Problem with ROMS running.

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lfelipem
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Joined: Thu Aug 15, 2013 1:54 pm
Location: Federal University of Bahia
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Problem with ROMS running.

#1 Unread post by lfelipem »

I'm running a simulation that technically runs on the COAWST versions without any problems, but the COAWST version has bugs in the biological module. I went back to the latest native version of ROMS, which compiles the biological module, and I noticed that when I run mpirun, it starts my files correctly, but when I run the first timestep it claims NaN, generalized.

Have you noticed this?

My files are attached.

Translated with DeepL.com (free version)

Code: Select all

 Power filter parameters, Fgamma, gamma =  0.28400   0.14200

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

 Minimum X-grid spacing, DXmin =  7.68697088E+00 km    Water points =  7.68697088E+00 km
 Maximum X-grid spacing, DXmax =  7.75282973E+00 km    Water points =  7.75282973E+00 km
 Minimum Y-grid spacing, DYmin =  7.67440062E+00 km    Water points =  7.67440062E+00 km
 Maximum Y-grid spacing, DYmax =  7.74015185E+00 km    Water points =  7.74015185E+00 km
 Minimum Z-grid spacing, DZmin =  1.28342346E-01 m     Water points =  1.28342346E-01 m
 Maximum Z-grid spacing, DZmax =  3.99865290E+02 m     Water points =  3.99865290E+02 m

 Minimum barotropic Courant Number =  1.91873093E-03
 Maximum barotropic Courant Number =  6.37473775E-02
 Maximum Coriolis   Courant Number =  2.80314720E-03

 Horizontal mixing scaled by grid area squared root, MAXVAL(grdscl) =  7.74648820E+00 km  (Water points)

  GET_STATE_NF90   - NLM: state initial conditions,                       2016-09-10 00:00:00.00
                      (Grid 01, t = 0.0000, File: ini_GLORYS_20160910.nc, Rec=0001, Index=1)
                   - free-surface
                      (Min = -5.35739839E-01 Max =  6.57110453E-01)
                   - vertically integrated u-momentum component
                      (Min = -3.03400576E-01 Max =  5.27763724E-01)
                   - vertically integrated v-momentum component
                      (Min = -4.11288381E-01 Max =  3.84088635E-01)
                   - u-momentum component
                      (Min = -1.07648885E+00 Max =  1.11721826E+00)
                   - v-momentum component
                      (Min = -1.86080062E+00 Max =  8.40811670E-01)
                   - potential temperature
                      (Min = -2.75410384E-01 Max =  2.38596420E+01)
                   - salinity
                      (Min =  1.52592547E-03 Max =  3.73637695E+01)
  GET_2DFLD_NF90   - surface u-wind component,                            2016-09-09 23:00:00.00
                      (Grid=01, Rec=24, Index=1, File: era5_u10_2016_roms.nc)
                      (Tmin=         -1.0000 Tmax=          8.9583)   t =         -0.0417
                      (Min =  1.00000000E+35 Max = -1.00000000E+35)   regrid = T
  GET_2DFLD_NF90   - surface v-wind component,                            2016-09-09 23:00:00.00
                      (Grid=01, Rec=24, Index=1, File: era5_v10_2016_roms.nc)
                      (Tmin=         -1.0000 Tmax=          8.9583)   t =         -0.0417
                      (Min =  1.00000000E+35 Max = -1.00000000E+35)   regrid = T
  GET_2DFLD_NF90   - surface air pressure,                                2016-09-09 23:00:00.00
                      (Grid=01, Rec=24, Index=1, File: era5_msl_2016_roms.nc)
                      (Tmin=         -1.0000 Tmax=          8.9583)   t =         -0.0417
                      (Min =  1.00000000E+35 Max = -1.00000000E+35)   regrid = T
  GET_2DFLD_NF90   - net solar shortwave radiation flux,                  2016-09-09 23:00:00.00
                      (Grid=01, Rec=24, Index=1, File: era5_msdwswrf_2016_roms.nc)
                      (Tmin=         -1.0000 Tmax=          8.9583)   t =         -0.0417
                      (Min =  1.00000000E+35 Max = -1.00000000E+35)   regrid = T
  GET_2DFLD_NF90   - downward longwave radiation flux,                    2016-09-09 23:00:00.00
                      (Grid=01, Rec=24, Index=1, File: era5_msdwlwrf_2016_roms.nc)
                      (Tmin=         -1.0000 Tmax=          8.9583)   t =         -0.0417
                      (Min =  1.00000000E+35 Max = -1.00000000E+35)   regrid = T
  GET_2DFLD_NF90   - surface air temperature,                             2016-09-09 23:00:00.00
                      (Grid=01, Rec=24, Index=1, File: era5_t2m_2016_roms.nc)
                      (Tmin=         -1.0000 Tmax=          8.9583)   t =         -0.0417
                      (Min =  1.00000000E+35 Max = -1.00000000E+35)   regrid = T
  GET_2DFLD_NF90   - surface air relative humidity,                       2016-09-09 23:00:00.00
                      (Grid=01, Rec=24, Index=1, File: era5_q_2016_roms.nc)
                      (Tmin=         -1.0000 Tmax=          8.9583)   t =         -0.0417
                      (Min =  1.00000000E+35 Max = -1.00000000E+35)   regrid = T
  GET_2DFLD_NF90   - rain fall rate,                                      2016-09-09 23:00:00.00
                      (Grid=01, Rec=24, Index=1, File: era5_tp_2016_roms.nc)
                      (Tmin=         -1.0000 Tmax=          8.9583)   t =         -0.0417
                      (Min =  1.00000000E+35 Max = -1.00000000E+35)   regrid = T
  GET_2DFLD_NF90   - sea surface temperature climatology,                 2016-09-10 00:00:00.00
                      (Grid=01, Rec=1, Index=1, File: oisst_roms_cor.nc)
                      (Tmin=          0.0000 Tmax=         10.0000)   t =          0.0000
                      (Min =  2.00625229E+01 Max =  2.28236008E+01)   regrid = F
  GET_2DFLD_NF90   - surface net heat flux sensitivity to SST,            2016-09-10 00:00:00.00
                      (Grid=01, Rec=1, Index=1, File: oisst_dQqSST_cor.nc)
                      (Tmin=          0.0000 Tmax=         10.0000)   t =          0.0000
                      (Min = -9.79282064E-06 Max = -9.79282064E-06)   regrid = F

 Basin information for Grid 01:

 Maximum grid stiffness ratios:  rx0 =   9.981603E-01 (Beckmann and Haidvogel)
                                 rx1 =   3.320217E+01 (Haney)

 Initial domain volumes:  TotVolume =  6.1664803598E+15 m3
                         MinCellVol =  7.7733445694E+06 m3
                         MaxCellVol =  2.3589033212E+10 m3
                            Max/Min =  3.0346053750E+03


 NL ROMS: started time-stepping: (Grid: 01 TimeSteps: 000000000001 - 000000017280)

  GET_2DFLD_NF90   - surface u-wind component,                            2016-09-10 00:00:00.00
                      (Grid=01, Rec=25, Index=2, File: era5_u10_2016_roms.nc)
                      (Tmin=         -1.0000 Tmax=          8.9583)   t =          0.0000
                      (Min =  1.00000000E+35 Max = -1.00000000E+35)   regrid = T
  GET_2DFLD_NF90   - surface v-wind component,                            2016-09-10 00:00:00.00
                      (Grid=01, Rec=25, Index=2, File: era5_v10_2016_roms.nc)
                      (Tmin=         -1.0000 Tmax=          8.9583)   t =          0.0000
                      (Min =  1.00000000E+35 Max = -1.00000000E+35)   regrid = T
  GET_2DFLD_NF90   - surface air pressure,                                2016-09-10 00:00:00.00
                      (Grid=01, Rec=25, Index=2, File: era5_msl_2016_roms.nc)
                      (Tmin=         -1.0000 Tmax=          8.9583)   t =          0.0000
                      (Min =  1.00000000E+35 Max = -1.00000000E+35)   regrid = T
  GET_2DFLD_NF90   - net solar shortwave radiation flux,                  2016-09-10 00:00:00.00
                      (Grid=01, Rec=25, Index=2, File: era5_msdwswrf_2016_roms.nc)
                      (Tmin=         -1.0000 Tmax=          8.9583)   t =          0.0000
                      (Min =  1.00000000E+35 Max = -1.00000000E+35)   regrid = T
  GET_2DFLD_NF90   - downward longwave radiation flux,                    2016-09-10 00:00:00.00
                      (Grid=01, Rec=25, Index=2, File: era5_msdwlwrf_2016_roms.nc)
                      (Tmin=         -1.0000 Tmax=          8.9583)   t =          0.0000
                      (Min =  1.00000000E+35 Max = -1.00000000E+35)   regrid = T
  GET_2DFLD_NF90   - surface air temperature,                             2016-09-10 00:00:00.00
                      (Grid=01, Rec=25, Index=2, File: era5_t2m_2016_roms.nc)
                      (Tmin=         -1.0000 Tmax=          8.9583)   t =          0.0000
                      (Min =  1.00000000E+35 Max = -1.00000000E+35)   regrid = T
  GET_2DFLD_NF90   - surface air relative humidity,                       2016-09-10 00:00:00.00
                      (Grid=01, Rec=25, Index=2, File: era5_q_2016_roms.nc)
                      (Tmin=         -1.0000 Tmax=          8.9583)   t =          0.0000
                      (Min =  1.00000000E+35 Max = -1.00000000E+35)   regrid = T
  GET_2DFLD_NF90   - rain fall rate,                                      2016-09-10 00:00:00.00
                      (Grid=01, Rec=25, Index=2, File: era5_tp_2016_roms.nc)
                      (Tmin=         -1.0000 Tmax=          8.9583)   t =          0.0000
                      (Min =  1.00000000E+35 Max = -1.00000000E+35)   regrid = T
  GET_2DFLD_NF90   - sea surface temperature climatology,                 2016-09-11 00:00:00.00
                      (Grid=01, Rec=2, Index=2, File: oisst_roms_cor.nc)
                      (Tmin=          0.0000 Tmax=         10.0000)   t =          1.0000
                      (Min =  2.00540314E+01 Max =  2.27781086E+01)   regrid = F
  GET_2DFLD_NF90   - surface net heat flux sensitivity to SST,            2016-09-11 00:00:00.00
                      (Grid=01, Rec=2, Index=2, File: oisst_dQqSST_cor.nc)
                      (Tmin=          0.0000 Tmax=         10.0000)   t =          1.0000
                      (Min = -9.79282064E-06 Max = -9.79282064E-06)   regrid = F

 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 2016-09-10 00:00:00.00  1.832622E-02  2.086062E+04  2.086063E+04  6.173537E+15
                     (104,004,32)  1.232032E-03  7.191476E-03  0.000000E+00  1.880842E+00
  DEF_HIS_NF90     - creating history file,            Grid 01: Projects/Procosta_bio/Out/procosta_his.nc
  WRT_HIS_NF90     - writing history     fields (Index=1,1) in record = 1
  DEF_RST_NF90     - creating restart file,            Grid 01: Projects/Procosta_bio/procosta_rst.nc
  GET_2DFLD_NF90   - surface u-wind component,                            2016-09-10 01:00:00.00
                      (Grid=01, Rec=26, Index=1, File: era5_u10_2016_roms.nc)
                      (Tmin=         -1.0000 Tmax=          8.9583)   t =          0.0417
                      (Min =  1.00000000E+35 Max = -1.00000000E+35)   regrid = T
  GET_2DFLD_NF90   - surface v-wind component,                            2016-09-10 01:00:00.00
                      (Grid=01, Rec=26, Index=1, File: era5_v10_2016_roms.nc)
                      (Tmin=         -1.0000 Tmax=          8.9583)   t =          0.0417
                      (Min =  1.00000000E+35 Max = -1.00000000E+35)   regrid = T
  GET_2DFLD_NF90   - surface air pressure,                                2016-09-10 01:00:00.00
                      (Grid=01, Rec=26, Index=1, File: era5_msl_2016_roms.nc)
                      (Tmin=         -1.0000 Tmax=          8.9583)   t =          0.0417
                      (Min =  1.00000000E+35 Max = -1.00000000E+35)   regrid = T
  GET_2DFLD_NF90   - net solar shortwave radiation flux,                  2016-09-10 01:00:00.00
                      (Grid=01, Rec=26, Index=1, File: era5_msdwswrf_2016_roms.nc)
                      (Tmin=         -1.0000 Tmax=          8.9583)   t =          0.0417
                      (Min =  1.00000000E+35 Max = -1.00000000E+35)   regrid = T
  GET_2DFLD_NF90   - downward longwave radiation flux,                    2016-09-10 01:00:00.00
                      (Grid=01, Rec=26, Index=1, File: era5_msdwlwrf_2016_roms.nc)
                      (Tmin=         -1.0000 Tmax=          8.9583)   t =          0.0417
                      (Min =  1.00000000E+35 Max = -1.00000000E+35)   regrid = T
  GET_2DFLD_NF90   - surface air temperature,                             2016-09-10 01:00:00.00
                      (Grid=01, Rec=26, Index=1, File: era5_t2m_2016_roms.nc)
                      (Tmin=         -1.0000 Tmax=          8.9583)   t =          0.0417
                      (Min =  1.00000000E+35 Max = -1.00000000E+35)   regrid = T
  GET_2DFLD_NF90   - surface air relative humidity,                       2016-09-10 01:00:00.00
                      (Grid=01, Rec=26, Index=1, File: era5_q_2016_roms.nc)
                      (Tmin=         -1.0000 Tmax=          8.9583)   t =          0.0417
                      (Min =  1.00000000E+35 Max = -1.00000000E+35)   regrid = T
  GET_2DFLD_NF90   - rain fall rate,                                      2016-09-10 01:00:00.00
                      (Grid=01, Rec=26, Index=1, File: era5_tp_2016_roms.nc)
                      (Tmin=         -1.0000 Tmax=          8.9583)   t =          0.0417
                      (Min =  1.00000000E+35 Max = -1.00000000E+35)   regrid = T
         1 2016-09-10 00:00:30.00           NaN           NaN           NaN           NaN
                     (000,000,00)  0.000000E+00  0.000000E+00  0.000000E+00 -1.000000E+20
 Found Error: 1    Line: 365      Source: ROMS/Nonlinear/main3d.F
 Found Error: 1    Line: 312      Source: ROMS/Drivers/nl_roms.h, ROMS_run

 Blowing-up: Saving latest model state into  RESTART file
     REASON: KEchar =      NaN, PEchar =      NaN

  WRT_RST_NF90     - writing re-start    fields (Index=2,2) in record = 1

Elapsed wall CPU time for each process (seconds):

 Node   #    1 CPU:       3.284
 Node   #   11 CPU:       3.283
 Node   #    2 CPU:       3.286
 Node   #    3 CPU:       3.284
 Node   #    4 CPU:       3.283
 Node   #    5 CPU:       3.282
 Node   #    6 CPU:       3.283
 Node   #    7 CPU:       3.284
 Node   #    8 CPU:       3.282
 Node   #    9 CPU:       3.283
 Node   #   10 CPU:       3.282
 Node   #    0 CPU:       3.281
 Total:                  39.398
 Average:                 3.283
 Minimum:                 3.281
 Maximum:                 3.286

 Nonlinear model elapsed CPU time profile, Grid: 01

  Allocation and array initialization ..............         2.069  ( 5.2506 %)
  Ocean state initialization .......................         0.142  ( 0.3601 %)
  Reading of input data ............................        14.552  (36.9346 %)
  Processing of input data .........................         0.048  ( 0.1213 %)
  Processing of output time averaged data ..........         0.000  ( 0.0006 %)
  Computation of vertical boundary conditions ......         0.003  ( 0.0066 %)
  Computation of global information integrals ......         0.068  ( 0.1729 %)
  Writing of output data ...........................         9.115  (23.1345 %)
  Model 2D kernel ..................................         0.912  ( 2.3141 %)
  2D/3D coupling, vertical metrics .................         0.238  ( 0.6034 %)
  Omega vertical velocity ..........................         0.070  ( 0.1778 %)
  Equation of state for seawater ...................         0.282  ( 0.7165 %)
  Atmosphere-Ocean bulk flux parameterization ......         0.036  ( 0.0909 %)
  GLS vertical mixing parameterization .............         0.927  ( 2.3524 %)
  3D equations right-side terms ....................         0.216  ( 0.5494 %)
  3D equations predictor step ......................         0.459  ( 1.1650 %)
  Pressure gradient ................................         0.074  ( 0.1867 %)
  Harmonic mixing of tracers, geopotentials ........         0.059  ( 0.1499 %)
  Harmonic stress tensor, S-surfaces ...............         0.078  ( 0.1975 %)
  Corrector time-step for 3D momentum ..............         0.090  ( 0.2274 %)
  Corrector time-step for tracers ..................         0.207  ( 0.5249 %)
                                              Total:        29.642   75.2370 %

  Unique kernel(s) regions profiled ................        29.642   75.2370 %
  Residual, non-profiled code ......................         9.756   24.7630 %


 All percentages are with respect to total time =           39.398


 MPI communications profile, Grid: 01

  Message Passage: 2D halo exchanges ...............         0.314  ( 0.7967 %)
  Message Passage: 3D halo exchanges ...............         0.586  ( 1.4882 %)
  Message Passage: 4D halo exchanges ...............         0.115  ( 0.2911 %)
  Message Passage: data broadcast ..................        14.087  (35.7554 %)
  Message Passage: data reduction ..................         0.868  ( 2.2026 %)
  Message Passage: data gathering ..................         4.359  (11.0645 %)
  Message Passage: data scattering..................         1.579  ( 4.0079 %)
  Message Passage: point data gathering ............         0.000  ( 0.0004 %)
  Message Passage: synchronization barrier .........         0.017  ( 0.0437 %)
                                              Total:        21.925   55.6504 %

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

 Dynamic and Automatic memory (MB) usage for Grid 01:  265x216x32  tiling: 4x3

     tile          Dynamic        Automatic            USAGE      MPI-Buffers

        0           214.79            30.73           245.52            30.73
        1             0.00            30.73            30.73             0.00
        2             0.00            30.73            30.73             0.00
        3             0.00            30.73            30.73             0.00
        4             0.00            30.73            30.73             0.00
        5             0.00            30.73            30.73             0.00
        6             0.00            30.73            30.73             0.00
        7             0.00            30.73            30.73             0.00
        8             0.00            30.73            30.73             0.00
        9             0.00            30.73            30.73             0.00
       10             0.00            30.73            30.73             0.00
       11             0.00            30.73            30.73             0.00

    TOTAL           214.79           368.79           583.58            30.73

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

 ROMS - Output NetCDF summary for Grid 01:
             number of time records written in HISTORY file = 1
             number of time records written in RESTART file = 1

 Analytical header files used:

     ROMS/Functionals/ana_btflux.h
     ROMS/Functionals/ana_fsobc.h
     ROMS/Functionals/ana_m2obc.h
     ROMS/Functionals/ana_srflux.h

 MAIN: Abnormal termination: BLOWUP.
 REASON: KEchar =      NaN, PEchar =      NaN
Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG IEEE_DIVIDE_BY_ZERO
ERROR STOP
Attachments
roms_bio_toy.in
(175.58 KiB) Downloaded 57 times
atmos_onlyroms.h
(1.26 KiB) Downloaded 57 times

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