Performance Factors

One of the main advantages of storing your data in TileDB arrays is the ability to tune performance for your particular use case. In this tutorial we list the most important factors influencing the performance when interacting with TileDB arrays.

Arrays

The following factors that influence performance must be considered when the array schema is designed. In general, designing an array schema that is effective and results in high performance depends on the type of data that the array will store, and the type of queries that will be issued to the array.

Dense vs. sparse arrays
Choosing a dense or sparse array representation depends on the particular data and use case. Sparse arrays in TileDB have additional overhead versus dense arrays due to the need to explicitly store cell coordinates of the non-empty cells. For a particular use case, this extra overhead may be outweighed by the storage savings of not storing dummy values for empty cells in the dense alternative, in which case a sparse array would be a good choice. Sparse array reads also have additional runtime overhead due to the potential need of sorting the cells based on their coordinates.
Space tiles
In dense arrays, the space tile shape and size determines the atomic unit of I/O and compression. All space tiles that intersect a read query’s subarray are read from disk whole, even if they only partially intersect with the query. Matching space tile shape and size closely with the typical read query can greatly improve performance. In sparse arrays, space tiles affect the order of the non-empty cells and, hence, the minimum bounding rectangle (MBR) shape and size. All tiles in a sparse array whose MBRs intersect a read query’s subarray are read from disk. Choosing the space tiles in a way that the shape of the resulting MBR’s is similar to the read access patterns can improve read performance, since fewer MBRs may then overlap with the typical read query.
Tile capacity
The tile capacity determines the number of cells in a data tile of a sparse fragment (recall that a sparse fragment can exist in both dense and sparse arrays), which is the atomic unit of I/O and compression. If the capacity is too small, the data tiles can be too small, requiring many small, independent read operations to fulfill a particular read query. Moreover, very small tiles could lead to poor compressibility. If the capacity is too large, I/O operations would become fewer and larger (a good thing in general), but the amount of wasted work may increase due to reading more d ata than necessary to fulfill the typical read query.
Dimensions vs. attributes
If read queries typically access the entire domain of a particular dimension, consider making that dimension an attribute instead. Dimensions should be used when read queries will issue ranges of that dimension of cells to retrieve, which facilitates TileDB to internally prune cell ranges or whole tiles from the data that must be read. Additionally, it is not possible to subselect on dimensions (i.e. a read query can specify only a subset of attributes should be read, but it must always specify all dimensions).
Filtering
Filtering (such as compression) of attributes can reduce persistent storage consumption, but at the expense of increased time to read/write tiles from/to the array. However, tiles on disk that are smaller due to compression can be read from disk in less time, which can improve performance. Additionally, many compressors offer different levels of compression, which can be used to fine-tune the tradeoff.

Queries

The following factors impact query performance, i.e., when reading/writing data from/to the array.

Number of array fragments
Each write to a TileDB array (with the exception of consecutive global-order writes) creates a new fragment. When reading from the array, read queries consider all fragments, sorting by timestamp to ensure the latest data is returned. However, large numbers of fragments can slow down performance during read queries, as TileDB must internally sort and determine potential overlap of cell data across all fragments. It therefore improves performance to consolidate arrays with a large number of fragments; consolidation collapses all fragments into a single one.
Attribute subsetting
A benefit of the column-oriented nature of attribute storage in TileDB is if a read query does not require data for some of the attributes in the array, those attributes will not be touched or read from disk at all. Therefore, specifying only the attributes actually needed for each read query will improve performance. In the current version of TileDB, write queries must still specify values for all attributes.
Read layout
When an ordered layout (row- or column-major) is used for a read query, if that layout differs from the array physical layout, TileDB must internally sort and reorganize the cell data that is read from the array into the requested order. If you do not care about the particular ordering of cells in the result buffers, you can specify a global order query layout, allowing TileDB to skip the sorting and reorganization steps.
Write layout
Similarly, if your specifies write layouts differs from the physcial layout of your array (i.e., the global cell order), then TileDB needs to internally sort and reorganize the cell data into global order before writing to the array. If your cells are already laid out in global order, issuing a write query with global-order allows TileDB to skip the sorting and reorganization step. Additionally, multiple consecutive global-order writes to an open array will append to a single fragment rather than creating a new fragment per write, which can improve later the read performance. Care must be taken for global-order writes, as it is an error to write data to a subarray that is not aligned with the space tiling of the array.
Opening/closing arrays
Before issuing queries, an array must be “opened.” When an array is opened, TileDB reads and decodes the array and fragment data, which may require disk operations (and potentially decompression). An array can be opened once, and many queries issued to it before closing. Minimizing the number of array open and close operations can improve performance.

Configuration Parameters

The following runtime configuration parameters can tune the performance of several internal TileDB subsystems.

Cache size – sm.tile_cache_size
When a read query causes a tile to be read from disk, TileDB places the uncompressed tile in an in-memory LRU cache associated with the query’s context. When subsequent read queries in the same context request that tile, it may be copied directly from the cache instead of re-fetched from disk. The sm.tile_cache_size config parameter determines the overall size in bytes of the in-memory tile cache. Increasing it can lead to a higher cache hit ratio, and better performance.
Coordinate deduplication – sm.dedup_coords and sm.check_coord_dups
During sparse writes, setting sm.dedup_coords to true will cause TileDB to internally deduplicate cells being written so that multiple cells with the same coordinate tuples are not written to the array (which is an error). A lighter-weight check is enabled by default with sm.check_coord_dups, meaning TileDB will simply perform the check for duplicates and return an error if any are found. Disabling these checks can lead to better performance on writes.
Coordinate out-of-bounds-check – sm.check_coord_oob
During sparse writes, setting sm.check_coord_oob to true (default) will cause TileDB to internally check whether the given coordinates fall outside the domain or not. If you are certain that this is not possible in your application, you can set this param to false, avoiding the check and thus boosting performance.
Async query concurrency – sm.num_async_threads
By default only one thread is allocated to handle async queries. Increasing this parameter value can lead to better performance if you are issuing many async queries.
Thread pool size – sm.num_tbb_threads
TileDB internally parallelizes many expensive operations such as coordinate sorting. A TBB-based thread pool is used for these operations, and changing this config parameter from the default (while not recommended) can lead to better performance in certain circumstances.
Reader thread pool size – sm.num_reader_threads
Read operations for read queries can be issued to the VFS layer in parallel (the VFS layer may additionally parallelize large I/O operations). For some hardware configurations, increasing the number of parallel VFS read operations with this parameter may increase performance.
Writer thread pool size – sm.num_writer_threads
Write operations for write queries can be issued to the VFS layer in parallel (the VFS layer may additionally parallelize large I/O operations). For some hardware configurations, increasing the number of parallel VFS write operations with this parameter may increase performance.
VFS thread pool size – vfs.num_threads
The virtual filesystem (VFS) subsystem in TileDB maintains a separate thread pool per context for I/O operations. Reducing or increasing the VFS thread pool size can help control the level of concurrency used for I/O operations, which may lead to better performance in certain circumstances.
VFS parallelism – vfs.min_parallel_size and vfs.file.max_parallel_ops
The vfs.min_parallel_size parameter sets the minimum number of bytes that can go in a parallel VFS operation. This can help ensure that I/O requests are not broken into too small pieces, even if there are enough threads in the VFS thread pool to do so. Similarly, vfs.file.max_parallel_ops controls the maximum number of parallel operations for file:/// URIs, independently of the thread pool size, allowing you to over- or under-subscribe VFS threads.
S3 parallelism – vfs.s3.max_parallel_ops
This controls the maximum number of parallel operations for s3:// URIs independently of the VFS thread pool size, allowing you to over- or under-subscribe VFS threads. Oversubscription can be helpful in some cases with S3, to help hide I/O latency.
S3 write size – vfs.s3.multipart_part_size
Replacing vfs.min_parallel_size for S3 objects, this parameter controls the minimum part size of S3 multipart writes. Note that vfs.s3.multipart_part_size * vfs.s3.max_parallel_ops bytes will be buffered in memory by TileDB before actually submitting an S3 write request, at which point all of the parts of the multipart write are issued in parallel.

System Parameters

Hardware concurrency
The number of cores and hardware threads of the machine impacts the amount of parallelism TileDB can use internally to accelerate reads, writes and compression/decompression.
Storage backend (S3, local, etc)
The different types of storage backend (S3, local disk, etc) have different throughput and latency characteristics, which can impact query time.