101073-0.0389222942264138 0.3874336481198977
 39 0.0001864631969805 0.0103892229422641-0.0387358310294334 0.3978228710621618
 40 0.0003605198990979 0.0103873583102943-0.0383753111303355 0.4082102293724562
 41 0.0005425590490165 0.0103837531113034-0.0378327520813190 0.4185939824837595
 42 0.0007325075227271 0.0103783275208132-0.0371002445585919 0.4289723100045727
 43 0.0009302866464954 0.0103710024455859-0.0361699579120965 0.4393433124501586
 44 0.0011358119228966 0.0103616995791210-0.0350341459891999 0.4497050120292796
 45 0.0013489927502484 0.0103503414598920-0.0336851532389515 0.4600553534891716
 46 0.0015697321354425 0.0103368515323895-0.0321154211035089 0.4703922050215611
 47 0.0017979264001745 0.0103211542110351-0.0303174947033344 0.4807133592325962
 48 0.0020334648805720 0.0103031749470333-0.0282840298227624 0.4910165341796295
 49 0.0022762296202215 0.0102828402982276-0.0260078002025408 0.5012993744778572
 50 0.0025260950565934 0.0102600780020254-0.0234817051459475 0.5115594524798827
 51 0.0027829277008656 0.0102348170514595-0.0206987774450819 0.5217942695313421
 52 0.0030465858111454 0.0102069877744508-0.0176521916339365 0.5320012573057930
 53 0.0033169190590902 0.0101765219163394-0.0143352725748463 0.5421777792221323
 54 0.0035937681899259 0.0101433527257485-0.0107415043849203 0.5523211319478808
 55 0.0038769646758645 0.0101074150438492-0.0068645397090558 0.5624285469917299
 56 0.0041663303629196 0.0100686453970906-0.0026982093461362 0.5724971923888205
 57 0.0044616771111203 0.0100269820934614 0.0017634677649840 0.5825241744822818
 58 0.0047628064281242 0.0099823653223502 0.0065262741931082 0.5925065398046320
 59 0.0050695090962281 0.0099347372580689 0.0115957832893363 0.6024412770627009
 60 0.0053815647927771 0.0098840421671066 0.0169773480821135 0.6123253192298075
 61 0.0056987417039731 0.0098302265191789 0.0226760897860865 0.6221555457489863
 62 0.0060207961320800 0.0097732391021391 0.0286968859181665 0.6319287848511255
 63 0.0063474720960293 0.0097130311408183 0.0350443580141958 0.6416418159919438
 64 0.0066785009254227 0.0096495564198580 0.0417228589396184 0.6512913724118019
 65 0.0070136008479335 0.0095827714106038 0.0487364597875519 0.6608741438224057
 66 0.0073524765701069 0.0095126354021245 0.0560889363576588 0.6703867792245302
 67 0.0076948188515579 0.0094391106364234 0.0637837552092167 0.6798258898609536
 68 0.0080403040725683 0.0093621624479078 0.0718240592817850 0.6891880523088615
 69 0.0083885937950820 0.0092817594071822 0.0802126530768670 0.6984698117160436
 70 0.0087393343170983 0.0091978734692313 0.0889519873939653 0.7076676851852749
 71 0.0090921562204639 0.0091104801260603 0.0980441436144293 0.7167781653113352
 72 0.0094466739120640 0.0090195585638557 0.1074908175264932 0.7257977238751909
 73 0.0098024851584102 0.0089250918247351 0.1172933026849035 0.7347228156999260
 74 0.0101591706136288 0.0088270669731510 0.1274524732985322 0.7435498826730770
 75 0.0105162933408455 0.0087254752670147 0.1379687666393777 0.7522753579400917
 76 0.0108733983269705 0.0086203123336062 0.1488421649663483 0.7608956702736980
 77 0.0112300119908805 0.0085115783503365 0.1600721769572288 0.7694072486240345
 78 0.0115856416849999 0.0083992782304277 0.1716578186422287 0.7778065268544623
 79 0.0119397751902801 0.0082834218135777 0.1835975938325088 0.7860899486680401
 80 0.0122918802045775 0.0081640240616749 0.1958894740370863 0.7942539727297150
 81 0.0126414038244295 0.0080411052596291 0.2085308778615158 0.8022950779893441
 82 0.0129877720202296 0.0079146912213848 0.2215186498817454 0.8102097692107290
 83 0.0133303891048003 0.0077848135011826 0.2348490389865456 0.8179945827119115
 84 0.0136686371953643 0.0076515096101345 0.2485176761819100 0.8256460923220460
 85 0.0140018756689153 0.0075148232381809 0.2625195518508252 0.8331609155602269
 86 0.0143294406109853 0.0073748044814918 0.2768489924618106 0.8405357200417186
 87 0.0146506442578125 0.0072315100753819 0.2914996367196231 0.8477672301171005
 88 0.0149647744319058 0.0070850036328038 0.3064644111515289 0.8548522337499043
 89 0.0152710939710086 0.0069353558884847 0.3217355051225375 0.8617875896383890
 90 0.0155688401504611 0.0067826449487746 0.3373043452729986 0.8685702345871636
 91 0.0158572240989606 0.0066269565472700 0.3531615693719592 0.8751971911344336
 92 0.0161354302077207 0.0064683843062804 0.3692969995796799 0.8816655754407140
 93 0.0164026155330280 0.0063070300042032 0.3856996151127079 0.8879726054449172
 94 0.0166579091921988 0.0061430038488729 0.4023575243049067 0.8941156092937901
 95 0.0169004117529325 0.0059764247569509 0.4192579360578392 0.9000920340507410
 96 0.0171291946160649 0.0058074206394216 0.4363871306739041 0.9058994546901626
 97 0.0173432993917185 0.0056361286932610 0.4537304300656226 0.9115355833834236
 98 0.0175417372688526 0.0054626956993438 0.4712721673344752 0.9169982790827673
 99 0.0177234883782110 0.0052872783266553 0.4889956557126862 0.9222855574094225
100 0.0178875011486682 0.0051100434428731 0.5068831568613544 0.9273956008522957
101 0.0180326916569743 0.0049311684313865 0.5249158485183287 0.9323267692836821
102 0.0181579429708980 0.0047508415148167 0.5430737914892267 0.9370776107984988
103 0.0182621044857684 0.0045692620851077 0.5613358959749951 0.9416468728836066
104 0.0183439912544149 0.0043866410402501 0.5796798872294100 0.9460335139238567
105 0.0184023833105056 0.0042032011277059 0.5980822705399156 0.9502367150515626
106 0.0184360249852842 0.0040191772946008 0.6165182955251998 0.9542558923461635
107 0.0184436242177053 0.0038348170447480 0.6349619197429051 0.9580907093909115
108 0.0184238518579681 0.0036503808025710 0.6533857716008732 0.9617410901934824
109 0.0183753409644487 0.0034661422839913 0.6717611125653219 0.9652072324774736
110 0.0182966860940303 0.0032823888743468 0.6900577986593522 0.9684896213518204
111 0.0181864425858324 0.0030994220134065 0.7082442412451847 0.9715890433652269
112 0.0180431258383383 0.0029175575875482 0.7262873670835230 0.9745066009527751
113 0.0178652105799207 0.0027371263291648 0.7441525776634437 0.9772437272819399
114 0.0176511301327661 0.0025584742233656 0.7618037077962098 0.9798022015053054
115 0.0173992756701974 0.0023819629220379 0.7792029834664072 0.9821841644273432
116 0.0171079954673952 0.0022079701653359 0.7963109789338024 0.9843921345926792
117 0.0167755941455171 0.0020368902106620 0.8130865730793195 0.9864290248033412
118 0.0164003319092156 0.0018691342692068 0.8294869049885351 0.9882981590725479
119 0.0159804237775546 0.0017051309501147 0.8454673287660897 0.9900032900226625
120 0.0155140388083243 0.0015453267123391 0.8609813675744140 0.9915486167350016
121 0.0149992993157544 0.0013901863242559 0.8759806668901684 0.9929388030592575
122 0.0144342800816253 0.0012401933310983 0.8904149469717937 0.9941789963903559
123 0.0138170075597788 0.0010958505302821 0.9042319545315725 0.9952748469206379
124 0.0131454590740262 0.0009576804546843 0.9173774136055987 0.9962325273753222
125 0.0124175620094554 0.0008262258639440 0.9297949756150540 0.9970587532392662
126 0.0116311929971360 0.0007020502438495 0.9414261686121900 0.9977608034831157
127 0.0107841770922234 0.0005857383138781 0.9522103457044133 0.9983465417969938
128 0.0098742869454606 0.0004778965429559 0.9620846326498740 0.9988244383399496
129 0.0088992419680793 0.0003791536735013 0.9709838746179533 0.9992035920134509
130 0.0078567074900984 0.0002901612538205 0.9788405821080517 0.9994937532672713
131 0.0067442939120218 0.0002115941789195 0.9855848760200735 0.9997053474461908
132 0.0055595558499342 0.0001441512397993 0.9911444318700077 0.9998494986859900
133 0.0042999912739953 0.0000885556812999 0.9954444231440029 0.9999380543672900
134 0.0029630406403327 0.0000455557685600 0.9984074637843356 0.9999836101358500
135 0.0015460860163330 0.0000159253621566 0.9999535498006686 0.9999995354980067
136 0.0000464501993315 0.0000004645019933 1.0000000000000002 1.0000000000000000

 ndtfast, nfast =  100 136   nfast/ndtfast =  1.36000

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

    1.000000000000 1.019196655660 0.509598327830 1.000000000000 1.000000000000

 Power filter parameters, Fgamma, gamma =  0.28400   0.25560

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

 Minimum X-grid spacing, DXmin =  2.93550402E-02 km
 Maximum X-grid spacing, DXmax =  2.98576841E-02 km
 Minimum Y-grid spacing, DYmin =  2.97880182E-02 km
 Maximum Y-grid spacing, DYmax =  3.06656174E-02 km
 Minimum Z-grid spacing, DZmin =  2.00000000E-15 m
 Maximum Z-grid spacing, DZmax =  2.30472405E+00 m

 Minimum barotropic Courant Number =  1.38959712E-02
 Maximum barotropic Courant Number =  1.40755645E-01
 Maximum Coriolis   Courant Number =  2.66097292E-03


 NLM: GET_STATE - Reading state initial conditions,                       0001-01-01 00:00:00.00
                   (Grid 01, t = 0.0000, File: oib_ini.nc, Rec=0001, Index=1)
                - free-surface
                   (Min =  0.00000000E+00 Max =  4.42551112E-02)
                - 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 =  0.00000000E+00 Max =  6.90543909E+00)
                - salinity
                   (Min =  0.00000000E+00 Max =  3.17981322E+01)
    GET_NGFLD   - free-surface western boundary condition,         0001-01-01 00:00:00.00
                   (Grid= 01, Rec=0000001, Index=2, File: oib_obc.nc)
                   (Tmin=          0.0000 Tmax=          0.0747)      t =          0.0000
                   (Min =  0.00000000E+00 Max =  0.00000000E+00)
    GET_NGFLD   - free-surface eastern boundary condition,         0001-01-01 00:00:00.00
                   (Grid= 01, Rec=0000001, Index=2, File: oib_obc.nc)
                   (Tmin=          0.0000 Tmax=          0.0747)      t =          0.0000
                   (Min =  0.00000000E+00 Max =  0.00000000E+00)
    GET_NGFLD   - free-surface southern boundary condition,        0001-01-01 00:00:00.00
                   (Grid= 01, Rec=0000001, Index=2, File: oib_obc.nc)
                   (Tmin=          0.0000 Tmax=          0.0747)      t =          0.0000
                   (Min =  0.00000000E+00 Max =  0.00000000E+00)
    GET_NGFLD   - 2D u-momentum western boundary condition,        0001-01-01 00:00:00.00
                   (Grid= 01, Rec=0000001, Index=2, File: oib_obc.nc)
                   (Tmin=          0.0000 Tmax=          0.0747)      t =          0.0000
                   (Min =  0.00000000E+00 Max =  0.00000000E+00)
    GET_NGFLD   - 2D v-momentum western boundary condition,        0001-01-01 00:00:00.00
                   (Grid= 01, Rec=0000001, Index=2, File: oib_obc.nc)
                   (Tmin=          0.0000 Tmax=          0.0747)      t =          0.0000
                   (Min =  0.00000000E+00 Max =  0.00000000E+00)
    GET_NGFLD   - 2D u-momentum eastern boundary condition,        0001-01-01 00:00:00.00
                   (Grid= 01, Rec=0000001, Index=2, File: oib_obc.nc)
                   (Tmin=          0.0000 Tmax=          0.0747)      t =          0.0000
                   (Min =  0.00000000E+00 Max =  0.00000000E+00)
    GET_NGFLD   - 2D v-momentum eastern boundary condition,        0001-01-01 00:00:00.00
                   (Grid= 01, Rec=0000001, Index=2, File: oib_obc.nc)
                   (Tmin=          0.0000 Tmax=          0.0747)      t =          0.0000
                   (Min =  0.00000000E+00 Max =  0.00000000E+00)
    GET_NGFLD   - 2D u-momentum southern boundary condition,       0001-01-01 00:00:00.00
                   (Grid= 01, Rec=0000001, Index=2, File: oib_obc.nc)
                   (Tmin=          0.0000 Tmax=          0.0747)      t =          0.0000
                   (Min =  0.00000000E+00 Max =  0.00000000E+00)
    GET_NGFLD   - 2D v-momentum southern boundary condition,       0001-01-01 00:00:00.00
                   (Grid= 01, Rec=0000001, Index=2, File: oib_obc.nc)
                   (Tmin=          0.0000 Tmax=          0.0747)      t =          0.0000
                   (Min =  0.00000000E+00 Max =  0.00000000E+00)

 Basin information for Grid 01:

 Maximum grid stiffness ratios:  rx0 =   2.000000E-01 (Beckmann and Haidvogel)
                                 rx1 =   1.800000E+00 (Haney)

 Initial domain volumes:  TotVolume =  4.6410819004E+07 m3
                         MinCellVol =  2.0581743846E+01 m3
                         MaxCellVol =  1.9942072251E+03 m3
                            Max/Min =  9.6892043744E+01

 NL ROMS/TOMS: started time-stepping: (Grid: 01 TimeSteps: 000000000001 - 000000000200)

    GET_NGFLD   - free-surface western boundary condition,         0001-01-01 00:00:28.00
                   (Grid= 01, Rec=0000002, Index=1, File: oib_obc.nc)
                   (Tmin=          0.0000 Tmax=          0.0747)      t =          0.0003
                   (Min = -3.78718571E-04 Max =  4.12897236E-04)
    GET_NGFLD   - free-surface eastern boundary condition,         0001-01-01 00:00:28.00
                   (Grid= 01, Rec=0000002, Index=1, File: oib_obc.nc)
                   (Tmin=          0.0000 Tmax=          0.0747)      t =          0.0003
                   (Min = -1.45746730E-04 Max =  1.80724703E-04)
    GET_NGFLD   - free-surface southern boundary condition,        0001-01-01 00:00:28.00
                   (Grid= 01, Rec=0000002, Index=1, File: oib_obc.nc)
                   (Tmin=          0.0000 Tmax=          0.0747)      t =          0.0003
                   (Min = -1.05794905E-04 Max = -9.69371904E-05)
    GET_NGFLD   - 2D u-momentum western boundary condition,        0001-01-01 00:00:28.00
                   (Grid= 01, Rec=0000002, Index=1, File: oib_obc.nc)
                   (Tmin=          0.0000 Tmax=          0.0747)      t =          0.0003
                   (Min =  0.00000000E+00 Max =  8.99481820E-04)
    GET_NGFLD   - 2D v-momentum western boundary condition,        0001-01-01 00:00:28.00
                   (Grid= 01, Rec=0000002, Index=1, File: oib_obc.nc)
                   (Tmin=          0.0000 Tmax=          0.0747)      t =          0.0003
                   (Min = -1.26960198E-03 Max =  2.68548756E-04)
    GET_NGFLD   - 2D u-momentum eastern boundary condition,        0001-01-01 00:00:28.00
                   (Grid= 01, Rec=0000002, Index=1, File: oib_obc.nc)
                   (Tmin=          0.0000 Tmax=          0.0747)      t =          0.0003
                   (Min =  0.00000000E+00 Max =  1.17361650E-03)
    GET_NGFLD   - 2D v-momentum eastern boundary condition,        0001-01-01 00:00:28.00
                   (Grid= 01, Rec=0000002, Index=1, File: oib_obc.nc)
                   (Tmin=          0.0000 Tmax=          0.0747)      t =          0.0003
                   (Min = -4.89090860E-04 Max =  6.61526399E-04)
    GET_NGFLD   - 2D u-momentum southern boundary condition,       0001-01-01 00:00:28.00
                   (Grid= 01, Rec=0000002, Index=1, File: oib_obc.nc)
                   (Tmin=          0.0000 Tmax=          0.0747)      t =          0.0003
                   (Min =  4.77489593E-05 Max =  8.93098040E-05)
    GET_NGFLD   - 2D v-momentum southern boundary condition,       0001-01-01 00:00:28.00
                   (Grid= 01, Rec=0000002, Index=1, File: oib_obc.nc)
                   (Tmin=          0.0000 Tmax=          0.0747)      t =          0.0003
                   (Min = -6.63306419E-05 Max = -1.19462557E-05)

 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
                      (000,000,0)  0.000000E+00  0.000000E+00  0.000000E+00  0.000000E+00
 Found Error: 01   Line: 298      Source: ROMS/Nonlinear/main3d.F
 Found Error: 01   Line: 299      Source: ROMS/Drivers/nl_ocean.h

 Elapsed CPU time (seconds):

 Node   #    0 CPU:       1.322
 Total:                   1.322

 Nonlinear model elapsed CPU time profile, Grid: 01

  Allocation and array initialization ..............         0.750  (56.6932 %)
  Ocean state initialization .......................         0.106  ( 7.9971 %)
  Reading of input data ............................         0.042  ( 3.1753 %)
  Processing of input data .........................         0.002  ( 0.1478 %)
  Computation of global information integrals ......         0.069  ( 5.2499 %)
  2D/3D coupling, vertical metrics .................         0.066  ( 5.0200 %)
  Omega vertical velocity ..........................         0.017  ( 1.2578 %)
  Equation of state for seawater ...................         0.078  ( 5.8947 %)
  Reading model state vector .......................         0.066  ( 5.0137 %)
                                              Total:         1.196   90.4493

 Nonlinear model message Passage profile, Grid: 01

  Message Passage: 2D halo exchanges ...............         0.000  ( 0.0227 %)
  Message Passage: 3D halo exchanges ...............         0.000  ( 0.0091 %)
  Message Passage: 4D halo exchanges ...............         0.000  ( 0.0016 %)
  Message Passage: data broadcast ..................         0.001  ( 0.0829 %)
  Message Passage: data reduction ..................         0.000  ( 0.0053 %)
  Message Passage: data scattering..................         0.028  ( 2.0892 %)
  Message Passage: boundary data gathering .........         0.000  ( 0.0041 %)
  Message Passage: synchronization barrier .........         0.000  ( 0.0011 %)
                                              Total:         0.029    2.2160

  Unique code regions profiled .....................         1.196   90.4493 %
  Residual, non-profiled code ......................         0.126    9.5507 %


 All percentages are with respect to total time =            1.322


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

 Dynamic and Automatic memory (MB) usage for Grid 01:  153x208x5  tiling: 1x1

     tile          Dynamic        Automatic            USAGE      MPI-Buffers

        0            81.59            11.46            93.06             1.30

    TOTAL            81.59            11.46            93.06             1.30

<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 Found Error: 01   Line: 68       Source: ROMS/Utility/close_io.F

 ROMS/TOMS - Output NetCDF summary for Grid 01:

 Analytical header files used:

     ROMS/Functionals/ana_btflux.h
     ROMS/Functionals/ana_smflux.h
     ROMS/Functionals/ana_stflux.h
 Found Error: 01   Line: 333      Source: ROMS/Utility/close_io.F

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

User avatar
kate
Posts: 4088
Joined: Wed Jul 02, 2003 5:29 pm
Location: CFOS/UAF, USA

Re: Blow up problem

#2 Unread post by kate »

For once I can't say try a shorter timestep because you are already in trouble before you've taken any timesteps:
0 0001-01-01 00:00:00.00 NaN NaN NaN NaN
(000,000,0) 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00
I'm not sure what has gone wrong.

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

Re: Blow up problem

#3 Unread post by jcwarner »

these values seem odd:

GET_GRID - mask on RHO-points: mask_rho
(Grid = 01, File: /gpfs/projects/WilsonGroup/ROMS/OIB/ROMS_Grid1_msk02.nc)
(Min = 0.00000000E+00 Max = 1.15000000E+02)
GET_GRID - mask on U-points: mask_u
(Grid = 01, File: /gpfs/projects/WilsonGroup/ROMS/OIB/ROMS_Grid1_msk02.nc)
(Min = 0.00000000E+00 Max = 1.17000000E+02)
GET_GRID - mask on V-points: mask_v
(Grid = 01, File: /gpfs/projects/WilsonGroup/ROMS/OIB/ROMS_Grid1_msk02.nc)
(Min = 0.00000000E+00 Max = 1.18000000E+02)
GET_GRID - mask on PSI-points: mask_psi
(Grid = 01, File: /gpfs/projects/WilsonGroup/ROMS/OIB/ROMS_Grid1_msk02.nc)
(Min = 0.00000000E+00 Max = 1.15000000E+02)


here is what i get:
GET_GRID - mask on RHO-points: mask_rho
(Grid = 02, File: /vortexfs1/scratch/jwarner/grids/CCBay_grd205.nc)
(Min = 0.00000000E+00 Max = 1.00000000E+00)
GET_GRID - mask on U-points: mask_u
(Grid = 02, File: /vortexfs1/scratch/jwarner/grids/CCBay_grd205.nc)
(Min = 0.00000000E+00 Max = 1.00000000E+00)
GET_GRID - mask on V-points: mask_v
(Grid = 02, File: /vortexfs1/scratch/jwarner/grids/CCBay_grd205.nc)
(Min = 0.00000000E+00 Max = 1.00000000E+00)
GET_GRID - mask on PSI-points: mask_psi
(Grid = 02, File: /vortexfs1/scratch/jwarner/grids/CCBay_grd205.nc)
(Min = 0.00000000E+00 Max = 2.00000000E+00)

check your grid masking.
--j

IBH123
Posts: 9
Joined: Wed Feb 27, 2019 8:24 pm
Location: Stony Brook University

Re: Blow up problem

#4 Unread post by IBH123 »

Thank you jcwarner and kate! It is really the wrong masking value that is causing problem, there was also a problem in the initial value, so I couldn't make the first step... The model is running now.

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