Default to the WRF output and rank settings measured in #89

[aethr]

Closes #89. Takes the four settings #89 measured to pay off and makes them the defaults, directly on main. It replaces #91, and leaves out #90's experiment-only environment variables (namelist overrides, extra mpirun arguments, quilting rank accounting), because the settings they tested either became defaults here or made no difference. Measured results are in #89 (comment).

Changes

Setting	Where	Measured effect (aust10km, c8id.16xlarge)	Output
history_begin_h = num_hours_spin_up	setup_for_wrf.py	−16%: 144 fewer frames written	byte-identical
use_netcdf_classic = .true.	setup_for_wrf.py	−33%: 8.7 s → 2.5 s per frame	byte-identical
debug_level = 0 (was 100)	setup_for_wrf.py; removed from every domains/*/namelist.wrf	−7% of compute	byte-identical
Ranks = physical cores	safe_mpi_tasks(), new physical_cpu_count()	−13% on top of the above	rounding-level differences (see #89)

Together: wrf-run 8,125 s → 4,163 s.

Notes

• Where the settings live: the three output settings are set when the namelist is generated rather than in the domain namelists, because they describe how we run wrf.exe, not the domain. history_begin_h follows the config's spin-up length.
• Physical cores: physical_cpu_count() counts distinct (physical id, core id) pairs in /proc/cpuinfo. It falls back to os.cpu_count() where those fields are missing, as on aarch64, which has no SMT anyway. NCPUS still overrides the default.
• Rank count by host: on the current 64-vCPU WrfStorageSpot hosts the default drops from 64 ranks to 32. A 96-vCPU host would get 48.
• Classic output: this only affects the history frames wrf.exe writes. average_fields() still compresses the hourly WRFOUT files.

Testing

• make test: passes, including new tests for physical_cpu_count() (hyperthreaded, two-socket, no core information).
• Each setting was run end to end in sandbox in wrf.exe spends over half its run writing history output; cut that before sizing ranks #89, against an in-batch control, by setting it at run time through Set wrf.exe namelist values and mpirun arguments from the environment #90's environment variables. This branch's defaults haven't been run as a whole.

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