ERROR M50: component_mod:check_fields NaN found in ATM instance

[oleson]

Yes, you would need the IHIST compset.

 

[LIN]

Hi @oleson and @kaeritai,
Yes, I think the problem came from corrupt atmospheric Precipitation files. I noticed that some files were really small compared to the average monthly GSWP precipitation files that were around 248M. @kaeritai can you check that your files are all good?
In my case I had to redownload the specific corrupt files with the command: check_input_data –download and it solved the error we were mentioning:
component_mod:check_fields NaN found in ATM instance: 1 field Faxa_rainc 1d
I hope this can help!
Gabriel

hi @Gabriel.Hes and @oleson
I have what looks like the same problem you have. However, your solution may not be suitable for me. I have checked my input data, and they are all normal values and regular data sizes compared with GSWP3 data.

 ERROR: component_mod:check_fields NaN found in ATM instance:    1 field Sa_u 1d global index:    11669
 ERROR: component_mod:check_fields NaN found in ATM instance:    1 field Sa_u 1d global index:    23337
 ERROR: component_mod:check_fields NaN found in ATM instance:    1 field Sa_u 1d global index:    35005
 ERROR: component_mod:check_fields NaN found in ATM instance:    1 field Sa_u 1d global index:    46673
 ERROR: component_mod:check_fields NaN found in ATM instance:    1 field Sa_u 1d global index:    58341

and I checked the input data, nothing seems to be wrong.


my atm forcing data head file:

default) [user@cesm2.2 SSP126_SP_QTP_0.125_04262]$ ncdump -h ~/cesmlab/CMFD_modify/Precip/prec_ITPCAS-CMFD_V0106_B-01_03hr_010deg_200002.nc
netcdf prec_ITPCAS-CMFD_V0106_B-01_03hr_010deg_200003 {
dimensions:
        scalar = 1 ;
        lon = 700 ;
        lat = 400 ;
        time = 248 ;
variables:
        float time(time) ;
                time:long_name = "observation time" ;
                time:units = "days since 2000-03-01 00:00:00" ;
                time:calendar = "noleap" ;
        float LONGXY(lat, lon) ;
                LONGXY:long_name = "longitude" ;
                LONGXY:units = "degrees_east" ;
                LONGXY:modes = "time-invariant" ;
        float LATIXY(lat, lon) ;
                LATIXY:long_name = "latitude" ;
                LATIXY:units = "degrees_north" ;
                LATIXY:modes = "time-invariant" ;
        float EDGEE(scalar) ;
                EDGEE:long_name = "eastern edge in atmospheric data" ;
                EDGEE:units = "degrees_east" ;
                EDGEE:modes = "time-invariant" ;
        float EDGEW(scalar) ;
                EDGEW:long_name = "western edge in atmospheric data" ;
                EDGEW:units = "degrees_west" ;
                EDGEW:modes = "time-invariant" ;
        float EDGES(scalar) ;
                EDGES:long_name = "southern edge in atmospheric data" ;
                EDGES:units = "degrees_south" ;
                EDGES:modes = "time-invariant" ;
        float EDGEN(scalar) ;
                EDGEN:long_name = "northern edge in atmospheric data" ;
                EDGEN:units = "degrees_north" ;
                EDGEN:modes = "time-invariant" ;
        float PRECTmms(time, lat, lon) ;
                PRECTmms:long_name = "PRECTmms total precipitation" ;
                PRECTmms:units = "mm H2O / sec" ;
                PRECTmms:modes = "time-dependent" ;
                PRECTmms:_FillValue = -32767.f ;
                PRECTmms:missing_value = -32767. ;
}

and my domain file of my own atm forcing data as follows:

netcdf domain.lnd.CMFD-ALL-noocean-230419 {
dimensions:
        n = 280000 ;
        ni = 700 ;
        nj = 400 ;
        nv = 4 ;
variables:
        double xc(nj, ni) ;
                xc:long_name = "longitude of grid cell center" ;
                xc:units = "degrees_east" ;
                xc:bounds = "xv" ;
        double yc(nj, ni) ;
                yc:long_name = "latitude of grid cell center" ;
                yc:units = "degrees_north" ;
                yc:bounds = "yv" ;
        double xv(nj, ni, nv) ;
                xv:long_name = "longitude of grid cell verticies" ;
                xv:units = "degrees_east" ;
        double yv(nj, ni, nv) ;
                yv:long_name = "latitude of grid cell verticies" ;
                yv:units = "degrees_north" ;
        int mask(nj, ni) ;
                mask:long_name = "domain mask" ;
                mask:note = "unitless" ;
                mask:coordinates = "xc yc" ;
                mask:comment = "0 value indicates cell is not active" ;
        double area(nj, ni) ;
                area:long_name = "area of grid cell in radians squared" ;
                area:coordinates = "xc yc" ;
                area:units = "radian2" ;
        double frac(nj, ni) ;
                frac:long_name = "fraction of grid cell that is active" ;
                frac:coordinates = "xc yc" ;
                frac:note = "unitless" ;
                frac:filter1 = "error if frac> 1.0+eps or frac < 0.0-eps; eps = 0.1000000E-11" ;
                frac:filter2 = "limit frac to [fminval,fmaxval]; fminval= 0.1000000E-02 fmaxval=  1.000000" ;

// global attributes:
                :title = "CESM domain data:" ;
                :Conventions = "CF-1.0" ;
                :source_code = "SVN $Id: gen_domain.F90 65202 2014-11-06 21:07:45Z mlevy@ucar.edu $" ;
                :SVN_url = " $URL: https://svn-ccsm-models.cgd.ucar.edu/tools/mapping/gen_domain/trunk/src/gen_domain.F90 $" ;
                :Compiler_Optimized = "TRUE" ;
                :hostname = "mgt" ;
                :history = "created by lmw, 2023-04-19 21:25:39" ;
                :source = "/gpfs/gpfs_fs/home/lmw/clm5.0/tools/mkmapdata/map_CMFD-ALL_noocean_to_CMFD-ALL_nomask_aave_da_230419.nc" ;
                :map_domain_a = "/gpfs/gpfs_fs/home/lmw/clm5.0/tools/mkmapgrids/SCRIPgrid_CMFD-ALL_noocean_c230419.nc" ;
                :map_domain_b = "/gpfs/gpfs_fs/home/lmw/clm5.0/tools/mkmapgrids/SCRIPgrid_CMFD-ALL_nomask_c230419.nc" ;
                :map_grid_file_ocn = "/gpfs/gpfs_fs/home/lmw/clm5.0/tools/mkmapgrids/SCRIPgrid_CMFD-ALL_noocean_c230419.nc" ;
                :map_grid_file_atm = "/gpfs/gpfs_fs/home/lmw/clm5.0/tools/mkmapgrids/SCRIPgrid_CMFD-ALL_nomask_c230419.nc" ;
}

My log file is in the attachment. I hope you will give me some advice. I am profoundly grateful!

 

[oleson]

Sa_u is wind (u-component). So you should check the values of wind in your forcing files. And make sure that there are valid values for all of the forcing data where the domain file has a mask value of 1.

 

[LIN]

Thank you, @oleson, I have solved this question!

 

[LiwenWu]

Thank you, @oleson, I have solved this question!

Hi Lin, We are using the same forcing dataset —— CMFD, and I have encountered the same error as you. Could you please tell me how how you solved this problem？My forcing dataset has NaN value after processing. Does this cause the error?