GitLab

Changes from ARL's Repo (C Wrappers, DSM rework, Custom Types, Templates, GridControllers, TIFF integration, XdmfAggregate)

Some style. Some fixes, especially for windows with the exports and template changes.

More so adapt this to work well as a subdirectory in a larger project. Don't force settings
that the parent project owns, allow parent project to turn on tests without xdmf's tests and
make the name of the library an option so that parent can have two xdmfs.

Rework of HeavyDataController and HDF5Controller to remove extra code and move HeavyDataController away from being too dependent on hdf5 style
XdmfFunction now supports negative numbers in addition to the - operator
Reworked the interaction between array references and reading
Cleaned up some warnings that showed up in pedantic
Adjusted mpi tests to test against the MPIEXEC variable as opposed to hard calling mpirun
Still needs to be changed to work better with Cray mpi style execution
Updates to XdmfArrayType to allow for signed and floating point checking
General test and Documentation updates

Add HDF5 tree writer test.

made changes for preparations to push to master; still need to finish documentation changes and line length changes

Only query hdf5 for number of datasets in a file when unavoidable.
On some machines, this can cause performance problems when writing
to large hdf5 files.

changes for file splitting and functions along with assorted changes to XdmfFortran for possible speed increases

changes to file splitting, hyperslab not completely working yet. changes to Fortran to allow for polylines and releasing data after standard write

Replace with visitor pattern that avoids the need for catching the exception.
Update the HDF5Writer to use stringstreams for error message output for
concatenating strings and error codes.

Current chunking mechanism produces chunks too large for hdf5 to handle.
Reduce sizes of chunks for multi-dimensional hdf5 datasets.
Chunks for multi-dimensional hdf5 datasets have shape resembling overarching
dataset.
Add test for this to TestXdmfArrayWriteRead.

Add tests for I/O of strings (to hdf5 and xml).
Fix bug in XdmfExodusReader when reading grid centered data.
Add string I/O in python and add tests.

Modified writer to utilize hyperslabs to write in parallel to file.
Updated DSM to newest version (0.9.9).
Modified DSM test to write in parallel to DSM buffer.
Add test for new hyperslab writing mode.

Choose dataset name more carefully to avoid querying the file many times.
Use a more efficient function to check if a dataset already exists in a file.
Get DSM working with new changes.
Fix gcc compiler warning in test.

Previously, each time a dataset was written to hdf5, the file was opened
and closed. This was implemented because inside the heavy data writer
we have no idea whether another dataset will be written, so we don't know
whether to keep the file open. After profiling large xdmf writes it was
determined that closing the file appeared to be a bottleneck so hooks were
added to the heavy data writer to open the file and keep it open while writing.
This is optional, but was incorporated into several higher level classes
like XdmfWriter where we know we can leave a file open until we finish writing
the XML. For our test problem we saw a 7 time performance gain.