Add support for raw MPI-IO and rework PencilIO

[jipolanco]

This PR changes the interface for parallel I/O to support multiple I/O drivers.

Both parallel HDF5 and (raw) MPI-IO drivers will be supported.

Things to do:

• [x] common interface for all drivers

• [x] add support for parallel HDF5 driver via Base.open

• [x] add MPI-IO writing functions

• [x] add MPI-IO reading functions

• [x] test write/read cycle

• [x] use MPI_File_set_view and derived datatypes to write discontiguous datasets (make this optional?). See also here, starting from slide 16.

• [x] deprecate / remove old ph5open function

• [x] update PencilIO docs

• [x] test both drivers with different open modes (read, write, append, ...)

• [x] MPI-IO: add support for array collections (vector fields)

• [x] MPI-IO: take dataset name in read!, and verify metadata

• [x] MPI-IO: support append mode (using metadata)

• [x] HDF5: accept user-provided property lists in open

• [x] maybe include MPI.Comm and MPI.Info in the PHDF5Driver and MPIIODriver structs

[codecov-commenter]

Codecov Report

Merging #7 into master will increase coverage by 0.86%. The diff coverage is 97.95%.

@@            Coverage Diff             @@
##           master       #7      +/-   ##
==========================================
+ Coverage   95.74%   96.60%   +0.86%     
==========================================
  Files          16       17       +1     
  Lines         705      884     +179     
==========================================
+ Hits          675      854     +179     
  Misses         30       30              

Impacted Files	Coverage Δ
src/PencilIO/hdf5.jl	93.80% <96.42%> (+3.51%)	:arrow_up:
src/PencilIO/mpi_io.jl	98.03% <98.03%> (ø)
src/PencilIO/PencilIO.jl	100.00% <100.00%> (ø)
src/arrays.jl	95.49% <100.00%> (+0.16%)	:arrow_up:

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[codecov-io]

Codecov Report

Merging #7 (8c079dc) into master (2276729) will increase coverage by 0.54%. The diff coverage is 96.51%.

@@            Coverage Diff             @@
##           master       #7      +/-   ##
==========================================
+ Coverage   95.73%   96.28%   +0.54%     
==========================================
  Files          16       17       +1     
  Lines         704      888     +184     
==========================================
+ Hits          674      855     +181     
- Misses         30       33       +3     

Impacted Files	Coverage Δ
src/PencilIO/PencilIO.jl	93.75% <92.30%> (-6.25%)	:arrow_down:
src/PencilIO/hdf5.jl	92.98% <93.10%> (+2.69%)	:arrow_up:
src/PencilIO/mpi_io.jl	97.43% <97.43%> (ø)
src/arrays.jl	95.49% <100.00%> (+0.16%)	:arrow_up:

---

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Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update 2276729...8c079dc. Read the comment docs.