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

[barlage]

@climbfuji I believe this is because the provided static file has not been recreated with the newer versions of the code that added the soil composition data and the need for the nSoilComps dimension (where the check is failing). I can provide you with a version that I created on hera and jet (or derecho) if you'd like.

[climbfuji]

@climbfuji I believe this is because the provided static file has not been recreated with the newer versions of the code that added the soil composition data and the need for the nSoilComps dimension (where the check is failing). I can provide you with a version that I created on hera and jet (or derecho) if you'd like.

Thanks for your reply, that sounds reasonable. Since the static data is coming from the MPAS repos, it would be good to update the data in the repo?

[barlage]

Yes, the data should be updated so would be good to keep this issue open. I ran into the same problem when I was starting to play around with MPAS several months ago. As part of our GSL testing framework, we regenerate this global 120km grid as part of the init_atmosphere testing so I have some versions lying around if you don't want to create your own.