Caching and Buffering in HDF5
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The document discusses caching and buffering mechanisms in HDF5, focusing on how data is managed during its lifecycle from application buffers to storage. It covers various dataset storage layouts (contiguous, chunked, compact), factors affecting I/O performance, and techniques to improve application efficiency. Key topics include metadata management, I/O operations, and the handling of variable-length data in HDF5.
![Examples of variable length data
• String
A[0] “the first string we want to write”
…………………………………
A[N-1] “the N-th string we want to write”
• Each element is a record of variable-length
A[0] (1,1,0,0,0,5,6,7,8,9) [length = 10]
A[1] (0,0,110,2005)
[length = 4]
………………………..
A[N] (1,2,3,4,5,6,7,8,9,10,11,12,….,M) [length = M]
Nov. 6, 2007
HDF-EOS Workshop XI Tutorial
42](https://image.slidesharecdn.com/hdf5-cach-buf-mfc-140217154851-phpapp01/85/Caching-and-Buffering-in-HDF5-42-320.jpg)
Caching and Buffering in HDF5
- 1. Caching and Buffering in HDF5 The HDF Group Nov. 6, 2007 HDF-EOS Workshop XI Tutorial 1
- 2. Software stack and the “magic box” • Life cycle: What happens to data when it is transferred from application buffer to HDF5 file? Application Data buffer Object API H5Dwrite Library internals Magic box Virtual file I/O Unbuffered I/O File or other “storage” Nov. 6, 2007 HDF-EOS Workshop XI Tutorial Data in a file 2
- 3. Inside the magic box • Understanding of what is happening to data inside the magic box will help to write efficient applications • HDF5 library has mechanisms to control behavior inside the magic box • Goals of this talk: Describe some basic operations and data structures and explain how they affect performance and storage sizes Give some “recipes” for how to improve performance Nov. 6, 2007 HDF-EOS Workshop XI Tutorial 3
- 4. Topics • Dataset metadata and array data storage layouts • Types of dataset storage layouts • Factors affecting I/O performance • • • • I/O with compact datasets I/O with contiguous datasets I/O with chunked datasets Variable length data and I/O Nov. 6, 2007 HDF-EOS Workshop XI Tutorial 4
- 5. HDF5 dataset metadata and array data storage layouts Nov. 6, 2007 HDF-EOS Workshop XI Tutorial 5
- 6. HDF5 Dataset • Data array • Ordered collection of identically typed data items distinguished by their indices • Metadata • • • • Dataspace: Rank, dimensions of dataset array Datatype: Information on how to interpret data Storage Properties: How array is organized on disk Attributes: User-defined metadata (optional) Nov. 6, 2007 HDF-EOS Workshop XI Tutorial 6
- 7. Separate Components of a Dataset Header Data array Dataspace Rank Dimensions 3 Dim_1 = 4 Dim_2 = 5 Dim_3 = 7 Datatype IEEE 32-bit float Storage info Attributes Time = 32.4 Chunked Pressure = 987 Compressed Temp = 56 Nov. 6, 2007 HDF-EOS Workshop XI Tutorial 7
- 8. Metadata cache and array data • Dataset array data typically kept in application memory • Dataset header in separate space – metadata cache Metadata cache Dataset header …………. Datatype Dataspace …………. Attributes … Dataset array data Application memory HDF5 metadata Dataset array data File Nov. 6, 2007 HDF-EOS Workshop XI Tutorial 8
- 9. Metadata and metadata cache • HDF5 metadata • Information about HDF5 objects used by the library • Examples: object headers, B-tree nodes for group, B-Tree nodes for chunks, heaps, super-block, etc. • Usually small compared to raw data sizes (KB vs. MB-GB) • Metadata cache • Space allocated to handle pieces of the HDF5 metadata • Allocated by the HDF5 library in application’s memory space • Cache behavior affects overall performance • Metadata cache implementation prior to HDF5 1.6.5 could cause performance degradation for some applications Nov. 6, 2007 HDF-EOS Workshop XI Tutorial 9
- 10. Types of data storage layouts Nov. 6, 2007 HDF-EOS Workshop XI Tutorial 10
- 11. HDF5 datasets storage layouts • Contiguous • Chunked • Compact Nov. 6, 2007 HDF-EOS Workshop XI Tutorial 11
- 12. Contiguous storage layout • Metadata header separate from raw data • Raw data stored in one contiguous block on disk Metadata cache Dataset array data Dataset header …………. Datatype Dataspace …………. Attributes … Application memory File Nov. 6, 2007 HDF-EOS Workshop XI Tutorial 12
- 13. Chunked storage • Chunking – storage layout where a dataset is partitioned in fixed-size multi-dimensional tiles or chunks • Used for extendible datasets and datasets with filters applied (checksum, compression) • HDF5 library treats each chunk as atomic object • Greatly affects performance and file sizes Nov. 6, 2007 HDF-EOS Workshop XI Tutorial 13
- 14. Chunked storage layout • Raw data divided into equal sized blocks (chunks). • Each chunk stored separately as a contiguous block on disk Metadata cache Dataset array data Dataset header A …………. Datatype Dataspace …………. Attributes … File B C D Chunk index Application memory header Nov. 6, 2007 Chunk index A C HDF-EOS Workshop XI Tutorial D 14 B
- 15. Compact storage layout • Data array and metadata stored together in the header Dataset header …………. Datatype Dataspace …………. Attributes … Array data Data Metadata cache Array data Application memory File* * “File” may in fact be a collection of files, memory, or other storage destination. Nov. 6, 2007 HDF-EOS Workshop XI Tutorial 15
- 16. Factors affecting I/O performance Nov. 6, 2007 HDF-EOS Workshop XI Tutorial 16
- 17. What goes on inside the magic box? • Operations on data inside the magic box • Copying to/from internal buffers • Datatype conversion • Scattering - gathering • Data transformation (filters, compression) • Data structures used • B-trees (groups, dataset chunks) • Hash tables • Local and Global heaps (variable length data: link names, strings, etc.) • Other concepts • HDF5 metadata, metadata cache • Chunking, chunk cache Nov. 6, 2007 HDF-EOS Workshop XI Tutorial 17
- 18. Operations on data inside the magic box • Copying to/from internal buffers • Datatype conversion, such as • float integer • LE BE • 64-bit integer to 16-bit integer • Scattering - gathering • Data is scattered/gathered from/to application buffers into internal buffers for datatype conversion and partial I/O • Data transformation (filters, compression) • Checksum on raw data and metadata (in 1.8.0) • Algebraic transform • GZIP and SZIP compressions • User-defined filters Nov. 6, 2007 HDF-EOS Workshop XI Tutorial 18
- 19. I/O performance depends on • • • • • • • Storage layouts Dataset storage properties Chunking strategy Metadata cache performance Datatype conversion performance Other filters, such as compression Access patterns Nov. 6, 2007 HDF-EOS Workshop XI Tutorial 19
- 20. I/O with different storage layouts Nov. 6, 2007 HDF-EOS Workshop XI Tutorial 20
- 21. Writing compact dataset Dataset header Metadata cache …………. Datatype Dataspace …………. Attributes … Array data Data Application memory One write to store header and data array File Nov. 6, 2007 HDF-EOS Workshop XI Tutorial 21
- 22. Writing contiguous dataset – no conversion Metadata cache Dataset header …………. Datatype Dataspace …………. Attributes … Dataset array data Application memory File Nov. 6, 2007 HDF-EOS Workshop XI Tutorial 22
- 23. Writing a contiguous dataset with datatype conversion Dataset header …………. Datatype Dataspace …………. Attribute 1 Attribute 2 ………… Metadata cache Dataset array data Conversion buffer 1MB Application memory File Nov. 6, 2007 HDF-EOS Workshop XI Tutorial 23
- 24. Partial I/O with contiguous datasets Nov. 6, 2007 HDF-EOS Workshop XI Tutorial 24
- 25. Writing whole dataset – contiguous rows N M One I/O operation Application data in memory M rows File Nov. 6, 2007 Data is contiguous in a file HDF-EOS Workshop XI Tutorial 25
- 26. Sub-setting of contiguous dataset Series of adjacent rows Application data in memory N M One I/O operation M rows Subset – contiguous in file File Entire dataset – contiguous in file Nov. 6, 2007 HDF-EOS Workshop XI Tutorial 26
- 27. Sub-setting of contiguous dataset Adjacent, partial rows Application data in memory N Several small I/O operation M N elements File Nov. 6, 2007 … Data is scattered in a file in M contiguous blocks HDF-EOS Workshop XI Tutorial 27
- 28. Sub-setting of contiguous dataset Extreme case: writing a column Application data in memory N Several small I/O operation M 1 element … Subset data is scattered in a file in M different locations Nov. 6, 2007 HDF-EOS Workshop XI Tutorial 28
- 29. Sub-setting of contiguous dataset Data sieve buffer Application data in memory N Data is gathered in a sieve buffer in memory 64K memcopy M 1 element File Nov. 6, 2007 … Data is scattered in a file in M contiguous blocks HDF-EOS Workshop XI Tutorial 29
- 30. Performance tuning for contiguous dataset • Datatype conversion • Avoid for better performance • Use H5Pset_buffer function to customize conversion buffer size • Partial I/O • Write/read in big contiguous blocks • Use H5Pset_sieve_buf_size to improve performance for complex subsetting Nov. 6, 2007 HDF-EOS Workshop XI Tutorial 30
- 31. I/O with Chunking Nov. 6, 2007 HDF-EOS Workshop XI Tutorial 31
- 32. Reminder – chunked storage layout Metadata cache Dataset array data Dataset header A …………. Datatype Dataspace …………. Attributes … File B C D Chunk index Application memory header Nov. 6, 2007 Chunk index A C HDF-EOS Workshop XI Tutorial D 32 B
- 33. Information about chunking • HDF5 library treats each chunk as atomic object • Compression is applied to each chunk • Datatype conversion, other filters applied per chunk • Chunk size greatly affects performance • Chunk overhead adds to file size • Chunk processing involves many steps • Chunk cache • • • • • • Caches chunks for better performance Created for each chunked dataset Size of chunk cache is set for file (default size 1MB) Each chunked dataset has its own chunk cache Chunk may be too big to fit into cache Memory may grow if application keeps opening datasets Nov. 6, 2007 HDF-EOS Workshop XI Tutorial 33
- 34. Chunk cache Dataset_1 header Metadata cache ………… ……… Dataset_N header Chunking B-tree nodes ………… Chunk cache Default size is 1MB Application memory Nov. 6, 2007 HDF-EOS Workshop XI Tutorial 34
- 35. Writing chunked dataset Chunked dataset A C Chunk cache C B Filter pipeline File B A ………….. C • Compression performed when chunk evicted from the chunk cache • Other filters applied as data goes through filter pipeline Nov. 6, 2007 HDF-EOS Workshop XI Tutorial 35
- 36. Partial I/O with Chunking Nov. 6, 2007 HDF-EOS Workshop XI Tutorial 36
- 37. Partial I/O for chunked dataset 1 2 3 4 • Example: write the green subset from the dataset , converting the data • Dataset is stored as six chunks in the file. • The subset spans four chunks, numbered 1-4 in the figure. • Hence four chunks must be written to the file. • But first, the four chunks must be read from the file, to preserve those parts of each chunk that are not to be overwritten. Nov. 6, 2007 HDF-EOS Workshop XI Tutorial 37
- 38. Partial I/O for chunked dataset • For each of the four chunks: 1 2 3 4 • Read chunk from file into chunk cache, unless it’s already there. • Determine which part of the chunk will be replaced by the selection. • Replace that part of the chunk in the cache with the corresponding elements from the application’s array. • Move those elements to conversion buffer and perform conversion • Move those elements back from conversion buffer to chunk cache. • Apply filters (compression) when chunk is flushed from chunk cache • For each element 3 memcopy performed Nov. 6, 2007 HDF-EOS Workshop XI Tutorial 38
- 39. Partial I/O for chunked dataset Application buffer Chunk cache 3 3 Chunk memcopy Elements participating in I/O are gathered into corresponding chunk Application memory Nov. 6, 2007 HDF-EOS Workshop XI Tutorial 39
- 40. Partial I/O for chunked dataset Chunk cache Memcopy Conversion buffer 3 Memcopy Application memory Compress and write to file File Nov. 6, 2007 Chunk HDF-EOS Workshop XI Tutorial 40
- 41. Variable length data and I/O Nov. 6, 2007 HDF-EOS Workshop XI Tutorial 41
- 42. Examples of variable length data • String A[0] “the first string we want to write” ………………………………… A[N-1] “the N-th string we want to write” • Each element is a record of variable-length A[0] (1,1,0,0,0,5,6,7,8,9) [length = 10] A[1] (0,0,110,2005) [length = 4] ……………………….. A[N] (1,2,3,4,5,6,7,8,9,10,11,12,….,M) [length = M] Nov. 6, 2007 HDF-EOS Workshop XI Tutorial 42
- 43. Variable length data in HDF5 • Variable length description in HDF5 application typedef struct { size_t length; void *p; }hvl_t; • Base type can be any HDF5 type H5Tvlen_create(base_type) • ~ 20 bytes overhead for each element • Data cannot be compressed Nov. 6, 2007 HDF-EOS Workshop XI Tutorial 43
- 44. How variable length data is stored in HDF5 Actual variable length data Global heap File Dataset header Nov. 6, 2007 Dataset with variable length elements Pointer into global heap HDF-EOS Workshop XI Tutorial 44
- 45. Variable length datasets and I/O • When writing variable length data, elements in application buffer point to global heaps in the metadata cache where actual data is stored. Raw data Application buffer Global heap Nov. 6, 2007 HDF-EOS Workshop XI Tutorial 45
- 46. There may be more than one global heap Raw data Application buffer Global heap Global heap Nov. 6, 2007 HDF-EOS Workshop XI Tutorial 46
- 47. Variable length datasets and I/O Raw data Global heap Global heap File Nov. 6, 2007 HDF-EOS Workshop XI Tutorial 47
- 48. VL chunked dataset in a file Chunk B-tree File Dataset header Heaps with VL data Nov. 6, 2007 Dataset chunks HDF-EOS Workshop XI Tutorial 48
- 49. Writing chunked VL datasets Metadata cache B-tree nodes Chunk cache Dataset header ………… Application memory Global heap ……… Raw data Chunk cache Conversion buffer Filter pipeline VL chunked dataset with selected region File Nov. 6, 2007 HDF-EOS Workshop XI Tutorial 49
- 50. Hints for variable length data I/O • Avoid closing/opening a file while writing VL datasets • Global heap information is lost • Global heaps may have unused space • Avoid alternately writing different VL datasets • Data from different datasets will go into to the same heap • If maximum length of the record is known, consider using fixed-length records and compression Nov. 6, 2007 HDF-EOS Workshop XI Tutorial 50
- 51. Thank you! Questions ? Nov. 6, 2007 HDF-EOS Workshop XI Tutorial 51