DIAG speed trouble / gridbuilder

Bug reports, work arounds and fixes

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hpd14thu
Posts: 55
Joined: Tue May 01, 2018 3:56 pm
Location: Tsinghua University

DIAG speed trouble / gridbuilder

#1 Post by hpd14thu » Wed Sep 11, 2019 1:22 pm

Dear all,

I'm trying to run ROMs by bulk forcing,and initial condition, but it blows up.

Because my area is near the coast and my blow-up point is in the shallow water area(~10m), I try to decrease my dt from 300s to 10s and decrease my N from 36 to 25.

It does work but it just delay the time of blow-up, not solve the problem.

So I think maybe there are some problems in my grid.file, and I generate my grid.nc by Gridbuilder, here is my result.out and grid.nc:

Thanks!!



Code: Select all

 Model Input Parameters:  ROMS/TOMS version 3.7  
                          Wednesday - September 11, 2019 -  6:00:18 PM
 -----------------------------------------------------------------------------

 mab

 Operating system : Linux
 CPU/hardware     : x86_64
 Compiler system  : gfortran
 Compiler command : /usr/bin/mpif90
 Compiler flags   : -frepack-arrays -O3 -ffast-math -ftree-vectorize -ftree-loop-linear -funroll-loops -w -ffree-form -ffree-line-length-none -frecord-marker=4 -fconvert=big-endian

 Input Script  : 

 SVN Root URL  : https:://myroms.org/svn/src
 SVN Revision  : 65M

 Local Root    : /home/ubuntu/app/COAWST_V3.2
 Header Dir    : /home/ubuntu/app/COAWST_V3.2/Projects/mab
 Header file   : mab.h
 Analytical Dir: /home/ubuntu/app/COAWST_V3.2/Projects/mab

 Resolution, Grid 01: 0166x0198x030,  Parallel Nodes:   1,  Tiling: 001x001


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

     138240  ntimes            Number of timesteps for 3-D equations.
     10.000  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.
        120  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.
          1  ntsAVG            Starting timestep for the accumulation of output
                                 time-averaged data.
        360  nAVG              Number of timesteps between the writing of
                                 time-averaged data into averages file.
 2.0000E-01  nl_tnu2(01)       NLM Horizontal, harmonic mixing coefficient
                                 (m2/s) for tracer 01: temp
 2.0000E-01  nl_tnu2(02)       NLM Horizontal, harmonic mixing coefficient
                                 (m2/s) for tracer 02: salt
 1.0000E-01  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
 1.0000E-06  Akt_bak(01)       Background vertical mixing coefficient (m2/s)
                                 for tracer 01: temp
 1.0000E-06  Akt_bak(02)       Background vertical mixing coefficient (m2/s)
                                 for tracer 02: salt
 1.0000E-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.
      0.000  wec_alpha         WEC factor for roller/breaking energy distribution.
 3.0000E-04  rdrg              Linear bottom drag coefficient (m/s).
 2.5000E-02  rdrg2             Quadratic bottom drag coefficient.
 2.0000E-02  Zob               Bottom roughness (m).
 2.0000E-02  Zos               Surface roughness (m).
 2.0000E+00  blk_ZQ            Height (m) of surface air humidity measurement.
 2.0000E+00  blk_ZT            Height (m) of surface air temperature measurement.
 1.0000E+01  blk_ZW            Height (m) of surface winds measurement.
          1  lmd_Jwt           Jerlov water type.
          2  Vtransform        S-coordinate transformation equation.
          4  Vstretching       S-coordinate stretching function.
 5.0000E+00  theta_s           S-coordinate surface control parameter.
 4.0000E-01  theta_b           S-coordinate bottom  control parameter.
     50.000  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  Tnudg_SSS         Nudging/relaxation time scale (days)
                                 for sea surface salinity.
 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(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(idTvar)      Write out tracer 01: temp
          T  Hout(idTvar)      Write out tracer 02: salt

          T  Aout(idSdif)      Write out averaged vertical diffusion: AKt(isalt).

 Output/Input Files:

             Output Restart File:  mab_rst.nc
             Output History File:  mab_his.nc
            Output Averages File:  mab_avg.nc
                 Input Grid File:  /home/ubuntu/app/COAWST_V3.2/Projects/mab/mab_grid.nc
    Input Nonlinear Initial File:  /home/ubuntu/app/COAWST_V3.2/Projects/mab/mab_init.nc
           Input Forcing File 01:  /home/ubuntu/app/COAWST_V3.2/Projects/mab/mab_wind.nc

 Tile partition information for Grid 01:  0166x0198x0030  tiling: 001x001

     tile     Istr     Iend     Jstr     Jend     Npts

 Number of tracers:            2
        0        1      166        1      198   986040

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

     tile     Xmin     Xmax     Ymin     Ymax     grid

        0     0.50   166.50     0.50   198.50  RHO-points

        0     1.00   166.00     0.50   198.50    U-points

        0     0.50   166.50     1.00   198.00    V-points

 Maximum halo size in XI and ETA directions:

               HaloSizeI(1) =     354
               HaloSizeJ(1) =     418
                TileSide(1) =     203
                TileSize(1) =   34713


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

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

 zeta                     1   Chapman Imp  Chapman Imp  Chapman Imp  Chapman Imp

 ubar                     1   Gradient     Gradient     Gradient     Gradient

 vbar                     1   Gradient     Gradient     Gradient     Gradient

 u                        1   Gradient     Gradient     Gradient     Gradient

 v                        1   Gradient     Gradient     Gradient     Gradient

 temp                     1   Gradient     Gradient     Gradient     Gradient

 salt                     1   Gradient     Gradient     Gradient     Gradient

 tke                      1   Gradient     Gradient     Gradient     Gradient

 Activated C-preprocessing Options:

 MAB                 mab
 ANA_BSFLUX          Analytical kinematic bottom salinity flux.
 ANA_BTFLUX          Analytical kinematic bottom temperature flux.
 ASSUMED_SHAPE       Using assumed-shape arrays.
 ATM_PRESS           Impose atmospheric pressure onto sea surface.
 AVERAGES            Writing out time-averaged nonlinear model fields.
 BULK_FLUXES         Surface bulk fluxes parameterization.
 CHARNOK             Charnok surface roughness from wind stress.
 CURVGRID            Orthogonal curvilinear grid.
 DJ_GRADPS           Parabolic Splines density Jacobian (Shchepetkin, 2002).
 DOUBLE_PRECISION    Double precision arithmetic.
 EMINUSP             Compute Salt Flux using E-P.
 GLS_MIXING          Generic Length-Scale turbulence closure.
 KANTHA_CLAYSON      Kantha and Clayson stability function formulation.
 MASKING             Land/Sea masking.
 MIX_GEO_TS          Mixing of tracers along geopotential surfaces.
 MIX_S_UV            Mixing of momentum along constant S-surfaces.
 MPI                 MPI distributed-memory configuration.
 NONLINEAR           Nonlinear Model.
 NONLIN_EOS          Nonlinear 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.
 RADIATION_2D        Use tangential phase speed in radiation conditions.
 !RST_SINGLE         Double precision fields in restart NetCDF file.
 SALINITY            Using salinity.
 SOLAR_SOURCE        Solar Radiation Source Term.
 SOLVE3D             Solving 3D Primitive Equations.
 TS_U3HADVECTION     Third-order upstream horizontal advection of tracers.
 TS_C4VADVECTION     Fourth-order centered vertical advection of tracers.
 TS_DIF2             Harmonic mixing of tracers.
 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.
 UV_LOGDRAG          Logarithmic bottom stress.
 UV_VIS2             Harmonic mixing of momentum.
 VAR_RHO_2D          Variable density barotropic mode.

 Process Information:

 Node #  0 (pid=    9629) is active.

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

 Vertical S-coordinate System, Grid 01:

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

    30   0.0000000   0.0000000        0.000       0.000       0.000       0.000
    29  -0.0333333  -0.0002307       -0.064      -0.839      -2.262      -2.912
    28  -0.0666667  -0.0009291       -0.128      -1.690      -5.791      -8.380
    27  -0.1000000  -0.0021144       -0.192      -2.553     -10.638     -16.508
    26  -0.1333333  -0.0038189       -0.257      -3.429     -16.892     -27.473
    25  -0.1666667  -0.0060892       -0.321      -4.319     -24.678     -41.529
    24  -0.2000000  -0.0089871       -0.385      -5.225     -34.164     -59.014
    23  -0.2333333  -0.0125913       -0.450      -6.148     -45.564     -80.359
    22  -0.2666667  -0.0169996       -0.514      -7.092     -59.141    -106.097
    21  -0.3000000  -0.0223307       -0.579      -8.058     -75.218    -136.878
    20  -0.3333333  -0.0287278       -0.643      -9.052     -94.182    -173.482
    19  -0.3666667  -0.0363614       -0.708     -10.076    -116.496    -216.843
    18  -0.4000000  -0.0454338       -0.773     -11.136    -142.706    -268.066
    17  -0.4333333  -0.0561830       -0.838     -12.238    -173.459    -328.450
    16  -0.4666667  -0.0688882       -0.903     -13.389    -209.509    -399.521
    15  -0.5000000  -0.0838752       -0.968     -14.597    -251.740    -483.061
    14  -0.5333333  -0.1015226       -1.033     -15.871    -301.177    -581.136
    13  -0.5666667  -0.1222681       -1.099     -17.223    -359.006    -696.139
    12  -0.6000000  -0.1466152       -1.165     -18.665    -426.590    -830.820
    11  -0.6333333  -0.1751391       -1.231     -20.212    -505.487    -988.324
    10  -0.6666667  -0.2084930       -1.298     -21.879    -597.467   -1172.218
     9  -0.7000000  -0.2474113       -1.365     -23.685    -704.518   -1386.515
     8  -0.7333333  -0.2927113       -1.433     -25.651    -828.855   -1635.681
     7  -0.7666667  -0.3452901       -1.501     -27.799    -972.908   -1924.618
     6  -0.8000000  -0.4061157       -1.570     -30.153   -1139.298   -2258.614
     5  -0.8333333  -0.4762095       -1.639     -32.739   -1330.792   -2643.251
     4  -0.8666667  -0.5566161       -1.709     -35.582   -1550.219   -3084.236
     3  -0.9000000  -0.6483588       -1.781     -38.709   -1800.352   -3587.160
     2  -0.9333333  -0.7523753       -1.853     -42.143   -2083.729   -4157.147
     1  -0.9666667  -0.8694298       -1.926     -45.902   -2402.422   -4798.372
     0  -1.0000000  -1.0000000       -2.000     -50.000   -2757.723   -5513.446

 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 =  4.68165556E+00 km
 Maximum X-grid spacing, DXmax =  5.28701590E+00 km
 Minimum Y-grid spacing, DYmin =  5.03543630E+00 km
 Maximum Y-grid spacing, DYmax =  5.03543631E+00 km
 Minimum Z-grid spacing, DZmin =  6.41203105E-02 m
 Maximum Z-grid spacing, DZmax =  7.15073607E+02 m

 Minimum barotropic Courant Number =  4.08021179E-04
 Maximum barotropic Courant Number =  2.13261516E-02
 Maximum Coriolis   Courant Number =  9.78217235E-04


 NLM: GET_STATE - Read state initial conditions,             t =     0 00:00:00
                   (Grid 01, File: mab_init.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 = -1.41334683E-01 Max =  3.04189892E+01)
                - salinity
                   (Min =  0.00000000E+00 Max =  3.67799568E+01)
    GET_2DFLD   - surface u-wind component,                  t =     0 00:00:00
                   (Rec=0000001, Index=1, File: mab_wind.nc)
                   (Tmin=          0.0000 Tmax=         16.0000)
                   (Min = -2.48879018E+00 Max =  9.48846082E+00)
    GET_2DFLD   - surface v-wind component,                  t =     0 00:00:00
                   (Rec=0000001, Index=1, File: mab_wind.nc)
                   (Tmin=          0.0000 Tmax=         16.0000)
                   (Min = -3.85694262E+00 Max =  8.27674899E+00)
    GET_2DFLD   - surface air pressure,                      t =     0 00:00:00
                   (Rec=0000001, Index=1, File: mab_wind.nc)
                   (Tmin=          0.0000 Tmax=         16.0000)
                   (Min =  9.41213884E+02 Max =  1.02045113E+03)
    GET_2DFLD   - surface air temperature,                   t =     0 00:00:00
                   (Rec=0000001, Index=1, File: mab_wind.nc)
                   (Tmin=          0.0000 Tmax=         16.0000)
                   (Min =  1.99932619E+01 Max =  2.83775444E+01)
    GET_2DFLD   - surface air relative humidity,             t =     0 00:00:00
                   (Rec=0000001, Index=1, File: mab_wind.nc)
                   (Tmin=          0.0000 Tmax=         16.0000)
                   (Min =  6.49802349E-01 Max =  9.73909050E-01)
    GET_2DFLD   - solar shortwave radiation flux,            t =     0 00:00:00
                   (Rec=0000001, Index=1, File: mab_wind.nc)
                   (Tmin=          0.0000 Tmax=         16.0000)
                   (Min =  5.84608824E-05 Max =  1.85498452E-04)
    GET_2DFLD   - net longwave radiation flux,               t =     0 00:00:00
                   (Rec=0000001, Index=1, File: mab_wind.nc)
                   (Tmin=          0.0000 Tmax=         16.0000)
                   (Min = -3.63744317E-05 Max =  8.11468262E-07)
    GET_2DFLD   - rain fall rate,                            t =     0 00:00:00
                   (Rec=0000001, Index=1, File: mab_wind.nc)
                   (Tmin=          0.0000 Tmax=         16.0000)
                   (Min = -7.73038670E-05 Max =  6.48162364E-04)

 Basin information for Grid 01:

 Maximum grid stiffness ratios:  rx0 =   1.000000E-01 (Beckmann and Haidvogel)
                                 rx1 =   5.221597E+00 (Haney)

 Initial basin volumes: TotVolume =  1.5937623726E+15 m3
                        MinVolume =  1.5137425177E+06 m3
                        MaxVolume =  1.8977905830E+10 m3
                          Max/Min =  1.2537076556E+04

 NL ROMS/TOMS: started time-stepping: (Grid: 01 TimeSteps: 00000001 - 00138240)

    GET_2DFLD   - surface u-wind component,                  t =     0 00:30:00
                   (Rec=0000002, Index=2, File: mab_wind.nc)
                   (Tmin=          0.0000 Tmax=         16.0000)
                   (Min = -2.67755614E+00 Max =  9.68387638E+00)
    GET_2DFLD   - surface v-wind component,                  t =     0 00:30:00
                   (Rec=0000002, Index=2, File: mab_wind.nc)
                   (Tmin=          0.0000 Tmax=         16.0000)
                   (Min = -3.95093540E+00 Max =  7.99857274E+00)
    GET_2DFLD   - surface air pressure,                      t =     0 00:30:00
                   (Rec=0000002, Index=2, File: mab_wind.nc)
                   (Tmin=          0.0000 Tmax=         16.0000)
                   (Min =  9.41149331E+02 Max =  1.02057863E+03)
    GET_2DFLD   - surface air temperature,                   t =     0 00:30:00
                   (Rec=0000002, Index=2, File: mab_wind.nc)
                   (Tmin=          0.0000 Tmax=         16.0000)
                   (Min =  2.01950278E+01 Max =  2.84300235E+01)
    GET_2DFLD   - surface air relative humidity,             t =     0 00:30:00
                   (Rec=0000002, Index=2, File: mab_wind.nc)
                   (Tmin=          0.0000 Tmax=         16.0000)
                   (Min =  5.93761673E-01 Max =  9.72107867E-01)
    GET_2DFLD   - solar shortwave radiation flux,            t =     0 00:30:00
                   (Rec=0000002, Index=2, File: mab_wind.nc)
                   (Tmin=          0.0000 Tmax=         16.0000)
                   (Min =  6.46495803E-05 Max =  1.92980171E-04)
    GET_2DFLD   - net longwave radiation flux,               t =     0 00:30:00
                   (Rec=0000002, Index=2, File: mab_wind.nc)
                   (Tmin=          0.0000 Tmax=         16.0000)
                   (Min = -3.78018656E-05 Max =  3.42369378E-07)
    GET_2DFLD   - rain fall rate,                            t =     0 00:30:00
                   (Rec=0000002, Index=2, File: mab_wind.nc)
                   (Tmin=          0.0000 Tmax=         16.0000)
                   (Min = -6.36967807E-05 Max =  6.65809200E-04)

   STEP   Day HH:MM:SS  KINETIC_ENRG   POTEN_ENRG    TOTAL_ENRG    NET_VOLUME
          C => (i,j,k)       Cu            Cv            Cw         Max Speed

       0     0 00:00:00  0.000000E+00  2.106255E+04  2.106255E+04  1.594152E+15
          (000,000,00)  0.000000E+00  0.000000E+00  0.000000E+00  0.000000E+00
      DEF_HIS   - creating history file, Grid 01: mab_his.nc
      WRT_HIS   - wrote history  fields (Index=1,1) into time record = 0000001
      DEF_AVG   - creating average file, Grid 01: mab_avg.nc
       1     0 00:00:10  1.474962E-05  2.106255E+04  2.106255E+04  1.594152E+15
          (067,045,01)  2.081455E-04  2.226696E-04  0.000000E+00  1.570205E-01
      WRT_HIS   - wrote history  fields (Index=1,2) into time record = 0000002
       2     0 00:00:20  5.726974E-05  2.106180E+04  2.106180E+04  1.594152E+15
          (159,118,30)  4.118950E-06  2.986013E-06  8.557346E-02  3.124298E-01
      WRT_HIS   - wrote history  fields (Index=1,1) into time record = 0000003
       3     0 00:00:30  1.130670E-04  2.106142E+04  2.106142E+04  1.594152E+15
          (070,050,30)  4.464227E-07  4.262684E-06  1.164615E-01  2.710172E-01
      WRT_HIS   - wrote history  fields (Index=1,2) into time record = 0000004
       4     0 00:00:40  1.969253E-04  2.106127E+04  2.106127E+04  1.594152E+15
          (164,122,30)  2.158154E-05  1.606934E-05  1.272829E-01  3.175687E-01
      WRT_HIS   - wrote history  fields (Index=1,1) into time record = 0000005
       5     0 00:00:50  3.167680E-04  2.106114E+04  2.106114E+04  1.594152E+15
          (074,045,30)  3.780017E-05  8.853016E-06  1.371968E-01  3.978551E-01
      WRT_HIS   - wrote history  fields (Index=1,2) into time record = 0000006
       6     0 00:01:00  4.717874E-04  2.106102E+04  2.106102E+04  1.594152E+15
          (132,105,30)  2.712113E-05  2.219168E-05  1.241226E-01  4.806186E-01
      WRT_HIS   - wrote history  fields (Index=1,1) into time record = 0000007
       7     0 00:01:10  6.546889E-04  2.106090E+04  2.106090E+04  1.594152E+15
          (157,118,30)  8.165194E-07  6.964529E-05  1.233353E-01  5.604440E-01
      WRT_HIS   - wrote history  fields (Index=1,2) into time record = 0000008
       8     0 00:01:20  8.636625E-04  2.106078E+04  2.106078E+04  1.594152E+15
          (068,048,30)  4.686715E-05  1.408874E-05  1.115997E-01  6.374340E-01
      WRT_HIS   - wrote history  fields (Index=1,1) into time record = 0000009
       9     0 00:01:30  1.098067E-03  2.106067E+04  2.106067E+04  1.594152E+15
          (069,050,30)  4.513706E-05  3.924901E-05  1.225895E-01  7.098138E-01
      WRT_HIS   - wrote history  fields (Index=1,2) into time record = 0000010
      10     0 00:01:40  1.357416E-03  2.106055E+04  2.106055E+04  1.594152E+15
          (069,050,30)  5.004504E-05  4.354835E-05  1.199431E-01  7.764920E-01
      WRT_HIS   - wrote history  fields (Index=1,1) into time record = 0000011
      11     0 00:01:50  1.641256E-03  2.106044E+04  2.106045E+04  1.594152E+15
          (159,118,30)  3.209828E-04  1.929475E-04  1.272818E-01  8.377186E-01
      WRT_HIS   - wrote history  fields (Index=1,2) into time record = 0000012
     
........

     619     0 01:43:10  1.658293E+00  2.107103E+04  2.107269E+04  1.596544E+15
          (140,167,30)  3.801504E-04  1.139325E-03  2.546639E-01  1.852424E+01
      WRT_HIS   - wrote history  fields (Index=1,2) into time record = 0000620
     620     0 01:43:20  1.661794E+00  2.107107E+04  2.107273E+04  1.596555E+15
          (140,167,30)  4.120010E-04  1.009199E-03  2.572201E-01  1.858495E+01
      WRT_HIS   - wrote history  fields (Index=1,1) into time record = 0000621
     621     0 01:43:30  1.665306E+00  2.107112E+04  2.107278E+04  1.596566E+15
          (140,167,30)  4.441568E-04  8.789347E-04  2.589819E-01  1.864356E+01
      WRT_HIS   - wrote history  fields (Index=1,2) into time record = 0000622
     622     0 01:43:40  1.668829E+00  2.107116E+04  2.107283E+04  1.596577E+15
          (140,167,30)  4.765161E-04  7.488287E-04  2.599243E-01  1.869997E+01
      WRT_HIS   - wrote history  fields (Index=1,1) into time record = 0000623
     623     0 01:43:50  1.672362E+00  2.107120E+04  2.107287E+04  1.596588E+15
          (140,167,30)  5.089691E-04  6.191760E-04  2.600256E-01  1.875406E+01
      WRT_HIS   - wrote history  fields (Index=1,2) into time record = 0000624
     624     0 01:44:00  1.675906E+00  2.107125E+04  2.107292E+04  1.596599E+15
          (140,167,30)  5.413992E-04  4.902709E-04  2.592699E-01  1.880570E+01
      WRT_HIS   - wrote history  fields (Index=1,1) into time record = 0000625
     625     0 01:44:10  1.679460E+00  2.107129E+04  2.107297E+04  1.596609E+15
          (140,167,30)  5.736834E-04  3.624010E-04  2.576449E-01  1.885473E+01
      WRT_HIS   - wrote history  fields (Index=1,2) into time record = 0000626
     626     0 01:44:20  1.683026E+00  2.107133E+04  2.107302E+04  1.596620E+15
          (140,167,30)  6.056935E-04  2.358515E-04  2.551452E-01  1.890101E+01
      WRT_HIS   - wrote history  fields (Index=1,1) into time record = 0000627
     627     0 01:44:30  1.686602E+00  2.107137E+04  2.107306E+04  1.596631E+15
          (140,167,30)  6.372968E-04  1.109013E-04  2.517701E-01  1.894441E+01
      WRT_HIS   - wrote history  fields (Index=1,2) into time record = 0000628
     628     0 01:44:40  1.690190E+00  2.107142E+04  2.107311E+04  1.596642E+15
          (140,167,30)  6.683570E-04  1.217988E-05  2.475228E-01  1.898484E+01
      WRT_HIS   - wrote history  fields (Index=1,1) into time record = 0000629
     629     0 01:44:50  1.693789E+00  2.107146E+04  2.107315E+04  1.596653E+15
          (140,167,30)  6.987361E-04  1.331444E-04  2.424144E-01  1.902216E+01
      WRT_HIS   - wrote history  fields (Index=1,2) into time record = 0000630
     630     0 01:45:00  1.697399E+00  2.107150E+04  2.107320E+04  1.596664E+15
          (139,167,30)  4.156946E-04  1.642476E-04  2.380592E-01  1.905627E+01
      WRT_HIS   - wrote history  fields (Index=1,1) into time record = 0000631
     631     0 01:45:10  1.701021E+00  2.107154E+04  2.107324E+04  1.596675E+15
          (139,167,30)  4.480066E-04  3.630090E-05  2.353832E-01  1.908706E+01
      WRT_HIS   - wrote history  fields (Index=1,2) into time record = 0000632
     632     0 01:45:20  1.704655E+00  2.107158E+04  2.107329E+04  1.596686E+15
          (139,167,30)  4.802085E-04  9.003822E-05  2.319888E-01  1.911437E+01
      WRT_HIS   - wrote history  fields (Index=1,1) into time record = 0000633
     633     0 01:45:30  1.708300E+00  2.107162E+04  2.107333E+04  1.596697E+15
          (139,167,30)  5.121477E-04  2.145089E-04  2.278763E-01  1.913807E+01
      WRT_HIS   - wrote history  fields (Index=1,2) into time record = 0000634
     634     0 01:45:40  1.711957E+00  2.107166E+04  2.107338E+04  1.596708E+15
          (138,167,30)  3.037492E-04  5.003511E-05  2.240180E-01  1.915798E+01
      WRT_HIS   - wrote history  fields (Index=1,1) into time record = 0000635
     635     0 01:45:50  1.715625E+00  2.107170E+04  2.107342E+04  1.596719E+15
          (138,167,30)  3.360824E-04  7.797287E-05  2.224510E-01  1.917396E+01
      WRT_HIS   - wrote history  fields (Index=1,2) into time record = 0000636
     636     0 01:46:00  1.719306E+00  2.107174E+04  2.107346E+04  1.596730E+15
          (141,168,30)  4.681722E-04  1.569754E-03  2.204796E-01  1.918581E+01
      WRT_HIS   - wrote history  fields (Index=1,1) into time record = 0000637
     637     0 01:46:10  1.722999E+00  2.107178E+04  2.107351E+04  1.596741E+15
          (141,168,30)  5.114005E-04  1.448164E-03  2.270326E-01  1.919337E+01
      WRT_HIS   - wrote history  fields (Index=1,2) into time record = 0000638
     638     0 01:46:20  1.726705E+00  2.107182E+04  2.107355E+04  1.596752E+15
          (141,168,30)  5.545455E-04  1.325004E-03  2.330064E-01  1.919646E+01
      WRT_HIS   - wrote history  fields (Index=1,1) into time record = 0000639
     639     0 01:46:30  1.730423E+00  2.107186E+04  2.107359E+04  1.596763E+15
          (141,168,30)  5.974899E-04  1.200562E-03  2.383535E-01  1.919491E+01
      WRT_HIS   - wrote history  fields (Index=1,2) into time record = 0000640
     640     0 01:46:40  1.734153E+00  2.107190E+04  2.107363E+04  1.596774E+15
          (141,168,30)  6.401129E-04  1.075132E-03  2.430289E-01  1.918855E+01
      WRT_HIS   - wrote history  fields (Index=1,1) into time record = 0000641
     641     0 01:46:50  1.737897E+00  2.107194E+04  2.107367E+04  1.596785E+15
          (141,168,30)  6.822854E-04  9.490107E-04  2.469923E-01  1.917722E+01
      WRT_HIS   - wrote history  fields (Index=1,2) into time record = 0000642
     642     0 01:47:00  1.741653E+00  2.107197E+04  2.107372E+04  1.596797E+15
          (141,168,30)  7.238744E-04  8.224959E-04  2.502056E-01  1.916079E+01
      WRT_HIS   - wrote history  fields (Index=1,1) into time record = 0000643
     643     0 01:47:10  1.745423E+00  2.107201E+04  2.107376E+04  1.596808E+15
          (141,168,30)  7.647434E-04  6.958907E-04  2.526361E-01  1.913909E+01
      WRT_HIS   - wrote history  fields (Index=1,2) into time record = 0000644
     644     0 01:47:20  1.749206E+00  2.107205E+04  2.107380E+04  1.596819E+15
          (141,168,30)  8.047537E-04  5.694942E-04  2.542537E-01  1.911200E+01
      WRT_HIS   - wrote history  fields (Index=1,1) into time record = 0000645
     645     0 01:47:30  1.753002E+00  2.107209E+04  2.107384E+04  1.596830E+15
          (140,168,30)  4.262115E-04  1.029449E-03  2.573854E-01  1.907935E+01
      WRT_HIS   - wrote history  fields (Index=1,2) into time record = 0000646
     646     0 01:47:40  1.756812E+00  2.107212E+04  2.107388E+04  1.596841E+15
          (140,168,30)  4.607835E-04  8.916500E-04  2.605302E-01  1.904100E+01
      WRT_HIS   - wrote history  fields (Index=1,1) into time record = 0000647
     647     0 01:47:50  1.760636E+00  2.107216E+04  2.107392E+04  1.596853E+15
          (140,168,30)  4.955185E-04  7.537136E-04  2.629026E-01  1.899628E+01
      WRT_HIS   - wrote history  fields (Index=1,2) into time record = 0000648
     648     0 01:48:00  1.764474E+00  2.107220E+04  2.107396E+04  1.596864E+15
          (140,168,30)  5.303083E-04  6.159594E-04  2.644709E-01  1.894445E+01
      WRT_HIS   - wrote history  fields (Index=1,1) into time record = 0000649
     649     0 01:48:10  1.768327E+00  2.107224E+04  2.107400E+04  1.596875E+15
          (140,168,30)  5.650380E-04  4.787081E-04  2.652086E-01  1.888488E+01
      WRT_HIS   - wrote history  fields (Index=1,2) into time record = 0000650
     650     0 01:48:20  1.772193E+00  2.107227E+04  2.107405E+04  1.596886E+15
          (140,168,30)  5.995872E-04  3.422804E-04  2.650944E-01  1.895415E+01
      WRT_HIS   - wrote history  fields (Index=1,1) into time record = 0000651
     651     0 01:48:30  1.776074E+00  2.107231E+04  2.107409E+04  1.596898E+15
          (139,168,30)  3.477611E-04  7.265965E-04  2.640069E-01  1.912164E+01
      WRT_HIS   - wrote history  fields (Index=1,2) into time record = 0000652
     652     0 01:48:40  1.779969E+00  2.107235E+04  2.107413E+04  1.596909E+15
          (139,168,30)  3.785930E-04  5.851489E-04  2.652985E-01  1.928908E+01
      WRT_HIS   - wrote history  fields (Index=1,1) into time record = 0000653
     653     0 01:48:50  1.783880E+00  2.107238E+04  2.107417E+04  1.596920E+15
          (139,168,30)  4.098338E-04  4.441161E-04  2.658315E-01  1.945642E+01
      WRT_HIS   - wrote history  fields (Index=1,2) into time record = 0000654
     654     0 01:49:00  1.787804E+00  2.107242E+04  2.107421E+04  1.596932E+15
          (139,168,30)  4.413740E-04  3.038135E-04  2.655815E-01  1.962355E+01
      WRT_HIS   - wrote history  fields (Index=1,1) into time record = 0000655
     655     0 01:49:10  1.791745E+00  2.107246E+04  2.107425E+04  1.596943E+15
          (139,168,30)  4.730971E-04  1.645623E-04  2.645303E-01  1.979045E+01
      WRT_HIS   - wrote history  fields (Index=1,2) into time record = 0000656
     656     0 01:49:20  1.795702E+00  2.107249E+04  2.107429E+04  1.596955E+15
          (139,168,30)  5.048801E-04  2.667614E-05  2.626610E-01  1.995709E+01
      WRT_HIS   - wrote history  fields (Index=1,1) into time record = 0000657
     657     0 01:49:30  1.799675E+00  2.107253E+04  2.107433E+04  1.596966E+15
          (139,168,30)  5.365946E-04  1.095268E-04  2.599640E-01  2.012343E+01
 DIAG speed trouble    20.123425742763210     

 Blowing-up: Saving latest model state into  RESTART file

      WRT_RST   - wrote re-start fields (Index=1,2) into time record = 0000003

 Elapsed CPU time (seconds):

 Node   #  0 CPU:     660.815
 Total:               660.815

 Nonlinear ocean model elapsed time profile, Grid: 01

  Allocation and array initialization ..............         0.100  ( 0.0152 %)
  Ocean state initialization .......................         0.012  ( 0.0018 %)
  Reading of input data ............................         0.040  ( 0.0061 %)
  Processing of input data .........................         0.274  ( 0.0414 %)
  Processing of output time averaged data ..........         0.848  ( 0.1284 %)
  Computation of vertical boundary conditions ......         0.655  ( 0.0991 %)
  Computation of global information integrals ......         3.277  ( 0.4959 %)
  Writing of output data ...........................       128.570  (19.4562 %)
  Model 2D kernel ..................................        85.940  (13.0052 %)
  2D/3D coupling, vertical metrics .................         3.385  ( 0.5123 %)
  Omega vertical velocity ..........................         2.972  ( 0.4497 %)
  Equation of state for seawater ...................        10.297  ( 1.5583 %)
  Atmosphere-Ocean bulk flux parameterization ......        38.018  ( 5.7533 %)
  GLS vertical mixing parameterization .............       257.001  (38.8916 %)
  3D equations right-side terms ....................        15.098  ( 2.2848 %)
  3D equations predictor step ......................        51.076  ( 7.7292 %)
  Pressure gradient ................................         8.158  ( 1.2346 %)
  Harmonic mixing of tracers, geopotentials ........        13.345  ( 2.0195 %)
  Harmonic stress tensor, S-surfaces ...............         6.764  ( 1.0236 %)
  Corrector time-step for 3D momentum ..............        13.868  ( 2.0986 %)
  Corrector time-step for tracers ..................        17.487  ( 2.6463 %)
                                              Total:       657.187   99.4509

 Nonlinear model message Passage profile, Grid: 01

  Message Passage: 2D halo exchanges ...............         0.310  ( 0.0468 %)
  Message Passage: 3D halo exchanges ...............         0.018  ( 0.0028 %)
  Message Passage: 4D halo exchanges ...............         0.005  ( 0.0008 %)
  Message Passage: data broadcast ..................         0.013  ( 0.0020 %)
  Message Passage: data reduction ..................         0.004  ( 0.0007 %)
  Message Passage: data gathering ..................        25.447  ( 3.8508 %)
  Message Passage: data scattering..................         0.020  ( 0.0030 %)
                                              Total:        25.817    3.9068

 All percentages are with respect to total time =          660.815


 ROMS/TOMS - Output NetCDF summary for Grid 01:
             number of time records written in HISTORY file = 00000657
             number of time records written in RESTART file = 00000006
             number of time records written in AVERAGE file = 00000001

 Analytical header files used:

     ROMS/Functionals/ana_btflux.h

 ROMS/TOMS: DONE... Wednesday - September 11, 2019 -  6:11:30 PM


Thank you!
Attachments
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(5.11 MiB) Downloaded 4 times
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User avatar
kate
Posts: 3718
Joined: Wed Jul 02, 2003 5:29 pm
Location: IMS/UAF, USA

Re: DIAG speed trouble / gridbuilder

#2 Post by kate » Wed Sep 11, 2019 4:52 pm

You might still need to reduce the timestep. You ran long enough that you should be getting close.

User avatar
wilkin
Posts: 510
Joined: Mon Apr 28, 2003 5:44 pm
Location: Rutgers University
Contact:

Re: DIAG speed trouble / gridbuilder

#3 Post by wilkin » Thu Sep 12, 2019 2:02 pm

With a minimum grid cell size of ~4 km you should be well within CFL stability with such a small time step, so that's not your problem.

The log indicates a 3rd record was written to the restart file on blow-up, so you should plot what's in there and look for a location that is causing trouble. It could be the boundary, or the interior, deep, or shallow, but it will give you some guidance.

Your choice of open boundary conditions is unconventional - gradient on all but zeta. If the blow-up is near a boundary you might experiment further there.

You have negative rainfall rates in your forcing file - what's that?
John Wilkin: DMCS Rutgers University
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Re: DIAG speed trouble / gridbuilder

#4 Post by hpd14thu » Sun Sep 15, 2019 6:01 pm

wilkin wrote:With a minimum grid cell size of ~4 km you should be well within CFL stability with such a small time step, so that's not your problem.

The log indicates a 3rd record was written to the restart file on blow-up, so you should plot what's in there and look for a location that is causes trouble. It could be the boundary, or the interior, deep, or shallow, but it will give you some guidance.

Your choice of open boundary conditions is unconventional - gradient on all but zeta. It the blow-up is near a boundary you might experiment further there.

You have negative rainfall rates in your forcing file - what's that?
Thank for your reply, Kate and Wilkin! I have modified my model, but there are still some problems

The blow-point is near the boudary, and if I change the boudary condition, it appears in the shallow water area, as shown in the picture below:

1)As for the boundary condition, because I don't have the boundary data and I just want to run a little case, I set GRA on all but zeta. Now I have change it into
Gra Clo Gra Clo, but it is still a little strange in my left-down corner, as shown in the picture below, which I think results from the boundary conditon;

2)As for the shallow water area, because my water depth varies from 2m to 4000m, I change hmin from 2m to 20m and turn on WET_DRY. But there is still wierd in right side of my result, as shown in the picture below;

3)As for the negative rainfall rates, that was my fault and I have modified it.
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