Hdf5 update

[mnagaso]

I created logical H5_COL flag in shared_param to control the IO mode of HDF5 easily (collective or independent). This is useful for the case that the machine does not like collective I/O (TACC Frontera).
I also modified the file write process of neighbors_adjncy in generate_databases to use 64-bit integer so that the code allows to count the number of the array elements which is larger than the maximum of 32 bit integer.

[codecov]

Codecov Report

Attention: Patch coverage is 0% with 3 lines in your changes missing coverage. Please review.

Project coverage is 50.68%. Comparing base (1b0d98c) to head (d1d0415).
Report is 17 commits behind head on devel.

Files with missing lines	Patch %	Lines
src/shared/check_mesh_resolution.f90	0.00%	3 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##            devel    #1738      +/-   ##
==========================================
- Coverage   50.92%   50.68%   -0.25%     
==========================================
  Files         270      271       +1     
  Lines       61506    61801     +295     
==========================================
  Hits        31322    31322              
- Misses      30184    30479     +295     

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[mnagaso]

Probably some other arrays' length need to be counted with integer(kind=8) for a large size mesh.