DuckDB Array Null Issue: Query-Dependent?

by SLV Team 42 views

Hey guys! Let's dive into a peculiar issue encountered in DuckDB where array columns mysteriously display NULL values depending on the query being executed. This can be quite a head-scratcher, so let's break it down and see what's going on.

The Mystery of the Disappearing Array Values

So, what's the deal? Imagine you have a table with an array column, and for some rows, the array values just vanish into thin air, showing up as NULL. This isn't a consistent issue; it pops up only under specific query conditions. Check out these scenarios to get a clearer picture:

Scenario 1: The Curious Case of LIMIT and OFFSET

When using LIMIT and OFFSET to paginate through your data, you might notice that the array column (esm_embed in this case) returns NULL for certain entries. It's like the data is playing hide-and-seek!

select accession, esm_embed from (select accession, esm_embed from embeddings) limit 50 offset 110;

In this query, some esm_embed values are incorrectly shown as NULL. This is definitely not the behavior we expect, and it can throw a wrench in our data analysis.

Scenario 2: The WHERE Clause to the Rescue

Now, here's where it gets even more interesting. When you use a WHERE clause that filters based on the accession column, the array values magically reappear! It's like the WHERE clause is a secret key that unlocks the missing data.

select accession, esm_embed from embeddings where accession in (select accession from embeddings limit 50 offset 110);

In this case, the esm_embed values are correctly displayed. This suggests that the issue might be related to how DuckDB optimizes certain queries, especially those involving LIMIT and OFFSET.

Scenario 3: Parquet File Peculiarities

To further investigate, the user tried exporting a sample set of values as a Parquet file. Interestingly, subsets of the data didn't exhibit the same issue. However, when querying the entire Parquet file, the false NULLs reappeared. This indicates that the problem might be tied to the size or structure of the data when it's processed in bulk.

select accession, esm_embed from (select accession, esm_embed from embeddings) limit 50 offset 110;

This query produces the false NULLs, as we've seen before.

select accession, esm_embed from (select accession, esm_embed from read_parquet('./embeddings.parquet')) limit 50 offset 110;

But when reading from the Parquet file, the values are correct. This inconsistency is a crucial clue in understanding the issue.

Reproducing the Issue

To reproduce this issue, you'll need a dataset with an array column and a significant number of rows. The user in this case had a 2.7GB Parquet file, which unfortunately couldn't be easily shared due to its size. However, the provided SQL snippets give us a good starting point for creating a similar test case.

Key Steps to Reproduce

  1. Create a Table with an Array Column: You'll need a table that includes a column with array data. This could be an array of integers, strings, or any other data type.
  2. Insert a Large Number of Rows: Populate the table with enough data to make pagination with LIMIT and OFFSET necessary.
  3. Run Queries with LIMIT and OFFSET: Execute queries similar to the ones provided, using LIMIT and OFFSET to retrieve specific subsets of the data.
  4. Compare Results with and Without WHERE Clause: Observe whether the array values are displayed correctly when using a WHERE clause compared to when they are not.
  5. Test with Parquet Files: Export the data to a Parquet file and then query the file to see if the issue persists.

By following these steps, you can recreate the conditions under which the NULL values appear and help identify the root cause.

Technical Details

Let's look at the technical environment where this issue was observed. Knowing the specific versions and configurations can help narrow down the problem.

  • Operating System: RHEL 9.5
  • DuckDB Version: 1.4.1
  • DuckDB Client: CLI
  • Hardware: HPC Cluster
  • Testing Environment: Stable Release

This setup indicates a fairly standard environment, which means the issue is likely within DuckDB itself rather than being caused by exotic hardware or software configurations.

Possible Causes and Workarounds

So, what could be causing this strange behavior? Here are a few potential explanations:

  1. Query Optimization Issues: DuckDB's query optimizer might be making incorrect assumptions when dealing with LIMIT and OFFSET, leading to incorrect data retrieval. The optimizer's decisions can sometimes result in unexpected behavior, especially with complex queries.
  2. Data Loading and Storage: The way DuckDB reads and stores array data, especially from Parquet files, might have a bug. There could be an issue in how the data is deserialized or accessed under certain conditions.
  3. Memory Management: It's possible that memory management issues are at play. When dealing with large datasets and array columns, memory allocation and deallocation can become tricky. A memory-related bug could cause data corruption or incorrect NULL values.

Potential Workarounds

While we try to nail down the root cause, here are some temporary workarounds you can try:

  • Use a WHERE Clause: As demonstrated, using a WHERE clause that filters the data can sometimes prevent the issue. This might force DuckDB to use a different query plan that avoids the bug.
  • Avoid LIMIT and OFFSET: If possible, try alternative pagination methods. For example, you could use range-based filtering instead of OFFSET.
  • Split the Data: If you're working with a large Parquet file, try splitting it into smaller chunks. This can reduce the chances of encountering the issue, although it's not an ideal long-term solution.
  • Upgrade DuckDB: Check if there's a newer version of DuckDB available. Bug fixes are often included in new releases, so upgrading might resolve the issue.

Community Input and Collaboration

Now, it's your turn! Have you encountered a similar issue with DuckDB or other database systems? Do you have any insights or suggestions on what might be causing this? Sharing your experiences and ideas can help us get to the bottom of this mystery.

What You Can Do

  • Share Your Experiences: If you've seen something similar, let us know in the comments. The more information we gather, the better.
  • Try to Reproduce the Issue: If you have the technical chops, try to reproduce the issue using the steps outlined above. This will help us confirm the bug and narrow down the conditions under which it occurs.
  • Contribute to the Discussion: If you have any theories or potential solutions, share them! Even if your ideas don't pan out, they might spark a breakthrough.

Conclusion

The case of the disappearing array values in DuckDB is a puzzling one, but with a collaborative effort, we can unravel the mystery. By understanding the conditions under which the issue occurs, exploring potential causes, and sharing our experiences, we can help improve DuckDB and make it even more reliable.

So, let's keep the discussion going and work together to solve this intriguing problem! If you guys have any thoughts or insights, don't hesitate to chime in. Let's get to the bottom of this!

If you're facing this issue, you're not alone. The user who reported this, Nick Sexson from the University of Florida, has highlighted a significant challenge that many others might encounter. By addressing this, we can make DuckDB a more robust and user-friendly database for everyone.

Keep an eye on this space for updates as we continue to investigate. And remember, your input is invaluable in this process. Let's solve this together!

Keywords: DuckDB, array columns, NULL values, query optimization, Parquet files, LIMIT, OFFSET, bug, reproduce, workarounds