PIO sync for potentially better robustness for gnu/cray-mpich and a few cleanups

[nmizukami]

We found that cesm-coupling.n02_v2.1.2 produces the history output problem for the gnu (12.2.0) / mpich (8.1.27) compiled executable. pio_sync was added after writing the history file and this reduces the occurrence of this error (but not completely eliminating this problem). Note: Jim mentioned when netcdf is closed, pio_sync happens so no explict call for pio_sync is needed.

Note: This problem does occur only for the executable compiled with gnu/mpich. gnu/openmpi (5.0.0) and intel/mpich work fine.

Further debugging for gnu/mpich is needed, but at this point, unclear about root cause of the problem. This might be related to #359

Switching netcdf type from pnetcdf to netcdf clear this problem (for gnu (12.2.0) / mpich (8.1.27)). Therefore, expose the pio_netcdf_type to user control file. so user can specify netcdf type without re-compiling the code (pio_netcdf_type was hard-coded as pnetcdf.)

Fixed library (PIO) Makefile bug that cause the compiling error when you use only netCDF and gcc.

Other changes include removing unused variables or routines

[nmizukami]

At least using standard netcdf for PIO works for gcc with mpich (not parallel-netcdf), and several compiling issues for recent compilers (both intel and gcc)

• issue on gcc and intel with mpich using standard parallel netcdf.
• issue on cmake flag
• issue on recent gcc compile (Rank mismatch between actual arguments)

So merge this now.