netCDF boundary plane write regression test fails after modifications

[rybchuk]

Bug description

I have a simulation with a refinement zone that touches the boundary, and I am write to write out the BCs for this simulation to netCDF, but it's failing. Marc pointed out that there's a regression test that does the same thing, but it succeeds. If I make some reasonable modifications, the simulation fails with the following message:

Shear Stress model: moeng
Heat Flux model: moeng
Creating output NetCDF file: bndry_file.nc
NetCDF file created successfully: bndry_file.nc

Writing NetCDF file bndry_file.nc at time 0
terminate called after throwing an instance of 'std::runtime_error'
  what():  Encountered NetCDF error; aborting
srun: error: x1006c0s4b1n1: task 177: Aborted (core dumped)

Here is the diff on abl.i:

9c9
< time.fixed_dt         =   0.5        # Use this constant dt if > 0
---
> time.fixed_dt         =   0.01 # 0.5        # Use this constant dt if > 0
52c52
< ABL.bndry_output_start_time = 2.0
---
> ABL.bndry_output_start_time = 0.0 # 2.0
58c58
< amr.n_cell              = 48 48 48    # Grid cells at coarsest AMRlevel
---
> amr.n_cell              = 320 320 240 # 48 48 48    # Grid cells at coarsest AMRlevel

I've also changed out static_box.txt:

1,7c1,3
< 2
< 2
< -100 -10 -100 1100 10 300
< -10 -100 -100 10 1100 300
< 2
< -100 -10 -100 1100 10 300
< -10 -100 -100 10 1100 300
---
> 1
> 1
> 0.0 0.0 100.0 1000.0 1000.0 150.0

Side note: It looks weird to me that the original static_box.txt has refinement zones that start at x=-100 even though xlo=0 in these simulations.

Other notes

• If I revert back from amr.n_cell = 320 320 240 to amr.n_cell = 48 48 48, the simulation runs fine
• If I change to ABL.bndry_output_format = native, the simulation runs fine
• If I set amr.max_level = 0, the simulation runs fine
• If I use the original static_box.txt, the simulation runs fine

Steps to reproduce

Steps to reproduce the behavior:

1. Compiler used
   • oneapi (Intel)
2. Operating system
   • Linux
3. Hardware:
   • CPU
4. Machine details ():
   Kestrel

Currently Loaded Modules:
  1) intel/2023.2.0	  7) cray-libsci/22.10.1.2
  2) craype/2.7.30        8) PrgEnv-intel/8.5.0
  3) cray-dsmml/0.2.2     9) cray-python/3.11.5
  4) libfabric/1.15.2.0  10) binutils/2.41
  5) craype-network-ofi  11) intel-oneapi-compilers/2023.2.0
  6) cray-mpich/8.1.28

5. Input file attachments
   failed_reg_test.zip

6. Error (paste or attach):
   See fail1.log in the ZIP

7. If this is a segfault, a stack trace from a debug build (paste or attach):
   This looks like a netCDF error?

Expected behavior

The simulation should not crash and should write out a boundary condition file in the netCDF format

AMR-Wind information

==============================================================================
                AMR-Wind (https://github.com/exawind/amr-wind)

  AMR-Wind version :: v3.2.0-21-g3e9d3a8b-DIRTY
  AMR-Wind Git SHA :: 3e9d3a8b4704e98ab6691cefeea2d240d24bef3f-DIRTY
  AMReX version    :: 24.09-45-g6d9c25b989f1

  Exec. time	   :: Sat Nov 30 08:28:59 2024
  Build time	   :: Nov 20 2024 07:39:48
  C++ compiler     :: IntelLLVM 2023.2.0

  MPI              :: ON    (Num. ranks = 192)
  GPU              :: OFF
  OpenMP           :: OFF

  Enabled third-party libraries:
    NetCDF    4.9.2

           This software is released under the BSD 3-clause license.
 See https://github.com/Exawind/amr-wind/blob/development/LICENSE for details.
------------------------------------------------------------------------------