Troubleshooting High CPU Usage in ClickHouse


“Don’t watch the clock; do what it does. Keep going.” – Sam Levenson

High CPU usage in ClickHouse can be a common challenge, especially when dealing with large datasets and complex queries. It can impact query response times and overall system performance. Understanding the reasons behind high CPU consumption and having effective troubleshooting strategies are crucial for maintaining a well-performing ClickHouse cluster.

Common Reasons for High CPU Usage in ClickHouse

  1. Complex Queries: Queries that involve aggregations, joins, and subqueries can be CPU-intensive, particularly when processing large volumes of data.
  2. Insufficient Indexing: Lack of appropriate indexes or inefficient use of existing indexes can lead to full scans of tables, increasing CPU load.
  3. High Cardinality Columns: Columns with high cardinality, which have many distinct values, can be computationally expensive to process.
  4. Inefficient Data Models: Poorly designed data models, including schema design and table structures, can contribute to high CPU usage.
  5. Data Volume: Large datasets and high ingestion rates can put significant CPU load on ClickHouse, especially during merge operations.
  6. Resource Contentions: Resource contentions, such as CPU contention between ClickHouse and other processes, can lead to spikes in CPU usage.
  7. Suboptimal Configurations: Incorrect configurations, including Merge Tree settings and memory allocations, can impact CPU performance.

Troubleshooting High CPU Usage in ClickHouse

  1. Monitor System Resources: Use system monitoring tools to track CPU utilization over time. Identify periods of high CPU usage and correlate them with specific queries or operations.
  2. Query Profiling: Enable query profiling in ClickHouse to analyze which parts of queries are consuming the most CPU resources. Optimize or rewrite queries that are resource-intensive.
  3. Indexing and Partitions: Ensure that your tables have appropriate indexes, and consider using partitioning to reduce the data volume ClickHouse needs to scan.
  4. Optimize Complex Queries: Review and optimize complex queries by reducing unnecessary calculations, using appropriate joins, and avoiding Cartesian products.
  5. Materialized Views: Implement materialized views to precompute and store frequently used aggregations or transformations, reducing the need for CPU-intensive calculations.
  6. High Cardinality Columns: Use approximate distinct count functions (uniqExact, uniqCombined, uniqUpTo) for high cardinality columns to reduce CPU load.
  7. Resource Isolation: Isolate ClickHouse processes from other resource-intensive processes running on the same server to prevent resource contention.
  8. Configuration Tuning: Adjust ClickHouse configurations, such as Merge Tree settings and memory allocations, to better align with your workload.
  9. Load Balancing: If you’re running a ClickHouse cluster, ensure that queries are distributed evenly across nodes to avoid overloading specific nodes.
  10. Upgrade ClickHouse: Keep ClickHouse up to date with the latest releases, as newer versions often include performance optimizations and bug fixes.


High CPU usage in ClickHouse can result from various factors, including query complexity, indexing, data volume, and resource contentions. Troubleshooting and optimizing CPU performance require a combination of monitoring, query profiling, configuration tuning, and efficient query design. By addressing these factors, you can maintain a responsive and performant ClickHouse environment for your analytics needs.

To know more about troubleshooting in ClickHouse, do consider reading the following articles: 

About Shiv Iyer 222 Articles
Open Source Database Systems Engineer with a deep understanding of Optimizer Internals, Performance Engineering, Scalability and Data SRE. Shiv currently is the Founder, Investor, Board Member and CEO of multiple Database Systems Infrastructure Operations companies in the Transaction Processing Computing and ColumnStores ecosystem. He is also a frequent speaker in open source software conferences globally.