Backups that depend on someone remembering to click a button don’t happen. This guide is for GoZen VPS and dedicated server users. The only backups that work are the ones that run themselves. This guide sets up automated file and database backups with offsite storage, so when something breaks at 3 AM, you have a clean copy to restore from.

What to Back Up

DataWhere It LivesHow Often
Website files/var/www/ or /home/*/public_html/Daily
DatabasesMySQL/MariaDB, PostgreSQLDaily (or more often for busy sites)
Server config/etc/nginx/, /etc/apache2/, /etc/php/Weekly or after changes
SSL certificates/etc/letsencrypt/Weekly
Cron jobscrontab -l outputWeekly
Mail data/var/mail/ or /home/*/Maildir/Daily (if hosting email)

Database Backups with mysqldump

Single Database 

  mysqldump -u root -p database_name > /backup/database_name_$(date +%Y%m%d).sql

All Databases 

  mysqldump -u root -p --all-databases > /backup/all_databases_$(date +%Y%m%d).sql

Skip the Password Prompt

Create a credentials file so scripts can run without interaction:

  sudo nano /root/.my.cnf
  
  [mysqldump]
user=root
password=your_mysql_root_password
  
  sudo chmod 600 /root/.my.cnf

Now mysqldump reads credentials automatically:

  mysqldump --all-databases > /backup/all_databases_$(date +%Y%m%d).sql

Compress on the Fly

Database dumps compress extremely well - 90%+ reduction is common:

  mysqldump --all-databases | gzip > /backup/all_databases_$(date +%Y%m%d).sql.gz

File Backups with rsync

rsync only copies files that changed since the last run, which makes incremental backups fast.

Local Backup 

  # Back up websites to a local backup directory
rsync -avz --delete /var/www/ /backup/www/

# Back up server configs
rsync -avz /etc/nginx/ /backup/nginx-config/
rsync -avz /etc/letsencrypt/ /backup/letsencrypt/
FlagWhat It Does
-aArchive mode - preserves permissions, timestamps, symlinks
-vVerbose - shows what’s being copied
-zCompress during transfer
--deleteRemove files in destination that no longer exist in source

Remote Backup (to Another Server) 

  rsync -avz -e "ssh -p 22" /var/www/ user@backup-server:/backup/www/

Set up SSH key authentication between servers so this runs without a password prompt (see Connecting via SSH).

Offsite Backups with rclone

rclone syncs files to cloud storage - S3, Backblaze B2, Google Drive, Wasabi, and 40+ others. It’s like rsync for cloud storage.

Install rclone 

  sudo apt install rclone -y    # Ubuntu/Debian
sudo dnf install rclone -y    # Rocky/AlmaLinux

# Or install the latest version directly
curl https://rclone.org/install.sh | sudo bash

Configure a Remote 

  rclone config

This walks you through an interactive setup. For Backblaze B2 (cheap, reliable, great for backups):

  1. Choose n for new remote
  2. Name it b2
  3. Select Backblaze B2 from the list
  4. Enter your Application Key ID and Application Key
  5. Leave other settings as defaults

For Amazon S3:

  1. Choose n for new remote
  2. Name it s3
  3. Select Amazon S3 from the list
  4. Enter your Access Key ID and Secret Access Key
  5. Choose your region

Test the Connection 

  # List buckets
rclone lsd b2:

# List files in a bucket
rclone ls b2:my-backup-bucket

Sync Files to Cloud Storage 

  # Push local backup directory to B2
rclone sync /backup/ b2:my-backup-bucket/servername/ --progress

# Sync only website files
rclone sync /var/www/ b2:my-backup-bucket/www/ --progress

# Sync with bandwidth limit (don't saturate your connection)
rclone sync /backup/ b2:my-backup-bucket/ --bwlimit 50M

rclone sync makes the destination match the source. Files deleted locally get deleted remotely too. If you want to keep old versions, use rclone copy instead or enable versioning on your bucket.

The Complete Backup Script

Here’s a production-ready script that backs up files and databases, compresses everything, and syncs to cloud storage:

  sudo nano /usr/local/bin/backup.sh
  
  #!/bin/bash
set -euo pipefail

# --- Configuration ---
BACKUP_DIR="/backup"
RETENTION_DAYS=14
DATE=$(date +%Y%m%d-%H%M%S)
RCLONE_REMOTE="b2:my-backup-bucket/$(hostname)"
LOG="/var/log/backup.log"

echo "=== Backup started at $(date) ===" >> "$LOG"

# --- Create backup directories ---
mkdir -p "$BACKUP_DIR/databases"
mkdir -p "$BACKUP_DIR/files"
mkdir -p "$BACKUP_DIR/config"

# --- Database backup ---
echo "Backing up databases..." >> "$LOG"
mysqldump --all-databases --single-transaction | gzip > "$BACKUP_DIR/databases/all_db_$DATE.sql.gz"
echo "Database backup: $(du -sh "$BACKUP_DIR/databases/all_db_$DATE.sql.gz" | cut -f1)" >> "$LOG"

# --- File backup ---
echo "Backing up website files..." >> "$LOG"
tar -czf "$BACKUP_DIR/files/www_$DATE.tar.gz" /var/www/ 2>/dev/null
echo "File backup: $(du -sh "$BACKUP_DIR/files/www_$DATE.tar.gz" | cut -f1)" >> "$LOG"

# --- Config backup ---
echo "Backing up server config..." >> "$LOG"
tar -czf "$BACKUP_DIR/config/config_$DATE.tar.gz" \
    /etc/nginx/ \
    /etc/letsencrypt/ \
    /etc/php/ \
    /etc/systemd/system/*.service \
    2>/dev/null
echo "Config backup: $(du -sh "$BACKUP_DIR/config/config_$DATE.tar.gz" | cut -f1)" >> "$LOG"

# --- Clean old local backups ---
echo "Cleaning backups older than $RETENTION_DAYS days..." >> "$LOG"
find "$BACKUP_DIR" -type f -name "*.gz" -mtime +$RETENTION_DAYS -delete

# --- Sync to cloud ---
echo "Syncing to cloud storage..." >> "$LOG"
rclone copy "$BACKUP_DIR" "$RCLONE_REMOTE" --log-file="$LOG" --log-level INFO

echo "=== Backup completed at $(date) ===" >> "$LOG"
echo "" >> "$LOG"
  
  sudo chmod +x /usr/local/bin/backup.sh

Key Details

  • --single-transaction - dumps InnoDB tables without locking them, so your sites stay online during backup
  • set -euo pipefail - the script stops on any error instead of silently continuing
  • Old backups get cleaned up after 14 days
  • rclone copy (not sync) keeps old offsite backups even if they’re deleted locally

Schedule It with Cron 

  sudo crontab -e
  
  # Run full backup daily at 3:00 AM
0 3 * * * /usr/local/bin/backup.sh

# Backup databases every 6 hours (for busy sites)
0 */6 * * * mysqldump --all-databases --single-transaction | gzip > /backup/databases/db_$(date +\%Y\%m\%d-\%H\%M).sql.gz

Verify Backups Are Running 

  # Check the log
tail -50 /var/log/backup.log

# Check when backup last ran
ls -la /backup/databases/ | tail -5

# Check cloud storage
rclone ls b2:my-backup-bucket/$(hostname)/databases/ | tail -5

Test Your Backups

A backup you’ve never tested is a backup that might not work. Test a restore at least once:

  # Test database restore (use a temporary database)
zcat /backup/databases/all_db_20260413-030000.sql.gz | mysql -u root test_restore_db

# Test file restore
mkdir /tmp/restore-test
tar -xzf /backup/files/www_20260413-030000.tar.gz -C /tmp/restore-test
ls /tmp/restore-test/var/www/

# Clean up
rm -rf /tmp/restore-test
mysql -u root -e "DROP DATABASE test_restore_db;"

Backup Costs

Offsite storage is cheap. For a typical VPS with 20 GB of sites and databases:

ProviderMonthly Cost (20 GB)Notes
Backblaze B2~$0.10$0.005/GB storage. Free egress to Cloudflare.
Wasabi~$1.40$0.0069/GB. No egress fees. 1 TB minimum billing.
AWS S3 (Glacier)~$0.08Cheapest for long-term archival. Slow retrieval.
Another VPSVariesGood if you already have a second server.

Troubleshooting

ProblemFix
mysqldump: “Access denied”Check /root/.my.cnf credentials. Or specify user: mysqldump -u root -p.
rclone: “Failed to create file”Check bucket permissions. Your API key needs read/write access.
Backup script runs but produces empty filesCheck disk space: df -h. The backup directory might be full.
Cron job doesn’t runCheck cron syntax. Use crontab -l to verify. Check /var/log/syslog for cron errors.
Backups are too largeExclude cache directories: add --exclude='wp-content/cache' to tar or rsync.
rclone is too slowAdd --transfers 4 for parallel uploads. Use --bwlimit to avoid saturating bandwidth during peak hours.

Last updated 21 Apr 2026, 08:08 +0300. history

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