Automating with Cron

Last updated on 2026-08-24 | Edit this page

Estimated time: 20 minutes

Overview

Questions

  • How can I schedule automatic syncs?
  • What is cron and how do I create cron jobs?
  • How do I debug scheduled sync jobs?

Objectives

  • Understand cron scheduling syntax
  • Create cron jobs for recurring rclone syncs
  • Build shell scripts with error handling and notifications
  • Debug common cron job issues

Why Schedule Syncs?

Instead of manually running rclone sync, you can schedule it to run automatically:

  • Daily backups: Sync your HPC work to Box every night
  • Regular downloads: Update your local data from cloud sources
  • Continuous mirroring: Keep two locations perfectly synchronized

Understanding Cron

Cron is a Linux job scheduler. A cron job runs a command at specified times.

Cron format:

minute hour day_of_month month day_of_week command

Examples:

0 2 * * *     # Every day at 2:00 AM
0 */4 * * *   # Every 4 hours
0 2 * * 1     # Every Monday at 2:00 AM; 1 = Monday
30 9 1 * *    # First day of month at 9:30 AM

Creating a Cron Job

Edit your cron table:

BASH 

crontab -e

Add a new line for your scheduled sync:

BASH 

# Sync HPC results to Box every night at 2 AM
0 2 * * * module load rclone && rclone sync /scratch/results pomona-box:/daily-backup --log-file ~/.rclone-sync.log

Save and exit the editor. Verify the job is scheduled:

BASH 

crontab -l

Checking Cron Logs

After your job runs, check if it succeeded:

BASH 

cat ~/.rclone-sync.log

If you see token errors, your token has expired. Use rclone config reconnect to refresh it.

Advanced: Shell Script for Scheduled Syncs

For complex syncing with error handling and notifications, create a shell script:

BASH 

#!/bin/bash
# File: ~/rclone-sync.sh

# Load modules
module load rclone

# Log file
LOGFILE="$HOME/.rclone-sync-$(date +%Y-%m-%d).log"

# Sync HPC results to Box
echo "Starting sync at $(date)" >> $LOGFILE
rclone sync /scratch/results pomona-box:/daily-backup \
  --log-file $LOGFILE \
  --backup-dir pomona-box:/results-archive

# Check result
if [ $? -eq 0 ]; then
  echo "Sync completed successfully" >> $LOGFILE
  echo "Sync successful!" | mail -s "rclone sync OK" $USER@pomona.edu
else
  echo "Sync FAILED" >> $LOGFILE
  echo "Check logs: $LOGFILE" | mail -s "rclone sync FAILED" $USER@pomona.edu
fi

echo "Sync finished at $(date)" >> $LOGFILE

Make it executable and schedule it:

BASH 

chmod +x ~/rclone-sync.sh
crontab -e
# Add: 0 2 * * * ~/rclone-sync.sh

Debugging Cron Jobs

Common issues when cron jobs don’t work:

  1. Module not loaded: module: command not found – cron doesn’t load your shell profile
  2. Path issues: Paths must be absolute (e.g., /scratch, not ~/results)
  3. Token expired: Re-authenticate with rclone config reconnect
  4. Permissions: User running cron might not have write permissions

Use Full Paths and Absolute References

BASH 

# WRONG - won't work in cron
0 2 * * * rclone sync ~/results myremote:/backup

# RIGHT - works in cron
0 2 * * * /usr/bin/rclone sync /rhome/<myusername>/results myremote:/backup
Challenge

Challenge 9.1: Create a Scheduled Sync Job

Create a cron job that syncs your test folder. First, create a test script:

BASH 

cat > ~/sync-test.sh << 'EOF'
#!/bin/bash
module load rclone
echo "Sync running at $(date)" >> $HOME/.sync-test.log
rclone copy ~/test-data.txt pomona-box:/scheduled-sync-test \
  --log-file $HOME/.sync-test-$(date +%Y-%m-%d).log
echo "Sync finished at $(date)" >> $HOME/.sync-test.log
EOF

chmod +x ~/sync-test.sh

Schedule it to run every 5 minutes for testing:

BASH 

crontab -e
# Add: */5 * * * * ~/sync-test.sh

Wait 5 minutes, then check the log and verify on Box. Once satisfied, remove the test job from crontab.

After waiting 5 minutes, check:

BASH 

cat ~/.sync-test.log

Expected output shows timestamps of each run. Verify the file reached Box:

BASH 

rclone ls pomona-box:/scheduled-sync-test

After confirming, remove the cron job with crontab -e and delete the test line. Verify removal with crontab -l.

Key Points
  • Cron jobs require absolute file paths and may need module load rclone in the command
  • Shell scripts with error handling and email notifications make automated syncs more robust
  • Always test cron jobs by running the command manually first before scheduling
  • Check cron logs regularly to catch token expiration and other failures early