Understanding the Mutation Compactor

Oct 13, 2025 by wbrum.org 123 views

Mutation Compactor: Ensuring Accurate Garbage Collection

Understanding the Mutation Compactor

The mutation compactor is a crucial component in modern databases, responsible for optimizing storage and improving performance by eliminating unnecessary data. In the context of ScyllaDB, a distributed NoSQL database, the mutation compactor plays a vital role in maintaining data consistency and reducing storage requirements. However, a recent issue has been identified in the mutation compactor's garbage collection (GC) mechanism, which can lead to data resurrection and compromise data integrity.

The Issue with can_gc

The can_gc function in the mutation compactor determines whether a partition can be garbage collected. This function uses either non-shadowable or shadowable purgeable timestamps for the entire partition. However, the current implementation does not account for the difference between these two types of timestamps, leading to potential issues.

The Problem with Shadowable Tombstones

In ScyllaDB, shadowable tombstones are a type of tombstone that can be used to mark deleted data. These tombstones have a more relaxed maximum GC timestamp compared to regular tombstones. However, the current implementation of the mutation compactor does not store the maximum GC timestamp for shadowable tombstones separately. As a result, the cache variable _max_purgeable stores the value of the maximum GC timestamp for the first type of tombstone queried, which can be either non-shadowable or shadowable.

Consequences of Data Resurrection

When a shadowable tombstone is queried first and has a more relaxed maximum timestamp than regular tombstones, the cache variable _max_purgeable will store this value. As a result, all subsequent GC attempts will use this value, potentially leading to data resurrection. Data resurrection occurs when a deleted record is inadvertently restored due to incorrect garbage collection.

Solution and Backport

To address this issue, a separate member variable is needed to cache the maximum GC timestamp for shadowable tombstones. This will ensure that the correct maximum timestamp is used for each type of tombstone, preventing data resurrection. The fix requires a backport to all releases that have the commit 7d893a5ed9a, which added support for separate maximum GC timestamps for shadowable and non-shadowable timestamps.

Code Changes

The code changes required to fix this issue involve adding a new member variable to cache the maximum GC timestamp for shadowable tombstones. This variable will be used in conjunction with the existing cache variable _max_purgeable to ensure accurate garbage collection.

// Add a new member variable to cache the maximum GC timestamp for shadowable tombstones
std::atomic<uint64_t> _max_purgeable_shadowable;

// Update the can_gc function to use the correct cache variable
bool can_gc() {
    // Use the correct cache variable based on the type of tombstone
    if (is_shadowable_tombstone()) {
        return _max_purgeable_shadowable.load() >= _max_gc_timestamp;
    } else {
        return _max_purgeable.load() >= _max_gc_timestamp;
    }
}

Conclusion

The mutation compactor is a critical component in ScyllaDB, responsible for optimizing storage and improving performance. However, a recent issue has been identified in the garbage collection mechanism, which can lead to data resurrection and compromise data integrity. By adding a separate member variable to cache the maximum GC timestamp for shadowable tombstones, we can ensure accurate garbage collection and prevent data resurrection. The fix requires a backport to all releases that have the commit 7d893a5ed9a, which added support for separate maximum GC timestamps for shadowable and non-shadowable timestamps.
Mutation Compactor: Q&A

Frequently Asked Questions

The mutation compactor is a complex component in ScyllaDB, and understanding its behavior can be challenging. In this article, we'll address some of the most frequently asked questions related to the mutation compactor and its garbage collection mechanism.

Q: What is the mutation compactor, and what is its purpose?

A: The mutation compactor is a component in ScyllaDB responsible for optimizing storage and improving performance by eliminating unnecessary data. Its primary purpose is to compact data in the database, reducing storage requirements and improving query performance.

Q: What is the issue with the current garbage collection mechanism?

A: The current garbage collection mechanism in the mutation compactor does not account for the difference between non-shadowable and shadowable purgeable timestamps. This can lead to data resurrection, where deleted records are inadvertently restored due to incorrect garbage collection.

Q: What is data resurrection, and how does it occur?

A: Data resurrection occurs when a deleted record is inadvertently restored due to incorrect garbage collection. In the context of the mutation compactor, data resurrection can occur when a shadowable tombstone is queried first and has a more relaxed maximum timestamp than regular tombstones. The cache variable _max_purgeable will store this value, and all subsequent GC attempts will use this value, potentially leading to data resurrection.

Q: How can the issue be fixed?

A: The issue can be fixed by adding a separate member variable to cache the maximum GC timestamp for shadowable tombstones. This variable will be used in conjunction with the existing cache variable _max_purgeable to ensure accurate garbage collection.

Q: What code changes are required to fix the issue?

A: The code changes required to fix the issue involve adding a new member variable to cache the maximum GC timestamp for shadowable tombstones. This variable will be used in conjunction with the existing cache variable _max_purgeable to ensure accurate garbage collection.

// Add a new member variable to cache the maximum GC timestamp for shadowable tombstones
std::atomic<uint64_t> _max_purgeable_shadowable;

// Update the can_gc function to use the correct cache variable
bool can_gc() {
    // Use the correct cache variable based on the type of tombstone
    if (is_shadowable_tombstone()) {
        return _max_purgeable_shadowable.load() >= _max_gc_timestamp;
    } else {
        return _max_purgeable.load() >= _max_gc_timestamp;
    }
}

Q: Why is a backport required to all releases that have the commit 7d893a5ed9a?

A: A backport is required to all releases that have the commit 7d893a5ed9a because this commit added support for separate maximum GC timestamps for shadowable and non-shadowable timestamps. The fix requires updating the garbage collection mechanism to account for this change, which affects all releases that have this commit.

Q: What are the benefits of fixing this issue?

A: Fixing this issue will ensure accurate garbage collection and prevent data resurrection. This will improve data integrity and reduce the risk of data corruption. Additionally, fixing this issue will improve the overall performance and reliability of the mutation compactor.

Conclusion

The mutation compactor is a critical component in ScyllaDB, and understanding its behavior is essential for ensuring data integrity and improving performance. By addressing the issue with the current garbage collection mechanism and adding a separate member variable to cache the maximum GC timestamp for shadowable tombstones, we can ensure accurate garbage collection and prevent data resurrection.