Test cases for StoreHDF5 read and write for issue #692

[anindex]

This PR proposes test cases for StoreHDF5::read and StoreHDF5::write with dash::Matrix. Test cases consist of 1D and 2D matrices with the default and unsigned index type.

[anindex]

I met some weird internal errors in HDF5 library when setting extend variable too small in 1D matrix test case.

HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) MPI-process 3:
  #000: ../../../src/H5Dio.c line 263 in H5Dwrite(): file selection+offset not within extent
    major: Dataspace
    minor: Out of range

Otherwise, all test cases pass successfully.

[codecov]

Codecov Report

Merging #699 into development will increase coverage by 0.53%.
The diff coverage is 100%.

@@               Coverage Diff               @@
##           development     #699      +/-   ##
===============================================
+ Coverage        83.65%   84.18%   +0.53%     
===============================================
  Files              336      336              
  Lines            24968    25072     +104     
  Branches         11354    11411      +57     
===============================================
+ Hits             20887    21108     +221     
- Misses            3692     3693       +1     
+ Partials           389      271     -118

Impacted Files	Coverage Δ
dart-impl/base/src/hwinfo.c	85% <100%> (ø)	⬆️
dash/test/io/HDF5MatrixTest.cc	100% <100%> (ø)	⬆️
dash/include/dash/GlobRef.h	76.99% <0%> (-13.28%)	⬇️
dash/include/dash/memory/UniquePtr.h	90% <0%> (-10%)	⬇️
dash/include/dash/view/ViewMod.h	92.94% <0%> (-7.06%)	⬇️
dash/include/dash/Team.h	80.41% <0%> (-5.16%)	⬇️
dash/include/dash/pattern/MakePattern.h	81.9% <0%> (-4.77%)	⬇️
...pi/include/dash/dart/mpi/dart_communication_priv.h	74.28% <0%> (-4.29%)	⬇️
dash/include/dash/view/IndexSet.h	94.21% <0%> (-3.31%)	⬇️
dash/include/dash/Dimensional.h	61.46% <0%> (-1.84%)	⬇️
... and 27 more

[anindex]

I have worked around the internal HDF5 errors of 1D dash::Matrix by initializing pattern_t and create the matrix instance using pattern_t:

typedef dash::TilePattern<1> pattern_t;
typedef dash::Matrix<value_t, 1> matrix_t;

pattern_t pattern(dash::SizeSpec<1, pattern_t::size_type>(8),
                           dash::DistributionSpec<1>(dash::TILE(2)),
                           dash::TeamSpec<1, pattern_t::index_type>());

...

matrix_t mat1(pattern);
...

As mentioned before, StoreHDF::write popups internal HDF5 library error if I use this initialization:

typedef dash::Matrix<value_t, 1> matrix_t;
auto size_spec = dash::SizeSpec<1>(8);

...

matrix_t mat1(size_spec);

...

[devreal]

@anindex

As mentioned before, StoreHDF::write popups internal HDF5 library error if I use this initialization:

typedef dash::Matrix<value_t, 1> matrix_t;
auto size_spec = dash::SizeSpec<1>(8);

matrix_t mat1(size_spec);

Which error exactly do you see there?

[anindex]

The error I posted in the previous comment and it is also the cause for CI failing last time we saw it.

HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) MPI-process 3:
  #000: ../../../src/H5Dio.c line 263 in H5Dwrite(): file selection+offset not within extent
    major: Dataspace
    minor: Out of range