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ERROR M50: component_mod:check_fields NaN found in ATM instance

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xueyanzhang520@...
ERROR M50: component_mod:check_fields NaN found in ATM instance

Hi, I only run CLM50 and build it successfully. However, when I ./case.submit, there is an error and the cesm.log showed:

84  (t_initf) Read in prof_inparm namelist from: drv_in

 85  (t_initf) Using profile_disable=          F

 86  (t_initf)       profile_timer=                      4

 87  (t_initf)       profile_depth_limit=                4

 88  (t_initf)       profile_detail_limit=               2

 89  (t_initf)       profile_barrier=          F

 90  (t_initf)       profile_outpe_num=                  1

 91  (t_initf)       profile_outpe_stride=               0

 92  (t_initf)       profile_single_file=      F

 93  (t_initf)       profile_global_stats=     T

 94  (t_initf)       profile_ovhd_measurement= F

 95  (t_initf)       profile_add_detail=       F

 96  (t_initf)       profile_papi_enable=      F

 97  ERROR:

 98  component_mod:check_fields NaN found in ATM instance:    1 field Sa_dens 1d glo

 99  bal index:     4578

100  ERROR:

101  component_mod:check_fields NaN found in ATM instance:    1 field Sa_dens 1d glo

102  bal index:     6782

103  ERROR:

104  component_mod:check_fields NaN found in ATM instance:    1 field Sa_dens 1d glo

105  bal index:     9155

106  ERROR:

107  component_mod:check_fields NaN found in ATM instance:    1 field Sa_dens 1d glo

108  bal index:    11344

109  ERROR:

110  component_mod:check_fields NaN found in ATM instance:    1 field Sa_dens 1d glo

111  bal index:    12538

112  ERROR:

113  component_mod:check_fields NaN found in ATM instance:    1 field Sa_dens 1d glo

114  bal index:    14727

115  ERROR:

116  component_mod:check_fields NaN found in ATM instance:    1 field Sa_dens 1d glo

117  bal index:     3392

118  ERROR:

119  component_mod:check_fields NaN found in ATM instance:    1 field Sa_dens 1d glo

120  bal index:     5772

121  ERROR:

122  component_mod:check_fields NaN found in ATM instance:    1 field Sa_dens 1d glo

123  bal index:    15921

124  ERROR:

125  component_mod:check_fields NaN found in ATM instance:    1 field Sa_dens 1d glo

126  bal index:    17115

127  ERROR:

128  component_mod:check_fields NaN found in ATM instance:    1 field Sa_dens 1d glo

129  bal index:    18110

130  ERROR:

131  component_mod:check_fields NaN found in ATM instance:    1 field Sa_dens 1d glo

132  bal index:    19304

133  ERROR:

134  component_mod:check_fields NaN found in ATM instance:    1 field Sa_dens 1d glo

135  bal index:    21493

136  ERROR:

137  component_mod:check_fields NaN found in ATM instance:    1 field Sa_dens 1d glo

138  bal index:    22687

139  ERROR:

140  component_mod:check_fields NaN found in ATM instance:    1 field Sa_dens 1d glo

141  bal index:    24876

 

I dont know this is because my forcing data or clm.

 

Work hard

oleson

This is an atm forcing data problem.  Sa_dens is air density.

xueyanzhang520@...

Hi, Thanks for reply! But forcing data does not include air density, this variable. It only has radiation, wind, humidity...

Work hard

oleson

What atmospheric forcing dataset are you using?

xueyanzhang520@...

NLDAS-2 forcing product

Work hard

oleson

If you are using 'CLMNCEP' mode for your forcing, then air density is calculated in cime/src/components/data_comps/datm/datm_comp_mod.F90 as:

 

          !--- density ---

          vp = (a2x%rAttr(kshum,n)*pbot) / (0.622_R8 + 0.378_R8 * a2x%rAttr(kshum,n))

          a2x%rAttr(kdens,n) = (pbot - 0.378_R8 * vp) / (tbot*rdair)

 

So maybe some combination of humidity, pressure, temperature is giving you a bad value of density?

xueyanzhang520@...

I used CLMNCEP! I saw air temperature used in this formula! So Can I have missing values in my forcing data to drive CLM model because I think this error maybe due to missing values of air temeprature from NLDAS-2

Work hard

oleson

Yes, that's possible.

xueyanzhang520@...

I checked the missing values in NLDAS data and set it as _Fillvalue (-1.e+36). I run the model again, but I found another error: 

2548  NetCDF: Variable not found

2549  ENDRUN:

2550  ENDRUN:

2551  lnd_import                       ERROR: Longwave down sent from the atmosphere

2552  model is negative or zero

2553  ERROR: Unknown error submitted to shr_abort_abort.

2554  ENDRUN:

2555  lnd_import                       ERROR: Longwave down sent from the atmosphere

2556  model is negative or zero

2557  ERROR: Unknown error submitted to shr_abort_abort.

2558  lnd_import                       ERROR: Longwave down sent from the atmosphere

2559  ENDRUN:

2560  lnd_import                       ERROR: Longwave down sent from the atmosphere

2561  model is negative or zero

2562  ERROR: Unknown error submitted to shr_abort_abort.

2563  model is negative or zero

2564  ERROR: Unknown error submitted to shr_abort_abort.

2565  ENDRUN:

 

 

Work hard

oleson

Maybe your domain file is not consistent with the NLDAS2 data.  The "mask" field on that file should have ones where there is valid forcing data and zeros where there is not.

The model is probably interpreting -1.e36 as a valid downward longwave value (longwave down sent from the atmosphere is negative or zero).

xueyanzhang520@...

Hi, I asked my fellow and they told me to use this command cdo fillmiss2 input.file output.file to replace all missing values. It works now! Thank you very much!

Work hard

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