ERROR: Abnormal termination: NetCDF OUTPUT

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remit
Posts: 15
Joined: Mon Jun 21, 2021 12:40 pm
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ERROR: Abnormal termination: NetCDF OUTPUT

#1 Unread post by remit »

After struggling in the compilation process finally arrived at the running stage. Now, I'm facing problems when running ROMS with:

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./romsS < ocean_sea.in
here is a snippet of the resulting error:

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 .
 .
 .
 Process Information:

 Thread #    0 (pid=   10262) is active.

 INITIAL: Configuring and initializing forward nonlinear model ...
 *******
 GET_GRID - Illegal output type, io_type = 0
 Found Error: 03   Line: 91       Source: ROMS/Utility/get_grid.F
 Found Error: 03   Line: 85       Source: ROMS/Utility/set_grid.F
 GET_STATE - Illegal output type, io_type = 0
 Found Error: 03   Line: 151      Source: ROMS/Utility/get_state.F
 Found Error: 03   Line: 416      Source: ROMS/Nonlinear/initial.F
 Found Error: 03   Line: 197      Source: ROMS/Drivers/nl_roms.h, ROMS_initialize

Elapsed wall CPU time for each process (seconds):

 Thread #    0 CPU:       0.009
 Total:                   0.009

 Nonlinear model elapsed CPU time profile, Grid: 01

  Allocation and array initialization ..............         0.008  (92.7778 %)
                                              Total:         0.008   92.7778 %

  Unique kernel(s) regions profiled ................         0.008   92.7778 %
  Residual, non-profiled code ......................         0.001    7.2222 %


 All percentages are with respect to total time =            0.009


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

 Dynamic and Automatic memory (MB) usage for Grid 01:  85x63x16  tiling: 1x1

     tile          Dynamic        Automatic            USAGE

        0            20.38             3.01            23.39

    TOTAL            20.38             3.01            23.39

<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 Found Error: 03   Line: 85       Source: ROMS/Utility/close_io.F, close_file_nf90
 Found Error: 03   Line: 85       Source: ROMS/Utility/close_io.F, close_file_nf90
 Found Error: 03   Line: 85       Source: ROMS/Utility/close_io.F, close_file_nf90
 Found Error: 03   Line: 85       Source: ROMS/Utility/close_io.F, close_file_nf90

 ROMS/TOMS - Output NetCDF summary for Grid 01:
 Found Error: 03   Line: 401      Source: ROMS/Utility/close_io.F, close_out

 ROMS/TOMS - Output error ............ exit_flag: 3


 ERROR: Abnormal termination: NetCDF OUTPUT.
 REASON: No error
ERROR STOP

Error termination. Backtrace:
#0  0x7fc48ecdcad0 in ???
#1  0x7fc48ecdd649 in ???
#2  0x7fc48ecdecb7 in ???
#3  0x55e85ab4ea76 in ???
#4  0x7fc48e8b6d8f in ???
#5  0x7fc48e8b6e3f in ???
#6  0x55e85ab4eac4 in ???
#7  0xffffffffffffffff in ???
any somebody helps me to solve this problem? :(
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arango
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Re: ERROR: Abnormal termination: NetCDF OUTPUT

#2 Unread post by arango »

ROMS is telling what is wrong:
GET_GRID - Illegal output type, io_type = 0
I believe that your roms.in is old and missing several parameters. For Example, you need to have logic for I/O:

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! Input and Output files processing library to use:
!
!   [1] Standard NetCDF-3 or NetCDF-4 library
!   [2] Serial or Parallel I/O with Parallel-IO (PIO) library (MPI only)

     INP_LIB =  1
     OUT_LIB =  1
and so on...

Update your roms.in to the latest version.
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remit
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Re: ERROR: Abnormal termination: NetCDF OUTPUT

#3 Unread post by remit »

tks arango for your replay, now I have a new problem about time forcing data:

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'
'
'
'
MULTIFILE_INFO_S2D - Error while processing forcing multi-files:
                      data does not include initialization time = 2022-09-01 12:00:00.00

 Found Error: 04   Line: 481      Source: ROMS/Utility/check_multifile.F, multifile_info_s2d
 Found Error: 04   Line: 188      Source: ROMS/Utility/check_multifile.F
 Found Error: 04   Line: 656      Source: ROMS/Nonlinear/initial.F
 Found Error: 04   Line: 197      Source: ROMS/Drivers/nl_roms.h, ROMS_initialize

Elapsed wall CPU time for each process (seconds):

 Thread #    0 CPU:       0.646
 Total:                   0.646

 Nonlinear model elapsed CPU time profile, Grid: 01

  Allocation and array initialization ..............         0.332  (51.3562 %)
  2D/3D coupling, vertical metrics .................         0.025  ( 3.8663 %)
  Omega vertical velocity ..........................         0.008  ( 1.1965 %)
  Equation of state for seawater ...................         0.027  ( 4.1328 %)
                                              Total:         0.391   60.5517 %

  Unique kernel(s) regions profiled ................         0.391   60.5517 %
  Residual, non-profiled code ......................         0.255   39.4483 %


 All percentages are with respect to total time =            0.646


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

 Dynamic and Automatic memory (MB) usage for Grid 01:  185x186x70  tiling: 2x2

     tile          Dynamic        Automatic            USAGE

        0           538.58            19.97           558.55
        1             0.00            19.97            19.97
        2             0.00            19.97            19.97
        3             0.00            19.97            19.97

    TOTAL           538.58            79.87           618.45

<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 Found Error: 04   Line: 85       Source: ROMS/Utility/close_io.F, close_file_nf90
 Found Error: 04   Line: 85       Source: ROMS/Utility/close_io.F, close_file_nf90
 Found Error: 04   Line: 85       Source: ROMS/Utility/close_io.F, close_file_nf90
 Found Error: 04   Line: 85       Source: ROMS/Utility/close_io.F, close_file_nf90

 ROMS/TOMS - Output NetCDF summary for Grid 01:
 Found Error: 04   Line: 401      Source: ROMS/Utility/close_io.F, close_out

 ROMS/TOMS - I/O error ............... exit_flag: 4


 ERROR: I/O related problem.
Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG
ERROR STOP

Error termination. Backtrace:
#0  0x7f3c804baad0 in ???
#1  0x7f3c804bb649 in ???
#2  0x7f3c804bccb7 in ???
#3  0x55b289aeda76 in ???
#4  0x7f3c80092d8f in ???
#5  0x7f3c80092e3f in ???
#6  0x55b289aedac4 in ???
#7  0xffffffffffffffff in ???
iuse 7 forcing data, namely:

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     NFFILES == 7                          ! number of unique forcing files

     FRCNAME == 	/mnt/c/Users/User/OneDrive/Desktop/ROMS_BALI/atm_forcing/lwrad_era5.nc | 
			/mnt/c/Users/User/OneDrive/Desktop/ROMS_BALI/atm_forcing/Pair_era5.nc |
			/mnt/c/Users/User/OneDrive/Desktop/ROMS_BALI/atm_forcing/Qair_era5.nc |
			/mnt/c/Users/User/OneDrive/Desktop/ROMS_BALI/atm_forcing/rain_era5.nc |
			/mnt/c/Users/User/OneDrive/Desktop/ROMS_BALI/atm_forcing/swrad_era5.nc |
			/mnt/c/Users/User/OneDrive/Desktop/ROMS_BALI/atm_forcing/Tair_era5.nc |
			/mnt/c/Users/User/OneDrive/Desktop/ROMS_BALI/atm_forcing/wind_era5.nc
this is the variable time from wind_era5 as an example:

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wind_time
           Size:       120x1
           Dimensions: wind_time
           Datatype:   double
           Attributes:
                       long_name = 'surface wind time'
                       units     = 'days since 1858-11-17 00:00:00'
                       calendar  = 'gregorian'
when I load the time using (in Matlab),

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time=ncread('wind_era5.nc','wind_time');
time1=datenum(1858,11,17,0,0,0)+time;
datestr(time1)
it will produce:

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ans =

  120×20 char array

    '01-Sep-2022 00:00:00'
    '01-Sep-2022 01:00:00'
    '01-Sep-2022 02:00:00'
    '01-Sep-2022 03:00:00'
    '01-Sep-2022 04:00:00'
    '01-Sep-2022 05:00:00'
    '01-Sep-2022 06:00:00'
    '01-Sep-2022 07:00:00'
    '01-Sep-2022 08:00:00'
    '01-Sep-2022 09:00:00'
    '01-Sep-2022 10:00:00'
    '01-Sep-2022 11:00:00'
    '01-Sep-2022 12:00:00'
    '01-Sep-2022 13:00:00'
    '01-Sep-2022 14:00:00'
    '01-Sep-2022 15:00:00'
    '01-Sep-2022 16:00:00'
    '01-Sep-2022 17:00:00'
    '01-Sep-2022 18:00:00'
    '01-Sep-2022 19:00:00'
    '01-Sep-2022 20:00:00'
    '01-Sep-2022 21:00:00'
    '01-Sep-2022 22:00:00'
    '01-Sep-2022 23:00:00'
    '02-Sep-2022 00:00:00'
    '02-Sep-2022 01:00:00'
    '02-Sep-2022 02:00:00'
    '02-Sep-2022 03:00:00'
    '02-Sep-2022 04:00:00'
    '02-Sep-2022 05:00:00'
    '02-Sep-2022 06:00:00'
    '02-Sep-2022 07:00:00'
    '02-Sep-2022 08:00:00'
    '02-Sep-2022 09:00:00'
    '02-Sep-2022 10:00:00'
    '02-Sep-2022 11:00:00'
    '02-Sep-2022 12:00:00'
    '02-Sep-2022 13:00:00'
    '02-Sep-2022 14:00:00'
    '02-Sep-2022 15:00:00'
    '02-Sep-2022 16:00:00'
    '02-Sep-2022 17:00:00'
    '02-Sep-2022 18:00:00'
    '02-Sep-2022 19:00:00'
    '02-Sep-2022 20:00:00'
    '02-Sep-2022 21:00:00'
    '02-Sep-2022 22:00:00'
    '02-Sep-2022 23:00:00'
    '03-Sep-2022 00:00:00'
    '03-Sep-2022 01:00:00'
    '03-Sep-2022 02:00:00'
    '03-Sep-2022 03:00:00'
    '03-Sep-2022 04:00:00'
    '03-Sep-2022 05:00:00'
    '03-Sep-2022 06:00:00'
    '03-Sep-2022 07:00:00'
    '03-Sep-2022 08:00:00'
    '03-Sep-2022 09:00:00'
    '03-Sep-2022 10:00:00'
    '03-Sep-2022 11:00:00'
    '03-Sep-2022 12:00:00'
    '03-Sep-2022 13:00:00'
    '03-Sep-2022 14:00:00'
    '03-Sep-2022 15:00:00'
    '03-Sep-2022 16:00:00'
    '03-Sep-2022 17:00:00'
    '03-Sep-2022 18:00:00'
    '03-Sep-2022 19:00:00'
    '03-Sep-2022 20:00:00'
    '03-Sep-2022 21:00:00'
    '03-Sep-2022 22:00:00'
    '03-Sep-2022 23:00:00'
    '04-Sep-2022 00:00:00'
    '04-Sep-2022 01:00:00'
    '04-Sep-2022 02:00:00'
    '04-Sep-2022 03:00:00'
    '04-Sep-2022 04:00:00'
    '04-Sep-2022 05:00:00'
    '04-Sep-2022 06:00:00'
    '04-Sep-2022 07:00:00'
    '04-Sep-2022 08:00:00'
    '04-Sep-2022 09:00:00'
    '04-Sep-2022 10:00:00'
    '04-Sep-2022 11:00:00'
    '04-Sep-2022 12:00:00'
    '04-Sep-2022 13:00:00'
    '04-Sep-2022 14:00:00'
    '04-Sep-2022 15:00:00'
    '04-Sep-2022 16:00:00'
    '04-Sep-2022 17:00:00'
    '04-Sep-2022 18:00:00'
    '04-Sep-2022 19:00:00'
    '04-Sep-2022 20:00:00'
    '04-Sep-2022 21:00:00'
    '04-Sep-2022 22:00:00'
    '04-Sep-2022 23:00:00'
    '05-Sep-2022 00:00:00'
    '05-Sep-2022 01:00:00'
    '05-Sep-2022 02:00:00'
    '05-Sep-2022 03:00:00'
    '05-Sep-2022 04:00:00'
    '05-Sep-2022 05:00:00'
    '05-Sep-2022 06:00:00'
    '05-Sep-2022 07:00:00'
    '05-Sep-2022 08:00:00'
    '05-Sep-2022 09:00:00'
    '05-Sep-2022 10:00:00'
    '05-Sep-2022 11:00:00'
    '05-Sep-2022 12:00:00'
    '05-Sep-2022 13:00:00'
    '05-Sep-2022 14:00:00'
    '05-Sep-2022 15:00:00'
    '05-Sep-2022 16:00:00'
    '05-Sep-2022 17:00:00'
    '05-Sep-2022 18:00:00'
    '05-Sep-2022 19:00:00'
    '05-Sep-2022 20:00:00'
    '05-Sep-2022 21:00:00'
    '05-Sep-2022 22:00:00'
    '05-Sep-2022 23:00:00'
and from this result, I don't know why ROMS produces error data does not include initialization time = 2022-09-01 12:00:00.00
even though the forcing data that I use is appropriate, i.e. 1 September 2022 to 5 September 2022.

Tks
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wilkin
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Re: ERROR: Abnormal termination: NetCDF OUTPUT

#4 Unread post by wilkin »

The "|" character is used to effectively concatenate files with sequential time records, e.g. one year at a time. When this is used it counts as only one file.

You should use the "\" character to end one file and go to the next, with a different variable, in a list.

What you have given is equivalent to one file NFFILES ==1 broken into pieces.

See the documentation at the top of the file:

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! Continuation lines in a parameter specification are allowed and must be 
! preceded by a backslash (\). 
! ...
!
! Multiple NetCDF files are allowed for input field(s).  This is useful when  !
! splitting input data (climatology,  boundary,  forcing)  time records into  !
! several files (say monthly, annual, etc). In this case, each multiple file  !
! entry line needs to be ended by the vertical bar (|) symbol. For example:   !
!                                                                             !
!    NFFILES == 7                          ! number of forcing files          !
!                                                                             !
!    FRCNAME == my_tides.nc       \                                           !
!               my_lwrad_year1.nc |                                           !
!               my_lwrad_year2.nc \                                           !
!               my_swrad_year1.nc |                                           !
!               my_swrad_year2.nc \                                           !
!               my_winds_year1.nc |                                           !
!               my_winds_year2.nc \                                           !
!               my_Pair_year1.nc  |                                           !
!               my_Pair_year2.nc  \                                           !
!               my_Qair_year1.nc  |                                           !
!               my_Qair_year2.nc  \                                           !
!               my_Tair_year1.nc  |                                           !
!               my_Tair_year2.nc
John Wilkin: DMCS Rutgers University
71 Dudley Rd, New Brunswick, NJ 08901-8521, USA. ph: 609-630-0559 jwilkin@rutgers.edu
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remit
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Joined: Mon Jun 21, 2021 12:40 pm
Location: bmkg

Re: ERROR: Abnormal termination: NetCDF OUTPUT

#5 Unread post by remit »

tks for your replay Wilkin, so I simply changed the NFFILES to 1 and the error was gone :idea:

Now, I'm facing with the another error:

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.
.
.
REGRID - input gridded data does not contain model grid:

          Gridded:  LonMin =  110.0000 LonMax =  115.0000
                    LatMin =  -10.0000 LatMax =   -5.0000
          Model:    LonMin =  110.0000 LonMax =  115.0224
                    LatMin =  -10.0000 LatMax =   -4.9954
 Found Error: 04   Line: 354      Source: ROMS/Utility/get_2dfld.F, get_2dfld_nf90

 GET_2DFLD_NF90 - error while reading variable: Uwind   at TIME index = 12
 Found Error: 04   Line: 112      Source: ROMS/Utility/get_2dfld.F
 Found Error: 04   Line: 169      Source: ROMS/Nonlinear/get_data.F
 Found Error: 04   Line: 670      Source: ROMS/Nonlinear/initial.F
 Found Error: 04   Line: 197      Source: ROMS/Drivers/nl_roms.h, ROMS_initialize

Elapsed wall CPU time for each process (seconds):

 Thread #    0 CPU:       1.684
 Total:                   1.684
for the information, I'm using bathymetry+initial data (clim,ini, and boundary)+atmospheric forcing with the same grid which is:
Lon = [110 115] and Lat = [-5 -10].
But why the ROMS issue the value for LonMax and LatMax which differ slightly from the initial grid?
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wilkin
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Re: ERROR: Abnormal termination: NetCDF OUTPUT

#6 Unread post by wilkin »

Read the documentation.

The | joins files with the same variables that are broken into time segments.

You want \ which goes to the next file - here you have different variables in each file in a list. You have 7 files.
John Wilkin: DMCS Rutgers University
71 Dudley Rd, New Brunswick, NJ 08901-8521, USA. ph: 609-630-0559 jwilkin@rutgers.edu
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remit
Posts: 15
Joined: Mon Jun 21, 2021 12:40 pm
Location: bmkg

Re: ERROR: Abnormal termination: NetCDF OUTPUT

#7 Unread post by remit »

Nice, thank you Wilkin.
I thought the problem had a different solution but it can be solved easily. :D
Now I'm finishing running ROMs to completion. Thanks again for the solution
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