Real-data test case with v8.2.2

[climbfuji]

It's been a while since I last ran MPAS ....

I downloaded release v8.2.2 and compiled the atmosphere and init_atmosphere cores with standard options using gfortran. All modules provided by spack-stack (only had to set a handful of environment variables to find NetCDF, Parallel NetCDF, etc.).

Then, I downloaded the real-data test case from https://mpas-dev.github.io/atmosphere/real_data.html

I didn't modify any of the files, simply dropped the init_atmosphere executable in the directory:

> ls -l
total 388724
-rwxr-xr-x 1 dom dom 240628936 May 27  2014 CFSR:2010-10-23_00
-rw-r--r-- 1 dom dom  81131458 May 27  2014 cfsr.2010102300.tar.gz
lrwxrwxrwx 1 dom dom        57 Mar 11 14:09 init_atmosphere_model -> ../../../build/core-init-atmosphere/init_atmosphere_model
-rw-r--r-- 1 dom dom       578 Mar 11 14:12 log.init_atmosphere.0000.err
-rw-r--r-- 1 dom dom      4245 Mar 11 14:12 log.init_atmosphere.0000.out
-rw-r--r-- 1 dom dom      1774 Jun  8  2019 namelist.atmosphere
-rw-r--r-- 1 dom dom      2494 Jun  8  2019 namelist_files.tar.gz
-rw-r--r-- 1 dom dom      1381 Jun  8  2019 namelist.init_atmosphere
-rw-r--r-- 1 dom dom      1203 Jun  8  2019 stream_list.atmosphere.diagnostics
-rw-r--r-- 1 dom dom       927 Jun  8  2019 stream_list.atmosphere.output
-rw-r--r-- 1 dom dom         9 Jun  8  2019 stream_list.atmosphere.surface
-rw-r--r-- 1 dom dom      1568 Jun  8  2019 streams.atmosphere
-rw-r--r-- 1 dom dom       959 Jun  8  2019 streams.init_atmosphere

When I kick off the init_atmosphere run as a serial task, no MPI, I get the following error:

> cat log.init_atmosphere.0000.out
----------------------------------------------------------------------
Beginning MPAS-init_atmosphere Output Log File for task       0 of       1
    Opened at 2025/03/11 14:12:31
----------------------------------------------------------------------


 MPAS Init-Atmosphere Version 8.2.2


 Output from 'git describe --dirty': v8.2.2

 Compile-time options:
   Build target: gfortran
   OpenMP support: no
   OpenACC support: no
   Default real precision: single
   Compiler flags: optimize
   I/O layer: SMIOL

 Run-time settings:
   MPI task count: 1

 Reading namelist from file namelist.init_atmosphere
 *** Encountered an issue while attempting to read namelist record physics
     The following values will be used for variables in this record:

         config_tsk_seaice_threshold = 100.000


 ----- I/O task configuration: -----

     I/O task count  = 1
     I/O task stride = 1

 Initializing MPAS_streamInfo from file streams.init_atmosphere
 Reading streams configuration from file streams.init_atmosphere
 Found mesh stream with filename template x1.40962.static.nc
 Using default io_type for mesh stream
  ** Attempting to bootstrap MPAS framework using stream: input
 Bootstrapping framework with mesh fields from input file 'x1.40962.static.nc'
  * Requested field lbc_scalars is deactivated due to packages, or is a scratch variable.
  * Requested field lbc_u is deactivated due to packages, or is a scratch variable.
  * Requested field lbc_w is deactivated due to packages, or is a scratch variable.
  * Requested field lbc_rho is deactivated due to packages, or is a scratch variable.
  * Requested field lbc_theta is deactivated due to packages, or is a scratch variable.

Parsing run-time I/O configuration from streams.init_atmosphere ...

 -----  found immutable stream "input" in streams.init_atmosphere  -----
         filename template:  x1.40962.static.nc
         filename interval:  none
         direction:          input
         reference time:     initial_time
         record interval:    -
         real precision:     4 bytes
         input alarm:        initial_only

 -----  found immutable stream "output" in streams.init_atmosphere  -----
         filename template:  x1.40962.init.nc
         filename interval:  none
         direction:          output
         reference time:     initial_time
         record interval:    -
         output alarm:       initial_only
         package:            initial_conds


 -----  found immutable stream "surface" in streams.init_atmosphere  -----
         filename template:  x1.40962.sfc_update.nc
         filename interval:  none
         direction:          output
         reference time:     initial_time
         record interval:    -
         output alarm:       86400
         package:            sfc_update


 -----  found immutable stream "lbc" in streams.init_atmosphere  -----
         filename template:  lbc.$Y-$M-$D_$h.$m.$s.nc
         filename interval:  3:00:00
         direction:          output
         reference time:     initial_time
         record interval:    -
         output alarm:       3:00:00
         package:            lbcs


 ----- done parsing run-time I/O from streams.init_atmosphere -----

  ** Validating streams


 Reading dimensions from input streams ...

 ----- reading dimensions from stream 'input' using file x1.40962.static.nc
        nCells = 40962
        nEdges = 122880
        nVertices = 81920
        TWO = 2
        maxEdges = 10
        maxEdges2 = 20
        vertexDegree = 3
        R3 = 3
        nMonths = 12
        nSoilComps *** not found in stream ***

ERROR: At least one fields to be read from the 'input' stream is dimensioned
ERROR: by 'nSoilComps', but the 'nSoilComps' dimension is not defined
ERROR: in the file x1.40962.static.nc
CRITICAL ERROR: Please check the input file(s) to be read by the 'input' input stream.

 -----------------------------------------
 Total log messages printed:
    Output messages =                   91
    Warning messages =                   0
    Error messages =                     3
    Critical error messages =            1
 -----------------------------------------
 Logging complete.  Closing file at 2025/03/11 14:12:31

It looks like the static.nc file is missing a recently added dimension nSoilComps? I saw that this dimension is tied to NoahMP, but it doesn't look like I can change the physics settings for the init_atmosphere run.

There is also this error, which seems to cause no harm / be unrelated:

 *** Encountered an issue while attempting to read namelist record physics
     The following values will be used for variables in this record:

         config_tsk_seaice_threshold = 100.000