The Good Doctor – Mastering the Art of PostgreSQL Health

We're inspired by the compelling and thought-provoking Netflix series "The Good Doctor" 
It follows the remarkable journey of Dr. Shaun Murphy, a young surgical resident with autism and savant syndrome. As he navigates the challenges of a prestigious hospital, Shaun's exceptional medical talents collide with societal prejudices and the complexities of interpersonal connections.

In the world of databases, PostgreSQL stands as a trusted and robust open-source relational database management system. Just like human health, a PostgreSQL database’s well-being is of utmost importance to ensure smooth operations, optimal performance, and data integrity. In this blog post, we will explore the role of a “doctor” for your PostgreSQL database and discuss the key practices that contribute to maintaining its health.

Regular Check-ups and Monitoring

Similar to routine health check-ups for individuals, PostgreSQL databases require constant monitoring to catch potential issues before they become critical. As a PostgreSQL doctor, your primary responsibility is to set up monitoring tools that keep an eye on various aspects such as disk space usage, query performance, connection counts, and replication status. This proactive approach helps you identify trends and patterns, allowing you to take corrective actions before problems escalate.

Check Disk Space Usage for All Tables:

SELECT 
schemaname,
tablename,
pg_size_pretty(pg_total_relation_size(schemaname || '.' || tablename)) AS size FROM 
pg_tables 
ORDER BY pg_total_relation_size(schemaname || '.' || tablename) DESC 
LIMIT 10;

Longest Running Queries:

SELECT 
query,
total_time 
FROM 
pg_stat_statements 
ORDER BY total_time DESC 
LIMIT 10;

Query Locks and Blocking Queries:

SELECT blocked_locks.pid AS blocked_pid,
blocking_locks.pid AS blocking_pid,
blocked_activity.query AS blocked_query,
blocking_activity.query AS blocking_query
FROM 
pg_locks blocked_locks
JOIN 
pg_stat_activity blocked_activity ON blocked_activity.pid = blocked_locks.pid
JOIN 
pg_locks blocking_locks ON blocking_locks.locktype = blocked_locks.locktype
AND 
blocking_locks.database IS NOT DISTINCT FROM blocked_locks.database
AND 
blocking_locks.relation IS NOT DISTINCT FROM blocked_locks.relation
JOIN 
pg_stat_activity blocking_activity ON blocking_activity.pid = blocking_locks.pid
WHERE 
blocked_locks.pid != blocking_locks.pid;

Replication Lag and Delay:

SELECT 
client_addr,
state,
pg_last_xact_replay_timestamp() - pg_last_xlog_receive_location() AS replication_lag 
FROM 
pg_stat_replication;

Checkpoint Activity:

SELECT 
checkpoint_time,
round(checkpoint_time - lag(checkpoint_time) OVER (ORDER BY checkpoint_time), 2) AS time_since_last_checkpoint 
FROM 
pg_stat_bgwriter;

Diagnosing Performance Bottlenecks

Performance issues can be a headache for both doctors and databases. PostgreSQL provides insightful tools like pg_stat_statements and pg_stat_activity that enable you to identify slow queries, resource-intensive operations, and areas requiring optimization. By diagnosing and addressing these bottlenecks, you ensure your database’s responsiveness and maintain a healthy performance level.

Identify Queries with High I/O:

SELECT 
query, 
pg_size_pretty(blk_read_time * current_setting('block_size')::bigint) AS read_time,
pg_size_pretty(blk_write_time * current_setting('block_size')::bigint) AS write_time
FROM 
pg_stat_statements
ORDER BY blk_read_time + blk_write_time DESC
LIMIT 10;

Analyze Temp File Usage:

SELECT 
query,
temp_blks_read,
tmp_blks_written 
FROM 
pg_stat_statements 
WHERE 
temp_blks_read > 0 OR temp_blks_written > 0 
ORDER BY temp_blks_read + temp_blks_written DESC
LIMIT 10;

Applying Regular Maintenance

Health maintenance is an ongoing process. PostgreSQL databases benefit from routine maintenance tasks like vacuuming, analyzing, and reindexing. The autovacuum process helps reclaim storage space and optimize the arrangement of data on disk, which prevents performance degradation over time. Regularly updating statistics through the ANALYZE command ensures that the query planner makes informed decisions about query execution plans.

Vacuuming and Analyzing Specific Schemas:

SELECT 
'VACUUM ANALYZE public.' || tablename || ';' AS vacuum_analyze_query 
FROM 
pg_tables
WHERE schemaname = 'public';

SELECT pg_stat_reset();  - - Reset stats after vacuum

Optimize Autovacuum Thresholds:

ALTER TABLE your_table_name SET (autovacuum_vacuum_scale_factor = 0.01);
ALTER TABLE your_table_name SET (autovacuum_analyze_scale_factor = 0.05);

Intensive Vacuum for High Update Tables:

Apply an aggressive vacuum on high-update tables to combat bloat.

VACUUM (FULL, ANALYZE) your_high_update_table_name;

Analyze Specific Tables More Frequently:

Schedule frequent automatic analyzes for specific tables to keep statistics fresh.

ALTER TABLE your_table_name SET (autovacuum_analyze_scale_factor = 0);

Reindex with Concurrently:

REINDEX INDEX CONCURRENTLY your_index_name;

Check Indexes Needing Reindexing:

Identify indexes that require reindexing based on fragmentation.

SELECT 
schemaname,
indexname,
pg_size_pretty(pg_total_relation_size(indexrelid)) AS index_size 
FROM 
pg_stat_user_indexes
WHERE
idx_scan = 0 
ORDER BY pg_total_relation_size(indexrelid) DESC

Reset Statistics and Activity Counters:

Reset both system statistics and query activity counters for accurate tracking.

SELECT pg_stat_reset();
SELECT pg_stat_reset_shared('bgwriter');

Backup and Disaster Recovery Plans

No doctor would leave their patient unprepared for emergencies, and the same applies to databases. As a PostgreSQL doctor, you must devise robust backup and disaster recovery plans. Implement regular backups, test their restore processes, and consider setting up point-in-time recovery options. This guarantees that in the event of data loss or corruption, your database can be swiftly restored to a healthy state.

Security Measures

Patient confidentiality is a priority in healthcare, just as data security is in databases. Safeguarding sensitive information stored in PostgreSQL databases is vital. Implement proper authentication and authorization mechanisms, use SSL/TLS for encrypted connections, and keep your PostgreSQL instance up to date with security patches. A secure database environment is essential for its overall health.

Implement Strong Authentication:

Set strong authentication mechanisms using pg_hba.conf

hostssl  	all     all     0.0.0.0/0     cert clientcert=1
hostnossl  	all     all     0.0.0.0/0     scram-sha-256

Configure PostgreSQL for SSL/TLS encryption:

— In postgresql.conf

ssl = on
ssl_cert_file = '/path/to/server.crt'
ssl_key_file = '/path/to/server.key'
ssl_ca_file = '/path/to/root.crt'
ssl_ciphers = 'HIGH:!aNULL:!MD5'
ssl_prefer_server_ciphers = on

Implement Role-Based Access Control (RBAC):

Apply fine-grained access control with roles and privileges:

— Create roles

CREATE ROLE doctor LOGIN PASSWORD 'securepassword';
GRANT doctor TO admin;

— Grant privileges

GRANT SELECT, INSERT, UPDATE, DELETE ON medical_records TO doctor;

Use Row-Level Security (RLS):

Enforce data access policies at the row level:

— Enable RLS

ALTER TABLE medical_records ENABLE ROW LEVEL SECURITY;

— Create security policy

CREATE POLICY restrict_confidentiality ON medical_records FOR ALL USING (doctor_id = current_user);

Enable Database Auditing:

audit_logging = 'on'
audit_directory = '/path/to/audit_logs'
audit_trail = 'on'

Frequent Security Patching:

# Apply PostgreSQL updates

sudo apt update
sudo apt upgrade postgresql

Probing into Bloat, unused Indexes and Dead Rows

Analyze table bloat and unproductive rows. Through insightful queries, pinpoint tables requiring optimization. Your in-depth understanding enhances both performance and resource utilization.
PostgreSQL trusted extensions are a toolkit for diagnosing, optimizing, and nurturing the well-being of your database environment, making you a proficient ‘doctor’ of PostgreSQL.

Conclusion

Becoming a proficient PostgreSQL doctor requires a combination of skills, vigilance, and dedication. By diligently monitoring, diagnosing, optimizing queries, performing maintenance tasks, and ensuring security, you contribute to the long-term health and optimal performance of PostgreSQL databases. Just as doctors play a critical role in keeping us healthy, your role as a PostgreSQL doctor ensures that data remains accessible, responsive, and reliable. So, put on your “white coat,” follow these practices, and nurture your PostgreSQL databases to lead a long and healthy tenure.