1. HDF5 Metadata and Page Buffering
Improving HDF5 metadata handling with L2 cache
May 30-31, 2012
HDF5 Workshop at PSI

2. HDF5 metadata Metadata – data about data HDF5 metadata
Structural metadata (describes HDF5 objects – groups, datasets, chunks, etc.)
Group header
B-Tree (to index objects, chunks)
Local heap (to store link names)
User defined metadata (HDF5 attributes)
Created via the H5A calls
Usually small – less than 1 KB
Accessed frequently
Small disk accesses are expensive
May 30-31, 2012
HDF5 Workshop at PSI

3. Current handling of HDF5 metadata
HDF5 implements metadata aggregators to allocate space in a file and to avoid small I/O
Aggregator minimum size can be controlled by application (default is 2K, 0 disables aggregation)
H5Pset_meta_block_size
Size of metadata block is limited only by the order of space allocations
Aggregator will go beyond minimum aggregation size if current allocation block is at the end of the file
May 30-31, 2012
HDF5 Workshop at PSI

4. HDF5 metadata allocation
Dataset array data
HDF5 File
Metadata is mixed with raw data in HDF5 file
2K metadata block; may be partially filled
HDF5 File
Metadata blocks of different lengths
May 30-31, 2012
HDF5 Workshop at PSI

5. Current handling of HDF5 metadata
Problems that affect metadata I/O
Size of aggregation varies and is not stored in the file
Library cannot take an advantage of reading metadata block since it doesn’t know the length of the block
Metadata blocks are not aligned to the block size of the underlying file system and do not have size of some multiple of the file system block size
May 30-31, 2012
HDF5 Workshop at PSI

6. Page buffering (L2 cache)
Implement metadata (MD) aggregation in 64K pages
MD pages are aligned in the file
Perform all I/O in page-sized blocks or greater
File format change
Store MD allocation parameters in the HDF5 superblock extension message; can be ignored by readers
Put a flag to indicate that some MD blocks are not aligned
Implement page buffering (L2 cache)
Currently in design stage
May 30-31, 2012
HDF5 Workshop at PSI

7. New aggregator API calls
Can set in file creation property lists
Only set on file creation
Permanent, stored in superblock when set
H5Pget/set_aggregator_block_size
May 30-31, 2012
HDF5 Workshop at PSI

8. HDF5 page buffering Page buffer contains MD pages (L2 cache)
Metadata blocks are aligned
HDF5 File
Metadata blocks are multiples of 64K
May 30-31, 2012
HDF5 Workshop at PSI

9. Data and metadata aggregators
The new aggregators pack small raw data and metadata allocations into aligned blocks which work with the page buffer.
data
metadata
HDF5 File
Small allocations
May 30-31, 2012
HDF5 Workshop at PSI

10. Thank You!
Questions?
May 30-31, 2012
HDF5 Workshop at PSI