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ROMS/TOMS

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PostPosted: Sat Aug 03, 2019 2:28 pm 
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Joined: Mon Jul 08, 2019 6:45 pm
Posts: 3
Location: yellow river institute of hydraulic research
Hi,all. I am new to ROMS. I have successfully built the roms with gfortran and mpich under ubuntu.
For the case, I didn't modify the roms_upwelling.in.

However, when I run the case of upwelling, the error goes.
I searched the similar errors on the web and tried to fix it, but finally failed.
Can you help me? thanks.

Code:
$mpirun -np 9 ./romsM roms_upwelling.in
**************************************************
--------------------------------------------------------------------------------
 Model Input Parameters:  ROMS/TOMS version 3.8 
                          Saturday - August 3, 2019 - 10:15:27 PM
--------------------------------------------------------------------------------

 Wind-Driven Upwelling/Downwelling over a Periodic Channel

 Operating system : Linux
 CPU/hardware     : x86_64
 Compiler system  : gfortran
 Compiler command : /usr/local/bin/mpif90
 Compiler flags   : -frepack-arrays -O3 -ffast-math -
 MPI Communicator : 1140850688  PET size = 9

 Input Script     : roms_upwelling.in

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

 Local Root       : /home/lairuixun/ROMS0803/trunk
 Header Dir       : /home/lairuixun/ROMS0803/test/upwelling
 Header file      : upwelling.h
 Analytical Dir   : /home/lairuixun/ROMS0803/test/upwelling

 Resolution, Grid 01: 41x80x16,  Parallel Nodes: 9,  Tiling: 3x3


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

        288  ntimes            Number of timesteps for 3-D equations.
    300.000  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.
         72  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).
         72  nHIS              Number of timesteps between the writing fields
                                 into history file.
          0  nQCK              Number of timesteps between the writing fields
                                 into quicksave file.
          F  LuvSponge         Turning OFF sponge on horizontal momentum.
          F  LtracerSponge(01) Turning OFF sponge on tracer 01: temp
          F  LtracerSponge(02) Turning OFF sponge on tracer 02: salt
 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.
 3.0000E-04  rdrg              Linear bottom drag coefficient (m/s).
 3.0000E-03  rdrg2             Quadratic bottom drag coefficient.
 2.0000E-02  Zob               Bottom roughness (m).
          2  Vtransform        S-coordinate transformation equation.
          4  Vstretching       S-coordinate stretching function.
 3.0000E+00  theta_s           S-coordinate surface control parameter.
 0.0000E+00  theta_b           S-coordinate bottom  control parameter.
     25.000  Tcline            S-coordinate surface/bottom layer width (m) used
                                 in vertical coordinate stretching.
   1025.000  rho0              Mean density (kg/m3) for Boussinesq approximation.
      0.000  dstart            Time-stamp assigned to model initialization (days).
       0.00  time_ref          Reference time for units attribute (yyyymmdd.dd)
 0.0000E+00  Tnudg(01)         Nudging/relaxation time scale (days)
                                 for tracer 01: temp
 0.0000E+00  Tnudg(02)         Nudging/relaxation time scale (days)
                                 for tracer 02: salt
 0.0000E+00  Znudg             Nudging/relaxation time scale (days)
                                 for free-surface.
 0.0000E+00  M2nudg            Nudging/relaxation time scale (days)
                                 for 2D momentum.
 0.0000E+00  M3nudg            Nudging/relaxation time scale (days)
                                 for 3D momentum.
 0.0000E+00  obcfac            Factor between passive and active
                                 open boundary conditions.
          F  VolCons(1)        NLM western  edge boundary volume conservation.
          F  VolCons(2)        NLM southern edge boundary volume conservation.
          F  VolCons(3)        NLM eastern  edge boundary volume conservation.
          F  VolCons(4)        NLM northern edge boundary volume conservation.
     14.000  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
          T  Hout(idDano)      Write out density anomaly.

 Output/Input Files:

               Output Restart File:  roms_rst.nc
               Output History File:  roms_his.nc

 Tile partition information for Grid 01:  41x80x16  tiling: 3x3

     tile     Istr     Iend     Jstr     Jend     Npts

        0        1       14        1       27     6048
        1       15       28        1       27     6048
        2       29       41        1       27     5616
        3        1       14       28       54     6048
        4       15       28       28       54     6048
        5       29       41       28       54     5616
        6        1       14       55       80     5824
        7       15       28       55       80     5824
        8       29       41       55       80     5408

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

     tile     Xmin     Xmax     Ymin     Ymax     grid

        0     0.50    14.50     0.50    27.50  RHO-points
        1    14.50    28.50     0.50    27.50  RHO-points
        2    28.50    41.50     0.50    27.50  RHO-points
        3     0.50    14.50    27.50    54.50  RHO-points
        4    14.50    28.50    27.50    54.50  RHO-points
        5    28.50    41.50    27.50    54.50  RHO-points
        6     0.50    14.50    54.50    80.50  RHO-points
        7    14.50    28.50    54.50    80.50  RHO-points
        8    28.50    41.50    54.50    80.50  RHO-points

        0     1.00    14.50     0.50    27.50    U-points
        1    14.50    28.50     0.50    27.50    U-points
        2    28.50    41.00     0.50    27.50    U-points
        3     1.00    14.50    27.50    54.50    U-points
        4    14.50    28.50    27.50    54.50    U-points
        5    28.50    41.00    27.50    54.50    U-points
        6     1.00    14.50    54.50    80.50    U-points
        7    14.50    28.50    54.50    80.50    U-points
        8    28.50    41.00    54.50    80.50    U-points

        0     0.50    14.50     1.00    27.50    V-points
        1    14.50    28.50     1.00    27.50    V-points
        2    28.50    41.50     1.00    27.50    V-points
        3     0.50    14.50    27.50    54.50    V-points
        4    14.50    28.50    27.50    54.50    V-points
        5    28.50    41.50    27.50    54.50    V-points
        6     0.50    14.50    54.50    80.00    V-points
        7    14.50    28.50    54.50    80.00    V-points
        8    28.50    41.50    54.50    80.00    V-points

 Maximum halo size in XI and ETA directions:

               HaloSizeI(1) =      81
               HaloSizeJ(1) =     117
                TileSide(1) =      33
                TileSize(1) =     693


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

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

 zeta                     1   Periodic     Closed       Periodic     Closed

 ubar                     1   Periodic     Closed       Periodic     Closed

 vbar                     1   Periodic     Closed       Periodic     Closed

 u                        1   Periodic     Closed       Periodic     Closed

 v                        1   Periodic     Closed       Periodic     Closed

 temp                     1   Periodic     Closed       Periodic     Closed

 salt                     1   Periodic     Closed       Periodic     Closed

 Activated C-preprocessing Options:

 UPWELLING               Wind-Driven Upwelling/Downwelling over a Periodic Channel
 ANA_BSFLUX              Analytical kinematic bottom salinity flux
 ANA_BTFLUX              Analytical kinematic bottom temperature flux
 ANA_GRID                Analytical grid set-up
 ANA_INITIAL             Analytical initial conditions
 ANA_SMFLUX              Analytical kinematic surface momentum flux
 ANA_SSFLUX              Analytical kinematic surface salinity flux
 ANA_STFLUX              Analytical kinematic surface temperature flux
 ANA_VMIX                Analytical vertical mixing coefficients
 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.
 MPI                     MPI distributed-memory configuration
 NONLINEAR               Nonlinear Model
 !NONLIN_EOS             Linear Equation of State for seawater
 POWER_LAW               Power-law shape time-averaging barotropic filter
 PROFILE                 Time profiling activated
 REDUCE_ALLGATHER        Using mpi_allgather in mp_reduce routine
 !RST_SINGLE             Double precision fields in restart NetCDF file
 SALINITY                Using salinity
 SOLVE3D                 Solving 3D Primitive Equations
 SPLINES_VDIFF           Parabolic Spline Reconstruction for Vertical Diffusion
 SPLINES_VVISC           Parabolic Spline Reconstruction for Vertical Viscosity
 TS_C4HADVECTION         Fourth-order centered horizontal advection of tracers
 TS_C4VADVECTION         Fourth-order centered vertical advection 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
 VAR_RHO_2D              Variable density barotropic mode

 CHECKDEFS - no bottom stress formulation is selected.
 Found Error: 05   Line: 1128     Source: ROMS/Utility/inp_par.F
 Found Error: 05   Line: 111      Source: ROMS/Drivers/nl_ocean.h

 Elapsed CPU time (seconds):

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

 Dynamic and Automatic memory (MB) usage for Grid 01:  41x80x16  tiling: 3x3

     tile          Dynamic        Automatic            USAGE      MPI-Buffers

        0             0.96             0.96             1.92             0.00
        1             0.96             0.96             1.92             0.00
        2             0.96             0.96             1.92             0.00
        3             0.96             0.96             1.92             0.00
        4             0.96             0.96             1.92             0.00
        5             0.96             0.96             1.92             0.00
        6             0.96             0.96             1.92             0.00
        7             0.96             0.96             1.92             0.00
        8             0.96             0.96             1.92             0.00

    TOTAL             8.65             8.63            17.28             0.00

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

 ROMS/TOMS - Output NetCDF summary for Grid 01:
 Found Error: 05   Line: 350      Source: ROMS/Utility/close_io.F

 ROMS/TOMS - Configuration error ..... exit_flag:   5

***************************************************************************************


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PostPosted: Sat Aug 03, 2019 3:15 pm 
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Joined: Wed Jul 02, 2003 5:29 pm
Posts: 3646
Location: IMS/UAF, USA
Here is the real error message:
Quote:
CHECKDEFS - no bottom stress formulation is selected.
The upwelling case should have one selected in the roms_upwelling.in file.


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PostPosted: Sat Aug 03, 2019 11:34 pm 
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Joined: Mon Jul 08, 2019 6:45 pm
Posts: 3
Location: yellow river institute of hydraulic research
Thanks,kate.
I searched other messages and finally add '#define UV_LDRAG' in upwelling.h.
After rebuild, it is work now.


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PostPosted: Sun Aug 04, 2019 4:21 pm 
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Joined: Wed Feb 26, 2003 4:41 pm
Posts: 1081
Location: IMCS, Rutgers University
The default upwelling example in ROMS test repository has UV_QDRAG activated in the build script. If you notice, there are various options in build_roms.sh:
Code:
# can be used to write time-averaged fields. Notice that you can have as
# many definitions as you want by appending values.

 setenv MY_CPP_FLAGS "${MY_CPP_FLAGS} -DAVERAGES"
 setenv MY_CPP_FLAGS "${MY_CPP_FLAGS} -DDIAGNOSTICS_TS"
 setenv MY_CPP_FLAGS "${MY_CPP_FLAGS} -DDIAGNOSTICS_UV"
 setenv MY_CPP_FLAGS "${MY_CPP_FLAGS} -DSTATIONS"
 setenv MY_CPP_FLAGS "${MY_CPP_FLAGS} -DFLOATS"
#setenv MY_CPP_FLAGS "${MY_CPP_FLAGS} -DFLOAT_OYSTER"
 setenv MY_CPP_FLAGS "${MY_CPP_FLAGS} -DFLOAT_VWALK"

#setenv MY_CPP_FLAGS "${MY_CPP_FLAGS} -DDEBUGGING"
#setenv MY_CPP_FLAGS "${MY_CPP_FLAGS} -DOUT_DOUBLE"
#setenv MY_CPP_FLAGS "${MY_CPP_FLAGS} -DPOSITIVE_ZERO"

 setenv MY_CPP_FLAGS "${MY_CPP_FLAGS} -DUV_VIS2"
#setenv MY_CPP_FLAGS "${MY_CPP_FLAGS} -DUV_VIS4"
 setenv MY_CPP_FLAGS "${MY_CPP_FLAGS} -DMIX_S_UV"
#setenv MY_CPP_FLAGS "${MY_CPP_FLAGS} -DMIX_GEO_UV"

 setenv MY_CPP_FLAGS "${MY_CPP_FLAGS} -DTS_DIF2"
 setenv MY_CPP_FLAGS "${MY_CPP_FLAGS} -DMIX_S_TS"
#setenv MY_CPP_FLAGS "${MY_CPP_FLAGS} -DMIX_GEO_TS"

#setenv MY_CPP_FLAGS "${MY_CPP_FLAGS} -DUV_LOGDRAG"
#setenv MY_CPP_FLAGS "${MY_CPP_FLAGS} -DUV_LDRAG"
 setenv MY_CPP_FLAGS "${MY_CPP_FLAGS} -DUV_QDRAG"
#setenv MY_CPP_FLAGS "${MY_CPP_FLAGS} -DUV_DRAG_GRID"
#setenv MY_CPP_FLAGS "${MY_CPP_FLAGS} -DANA_DRAG"

 setenv MY_CPP_FLAGS "${MY_CPP_FLAGS} -DTS_U3HADVECTION"
 setenv MY_CPP_FLAGS "${MY_CPP_FLAGS} -DTS_C4VADVECTION"
#setenv MY_CPP_FLAGS "${MY_CPP_FLAGS} -DTS_MPDATA"

 setenv MY_CPP_FLAGS "${MY_CPP_FLAGS} -DBIO_FENNEL"
#setenv MY_CPP_FLAGS "${MY_CPP_FLAGS} -DECOSIM"
#setenv MY_CPP_FLAGS "${MY_CPP_FLAGS} -DNEMURO"
#setenv MY_CPP_FLAGS "${MY_CPP_FLAGS} -DNPZD_FRANKS"
#setenv MY_CPP_FLAGS "${MY_CPP_FLAGS} -DNPZD_IRON"
#setenv MY_CPP_FLAGS "${MY_CPP_FLAGS} -DNPZD_POWELL"

#setenv MY_CPP_FLAGS "${MY_CPP_FLAGS} -DGLS_MIXING"
#setenv MY_CPP_FLAGS "${MY_CPP_FLAGS} -DMY25_MIXING"

The strategy here is to play with several options in the build script and not modifying header file upwelling.h. Of course, you need to have some knowledge of ROMS and be able to read the standard file and assimilate what in ROMS is telling you. It needs a scheme for bottom friction! and you commented it out UV_QDRAG for some reason.

:idea: It is that simple, and you need to pay attention to what you are modifying.


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