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Optimize RocksDB Compaction for Openos BlockStore

This document explores RocksDB based solutions for Openos BlockStore mentioned in issue #16234.

Background​

Openos uses RocksDB as the underlying storage for its blockstore. RocksDB is a LSM-based key value store which consists of multiple logical levels, and data in each level is sorted by key (read amplification). In such leveled structure, each read hits at most one file for each level, while all other mutable operations including writes, deletions, and merge operations are implemented as append operations and will eventually create more logical levels which makes the read performance worse over time.

To make reads more performant over time, RocksDB periodically reduces the number of logical levels by running compaction in background, where part or multiple logical levels are merged into one, which increases the number of disk I/Os (write amplification) and storage (space amplification) required for storing each entry. In other words, RocksDB uses compactions to balance write, space, and read amplifications.

As different workloads have different requirements, RocksDB makes its options highly configurable. However, it also means its default settings might not be always suitable. This document focuses on RocksDB's compaction optimization for Openos's Blockstore.

Problems​

As mentioned in #16234, there're several issues in the Openos's BlockStore which runs RocksDB with level compaction. Here's a quick summary of the issues:

Long Write Stalls on Shred Insertions​

Remember that RocksDB periodically runs background compactions in order to keep the number of logical levels small in order to reach the target read amplification. However, when the background compactions cannot catch up the write rate, the number of logical levels will eventually exceeds the configured limit. In such case, RocksDB will rate-limit / stop all writes when it reaches soft / hard threshold.

In #14586, it is reported that the write stalls in Openos's use case can be 40 minutes long. It is also reported in #16234 that writes are also slowed-down, indicating the underlying RocksDB instance has reach the soft limit for write stall.

Deletions are not Processed in Time​

Deletions are processed in the same way as other write operations in RocksDB, where multiple entries associated with the same key are merged / deleted during the background compaction. Although the deleted entries will not be visible from the read side right after the deletion is issued, the deleted entries (including the original data entries and its deletion entries) will still occupy disk storage.

TBD: explain how write-key order makes this worse

High Write I/O from Write Amplification​

In addition to write stalls, it is also observed that compactions cause unwanted high write I/O. With the current design where level compaction is configured for BlockStore, it has ~30x write amplification (10x write amp per level and assuming three levels in average).

Current Design​

Blockstore stores three types of data in RocksDB: shred data, metadata, accounts and transactional data. Each stores in multiple different column families. For shred insertions, write batches are used to combine several shred insertions that update both shred data and metadata related column families, while column families related to accounts and transactional are unrelated.

In the current BlockStore, the default level compaction is used for all column families. As deletions are not processed in time by RocksDB, a slot-ID based compaction filter with periodic manual compactions is used in order to force the deletions to be processed. While this approach can guarantees deletions are processed for specified period of time which mitigates the write stall issue, period manual compactions will introduce additional write amplification.

The Proposed Design​

As all the above issues are compaction related, it can be solved with a proper compaction style and deletion policy. Fortunately, shred data column families, ShredData and ShredCode, which contribute to 99% of the storage size in shred insertion, have an unique write workload where write-keys are mostly monotonically increasing over time. This allows data to be persisted in sorted order naturally without compaction, and the deletion policy can be as simple as deleting the oldest file when the storage size reaches the cleanup trigger.

In the proposed design, we will leverage such unique property to aggressively config RocksDB to run as few compactions as possible while offering low read amplification with no write stalls.

Use FIFO Compaction for Shred Data Column Families​

As mentioned above, shred data column families, ShredData and ShredCode, which contribute to 99% of the storage size in shred insertion, have an unique write workload where write-keys are mostly monotonically increasing over time. As a result, after entries are flushed from memory into SST files, the keys are naturally sorted across multiple SST files where each SST file might have a small overlapping key range between at most two other SST files. In other words, files are sorted naturally from old to new, which allows us to use the First-In-First-Out compaction, or FIFO Compaction.

FIFO Compaction actually does not compact files. Instead, it simply deletes the oldest files when the storage size reaches the specified threshold. As a result, it has a constant 1 write amplification. In addition, as keys are naturally sorted across multiple SST files, each read can be answered by hitting mostly only one (or in the boundary case, two) file. This gives us close to 1 read amplification. As each key is only inserted once, we have space amplification 1.

Use Current Settings for Metadata Column Families​

The second type of the column families related to shred insertion is metadata column families. These metadata column families contributes ~1% of the shred insertion data in size. The largest metadata column family here is the Index column family, which occupies 0.8% of the shred insertion data.

As these column families only contribute ~1% of the shred insertion data in size, the current settings with default level compaction with compaction filter should be good enough for now. We can revisit later if these metadata column families become the performance bottleneck after we've optimized the shred data column families.

Benefits​

No More Write Stalls​

Write stall is a RocksDB's mechanism to slow-down or stop writes in order to allow compactions to catch up in order to keep read amplification low. Luckily, because keys in data shred column families are written in mostly monotonically increasing order, the resulting SST files are naturally sorted that always keeps read amplification close to 1. As a result, there is no need to stall writes in order to maintain the read amplification.

Deletions are Processed in time​

In FIFO compactions, deletions are happened immediately when the size of the column family reaches the configured trigger. As a result, deletions are always processed in time, and we don't need to worry about whether RocksDB picks the correct file to process the deletion as FIFO compaction always pick the oldest one, which is the correct deletion policy for shred data.

Low I/Os with Minimum Amplification Factors​

FIFO Compaction offers constant write amplification as it does not run any compactions in background while it usually has a large read amplification as each read must be answered by reaching every single SST file. However, it is not the case in the shred data column families because SST files are naturally sorted as write keys are inserted in mostly monotonically increasing order without duplication. This gives us 1 space amplification and close to 1 read amplification.

To sum up, if no other manual compaction is issued for quickly picking up deletions, FIFO Compaction offers the following amplification factors in Openos's BlockStore use case:

  • Write Amplification: 1 (all data is written once without compaction.)
  • Read Amplification: < 1.1 (assuming each SST file has 10% overlapping key range with another SST file.)
  • Space Amplification: 1 (same data never be written in more than one SST file, and no additional temporary space required for compaction.)

Migration​

Here we discuss Level to FIFO and FIFO to Level migrations:

Level to FIFO​

Theoretically, FIFO compaction is the superset of all other compaction styles, as it does not have any assumption of the LSM tree structure. However, the current RocksDB implementation does not offer such flexibility while it is theoretically doable.

As the current RocksDB implementation doesn't offer such flexibility, the best option is to extend the copy tool in the ledger tool to allow it also specifying the destired compaction style of the output DB. This approach also ensures the resulting FIFO compacted DB can clean up the SST files in the correct order, as the copy tool iterates from smaller (older) slots to bigger (latest) slots, leaving the resulting SST files generated in the correct time order, which allows FIFO compaction to delete the oldest data just by checking the file creation time during its clean up process.

FIFO to Level​

While one can opens a FIFO-compacted DB using level compaction, the DB will likely to encounter long write stalls. It is because FIFO compaction puts all files in level 0, and write stalls trigger when the number of level-0 files exceed the limit until all the level-0 files are compacted into other levels.

To avoid the start-up write stalls, a more efficient way to perform FIFO to level compaction is to do a manual compaction first, then open the DB.

Release Plan​

As the migration in either way cannot not be done smoothly in place, the release will be divided into the following steps:

  • v0 - merge FIFO compaction implementation with visible args.
  • v1 - visible args with a big warning stating you'll lose your ledger if you enable it
  • v2 - slow-roll and monitor FIFO compaction, fix any issues.
  • v3 - if needed, add migration support.

In step v1, FIFO will use a different rocksdb directory (something like rocksdb-v2 or rocksdb-fifo) to ensure that the validator will never mix two different formats and panic.

Experiments​

Single Node Benchmark Results​

To verify the effectiveness, I ran both 1m slots and 100m slots shred insertion benchmarks on my n2-standard-32 GC instance (32 cores 2800MHz cpu, 128GB memory, 2048GB SSD). Each slot contains 25 shreds, and the shreds are inserted with with 8 writers. Here are the summary of the result:

  • FIFO based validator: Shred insertion took 13450.8s, 185.8k shreds/s
  • Current setting: shred insertion took 30337.2s, 82.4k shreds/s

If we further remove the write lock inside the shred insertion to allow fully concurrent shred insertion, the proposed FIFO setting can inserts 295k shreds/s:

  • FIFO + no write lock: Shred insertion took 8459.3s, 295.5k shreds/s

The possibility of enabling fully concurrent multi-writer shred insertion is discussed in #21657.

Results from the Mainnet-Beta​

To further understand the performance, I setup two validator instances joining the Mainnet-Beta, but one with FIFO based validator and the other is based on the current setting. Two validators have the same machine spec (24-core 2.8kMHz CPU, 128GB memory, 768GB SSD for blockstore, and everything else stored in the 1024GB SSD.) Below are the results.

Disk Write Bytes​

I first compared the disk write bytes of the SSD for blockstore of the two instances. This number represents how many bytes written are required in order to store the same amount of logical data. It also reflects the write amplification factor of the storage.

  • FIFO based validator: ~15~20 MB/s
  • Current setting: vs 25~30 MB/s

The result shows that FIFO-based validator writes ~33% less data to perform the same task compared to the current setting.

Compaction Stats on Data and Coding Shred Column Family​

Another data point we have is the RocksDB compaction stats, which tells us how much resource is spent in compaction. Below shows the compaction stats on data and coding shreds:

  • FIFO based validator: 188.24 GB write, 1.27 MB/s write, 0.00 GB read, 0.00 MB/s read, 870.4 seconds
  • Current setting: 719.87 GB write, 4.88 MB/s write, 611.61 GB read, 4.14 MB/s read, 5782.6 seconds

The compaction stats show that FIFO based validator is 6.5x faster in compacting data shreds and coding shreds with fewer than 1/3 disk writes. In addition, there is no disk read involved in FIFO's compaction process.

Summary​

This documents proposes a FIFO-compaction based solution to the performance issues of blockstore #16234. It minimizes read / write / space amplification factors by leveraging the unique property of Openos BlockStore workload where write-keys are mostly monotonically increasing over time. Experimental results from the single node 100m slots insertion indicate the proposed solution can insert 185k shred/s, which is ~2.25x faster than current design that inserts 82k shreds/s. Experimental results from Mainnet-Beta also shows that the proposed FIFO-based solution can achieve same task with 33% fewer disk writes compared to the current design.