Best Practices for Optmizing ClickHouse MergeTree on S3

Best Practices for Optmizing ClickHouse MergeTree on S3

ClickHouse’s integration with Amazon S3 storage provides powerful capabilities for managing large-scale data warehouses with cost-effective storage solutions. When implementing MergeTree tables with S3 backing, proper administrative practices are crucial for maintaining data integrity, performance, and operational efficiency.

Architecture Overview

Before diving into best practices, it’s essential to understand how ClickHouse utilises S3 storage. MergeTree tables can store data parts directly in S3 buckets while maintaining metadata locally. This hybrid approach allows for virtually unlimited storage capacity while preserving ClickHouse’s query performance characteristics.

Essential S3 Bucket Configuration

Recommended S3 Bucket Settings

Proper bucket configuration forms the foundation of a reliable ClickHouse S3 deployment:

Multi-part Upload Management

• Configure bucket lifecycle policies to automatically terminate incomplete multi-part uploads after 3-7 days
• This prevents accumulation of orphaned upload fragments that consume storage and increase costs
• Set up monitoring for failed uploads to identify potential connectivity or permission issues

File Management Policies

• Never implement automatic file deletion policies on ClickHouse S3 buckets
• Only ClickHouse itself or informed administrators should delete S3 objects
• Avoid mixing ClickHouse data with other applications in the same bucket to prevent accidental deletions

Access Control and Security

• Implement least-privilege IAM policies for ClickHouse service accounts
• Enable S3 bucket versioning for additional data protection
• Configure server-side encryption (SSE-S3 or SSE-KMS) for data at rest

Storage Configuration Setup

Defining S3 Storage Policies

<storage_configuration>
    <disks>
        <s3_disk>
            <type>s3</type>
            <endpoint>https://s3.amazonaws.com/your-clickhouse-bucket/</endpoint>
            <access_key_id>YOUR_ACCESS_KEY</access_key_id>
            <secret_access_key>YOUR_SECRET_KEY</secret_access_key>
            <region>us-east-1</region>
            <metadata_type>plain</metadata_type>
            <cache_enabled>true</cache_enabled>
            <cache_path>/var/lib/clickhouse/disks/s3_cache/</cache_path>
            <cache_size>10Gi</cache_size>
        </s3_disk>
    </disks>
    <policies>
        <s3_main>
            <volumes>
                <main>
                    <disk>s3_disk</disk>
                </main>
            </volumes>
        </s3_main>
    </policies>
</storage_configuration>

Performance Optimization Settings

Key configuration parameters for optimal performance:

• max_single_part_upload_size: Set to 32MB-64MB for better upload efficiency
• min_bytes_for_wide_part: Configure based on your typical part sizes
• s3_max_connections: Increase for high-throughput workloads (default: 1024)

Creating and Managing S3-Backed Tables

Table Creation Best Practices

CREATE TABLE events_s3
(
    event_date Date,
    user_id UInt64,
    event_type String,
    properties String
)
ENGINE = MergeTree()
PARTITION BY toYYYYMM(event_date)
ORDER BY (event_date, user_id)
SETTINGS storage_policy = 's3_main';

Table Deletion Considerations

When dropping S3-backed tables:

-- Safe deletion with cleanup
DROP TABLE events_s3 SYNC;

-- Verify S3 cleanup (may take time)
SELECT * FROM system.s3queue WHERE table = 'events_s3';

Important: Table deletion may not immediately remove S3 objects. Monitor cleanup processes and manually verify S3 bucket contents if necessary.

Zero-Copy Replication Management

Understanding Zero-Copy Replication

Zero-copy replication allows multiple ClickHouse replicas to share the same S3 data without duplicating storage. While this reduces costs, it introduces complexity in data management.

When to Disable Zero-Copy Replication

Consider disabling zero-copy replication when:

• Data consistency is more critical than storage costs
• Troubleshooting replication issues
• Operating in environments with unreliable network connectivity

-- Disable zero-copy replication for specific table
ALTER TABLE events_s3 MODIFY SETTING allow_s3_zero_copy_replication = 0;

-- Global setting in config.xml
<merge_tree>
    <allow_s3_zero_copy_replication>0</allow_s3_zero_copy_replication>
</merge_tree>

Monitoring and Maintenance

Essential Monitoring Queries

Track S3 file locations and storage usage:

-- Monitor S3 parts distribution
SELECT 
    table,
    disk_name,
    count() as parts_count,
    sum(bytes_on_disk) as total_bytes
FROM system.parts 
WHERE disk_name LIKE '%s3%'
GROUP BY table, disk_name;

-- Check for orphaned S3 objects
SELECT 
    database,
    table,
    name,
    disk_name,
    path
FROM system.parts 
WHERE disk_name LIKE '%s3%' 
    AND modification_time < now() - INTERVAL 1 DAY;

Performance Monitoring

-- S3 operation metrics
SELECT 
    event,
    value
FROM system.events 
WHERE event LIKE '%S3%'
ORDER BY event;

-- Cache hit rates for S3 disk
SELECT 
    disk_name,
    cache_hits,
    cache_misses,
    cache_hits / (cache_hits + cache_misses) as hit_rate
FROM system.disk_cache;

Troubleshooting Common Issues

Connection and Authentication Problems

• Verify IAM permissions include s3:GetObject, s3:PutObject, s3:DeleteObject
• Check network connectivity and DNS resolution for S3 endpoints
• Validate AWS credentials and region settings

Performance Issues

• Monitor cache hit rates and adjust cache size accordingly
• Review S3 request patterns and optimize part sizes
• Consider using S3 Transfer Acceleration for geographically distributed deployments

Data Consistency Concerns

• Implement regular data validation checks
• Monitor replication lag in multi-replica setups
• Establish backup and recovery procedures for critical data

Security Best Practices

Access Control

• Use IAM roles instead of access keys when possible
• Implement bucket policies to restrict access by IP or VPC
• Enable CloudTrail logging for audit purposes

Data Protection

• Configure cross-region replication for disaster recovery
• Implement MFA delete protection for critical buckets
• Regular security audits of bucket permissions and policies

Cost Optimization Strategies

Storage Class Management

• Use S3 Intelligent Tiering for automatic cost optimization
• Consider Glacier storage for long-term archival of old partitions
• Monitor storage costs and usage patterns regularly

Transfer Cost Reduction

• Minimize cross-region data transfers
• Use VPC endpoints to avoid internet gateway charges
• Optimize query patterns to reduce unnecessary S3 requests

Conclusion

Successful administration of ClickHouse MergeTree tables on S3 requires careful attention to bucket configuration, storage policies, and ongoing monitoring. By following these best practices, administrators can ensure reliable, performant, and cost-effective S3-backed ClickHouse deployments.

The key to success lies in understanding the unique characteristics of S3 storage, properly configuring both ClickHouse and AWS services, and maintaining vigilant monitoring of system performance and data integrity. Regular review and optimization of these practices will help maintain optimal performance as your data warehouse scales.

For organizations seeking expert guidance on ClickHouse S3 implementations, ChistaDATA offers fully managed services with 24/7 support to simplify your ClickHouse experience in both BYOC and cloud environments.

Further Reading:

ClickHouse® ReplacingMergeTree Explained: The Good, The Bad, and The Ugly

Pro Tricks to Build Cost-Efficient Analytics: Snowflake vs BigQuery vs ClickHouse® for Any Business

Using ClickHouse-Backup for Comprehensive ClickHouse® Backup and Restore Operations

Avoiding ClickHouse Fan Traps : A Technical Guide for High-Performance Analytics

Open Source Data Warehousing and Analytics

Integrating S3 with ClickHouse 

References

Integrating S3 with ClickHouse