Why we spent the last month eliminating PostgreSQL subtransactions

Stan Hu and Grzegorz Bizon ·
Sep 29, 2021 · 20 min read · Leave a comment

Since last June, we noticed the database on GitLab.com would mysteriously stall for minutes, which would lead to users seeing 500 errors during this time. Through a painstaking investigation over several weeks, we finally uncovered the cause of this: initiating a subtransaction via the SAVEPOINT SQL query while a long transaction is in progress can wreak havoc on database replicas. Thus launched a race, which we recently completed, to eliminate all SAVEPOINT queries from our code. Here's what happened, how we discovered the problem, and what we did to fix it.

The symptoms begin

On June 24th, we noticed that our CI/CD runners service reported a high error rate:

runners errors

A quick investigation revealed that database queries used to retrieve CI/CD builds data were timing out and that the unprocessed builds backlog grew at a high rate:

builds queue

Our monitoring also showed that some of the SQL queries were waiting for PostgreSQL lightweight locks (LWLocks):

aggregated lwlocks

In the following weeks we had experienced a few incidents like this. We were surprised to see how sudden these performance degradations were, and how quickly things could go back to normal:

ci queries latency

Introducing Nessie: Stalled database queries

In order to learn more, we extended our observability tooling to sample more data from pg_stat_activity. In PostgreSQL, the pg_stat_activity virtual table contains the list of all database connections in the system as well as what they are waiting for, such as a SQL query from the client. We observed a consistent pattern: the queries were waiting on SubtransControlLock. Below shows a graph of the URLs or jobs that were stalled:

endpoints locked

The purple line shows the sampled number of transactions locked by SubtransControlLock for the POST /api/v4/jobs/request endpoint that we use for internal communication between GitLab and GitLab Runners processing CI/CD jobs.

Although this endpoint was impacted the most, the whole database cluster appeared to be affected as many other, unrelated queries timed out.

This same pattern would rear its head on random days. A week would pass by without incident, and then it would show up for 15 minutes and disappear for days. Were we chasing the Loch Ness Monster?

Let's call these stalled queries Nessie for fun and profit.

What is a SAVEPOINT?

To understand SubtransControlLock (PostgreSQL 13 renamed this to SubtransSLRU), we first must understand how subtransactions work in PostgreSQL. In PostgreSQL, a transaction can start via a BEGIN statement, and a subtransaction can be started with a subsequent SAVEPOINT query. PostgreSQL assigns each of these a transaction ID (XID for short) when a transaction or a subtransaction needs one, usually before a client modifies data.

Why would you use a SAVEPOINT?

For example, let's say you were running an online store and a customer placed an order. Before the order is fullfilled, the system needs to ensure a credit card account exists for that user. In Rails, a common pattern is to start a transaction for the order and call find_or_create_by. For example:

Order.transaction do
  begin
    CreditAccount.transaction(requires_new: true) do
      CreditAccount.find_or_create_by(customer_id: customer.id)
  rescue ActiveRecord::RecordNotUnique
    retry
  end
  # Fulfill the order
  # ...
end

If two orders were placed around the same time, you wouldn't want the creation of a duplicate account to fail one of the orders. Instead, you would want the system to say, "Oh, an account was just created; let me use that."

That's where subtransactions come in handy: the requires_new: true tells Rails to start a new subtransaction if the application already is in a transaction. The code above translates into several SQL calls that look something like:

--- Start a transaction
BEGIN
SAVEPOINT active_record_1
--- Look up the account
SELECT * FROM credit_accounts WHERE customer_id = 1
--- Insert the account; this may fail due to a duplicate constraint
INSERT INTO credit_accounts (customer_id) VALUES (1)
--- Abort this by rolling back
ROLLBACK TO active_record_1
--- Retry here: Start a new subtransaction
SAVEPOINT active_record_2
--- Find the newly-created account
SELECT * FROM credit_accounts WHERE customer_id = 1
--- Save the data
RELEASE SAVEPOINT active_record_2
COMMIT

On line 7 above, the INSERT might fail if the customer account was already created, and the database unique constraint would prevent a duplicate entry. Without the first SAVEPOINT and ROLLBACK block, the whole transaction would have failed. With that subtransaction, the transaction can retry gracefully and look up the existing account.

What is SubtransControlLock?

As we mentioned earlier, Nessie returned at random times with queries waiting for SubtransControlLock. SubtransControlLock indicates that the query is waiting for PostgreSQL to load subtransaction data from disk into shared memory.

Why is this data needed? When a client runs a SELECT, for example, PostgreSQL needs to decide whether each version of a row, known as a tuple, is actually visible within the current transaction. It's possible that a tuple has been deleted or has yet to be committed by another transaction. Since only a top-level transaction can actually commit data, PostgreSQL needs to map a subtransaction ID (subXID) to its parent XID.

This mapping of subXID to parent XID is stored on disk in the pg_subtrans directory. Since reading from disk is slow, PostgreSQL adds a simple least-recently used (SLRU) cache in front for each backend process. The lookup is fast if the desired page is already cached. However, as Laurenz Albe discussed in his blog post, PostgreSQL may need to read from disk if the number of active subtransactions exceeds 64 in a given transaction, a condition PostgreSQL terms suboverflow. Think of it as the feeling you might get if you ate too many Subway sandwiches.

Suboverflowing (is that a word?) can bog down performance because as Laurenz said, "Other transactions have to update pg_subtrans to register subtransactions, and you can see in the perf output how they vie for lightweight locks with the readers."

Hunting for nested subtransactions

Laurenz's blog post suggested that we might be using too many subtransactions in one transaction. At first, we suspected we might be doing this in some of our expensive background jobs, such as project export or import. However, while we did see numerous SAVEPOINT calls in these jobs, we didn't see an unusual degree of nesting in local testing.

To isolate the cause, we started by adding Prometheus metrics to track subtransactions as a Prometheus metric by model. This led to nice graphs as the following:

subtransactions plot

While this was helpful in seeing the rate of subtransactions over time, we didn't see any obvious spikes that occurred around the time of the database stalls. Still, it was possible that suboverflow was happening.

To see if that was happening, we instrumented our application to track subtransactions and log a message whenever we detected more than 32 SAVEPOINT calls in a given transaction. Rails makes it possible for the application to subscribe to all of its SQL queries via ActiveSupport notifications. Our instrumentation looked something like this, simplified for the purposes of discussion:

ActiveSupport::Notifications.subscribe('sql.active_record') do |event|
  sql = event.payload.dig(:sql).to_s
  connection = event.payload[:connection]
  manager = connection&.transaction_manager

  context = manager.transaction_context
  return if context.nil?

  if sql.start_with?('BEGIN')
    context.set_depth(0)
  elsif cmd.start_with?('SAVEPOINT', 'EXCEPTION')
    context.increment_savepoints
  elsif cmd.start_with?('ROLLBACK TO SAVEPOINT')
    context.increment_rollbacks
  elsif cmd.start_with?('RELEASE SAVEPOINT')
    context.increment_releases
  elsif sql.start_with?('COMMIT', 'ROLLBACK')
    context.finish_transaction
  end
end

This code looks for the key SQL commands that initiate transactions and subtransactions and increments counters when they occurred. After a COMMIT, we log a JSON message that contained the backtrace and the number of SAVEPOINT and RELEASES calls. For example:

{
  "sql": "/*application:web,correlation_id:01FEBFH1YTMSFEEHS57FA8C6JX,endpoint_id:POST /api/:version/projects/:id/merge_requests/:merge_request_iid/approve*/ BEGIN",
  "savepoints_count": 1,
  "savepoint_backtraces": [
    [
      "app/models/application_record.rb:75:in `block in safe_find_or_create_by'",
      "app/models/application_record.rb:75:in `safe_find_or_create_by'",
      "app/models/merge_request.rb:1859:in `ensure_metrics'",
      "ee/lib/analytics/merge_request_metrics_refresh.rb:11:in `block in execute'",
      "ee/lib/analytics/merge_request_metrics_refresh.rb:10:in `each'",
      "ee/lib/analytics/merge_request_metrics_refresh.rb:10:in `execute'",
      "ee/app/services/ee/merge_requests/approval_service.rb:57:in `calculate_approvals_metrics'",
      "ee/app/services/ee/merge_requests/approval_service.rb:45:in `block in create_event'",
      "ee/app/services/ee/merge_requests/approval_service.rb:43:in `create_event'",
      "app/services/merge_requests/approval_service.rb:13:in `execute'",
      "ee/app/services/ee/merge_requests/approval_service.rb:14:in `execute'",
      "lib/api/merge_request_approvals.rb:58:in `block (3 levels) in <class:MergeRequestApprovals>'",
    ]
  "rollbacks_count": 0,
  "releases_count": 1
}

This log message contains not only the number of subtransactions via savepoints_count, but it also contains a handy backtrace that identifies the exact source of the problem. The sql field also contains Marginalia comments that we tack onto every SQL query. These comments make it possible to identify what HTTP request initiated the SQL query.

Taking a hard look at PostgreSQL

The new instrumentation showed that while the application regularly used subtransactions, it never exceeded 10 nested SAVEPOINT calls.

Meanwhile, Nikolay Samokhvalov, founder of Postgres.ai, performed a battery of tests trying to replicate the problem. He replicated Laurenz's results when a single transaction exceeded 64 subtransactions, but that wasn't happening here.

When the database stalls occurred, we observed a number of patterns:

  1. Only the replicas were affected; the primary remained unaffected.
  2. There was a long-running transaction, usually relating to PostgreSQL's autovacuuming, during the time. The stalls stopped quickly after the transaction ended.

Why would this matter? Analyzing the PostgreSQL source code, Senior Support Engineer Catalin Irimie posed an intriguing question that led to a breakthrough in our understanding:

Does this mean that, having subtransactions spanning more than 32 cache pages, concurrently, would trigger the exclusive SubtransControlLock because we still end up reading them from the disk?

Reproducing the problem with replicas

To answer this, Nikolay immediately modified his test to involve replicas and long-running transactions. Within a day, he reproduced the problem:

Nikolay experiment

The image above shows that transaction rates remain steady around 360,000 transactions per second (TPS). Everything was proceeding fine until the long-running transaction started on the primary. Then suddenly the transaction rates plummeted to 50,000 TPS on the replicas. Canceling the long transaction immediately caused the transaction rate to return.

What is going on here?

In his blog post, Nikolay called the problem Subtrans SLRU overflow. In a busy database, it's possible for the size of the subtransaction log to grow so large that the working set no longer fits into memory. This results in a lot of cache misses, which in turn causes a high amount of disk I/O and CPU as PostgreSQL furiously tries to load data from disk to keep up with all the lookups.

As mentioned earlier, the subtransaction cache holds a mapping of the subXID to the parent XID. When PostgreSQL needs to look up the subXID, it calculates in which memory page this ID would live, and then does a linear search to find in the memory page. If the page is not in the cache, it evicts one page and loads the desired one into memory. The diagram below shows the memory layout of the subtransaction SLRU.

Subtrans SLRU

By default, each SLRU page is an 8K buffer holding 4-byte parent XIDs. This means 8192/4 = 2048 transaction IDs can be stored in each page.

Note that there may be gaps in each page. PostgreSQL will cache XIDs as needed, so a single XID can occupy an entire page.

There are 32 (NUM_SUBTRANS_BUFFERS) pages, which means up to 65K transaction IDs can be stored in memory. Nikolay demonstrated that in a busy system, it took about 18 seconds to fill up all 65K entries. Then performance dropped off a cliff, making the database replicas unusable.

To our surprise, our experiments also demonstrated that a single SAVEPOINT during a long-transaction could initiate this problem if many writes also occurred simultaneously. That is, it wasn't enough just to reduce the frequency of SAVEPOINT; we had to eliminate them completely.

Why does a single SAVEPOINT cause problems?

To answer this question, we need to understand what happens when a SAVEPOINT occurs in one query while a long-running transaction is running.

We mentioned earlier that PostgreSQL needs to decide whether a given row is visible to support a feature called multi-version concurrency control, or MVCC for short. It does this by storing hidden columns, xmin and xmax, in each tuple.

xmin holds the XID of when the tuple was created, and xmax holds the XID when it was marked as dead (0 if the row is still present). In addition, at the beginning of a transaction, PostgreSQL records metadata in a database snapshot. Among other items, this snapshot records the oldest XID and the newest XID in its own xmin and xmax values.

This metadata helps PostgreSQL determine whether a tuple is visible. For example, a committed XID that started before xmin is definitely visible, while anything after xmax is invisible.

What does this have to do with long transactions?

Long transactions are bad in general because they can tie up connections, but they can cause a subtly different problem on a replica. On the replica, a single SAVEPOINT during a long transaction causes a snapshot to suboverflow. Remember that dragged down performance in the case where we had more than 64 subtransactions.

Fundamentally, the problem happens because a replica behaves differently from a primary when creating snapshots and checking for tuple visibility. The diagram below illustrates an example with some of the data structures used in PostgreSQL:

Diagram of subtransaction handling in replicas

On the top of this diagram, we can see the XIDs increase at the beginning of a subtransaction: the INSERT after the BEGIN gets 1, and the subsequent INSERT in SAVEPOINT gets 2. Another client comes along and performs a INSERT and SELECT at XID 3.

On the primary, PostgreSQL stores the transactions in progress in a shared memory segment. The process array (procarray) stores XID 1 with the first connection, and the database also writes that information to the pg_xact directory. XID 2 gets stored in the pg_subtrans directory, mapped to its parent, XID 1.

If a read happens on the primary, the snapshot generated contains xmin as 1, and xmax as 3. txip holds a list of transactions in progress, and subxip holds a list of subtransactions in progress.

However, neither the procarray nor the snapshot are shared directly with the replica. The replica receives all the data it needs from the write-ahead log (WAL).

Playing the WAL back one entry at time, the replica populates a shared data structure called KnownAssignedIds. It contains all the transactions in progress on the primary. Since this structure can only hold a limited number of IDs, a busy database with a lot of active subtransactions could easily fill this buffer. PostgreSQL made a design choice to kick out all subXIDs from this list and store them in the pg_subtrans directory.

When a snapshot is generated on the replica, notice how txip is blank. A PostgreSQL replica treats all XIDs as though they are subtransactions and throws them into the subxip bucket. That works because if a XID has a parent XID, then it's a subtransaction. Otherwise, it's a normal transaction. The code comments explain the rationale.

However, this means the snapshot is missing subXIDs, and that could be bad for MVCC. To deal with that, the replica also updates lastOverflowedXID:

 * When we throw away subXIDs from KnownAssignedXids, we need to keep track of
 * that, similarly to tracking overflow of a PGPROC's subxids array.  We do
 * that by remembering the lastOverflowedXID, ie the last thrown-away subXID.
 * As long as that is within the range of interesting XIDs, we have to assume
 * that subXIDs are missing from snapshots.  (Note that subXID overflow occurs
 * on primary when 65th subXID arrives, whereas on standby it occurs when 64th
 * subXID arrives - that is not an error.)

What is this "range of interesting XIDs"? We can see this in the code below:

if (TransactionIdPrecedesOrEquals(xmin, procArray->lastOverflowedXid))
    suboverflowed = true;

If lastOverflowedXid is smaller than our snapshot's xmin, it means that all subtransactions have completed, so we don't need to check for subtransactions. However, in our example:

  1. xmin is 1 because of the transaction.
  2. lastOverflowXid is 2 because of the SAVEPOINT.

This means suboverflowed is set to true here, which tells PostgreSQL that whenever a XID needs to be checked, check to see if it has a parent XID. Remember that this causes PostgreSQL to:

  1. Look up the subXID for the parent XID in the SLRU cache.
  2. If this doesn't exist in the cache, fetch the data from pg_trans.

In a busy system, the requested XIDs could span an ever-growing range of values, which could easily exhaust the 64K entries in the SLRU cache. This range will continue to grow as long as the transaction runs; the rate of increase depends on how many updates are happening on the prmary. As soon as the transaction terminates, the suboverflowed state gets set to false.

In other words, we've replicated the same conditions as we saw with 64 subtransactions, only with a single SAVEPOINT and a long transaction.

What can we do about getting rid of Nessie?

There are three options:

  1. Eliminate SAVEPOINT calls completely.
  2. Eliminate all long-running transactions.
  3. Apply Andrey Borodin's patches to PostgreSQL and increase the subtransaction cache.

We chose the first option because most uses of subtransaction could be removed fairly easily. There were a number of approaches we took:

  1. Perform updates outside of a subtransaction. Examples: 1, 2
  2. Rewrite a query to use a INSERT or an UPDATE with an ON CONFLICT clause to deal with duplicate constraint violations. Examples: 1, 2, 3
  3. Live with a non-atomic find_or_create_by. We used this approach sparingly. Example: 1

In addition, we added an alert whenever the application used a a single SAVEPOINT:

subtransaction alert

This had the side benefit of flagging a minor bug.

Why not eliminate all long-running transactions?

In our database, it wasn't practical to eliminate all long-running transactions because we think many of them happened via database autovacuuming, but we're not able to reproduce this yet. We are working on partitioning the tables and sharding the database, but this is a much more time-consuming problem than removing all subtransactions.

What about the PostgreSQL patches?

Although we tested Andrey's PostgreSQL patches, we did not feel comfortable deviating from the official PostgreSQL releases. Plus, maintaining a custom patched release over upgrades would add a significant maintenance burden for our infrastructure team. Our self-managed customers would also not benefit unless they used a patched database.

Andrey's patches do two main things:

  1. Allow administrators to change the SLRU size to any value.
  2. Adds an associative cache. to make it performant to use a large cache value.

Remember that the SLRU cache does a linear search for the desired page. That works fine when there are only 32 pages to search, but if you increase the cache size to 100 MB the search becomes much more expensive. The associative cache makes the lookup fast by indexing pages with a bitmask and looking up the entry with offsets from the remaining bits. This mitigates the problem because a transaction would need to be several magnitudes longer to cause a problem.

Nikolay demonstrated that the SAVEPOINT problem disappeared as soon as we increased the SLRU size to 100 MB with those patches. With a 100 MB cache, PostgreSQL can cache 26.2 million IDs (104857600/4), far more than the measely 65K.

These patches are currently awaiting review, but in our opinion they should be given high priority for PostgreSQL 15.

Conclusion

Since removing all SAVEPOINT queries, we have not seen Nessie rear her head again. If you are running PostgreSQL with read replicas, we strongly recommend that you also remove all subtransactions until further notice.

PostgreSQL is a fantastic database, and its well-commented code makes it possible to understand its limitations under different configurations.

We would like to thank the GitLab community for bearing with us while we iron out this production issue.

We are also grateful for the support from Nikolay Samokhvalov and Catalin Irimie, who contributed to understanding where our Loch Ness Monster was hiding.

Cover image by Khadi Ganiev on iStock, licensed under standard license

“Follow along as we investigate the mysterious case of the Loch Ness Monster hiding in the stalled database (really!). We banished Nessie by eliminating PostgreSQL subtransactions. Here's a step-by-step look at what we did, and why you might want to do this as well.” – Stan Hu and Grzegorz Bizon

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