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Tuesday, December 16, 2025

Costly Delta Lake S3 Storage Errors (And Tips on how to Repair Them)


1. Introduction: The Basis

Cloud object storage, reminiscent of S3, is the muse of any Lakehouse Structure. You’re the proprietor for the info saved in your Lakehouse, not the methods that use it. As knowledge quantity will increase, both as a consequence of ETL pipelines or extra customers querying tables, so do cloud storage prices.

In apply, we’ve recognized widespread pitfalls in how these storage buckets are configured, which lead to pointless prices for Delta Lake tables. Left unchecked, these habits can result in wasted storage and elevated community prices.

On this weblog, we’ll focus on the commonest errors and provide tactical steps to each detect and repair them. We’ll use a steadiness of instruments and techniques that leverage each the Databricks Information Intelligence Platform and AWS providers.

2. Key Architectural Issues

There are three facets of cloud storage for Delta tables we’ll contemplate on this weblog when optimizing prices:

Object vs. Desk Versioning

Cloud-native options alone for object versioning don’t work intuitively for Delta Lake tables. The truth is, it primarily contradicts Delta Lake as the 2 are competing to resolve the identical drawback–knowledge retention–in several methods.

To grasp this, let’s overview how Delta tables deal with versioning after which evaluate that with S3’s native object versioning.

How Delta Tables Deal with Versioning

Delta Lake tables write every transaction as a manifest file (in JSON or Parquet format) within the _delta_log/ listing, and these manifests level to the desk’s underlying knowledge information (in Parquet format). When knowledge is added, modified, or deleted, new knowledge information are created. Thus, at a file stage, every object is immutable. This method optimizes for environment friendly knowledge entry and strong knowledge integrity.

Delta Lake inherently manages knowledge versioning by storing all adjustments as a sequence of transactions within the transaction log. Every transaction represents a brand new model of the desk, permitting customers to time-travel to earlier states, revert to an older model, and audit knowledge lineage.

How S3 Handles Object Versioning

S3 additionally provides native object versioning as a bucket-level characteristic. When enabled, S3 retains a number of variations of an object; these can solely be 1 present model of the thing, and there could be a number of noncurrent variations.

When an object is overwritten or deleted, S3 marks the earlier model as noncurrent after which creates the brand new model as present. This provides safety towards unintentional deletions or overwrites.

The issue with that is that it conflicts with Delta Lake versioning in two methods:

  1. Delta Lake solely writes new transaction information and knowledge information; it doesn’t overwrite them.
    • If storage objects are a part of a Delta desk, we should always solely function on them utilizing a Delta Lake shopper such because the native Databricks Runtime or any engine that helps the open-source Unity Catalog REST API.
    • Delta Lake already supplies safety towards unintentional deletion by way of table-level versioning and time-travel capabilities.
  2. We vacuum Delta tables to take away information which are not referenced within the transaction log.
    • Nevertheless, due to S3’s object versioning, this doesn’t totally delete the info; as an alternative, it turns into a noncurrent model, which we nonetheless pay for.

Storage Tiers

Evaluating Storage Lessons

S3 provides versatile storage courses for storing knowledge at relaxation, which could be broadly categorized as scorching, cool, chilly, and archive. These check with how incessantly knowledge is accessed and the way lengthy it takes to retrieve:

Colder storage courses have a decrease price per GB to retailer knowledge, however incur greater prices and latency when retrieving it. We need to benefit from these for Lakehouse storage as properly, but when utilized with out warning, they will have important penalties for question efficiency and even lead to greater prices than merely storing every part in S3 Commonplace.

Storage Class Errors

Utilizing lifecycle insurance policies, S3 can routinely transfer information to totally different storage courses after a time frame from when the thing was created. Cool tiers like S3-IA look like a protected possibility on the floor as a result of they nonetheless have a quick retrieval time; nonetheless, this relies on precise question patterns.

For instance, let’s say we now have a Delta desk that’s partitioned by a created_dt DATE column, and it serves as a gold desk for reporting functions. We apply a lifecycle coverage that strikes information to S3-IA after 30 days to save lots of prices. Nevertheless, an analyst queries the desk with out a WHERE clause, or wants to make use of knowledge additional again, and makes use of WHERE created_dt >= curdate() – INTERVAL 90 DAYS, then a number of information in S3-IA shall be retrieved and incur the upper retrieval price. To the analyst, they might not notice they’re doing something improper, however the FinOps group will discover elevated S3-IA retrieval prices.

Even worse, let’s say after 90 days, we transfer the objects to the S3 Glacier Deep Archive or Glacier Versatile Retrieval class. The identical drawback happens, however this time the question really fails as a result of it makes an attempt to entry information that have to be restored or thawed prior to make use of. This restoration is a guide course of sometimes carried out by a cloud engineer or platform administrator, which might take as much as 12 hours to finish. Alternatively, you possibly can select the “Expedited” retrieval methodology, which takes 1-5 minutes. See Amazon’s docs for extra particulars on restoring objects from Glacier archival storage courses.

We’ll see easy methods to mitigate these storage class pitfalls shortly.

Information Switch Prices

The third class of high-priced Lakehouse storage errors is knowledge switch. Think about which cloud area your knowledge is saved in, from the place it’s accessed, and the way requests are routed inside your community.

When S3 knowledge is accessed from a area totally different than the S3 bucket, knowledge egress prices are incurred. This will rapidly grow to be a major line merchandise in your invoice and is extra widespread in use circumstances that require multi-region help, reminiscent of high-availability or disaster-recovery situations.

NAT Gateways

The most typical mistake on this class is letting your S3 site visitors route via your NAT Gateway. By default, sources in personal subnets will entry S3 by routing site visitors to the public S3 endpoint (e.g., s3.us-east-1.amazonaws.com). Since this can be a public host, the site visitors will route via your subnet’s NAT Gateway, which prices roughly $0.045 per GB. This may be present in AWS Price Explorer underneath Service = Amazon EC2 and Utilization Sort = NatGateway-Bytes or Utilization Sort = -DataProcessing-Bytes.

This consists of EC2 situations launched by Databricks basic clusters and warehouses, as a result of the EC2 situations are launched inside your AWS VPC. In case your EC2 situations are in a special Availability Zone (AZ) than the NAT Gateway, you additionally incur an extra price of roughly $0.01 per GB. This may be present in AWS Price Explorer underneath Service = Amazon EC2 and Utilization Sort = -DataTransfer-Regional-Bytes or Utilization Sort = DataTransfer-Regional-Bytes.

With these workloads sometimes being a major supply of S3 reads and writes, this error might account for a considerable proportion of your S3-related prices. Subsequent, we’ll break down the technical options to every of those issues.

3. Technical Answer Breakdown

Fixing NAT Gateway S3 Prices

S3 Gateway Endpoints

Let’s begin with presumably the simplest drawback to repair – VPC networking, in order that S3 site visitors doesn’t use the NAT Gateway and go over the general public Web. The only resolution is to make use of an S3 Gateway Endpoint, a regional VPC Endpoint Service that handles S3 site visitors for a similar area as your VPC, bypassing the NAT Gateway. S3 Gateway Endpoints don’t incur any prices for the endpoint or the info transferred via it.

Script: Establish Lacking S3 Gateway Endpoints

We offer the next Python script for finding VPCs inside a area that don’t at present have an S3 Gateway Endpoint.

Be aware: To make use of this or another scripts on this weblog, you need to have put in Python 3.9+ and boto3 (pip set up boto3). Moreover, these scripts can’t be run on Serverless compute with out utilizing Unity Catalog Service Credentials, as entry to your AWS sources is required.

Save the script to check_vpc_s3_endpoints.py and run the script with:

You need to see an output like the next:

After you have recognized these VPC candidates, please check with the AWS documentation to create S3 Gateway Endpoints.

Multi-Area S3 Networking

For superior use circumstances that require multi-region S3 patterns, we will make the most of S3 Interface Endpoints, which require extra setup effort. Please see our full weblog with instance price comparisons for extra particulars on these entry patterns:
https://www.databricks.com/weblog/optimizing-aws-s3-access-databricks

Basic vs Serverless Compute

Databricks additionally provides totally managed Serverless compute, together with Serverless Lakeflow Jobs, Serverless SQL Warehouses, and Serverless Lakeflow Spark Declarative Pipelines. With serverless compute, Databricks does the heavy lifting for you and already routes S3 site visitors via S3 Gateway Endpoints!

See Serverless compute airplane networking for extra particulars on how Serverless compute routes site visitors to S3.

Archival Assist in Databricks

Databricks provides archival help for S3 Glacier Deep Archive and Glacier Versatile Retrieval, out there in Public Preview for Databricks Runtime 13.3 LTS and later. Use this characteristic in case you should implement S3 storage class lifecycle insurance policies, however need to mitigate the sluggish/costly retrieval mentioned beforehand. Enabling archival help successfully tells Databricks to disregard information which are older than the desired interval.

Archival help solely permits queries that may be answered appropriately with out touching archived information. Due to this fact, it’s extremely beneficial to make use of VIEWs to limit queries to solely entry unarchived knowledge in these tables. In any other case, queries that require knowledge in archived information will nonetheless fail, offering customers with an in depth error message.

Be aware: Databricks doesn’t instantly work together with lifecycle administration insurance policies on the S3 bucket. It’s essential to use this desk property together with an everyday S3 lifecycle administration coverage to completely implement archival. For those who allow this setting with out setting lifecycle insurance policies in your cloud object storage, Databricks nonetheless ignores information based mostly on the desired threshold, however no knowledge is archived.

To make use of archival help in your desk, first set the desk property:

Then create a S3 lifecycle coverage on the bucket to transition objects to Glacier Deep Archive or Glacier Versatile Retrieval after the identical variety of days specified within the desk property.

Establish Dangerous Buckets

Subsequent, we’ll establish S3 bucket candidates for price optimization. The next script iterates S3 buckets in your AWS account and logs buckets which have object versioning enabled however no lifecycle coverage for deleting noncurrent variations.

The script ought to output candidate buckets like so:

Estimate Price Financial savings

Subsequent, we will use Price Explorer and S3 Lens to estimate the potential price financial savings for a S3 bucket’s unchecked noncurrent objects.

Amazon launched the S3 Lens service that delivers an out-of-the-box dashboard for S3 utilization, which is normally out there at https://console.aws.amazon.com/s3/lens/dashboard/default.

First, navigate to your S3 Lens dashboard > Overview > Traits and distributions. For the first metric, choose % noncurrent model bytes, and for the secondary metric, choose Noncurrent model bytes. You’ll be able to optionally filter by Account, Area, Storage Class, and/or Buckets on the prime of the dashboard.

Within the above instance, 40% of the storage is occupied by noncurrent model bytes, or ~40 TB of bodily knowledge.

Subsequent, navigate to AWS Price Explorer. On the precise aspect, change the filters:

  • Service: S3 (Easy Storage Service)
  • Utilization kind group: choose all the S3: Storage * utilization kind teams that apply:
    • S3: Storage – Categorical One Zone
    • S3: Storage – Glacier
    • S3: Storage – Glacier Deep Archive
    • S3: Storage – Clever Tiering
    • S3: Storage – One Zone IA
    • S3: Storage – Decreased Redundancy
    • S3: Storage – Commonplace
    • S3: Storage – Commonplace Rare Entry

Apply the filters, and alter the Group By to API operation to get a chart like the next:

Be aware: in case you filtered to particular buckets in S3 Lens, you need to match that scope in Price Explorer by filtering on Tag:Title to the title of your S3 bucket.

Combining these two experiences, we will estimate that by eliminating the noncurrent model bytes from our S3 buckets used for Delta Lake tables, we’d save ~40% of the typical month-to-month S3 storage price ($24,791) → $9,916 monthly!

Implement Optimizations

Subsequent, we start implementing the optimizations for noncurrent variations in a 2-step course of:

  1. Implement lifecycle insurance policies for noncurrent variations.
  2. (Optionally available) Disable object versioning on the S3 bucket.

Lifecycle Insurance policies for Noncurrent Variations

Within the AWS console (UI), navigate to the S3 bucket’s Administration tab, then click on Create lifecycle rule.

Select a rule scope:

  • In case your bucket solely shops Delta tables, choose ‘Apply to all objects within the bucket’.
  • In case your Delta tables are remoted to a prefix inside the bucket, choose ‘Restrict the scope of this rule utilizing a number of filters’, and enter the prefix (e.g., delta/).

Subsequent, verify the field Completely delete noncurrent variations of objects.

Subsequent, enter what number of days you need to hold noncurrent objects after they grow to be noncurrent. Be aware: This serves as a backup to guard towards unintentional deletion. For instance, if we use 7 days for the lifecycle coverage, then once we VACUUM a Delta desk to take away unused information, we could have 7 days to revive the noncurrent model objects in S3 earlier than they’re completely deleted.

Assessment the rule earlier than persevering with, then click on ‘Create rule’ to complete the setup.

This may also be achieved in Terraform with the aws_s3_bucket_lifecycle_configuration useful resource:

Disable Object Versioning

To disable object versioning on an S3 bucket utilizing the AWS console, navigate to the bucket’s Properties tab and edit the bucket versioning property.

Be aware: For current buckets which have versioning enabled, you possibly can solely droop versioning, not disable it. This suspends the creation of object variations for all operations however preserves any current object variations.

This may also be achieved in Terraform with the aws_s3_bucket_versioning useful resource:

Templates for Future Deployments

To make sure future S3 buckets are deployed with the very best practices, please use the Terraform modules offered in terraform-databricks-sra, such because the unity_catalog_catalog_creation module, which routinely creates the next sources:

Along with the Safety Reference Structure (SRA) modules, chances are you’ll check with the Databricks Terraform supplier guides for deploying VPC Gateway Endpoints for S3 when creating new workspaces.

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