Recreated: Debug/updates for hdf5 routines

[mnagaso]

I made a few updates on hdf5 routines for solving a few runtime issues.

and please ignore my last 2 PRs.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 48.82%. Comparing base (300bf37) to head (4ee070d).
⚠️ Report is 4 commits behind head on devel.

Additional details and impacted files

@@           Coverage Diff           @@
##            devel    #1825   +/-   ##
=======================================
  Coverage   48.82%   48.82%           
=======================================
  Files         273      273           
  Lines       64785    64785           
=======================================
  Hits        31629    31629           
  Misses      33156    33156           

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