Added HDF5 optimisation

 * Configured chunk cache size to contain a full set of cached frames
 * Set the chunk boundary alignment to 4MB
 * Only flush when local cache is to be written
Log configuration tweaks
Tidy up #include statements
Frame loading read chunk configuration
Writer use chunking from test data Frame
Writer: remove sleep in loop
Progressbar can now print an optional rate measurement
Writer performance measurements added

The writer loop now takes a delta-time every time the cache is flushed and data is written to disk. The data rate is calculated and printed.
Removed writer CLI option to specify loop period
Adding timestamp and report to writer
Merge branch 'hdf5_optimisations'