Clickhouse Best Practices

ClickHouse Best Practices

Comprehensive guidance for ClickHouse covering schema design, query optimization, data ingestion, and AI agent connectivity. Contains 31 rules across 4 main categories (schema, query, insert, agent), prioritized by impact.

Official docs: ClickHouse Best Practices

IMPORTANT: How to Apply This Skill

Before answering ClickHouse questions, follow this priority order:

1. Check for applicable rules in the rules/ directory
2. If rules exist: Apply them and cite them in your response using "Per rule-name..."
3. If no rule exists: Use the LLM's ClickHouse knowledge or search documentation
4. If uncertain: Use web search for current best practices
5. Always cite your source: rule name, "general ClickHouse guidance", or URL

Why rules take priority: ClickHouse has specific behaviors (columnar storage, sparse indexes, merge tree mechanics) where general database intuition can be misleading. The rules encode validated, ClickHouse-specific guidance.

Agent Connectivity & Query Workflow

Before querying ClickHouse, agents must establish a connection and follow the discovery workflow:

1. rules/agent-connect-mcp.md - Connection setup (MCP + CLI), credential discovery, output format selection
2. rules/agent-discovery-schema.md - CRITICAL: 7-step schema discovery workflow
3. rules/agent-query-safety.md - CRITICAL: LIMIT, timeouts, progressive exploration

Every agent session should follow this sequence:

1. Connect — establish connection via MCP or CLI (see agent-connect-mcp)
2. Discover — databases → tables → columns + comments → sort keys → skip indexes → sample → EXPLAIN
3. Plan — use sort key and skip index knowledge to write efficient WHERE clauses
4. Execute — run queries with LIMIT and timeouts
5. Recover — on timeout/memory errors, narrow filters and retry (see agent-query-safety)

Subagent architecture notes

If your system dispatches ClickHouse tasks to specialized subagents:

• Schema discovery + query execution: any model — the steps are procedural
• EXPLAIN analysis + query optimization: benefits from mid-tier reasoning
• Schema design review against all 28 rules: benefits from mid-tier reasoning

Review Procedures

For Schema Reviews (CREATE TABLE, ALTER TABLE)

Read these rule files in order:

1. rules/schema-pk-plan-before-creation.md - ORDER BY is immutable
2. rules/schema-pk-cardinality-order.md - Column ordering in keys
3. rules/schema-pk-prioritize-filters.md - Filter column inclusion
4. rules/schema-types-native-types.md - Proper type selection
5. rules/schema-types-minimize-bitwidth.md - Numeric type sizing
6. rules/schema-types-lowcardinality.md - LowCardinality usage
7. rules/schema-types-avoid-nullable.md - Nullable vs DEFAULT
8. rules/schema-partition-low-cardinality.md - Partition count limits
9. rules/schema-partition-lifecycle.md - Partitioning purpose

Check for:

• PRIMARY KEY / ORDER BY column order (low-to-high cardinality)
• Data types match actual data ranges
• LowCardinality applied to appropriate string columns
• Partition key cardinality bounded (100-1,000 values)
• ReplacingMergeTree has version column if used

For Query Reviews (SELECT, JOIN, aggregations)

Read these rule files:

1. rules/query-join-choose-algorithm.md - Algorithm selection
2. rules/query-join-filter-before.md - Pre-join filtering
3. rules/query-join-use-any.md - ANY vs regular JOIN
4. rules/query-index-skipping-indices.md - Secondary index usage
5. rules/schema-pk-filter-on-orderby.md - Filter alignment with ORDER BY

Check for:

• Filters use ORDER BY prefix columns
• JOINs filter tables before joining (not after)
• Correct JOIN algorithm for table sizes
• Skipping indices for non-ORDER BY filter columns

For Insert Strategy Reviews (data ingestion, updates, deletes)

Read these rule files:

1. rules/insert-batch-size.md - Batch sizing requirements
2. rules/insert-mutation-avoid-update.md - UPDATE alternatives
3. rules/insert-mutation-avoid-delete.md - DELETE alternatives
4. rules/insert-async-small-batches.md - Async insert usage
5. rules/insert-optimize-avoid-final.md - OPTIMIZE TABLE risks

Check for:

• Batch size 10K-100K rows per INSERT
• No ALTER TABLE UPDATE for frequent changes
• ReplacingMergeTree or CollapsingMergeTree for update patterns
• Async inserts enabled for high-frequency small batches

Output Format

Structure your response as follows:

## Rules Checked
- `rule-name-1` - Compliant / Violation found
- `rule-name-2` - Compliant / Violation found
...

## Findings

### Violations
- **`rule-name`**: Description of the issue
  - Current: [what the code does]
  - Required: [what it should do]
  - Fix: [specific correction]

### Compliant
- `rule-name`: Brief note on why it's correct

## Recommendations
[Prioritized list of changes, citing rules]

Rule Categories by Priority