@cubis/foundry 0.3.10

package/Ai Agent Workflow/skills/database-optimizer/references/mysql-tuning.md

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+# MySQL Tuning
+
+> Reference for: Database Optimizer
+> Load when: MySQL-specific optimizations, InnoDB tuning
+
+## InnoDB Memory Configuration
+
+### Buffer Pool
+
+```sql
+-- Recommended: 70-80% of system RAM for dedicated MySQL server
+-- For 16GB RAM server:
+SET GLOBAL innodb_buffer_pool_size = 12884901888;  -- 12GB
+
+-- Check buffer pool usage
+SHOW GLOBAL STATUS LIKE 'Innodb_buffer_pool_%';
+
+-- Buffer pool hit ratio (target: >99%)
+SELECT
+    (1 - (Innodb_buffer_pool_reads / Innodb_buffer_pool_read_requests)) * 100 as hit_ratio
+FROM (
+    SELECT
+        VARIABLE_VALUE as Innodb_buffer_pool_reads
+    FROM performance_schema.global_status
+    WHERE VARIABLE_NAME = 'Innodb_buffer_pool_reads'
+) reads,
+(
+    SELECT
+        VARIABLE_VALUE as Innodb_buffer_pool_read_requests
+    FROM performance_schema.global_status
+    WHERE VARIABLE_NAME = 'Innodb_buffer_pool_read_requests'
+) requests;
+
+-- Buffer pool instances (for multi-core systems)
+-- Recommended: 1 instance per 1GB, max 64
+SET GLOBAL innodb_buffer_pool_instances = 8;
+```
+
+### Sort and Join Buffers
+
+```sql
+-- Sort buffer per connection
+SET GLOBAL sort_buffer_size = 2097152;  -- 2MB
+
+-- Join buffer for full joins
+SET GLOBAL join_buffer_size = 2097152;  -- 2MB
+
+-- Temporary table size
+SET GLOBAL tmp_table_size = 67108864;  -- 64MB
+SET GLOBAL max_heap_table_size = 67108864;  -- 64MB
+
+-- Monitor temp table usage
+SHOW GLOBAL STATUS LIKE 'Created_tmp%';
+```
+
+## Query Cache (Deprecated in 8.0)
+
+```sql
+-- MySQL 5.7 and earlier
+-- Note: Removed in MySQL 8.0
+SET GLOBAL query_cache_type = 1;
+SET GLOBAL query_cache_size = 67108864;  -- 64MB
+
+-- Check query cache effectiveness
+SHOW STATUS LIKE 'Qcache%';
+
+-- Query cache hit ratio
+SELECT
+    Qcache_hits / (Qcache_hits + Com_select) * 100 as cache_hit_ratio
+FROM (
+    SELECT VARIABLE_VALUE as Qcache_hits
+    FROM performance_schema.global_status
+    WHERE VARIABLE_NAME = 'Qcache_hits'
+) hits,
+(
+    SELECT VARIABLE_VALUE as Com_select
+    FROM performance_schema.global_status
+    WHERE VARIABLE_NAME = 'Com_select'
+) selects;
+```
+
+## InnoDB Performance Settings
+
+### Log Files and Flushing
+
+```sql
+-- InnoDB log file size (larger = better write performance)
+-- Recommended: 1-2GB for write-heavy workloads
+SET GLOBAL innodb_log_file_size = 1073741824;  -- 1GB
+
+-- Log buffer size
+SET GLOBAL innodb_log_buffer_size = 16777216;  -- 16MB
+
+-- Flush method (O_DIRECT for dedicated server, avoids double buffering)
+-- Set in my.cnf
+innodb_flush_method = O_DIRECT
+
+-- Flush log at transaction commit
+-- 1 = full ACID (default, safest)
+-- 2 = write to OS cache, flush every second
+-- 0 = write and flush every second (fastest, risk data loss)
+SET GLOBAL innodb_flush_log_at_trx_commit = 1;
+
+-- For replication slaves or analytics (trade safety for speed)
+SET GLOBAL innodb_flush_log_at_trx_commit = 2;
+```
+
+### I/O Configuration
+
+```sql
+-- Read I/O threads
+SET GLOBAL innodb_read_io_threads = 8;
+
+-- Write I/O threads
+SET GLOBAL innodb_write_io_threads = 8;
+
+-- I/O capacity (IOPS your storage can handle)
+-- For SSD: 5000-20000
+SET GLOBAL innodb_io_capacity = 10000;
+SET GLOBAL innodb_io_capacity_max = 20000;
+
+-- Flush method for optimal I/O
+-- my.cnf:
+innodb_flush_method = O_DIRECT
+innodb_flush_neighbors = 0  -- Disable for SSD
+```
+
+### Thread Configuration
+
+```sql
+-- Max connections
+SET GLOBAL max_connections = 200;
+
+-- Thread cache (reuse threads)
+SET GLOBAL thread_cache_size = 100;
+
+-- Check thread cache effectiveness
+SHOW STATUS LIKE 'Threads_%';
+SHOW STATUS LIKE 'Connections';
+
+-- Thread cache hit ratio (target: >90%)
+SELECT
+    (1 - (Threads_created / Connections)) * 100 as thread_cache_hit_ratio
+FROM (
+    SELECT VARIABLE_VALUE as Threads_created
+    FROM performance_schema.global_status
+    WHERE VARIABLE_NAME = 'Threads_created'
+) created,
+(
+    SELECT VARIABLE_VALUE as Connections
+    FROM performance_schema.global_status
+    WHERE VARIABLE_NAME = 'Connections'
+) conns;
+```
+
+## Query Optimization
+
+### Slow Query Log
+
+```sql
+-- Enable slow query logging
+SET GLOBAL slow_query_log = 'ON';
+SET GLOBAL long_query_time = 1.0;  -- Log queries > 1 second
+SET GLOBAL log_queries_not_using_indexes = 'ON';
+
+-- Slow query log file location
+SET GLOBAL slow_query_log_file = '/var/log/mysql/slow-query.log';
+
+-- Analyze slow query log with pt-query-digest
+-- $ pt-query-digest /var/log/mysql/slow-query.log
+
+-- Check slow query status
+SHOW GLOBAL STATUS LIKE 'Slow_queries';
+```
+
+### Performance Schema
+
+```sql
+-- Enable performance schema (my.cnf)
+performance_schema = ON
+
+-- Top queries by total execution time
+SELECT
+    DIGEST_TEXT,
+    COUNT_STAR as exec_count,
+    ROUND(AVG_TIMER_WAIT / 1000000000000, 3) as avg_time_sec,
+    ROUND(SUM_TIMER_WAIT / 1000000000000, 3) as total_time_sec,
+    ROUND((SUM_TIMER_WAIT / SUM(SUM_TIMER_WAIT) OVER ()) * 100, 2) as pct
+FROM performance_schema.events_statements_summary_by_digest
+ORDER BY SUM_TIMER_WAIT DESC
+LIMIT 10;
+
+-- Full table scans
+SELECT * FROM sys.statements_with_full_table_scans
+ORDER BY exec_count DESC
+LIMIT 10;
+
+-- Tables with high I/O
+SELECT
+    object_schema,
+    object_name,
+    count_read,
+    count_write,
+    count_fetch,
+    SUM_TIMER_WAIT / 1000000000000 as total_latency_sec
+FROM performance_schema.table_io_waits_summary_by_table
+WHERE object_schema NOT IN ('mysql', 'performance_schema', 'sys')
+ORDER BY SUM_TIMER_WAIT DESC
+LIMIT 10;
+```
+
+## Index Optimization
+
+### Index Statistics
+
+```sql
+-- Update index statistics
+ANALYZE TABLE users;
+
+-- Check index cardinality
+SHOW INDEX FROM users;
+
+-- Find duplicate/redundant indexes
+SELECT
+    a.table_schema,
+    a.table_name,
+    a.index_name as index1,
+    a.column_name,
+    b.index_name as index2
+FROM information_schema.statistics a
+JOIN information_schema.statistics b
+    ON a.table_schema = b.table_schema
+    AND a.table_name = b.table_name
+    AND a.seq_in_index = b.seq_in_index
+    AND a.column_name = b.column_name
+    AND a.index_name != b.index_name
+WHERE a.table_schema NOT IN ('mysql', 'information_schema', 'performance_schema', 'sys')
+ORDER BY a.table_schema, a.table_name, a.index_name;
+
+-- Find unused indexes
+SELECT
+    object_schema,
+    object_name,
+    index_name
+FROM performance_schema.table_io_waits_summary_by_index_usage
+WHERE index_name IS NOT NULL
+  AND count_star = 0
+  AND object_schema NOT IN ('mysql', 'performance_schema', 'sys')
+ORDER BY object_schema, object_name;
+```
+
+### Covering Indexes
+
+```sql
+-- Create covering index
+CREATE INDEX idx_users_email_name_created
+ON users(email, name, created_at);
+
+-- Query can use covering index
+EXPLAIN
+SELECT name, created_at FROM users WHERE email = 'user@example.com';
+-- Look for "Using index" in Extra column
+
+-- Force index usage for testing
+SELECT name FROM users FORCE INDEX (idx_users_email_name_created)
+WHERE email = 'user@example.com';
+```
+
+## Partitioning
+
+### Range Partitioning
+
+```sql
+-- Create partitioned table
+CREATE TABLE events (
+    id BIGINT NOT NULL AUTO_INCREMENT,
+    event_type VARCHAR(50),
+    created_at DATETIME NOT NULL,
+    data JSON,
+    PRIMARY KEY (id, created_at)
+) PARTITION BY RANGE (YEAR(created_at)) (
+    PARTITION p2023 VALUES LESS THAN (2024),
+    PARTITION p2024 VALUES LESS THAN (2025),
+    PARTITION p2025 VALUES LESS THAN (2026),
+    PARTITION pmax VALUES LESS THAN MAXVALUE
+);
+
+-- Query with partition pruning
+EXPLAIN PARTITIONS
+SELECT * FROM events
+WHERE created_at >= '2024-01-01' AND created_at < '2024-02-01';
+-- Should show "partitions: p2024"
+
+-- Add new partition
+ALTER TABLE events
+ADD PARTITION (PARTITION p2026 VALUES LESS THAN (2027));
+
+-- Drop old partition (fast delete)
+ALTER TABLE events DROP PARTITION p2023;
+```
+
+### List Partitioning
+
+```sql
+-- Partition by discrete values
+CREATE TABLE orders (
+    id BIGINT NOT NULL AUTO_INCREMENT,
+    user_id BIGINT,
+    status VARCHAR(20),
+    PRIMARY KEY (id, status)
+) PARTITION BY LIST COLUMNS(status) (
+    PARTITION p_pending VALUES IN ('pending', 'processing'),
+    PARTITION p_completed VALUES IN ('completed', 'shipped'),
+    PARTITION p_cancelled VALUES IN ('cancelled', 'refunded')
+);
+```
+
+## Replication Optimization
+
+### Binary Log Settings
+
+```sql
+-- Binary log format
+SET GLOBAL binlog_format = 'ROW';  -- ROW, STATEMENT, or MIXED
+
+-- Binary log cache size
+SET GLOBAL binlog_cache_size = 1048576;  -- 1MB per transaction
+
+-- Sync binary log (durability vs performance)
+SET GLOBAL sync_binlog = 1;  -- Safest, sync after each commit
+-- sync_binlog = 0  -- Fastest, let OS handle flushing
+
+-- Expire binary logs after N days
+SET GLOBAL binlog_expire_logs_seconds = 604800;  -- 7 days
+```
+
+### Replication Lag Monitoring
+
+```sql
+-- On replica: Check replication lag
+SHOW SLAVE STATUS\G
+
+-- Parse seconds behind master
+SELECT
+    IF(Slave_IO_Running = 'Yes' AND Slave_SQL_Running = 'Yes',
+       Seconds_Behind_Master,
+       NULL) as replication_lag_seconds
+FROM (SHOW SLAVE STATUS) s;
+
+-- Parallel replication (MySQL 8.0+)
+SET GLOBAL slave_parallel_workers = 4;
+SET GLOBAL slave_parallel_type = 'LOGICAL_CLOCK';
+```
+
+## Table Optimization
+
+### Table Maintenance
+
+```sql
+-- Optimize table (rebuilds, reclaims space)
+OPTIMIZE TABLE users;
+
+-- Check table for errors
+CHECK TABLE users;
+
+-- Repair table if corrupted
+REPAIR TABLE users;
+
+-- Analyze table statistics
+ANALYZE TABLE users;
+
+-- Check fragmentation
+SELECT
+    table_schema,
+    table_name,
+    ROUND(data_length / 1024 / 1024, 2) as data_mb,
+    ROUND(data_free / 1024 / 1024, 2) as free_mb,
+    ROUND(data_free / data_length * 100, 2) as fragmentation_pct
+FROM information_schema.tables
+WHERE table_schema NOT IN ('mysql', 'information_schema', 'performance_schema', 'sys')
+  AND data_free > 0
+ORDER BY fragmentation_pct DESC;
+```
+
+### Table Compression
+
+```sql
+-- InnoDB compression (requires ROW_FORMAT=COMPRESSED)
+CREATE TABLE compressed_logs (
+    id BIGINT AUTO_INCREMENT PRIMARY KEY,
+    message TEXT,
+    created_at DATETIME
+) ROW_FORMAT=COMPRESSED KEY_BLOCK_SIZE=8;
+
+-- Check compression ratio
+SELECT
+    table_schema,
+    table_name,
+    ROUND(data_length / 1024 / 1024, 2) as data_mb,
+    ROUND(index_length / 1024 / 1024, 2) as index_mb,
+    create_options
+FROM information_schema.tables
+WHERE row_format = 'Compressed';
+```
+
+## Configuration File Example
+
+```ini
+# my.cnf - Production optimized for 16GB RAM server
+
+[mysqld]
+# InnoDB Settings
+innodb_buffer_pool_size = 12G
+innodb_buffer_pool_instances = 8
+innodb_log_file_size = 1G
+innodb_log_buffer_size = 16M
+innodb_flush_log_at_trx_commit = 1
+innodb_flush_method = O_DIRECT
+innodb_flush_neighbors = 0
+
+# I/O Settings
+innodb_read_io_threads = 8
+innodb_write_io_threads = 8
+innodb_io_capacity = 10000
+innodb_io_capacity_max = 20000
+
+# Connection Settings
+max_connections = 200
+thread_cache_size = 100
+
+# Query Cache (MySQL 5.7)
+# query_cache_type = 1
+# query_cache_size = 64M
+
+# Temporary Tables
+tmp_table_size = 64M
+max_heap_table_size = 64M
+
+# Slow Query Log
+slow_query_log = ON
+long_query_time = 1
+log_queries_not_using_indexes = ON
+
+# Binary Log
+binlog_format = ROW
+sync_binlog = 1
+binlog_expire_logs_seconds = 604800
+
+# Performance Schema
+performance_schema = ON
+
+# Character Set
+character_set_server = utf8mb4
+collation_server = utf8mb4_unicode_ci