How to Safely Fix JetMongoDB Journal Disk Space Issues

JetMongoDB journal files can unexpectedly consume massive amounts of disk space, often growing to 80GB or more in the /usr/local/jetapps/var/lib/mongod/journal directory. This common issue occurs when MongoDB journal files accumulate without proper cleanup, leading to critical disk space shortages that can affect system performance and stability.

This comprehensive guide provides a safe and systematic approach to fix JetMongoDB journal disk space issues without risking data loss or service interruption.

Understanding JetMongoDB Journal Files

MongoDB journal files are write-ahead log files that ensure data durability and crash recovery. In JetMongoDB installations, these files are stored in /usr/local/jetapps/var/lib/mongod/journal/ and can grow significantly over time.

What Are Journal Files?

Why Journal Files Grow Large

Common causes of excessive journal file growth:

1. High Write Operations: Frequent database writes increase journal size
2. Checkpoint Delays: Delayed checkpoints prevent journal cleanup
3. Service Interruptions: Improper shutdowns leave incomplete journal entries
4. Backup Processes: JetBackup operations generate additional journal entries
5. System Crashes: Unexpected shutdowns prevent journal rotation

Symptoms of Journal Space Issues

Prerequisites

Before proceeding with journal cleanup, ensure you have:

System Requirements

• Root Access: Administrative privileges required
• Service Control: Ability to stop/start system services
• Disk Space: Sufficient space for backup operations
• Backup Strategy: Current database backups available

Required Commands

• systemctl: Service management
• mongod: MongoDB repair operations
• mv/rm: File management operations
• du/df: Disk usage monitoring

Safety Checklist

• Database Backups: Recent backups available
• Service Dependencies: Understanding of affected services
• Maintenance Window: Low-traffic period scheduled
• Rollback Plan: Recovery procedures documented

Step-by-Step Journal Cleanup Process

Step 1: Stop Required Services

Safely stop JetMongoDB and JetBackup services to prevent data corruption:

# Stop JetMongoDB service
sudo systemctl stop jetmongod

# Stop JetBackup service
sudo systemctl stop jetbackup5d

# Verify services are stopped
sudo systemctl status jetmongod
sudo systemctl status jetbackup5d

Important: Ensure both services are completely stopped before proceeding. Running MongoDB repair while services are active can cause data corruption.

Step 2: Verify Service Status

Confirm all services are properly stopped:

# Check service status
sudo systemctl is-active jetmongod
sudo systemctl is-active jetbackup5d

# Check for any remaining MongoDB processes
ps aux | grep mongod
ps aux | grep jetbackup

# Verify no MongoDB connections
netstat -tlnp | grep 27017

Expected output: Services should show as "inactive" and no MongoDB processes should be running.

Step 3: Backup Journal Directory

Create backup of journal directory before removal:

# Create backup directory with timestamp
sudo mkdir -p /usr/local/jetapps/var/lib/mongod/journal.backup.$(date +%Y%m%d_%H%M%S)

# Move journal directory to backup location
sudo mv /usr/local/jetapps/var/lib/mongod/journal /usr/local/jetapps/var/lib/mongod/journal.backup.$(date +%Y%m%d_%H%M%S)

# Verify backup creation
ls -la /usr/local/jetapps/var/lib/mongod/
du -sh /usr/local/jetapps/var/lib/mongod/journal.backup.*

Backup naming convention:

• Format: journal.backup.YYYYMMDD_HHMMSS
• Example: journal.backup.20241219_143022
• Retention: Keep for at least 7 days before removal

Step 4: Perform MongoDB Repair

Execute MongoDB repair to ensure database consistency:

# Navigate to JetMongoDB directory
cd /usr/local/jetapps/var/lib/mongod

# Run MongoDB repair operation
sudo /usr/local/jetapps/usr/bin/mongod --dbpath /usr/local/jetapps/var/lib/mongod --repair

Repair process details:

• Duration: Can take several minutes depending on database size
• Output: Look for "repair completed successfully" message
• Errors: Address any repair errors before continuing
• Logs: Monitor repair progress in terminal output

Common repair messages:

[initandlisten] MongoDB starting : pid=12345 port=27017 dbpath=/usr/local/jetapps/var/lib/mongod
[initandlisten] repair database local
[initandlisten] repair database admin
[initandlisten] repair database jetbackup
[initandlisten] repair completed successfully

Step 5: Restart Services

Safely restart JetMongoDB and JetBackup services:

# Start JetMongoDB service
sudo systemctl start jetmongod

# Wait for MongoDB to fully initialize
sleep 10

# Start JetBackup service
sudo systemctl start jetbackup5d

# Verify services are running
sudo systemctl status jetmongod
sudo systemctl status jetbackup5d

Service startup sequence:

1. JetMongoDB first: Database must be available before JetBackup
2. Wait period: Allow MongoDB to initialize journal files
3. JetBackup second: Start after database is ready

Step 6: Verify Service Health

Confirm services are functioning correctly:

# Check service status
sudo systemctl is-active jetmongod
sudo systemctl is-active jetbackup5d

# Check MongoDB connection
/usr/local/jetapps/usr/bin/mongo --eval "db.runCommand('ping')"

# Monitor journal directory size
du -sh /usr/local/jetapps/var/lib/mongod/journal

# Check system logs for errors
sudo journalctl -u jetmongod -n 50
sudo journalctl -u jetbackup5d -n 50

Health indicators:

• Services: Both services show as "active"
• MongoDB: Responds to ping command
• Journal size: Should be minimal (few MB)
• Logs: No critical errors in service logs

Post-Cleanup Verification

Disk Space Recovery

Verify disk space has been recovered:

# Check overall disk usage
df -h

# Check specific directory sizes
du -sh /usr/local/jetapps/var/lib/mongod/*
du -sh /usr/local/jetapps/var/lib/mongod/journal*

# Compare before/after sizes
echo "Before cleanup: 80GB+ (estimated)"
echo "After cleanup: $(du -sh /usr/local/jetapps/var/lib/mongod/journal | cut -f1)"

Expected results:

• Journal directory: Few MB instead of 80GB+
• Total mongod directory: Significantly reduced size
• Available disk space: Substantially increased

Database Functionality Test

Test database operations to ensure functionality:

# Test basic MongoDB operations
/usr/local/jetapps/usr/bin/mongo --eval "
  db.runCommand('ping');
  db.adminCommand('listDatabases');
  db.runCommand('dbStats');
"

# Test JetBackup functionality
sudo systemctl status jetbackup5d

Functionality checklist:

• MongoDB ping: Responds successfully
• Database listing: Shows all databases
• Statistics: Database stats accessible
• JetBackup: Service running normally

Journal Directory Management

Understanding Journal Structure

New journal directory will contain:

/usr/local/jetapps/var/lib/mongod/journal/
├── WiredTiger.lock          # Database lock file
├── WiredTigerLog.0000000001 # Current log file
├── WiredTigerPreplog.0000000001 # Preplog file
└── WiredTiger.wt           # WiredTiger metadata

Journal File Lifecycle

Journal files follow this lifecycle:

1. Creation: New journal file created during startup
2. Growth: File grows with database operations
3. Checkpoint: MongoDB creates checkpoints periodically
4. Cleanup: Old journal entries removed after checkpoint
5. Rotation: New journal file created when needed

Preventing Future Issues

Implement these practices to prevent journal bloat:

# Regular monitoring script
#!/bin/bash
JOURNAL_SIZE=$(du -sh /usr/local/jetapps/var/lib/mongod/journal | cut -f1)
JOURNAL_SIZE_NUM=$(du -s /usr/local/jetapps/var/lib/mongod/journal | cut -f1)

# Alert if journal exceeds 10GB
if [ $JOURNAL_SIZE_NUM -gt 10485760 ]; then
    echo "WARNING: Journal directory size: $JOURNAL_SIZE"
    echo "Consider running journal cleanup procedure"
fi

Monitoring schedule:

• Daily: Check journal directory size
• Weekly: Review MongoDB logs for issues
• Monthly: Perform preventive maintenance

Troubleshooting Common Issues

Issue 1: Service Won't Start

Symptoms: JetMongoDB or JetBackup fails to start after cleanup

Solutions:

# Check service logs
sudo journalctl -u jetmongod -n 100
sudo journalctl -u jetbackup5d -n 100

# Verify directory permissions
ls -la /usr/local/jetapps/var/lib/mongod/
sudo chown -R jetapps:jetapps /usr/local/jetapps/var/lib/mongod/

# Check MongoDB configuration
sudo cat /etc/systemd/system/jetmongod.service

Issue 2: Database Corruption

Symptoms: MongoDB repair fails or database errors occur

Solutions:

# Restore from backup
sudo mv /usr/local/jetapps/var/lib/mongod/journal.backup.* /usr/local/jetapps/var/lib/mongod/journal

# Restart services
sudo systemctl restart jetmongod
sudo systemctl restart jetbackup5d

# Contact JetApps support if issues persist

Issue 3: Insufficient Disk Space

Symptoms: Not enough space for backup operations

Solutions:

# Clean up other large files
sudo find /var/log -name "*.log" -size +100M -delete
sudo find /tmp -type f -mtime +7 -delete

# Compress existing backups
sudo tar -czf /backup/journal-backup-$(date +%Y%m%d).tar.gz /usr/local/jetapps/var/lib/mongod/journal.backup.*

# Remove compressed backups after verification
sudo rm -rf /usr/local/jetapps/var/lib/mongod/journal.backup.*

Best Practices

Safety Best Practices

1. Always Backup First: Never delete journal files without backup
2. Service Order: Stop services before any file operations
3. Verification: Test services after each step
4. Documentation: Record all actions taken
5. Rollback Plan: Know how to restore from backup

Performance Best Practices

1. Regular Monitoring: Check journal size daily
2. Scheduled Maintenance: Plan cleanup during low-traffic periods
3. Automated Alerts: Set up disk space monitoring
4. Preventive Actions: Address issues before they become critical
5. Performance Testing: Verify system performance after cleanup

Maintenance Best Practices

1. Backup Strategy: Maintain multiple backup copies
2. Service Dependencies: Understand service relationships
3. Log Analysis: Regular review of service logs
4. Capacity Planning: Monitor disk usage trends
5. Update Procedures: Keep JetApps software updated

Conclusion

JetMongoDB journal disk space issues can be safely resolved by following this systematic approach. The key is to stop services first, repair the database, backup journal files, and restart services in the correct order.

Key Benefits Achieved

• Disk Space Recovery: Reclaim 80GB+ of disk space
• Service Stability: Restore normal JetMongoDB and JetBackup operation
• Data Safety: Maintain database integrity throughout the process
• Prevention: Establish monitoring to prevent future issues

Success Indicators

Maintenance Schedule

Recommended maintenance intervals:

• Daily: Monitor journal directory size
• Weekly: Review service logs and performance
• Monthly: Check disk usage trends
• Quarterly: Perform preventive journal cleanup
• As Needed: Address issues when journal exceeds 10GB

By following this guide, you can safely resolve JetMongoDB journal disk space issues while maintaining data integrity and service availability. Regular monitoring and preventive maintenance will help prevent these issues from recurring in the future.

Remember: Always backup before making changes, stop services before file operations, and verify functionality after each step. When in doubt, consult JetApps support or restore from backup.