Error in ROMS execution

[cloudy4568]

Hi all,

I am running my customized example for the first time. The source code I use is Kate's trunk (https://github.com/kshedstrom/roms.git), and the grid file, forcing files, boundary and initial files are prepared. The error is:

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 READ_PHYPAR - Variable index not yet loaded, idpthR
 Found Error: 05   Line: 162      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:  81x59x11  tiling: 1x1

     tile          Dynamic        Automatic            USAGE

        0             1.00             0.97             1.97

    TOTAL             1.00             0.97             1.97

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

 ROMS/TOMS - Output NetCDF summary for Grid 01:
 Found Error: 05   Line: 443      Source: ROMS/Utility/close_io.F

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


 ERROR: Illegal model configuration.

I have replaced the varinfo.dat for the newest version, the error still exists and is:

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READ_PHYPAR - Variable index not yet loaded, idUairE

Do you know how to solve this? Thanks in advance.

[kate]

Oh, yeah, sorry. There needs to be a chunk in varinfo.dat with:

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'Uwind_eastward'                                   ! Output
  'eastward surface wind component at RHO-points'
  'meter second-1'                                 ! [m/s]
  'Uwind_eastward, scalar, series'
  'ocean_time'
  'idUairE'
  'r2dvar'
  1.0d0

'Vwind_northward'                                  ! Output
  'northward surface wind component at RHO-points'
  'meter second-1'                                 ! [m/s]
  'Vwind_northward, scalar, series'
  'ocean_time'
  'idVairN'
  'r2dvar'
  1.0d0

Rather than fight with Hernan's updates to varinfo.dat, I have my own versions in the Apps repository.

[cloudy4568]

Thank you Kate, this problem has been solved.

[cloudy4568]

Then there is another error:

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forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image              PC                Routine            Line        Source             
romsS              00000000009D6963  Unknown               Unknown  Unknown
libpthread-2.27.s  00007F83AFE81890  Unknown               Unknown  Unknown
romsS              00000000007DF325  inp_decode_mod_mp        1662  inp_decode.f90
romsS              000000000079968E  read_phypar_             1914  read_phypar.f90
romsS              00000000006AB0FA  inp_par_                   67  inp_par.f90
romsS              00000000004039B1  ocean_control_mod          73  ocean_control.f90
romsS              00000000004034FD  MAIN__                     73  master.f90
romsS              0000000000403382  Unknown               Unknown  Unknown
libc-2.27.so       00007F83AF89BB97  __libc_start_main     Unknown  Unknown
romsS              000000000040326A  Unknown               Unknown  Unknown

Do you have any idea about this error?

[kate]

Probaby, if you tell me what is on this line:

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 1914  read_phypar.f90

Note that this file is in the build directory.

[cloudy4568]

It is:

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      max_Ffiles=MAXVAL(nSSFfiles)
              allocate ( SSF(max_Ffiles,Ngrids) )
              allocate ( SSFids(max_Ffiles,Ngrids) )
              allocate ( NSSFcount(max_Ffiles,Ngrids) )
              SSFids(1:max_Ffiles,1:Ngrids)=-1
              NSSFcount(1:max_Ffiles,1:Ngrids)=0
            CASE ('SSFNAME')
              label='SSF - Sources/Sinks forcing fields'
              Npts=load_s2d(Nval, Cval, Cdim, line, label, issffile,    &          ! LN 1914
     &                      igrid, Ngrids, nSSFfiles, NSSFcount,        &
     &                      max_Ffiles, SSF)
            CASE ('TIDENAME')
              label='TIDE - Tidal forcing fields'
              Npts=load_s1d(Nval, Cval, Cdim, line, label, igrid,       &
     &                      Nfiles, TIDE)

[kate]

You need to set NSSFFILES in your roms.in file, such as:

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    NSSFFILES == 2                          ! number of boundary files
     SSFNAME == /center1/AKWATERS/kshedstrom/Chukchi/Files/JRA_Chukchi_rivers_1993.nc |
                /center1/AKWATERS/kshedstrom/Chukchi/Files/JRA_Chukchi_rivers_1994.nc |
                /center1/AKWATERS/kshedstrom/Chukchi/Files/JRA_Chukchi_rivers_1995.nc \
                /center1/AKWATERS/kshedstrom/Chukchi/Files/river_tracers.nc

If you try to set SSFNAME first, it hasn't allocated the necessary arrays yet. This is a change in my code from the trunk.

[cloudy4568]

Thank you, Kate. Then there is another error,

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 Tile partition information for Grid 01:  81x59x11  tiling: 1x1

     tile     Istr     Iend     Jstr     Jend     Npts

 Number of tracers:            2
        0        1       81        1       59    52569

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

     tile     Xmin     Xmax     Ymin     Ymax     grid

        0     0.50    81.50     0.50    59.50  RHO-points

        0     0.00    81.00     0.50    59.50    U-points

        0     0.50    81.50     0.00    59.00    V-points

 READ_IcePar - variable info not yet loaded, idUiceE

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

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

 zeta                     1   Closed       Closed       Chapman Exp  Closed

 ubar                     1   Closed       Closed       Shchepetkin  Closed

 vbar                     1   Closed       Closed       Shchepetkin  Closed

 u                        1   Closed       Closed       Rad + Nud    Closed

 v                        1   Closed       Closed       Rad + Nud    Closed

 temp                     1   Closed       Closed       Closed       Closed

 salt                     1   Closed       Closed       Closed       Closed

 tke                      1   Closed       Closed       Closed       Closed

 uice                     1   Closed       Closed       Closed       Closed

 vice                     1   Gradient     Gradient     Gradient     Gradient

 aice                     1   Closed       Closed       Closed       Closed

 hice                     1   Closed       Closed       Closed       Closed

 tisrf                    1   Closed       Closed       Closed       Closed

 snow_thick               1   Closed       Closed       Closed       Closed

  1ClosedClosedClosedClosed

  1ClosedClosedClosedClosed

 sig11                    1   Closed       Closed       Closed       Closed

 sig12                    1   Closed       Closed       Closed       Closed

 sig22                    1   Closed       Closed       Closed       Closed
 Found Error: 05   Line: 855      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:  81x59x11  tiling: 1x1

     tile          Dynamic        Automatic            USAGE

        0             1.00             3.83             4.83

    TOTAL             1.00             3.83             4.83

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

 ROMS/TOMS - Output NetCDF summary for Grid 01:
 Found Error: 05   Line: 443      Source: ROMS/Utility/close_io.F

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


 ERROR: Illegal model configuration.

I have turned LuvSrc, LwSrc and LtracerSrc all F(no river.nc input). Others are almost the same with your NWGOA example.

[kate]

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READ_IcePar - variable info not yet loaded, idUiceE

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'uice_eastward'                                    ! Output
  'ice eastward momentum component at RHO-points'
  'meter second-1'                                 ! [m/s]
  'uice_eastward, scalar, series'
  'ocean_time'
  'idUiceE'
  'r2dvar'
  1.0d0

'vice_northward'                                   ! Output
  'ice northward momentum component at RHO-points'
  'meter second-1'                                 ! [m/s]
  'vice_northward, scalar, series'
  'ocean_time'
  'idViceN'
  'r2dvar'
  1.0d0

[cloudy4568]

Thank you, Kate! I have replaced varinfo.dat with the one in your Apps repository. But another error happened:

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

 GET_GRID - unable to open grid NetCDF file: wtype_grid

 GET_GRID - unable to open grid NetCDF file: /home/cyue/cyue/bohai/data/bohai24.nc
 Found Error: 02   Line: 301      Source: ROMS/Nonlinear/initial.F
 Found Error: 02   Line: 188      Source: ROMS/Drivers/nl_ocean.h

 Elapsed CPU time (seconds):

 Thread #    0 CPU:       0.027
 Total:                   0.027

 Nonlinear ocean model elapsed time profile, Grid: 01

  Allocation and array initialization ..............         0.027  (99.0968 %)
                                              Total:         0.027   99.0968

  Unique code regions profiled .....................         0.027   99.0968 %
  Residual, non-profiled code ......................         0.000    0.9032 %


 All percentages are with respect to total time =            0.027


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

 Dynamic and Automatic memory (MB) usage for Grid 01:  81x59x11  tiling: 1x1

     tile          Dynamic        Automatic            USAGE

        0            33.37             3.83            37.20

    TOTAL            33.37             3.83            37.20

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

 ROMS/TOMS - Output NetCDF summary for Grid 01:
 Found Error: 02   Line: 443      Source: ROMS/Utility/close_io.F

 ROMS/TOMS - Input error ............. exit_flag:   2


 ERROR: Abnormal termination: NetCDF INPUT.
 REASON: No error                                              

I have checked my grid NC file, it's good and I can open it with ncview. What is wtype_grid? Should I 'undef wtype_grid' in the .h file?

[robertson]

Are you sure that the grid file is at /home/cyue/cyue/bohai/data? It looks like your username (cyue) is doubled in there.

[cloudy4568]

Thank you, but I think the path is right. And I have modified the grid NC file already, last time the error is that it can't find 'xl' in the grid NC file, then I added it to the NC file.

[kate]

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GET_GRID - unable to open grid NetCDF file: wtype_grid

I am adding this field to the grid file and it is saying you are missing the field. You can turn off having a spatially variable water type or you can provide the field. I set it as a function of depth using the attached script.