Troubleshooting Common Issues in MonetDB 5MonetDB 5 introduces performance improvements, new features, and architectural changes that can improve analytics workloads — but like any major release, it also brings new failure modes and migration-related gotchas. This guide walks through common issues users encounter with MonetDB 5, diagnostic steps, and practical fixes. It covers installation, startup, connectivity, query performance, storage and disk problems, migration pitfalls, and logging/monitoring tips.
Table of contents
- Installation and startup failures
- Server won’t accept connections
- Authentication and access control problems
- Query performance regressions
- Memory pressure and crashes
- Disk space, I/O, and storage corruption
- Migration from MonetDB 4 to MonetDB 5
- Backup, restore, and consistency checks
- Logging, monitoring, and metrics
- Preventive practices and tuning checklist
Installation and startup failures
Symptoms:
- MonetDB daemon (mserver5) fails to start or crashes immediately.
- Error messages referring to missing shared libraries or incompatible ABI.
- Package manager reports conflicts or unmet dependencies.
Diagnostics:
- Start mserver5 from the shell to observe stderr output:
mserver5 -d <dbfarm>
and note the first error lines. - Check system logs (journalctl or /var/log/) for OS-level errors.
- Verify library versions: run
ldd /usr/bin/mserver5
(or the installed binary path) to see unresolved libraries. - Confirm OS and distribution compatibility against MonetDB 5 release notes.
Common fixes:
- Install missing dependencies (C runtime, libmapi, libssl, etc.) using your package manager.
- Use the MonetDB-provided packages for your distribution or build from source with the supported compiler toolchain.
- If binaries are incompatible, recompile MonetDB 5 on the host system.
- Ensure correct permissions for the dbfarm directory and that the user running mserver5 owns it.
Server won’t accept connections
Symptoms:
- Clients (mclient, ODBC/JDBC, BI tools) can’t connect: connection refused or timeout.
- Connections work locally but fail from remote hosts.
Diagnostics:
- Confirm mserver5 is running:
pgrep -a mserver5
orsystemctl status monetdb
(if installed as a service). - Check which address/port mserver5 is listening on:
ss -ltnp | grep mserver5
ornetstat -ltnp
. - Inspect MonetDB configuration (monetdb5.conf or the service unit) for listen address and port settings.
- Test local connectivity:
mclient -u monetdb -d demo
(adjust user/db). - Test remote connectivity with telnet/nc:
nc -vz <host> 50000
(default port 50000) to see if TCP accepts connections. - Firewall/iptables or cloud security groups may be blocking external access.
Common fixes:
- Configure MonetDB to listen on the correct network interface (0.0.0.0 for all addresses) by editing the service start options or setting appropriate mserver5 flags.
- Open the MonetDB port in firewall and cloud security group rules.
- Ensure the server’s TCP backlog isn’t exhausted by inspecting kernel TCP settings and increasing them if needed.
- If using TLS, ensure certificates are valid and that client tools are configured for TLS.
Authentication and access control problems
Symptoms:
- “Authentication failed” for valid credentials.
- Permission denied when creating databases, tables, or running commands.
Diagnostics:
- Check MonetDB user accounts and roles via mclient:
SELECT * FROM sys.user;
andSELECT * FROM sys.database;
. - Inspect mclient and server-side error messages; MonetDB logs authentication attempts.
- Confirm the authentication backend in use (native, PAM, or other) and configuration for user mapping.
- Verify the database farm permissions and filesystem ownership.
Common fixes:
- Reset or recreate the MonetDB user with the correct password:
CREATE USER username PASSWORD 'pw';
orALTER USER ...
. - Ensure the OS user running mserver5 has proper rights to the dbfarm directory.
- If using external auth (LDAP/PAM), validate that the integration is configured and reachable.
Query performance regressions
Symptoms:
- Queries that were fast in MonetDB 4 are slower in MonetDB 5.
- Increased CPU usage, longer execution times, or higher memory consumption.
Diagnostics:
- Capture query plans and execution statistics: use EXPLAIN ANALYZE (or MonetDB-equivalent profiling) to inspect operator breakdown.
- Compare query plans between MonetDB 4 and MonetDB 5 for the same workload to see plan changes.
- Monitor system resources (cpu, iowait, memory) during query execution.
- Check wait events and operator-level timings in the MonetDB profiler output.
Common causes and fixes:
- Optimizer behavior changes: MonetDB 5’s optimizer may choose different join orders or algorithms. Force desired plans with hints or rewrite queries to guide the optimizer.
- Missing or changed statistics: collect or update table statistics so the optimizer can make correct choices.
- Column-store encoding/fragmentation: Reorganize or recluster tables if fragmentation increases scan costs.
- New default settings: Compare default configuration parameters (join methods, parallelism) with prior versions and adjust them in monetdb5.conf.
- Increase parallelism or adjust worker thread counts if single-threaded operators are bottlenecks.
- Use prepared statements for repeated queries to avoid repeated planning overhead.
Example fixes:
- Recompute statistics:
ANALYZE table_name;
- Force join order via explicit JOIN/ON structure or use hints if available.
- Adjust optimizer thresholds in configuration and restart mserver5.
Memory pressure and crashes
Symptoms:
- mserver5 gets killed by the OS (OOM killer).
- Server crashes with segmentation faults or assertions.
- Excessive swap usage or paging during large queries.
Diagnostics:
- Inspect kernel logs (
dmesg
or journalctl) for OOM killer entries. - Check MonetDB logs for stack traces or assertion messages.
- Monitor resident set size (RSS) and virtual memory of the mserver5 process during workload using top/htop or ps.
- Run diagnostics to reproduce and capture core dumps (system must be configured to permit core dumps).
Common fixes:
- Reduce memory usage by tuning MonetDB memory-related settings (e.g., memory budget for operators) in monetdb5.conf.
- Increase available physical memory or add swap as a temporary mitigation.
- Limit concurrency or reduce per-query memory limits to prevent multiple large queries from exhausting RAM.
- If crashes indicate bugs (segfaults, assertions), capture logs and core dumps and file a reproducible bug report with MonetDB maintainers including schema, query, and stack traces.
- Upgrading to a newer patch of MonetDB 5 may include bug fixes for crashes.
Disk space, I/O, and storage corruption
Symptoms:
- Running out of disk space; writes failing; transactions failing.
- Corrupt tables, errors like “inconsistent repository”, or unexpected data loss.
- Slow I/O, high latency on scans and writes.
Diagnostics:
- Check free space:
df -h
and check inode usage withdf -i
. - Inspect MonetDB dbfarm directory for large files and unexpected growth (heap, column files, logs).
- Monitor I/O stats (iostat, vmstat) during workload for high utilization or long service times.
- Use MonetDB integrity checks if provided (or offline consistency checks).
Common fixes:
- Free space by archiving or removing old logs, exports, and noncritical datasets.
- Move dbfarm to a larger disk or to faster storage (NVMe, SSD) if I/O-bound.
- Ensure the filesystem and underlying storage are healthy (smartctl, fsck).
- If corruption is detected, restore from the most recent clean backup. Do not run repair operations without backups.
- Configure MonetDB to place temporary files on fast storage and ensure temp directories have sufficient space.
Migration from MonetDB 4 to MonetDB 5
Common pitfalls:
- Schema or metadata incompatibilities.
- Differences in default settings and optimizer behavior.
- Third-party drivers or connectors that expect older protocol behavior.
Migration checklist and fixes:
- Read MonetDB 5 release notes for breaking changes and deprecated features.
- Test application workloads in a staging environment before production migration.
- Export and import schema and data using safe, versioned methods:
- Use mclient to dump schema and data:
mclient -d dbname -s "SCRIPT TO FILE"
or MonetDB-provided dump tools. - Consider logical export (CSV/Parquet) and re-importing into MonetDB 5 to avoid low-level format incompatibilities.
- Use mclient to dump schema and data:
- Validate application queries and stored procedures; adjust any queries dependent on specific execution plans or optimizer quirks.
- Upgrade client drivers (ODBC/JDBC) to versions compatible with MonetDB 5.
Backup, restore, and consistency checks
Best practices:
- Maintain regular backups (logical and physical). A combination of full physical snapshots and logical exports gives flexibility.
- Test restores regularly in a staging environment.
Common backup/restore issues:
- Restores failing due to version mismatch — ensure the restore target is running compatible MonetDB 5 version.
- Logical backups (CSV/Parquet) may lose metadata (privileges, constraints) which then must be re-applied.
Commands and tips:
- Use filesystem-level snapshots for quick full-disk backups when possible, but ensure the DB is quiesced or consistent at snapshot time.
- For logical exports, prefer formats that preserve types precisely (Parquet) where supported.
- After restore, run ANALYZE and verify constraints and indexes.
Logging, monitoring, and metrics
Useful logs:
- MonetDB server log in the dbfarm directory or configured logging path.
- Client-side logs (mclient) for query errors.
- System logs for resource-related messages.
Monitoring recommendations:
- Collect metrics: CPU, memory, disk I/O, network, and MonetDB-specific counters (active queries, connection counts).
- Use existing monitoring stacks (Prometheus + Grafana) with exporters or scripts to scrape MonetDB metrics if available.
- Alert on long-running queries, high queue lengths, OOM events, and disk usage thresholds.
Preventive practices and tuning checklist
- Keep MonetDB 5 up to date with patch releases.
- Test upgrades in staging with representative workloads.
- Maintain recent backups and test restores.
- Monitor system resources and set alerts for disk, memory, and CPU.
- Tune configuration (monetdb5.conf) for your workload: memory budgets, worker threads, I/O settings.
- Recompute statistics after major data loads:
ANALYZE table_name;
- Use filesystem snapshots and storage with good IOPS for columnar scans.
- Limit concurrency or set quotas for heavy user workloads.
If you want, I can:
- Add exact monetdb5.conf parameter examples tuned for OLAP vs mixed workloads.
- Provide step-by-step commands to reproduce and capture core dumps and logs for a crash.
- Draft a migration playbook (export/import commands, sample scripts) from MonetDB 4 → 5.