Fixing ZFS DKMS Build Failures on Debian 12 VPS with Limited RAM

If you’re running ZFS on a small VPS and have encountered compilation failures during system updates, you’re not alone. This tutorial covers a common issue that affects many system administrators managing ZFS on memory-constrained virtual private servers.

The Problem

During a routine system update on a Hetzner Cloud CAX11 VPS (2 vCPU, 4GB RAM) running Debian 12 with ZFS, the zfs-dkms module compilation failed with the following error:

CC [M] /var/lib/dkms/zfs/2.3.1/build/module/zfs/arc.o
gcc-12: fatal error: Killed signal terminated program cc1
compilation terminated.
make[4]: *** [/usr/src/linux-headers-6.1.0-34-common/scripts/Makefile.build:255: /var/lib/dkms/zfs/2.3.1/build/module/zstd/lib/compress/zstd_opt.o] Error 1

The telltale sign here is gcc-12: fatal error: Killed signal terminated program cc1 – this indicates that the GCC compiler process was killed by the system, typically due to memory exhaustion.

Understanding the Root Cause

Why This Happens

1. Memory-Intensive Compilation: ZFS DKMS compilation is particularly memory-hungry, especially when compiling complex modules like the ZSTD compression components
2. Small VPS Limitations: VPS instances with 4GB RAM or less often lack sufficient memory for large compilation tasks
3. No Swap Configuration: Many VPS providers don’t configure swap by default, leaving the system without memory overflow protection
4. Kernel Build Process: DKMS rebuilds kernel modules against the current kernel headers, which requires substantial memory allocation

The Update Process Chain

The issue typically occurs during:

1. apt update && apt upgrade – works fine initially
2. ZFS packages are “kept back” due to dependency conflicts
3. apt dist-upgrade is required to resolve dependencies
4. ZFS DKMS compilation begins and fails due to memory constraints

The Solution: Adding Swap Space

The most effective solution is to temporarily add swap space before attempting the upgrade.

Step 1: Check Current Memory Usage

# Check available memory
free -h

# Check if swap is already configured
swapon --show

Step 2: Create Swap File

Create a 2GB swap file (adjust size based on your needs):

# Create a 2GB swap file
sudo fallocate -l 2G /swapfile

# Alternatively, if fallocate isn't available:
# sudo dd if=/dev/zero of=/swapfile bs=1024 count=2097152

Step 3: Configure Swap

# Set correct permissions
sudo chmod 600 /swapfile

# Set up swap space
sudo mkswap /swapfile

# Enable swap
sudo swapon /swapfile

# Verify swap is active
swapon --show
free -h

Step 4: Retry the Upgrade

# Now retry the upgrade
sudo apt dist-upgrade

Step 5: Clean Up (Optional)

After the successful upgrade, you can remove the swap file if desired:

# Disable swap
sudo swapoff /swapfile

# Remove swap file
sudo rm /swapfile

Alternative Solutions

Permanent Swap Configuration

If you frequently compile software or update DKMS modules, consider making swap permanent:

# Add to /etc/fstab for persistent swap
echo '/swapfile none swap sw 0 0' | sudo tee -a /etc/fstab

Swap Optimization

Configure swap behavior for better performance:

# Set swappiness (how aggressively to use swap)
echo 'vm.swappiness=10' | sudo tee -a /etc/sysctl.conf

# Set cache pressure
echo 'vm.vfs_cache_pressure=50' | sudo tee -a /etc/sysctl.conf

Using Pre-compiled Packages

Consider using pre-compiled ZFS packages when available:

# Check if pre-compiled packages are available
apt search zfs-dkms

# Some distributions offer pre-built kernel modules
apt search zfs-modules

Prevention Strategies

1. Monitor Memory During Updates

# Monitor memory usage in real-time during updates
watch -n 1 'free -h && echo "---" && ps aux --sort=-%mem | head -10'

2. Staged Updates

Break large updates into smaller chunks:

# Update system packages first
sudo apt upgrade

# Handle held packages separately
sudo apt install zfs-dkms zfsutils-linux

3. VPS Monitoring

Set up basic monitoring to track memory usage trends:

# Simple memory logging
echo "$(date): $(free -m | grep Mem:)" >> /var/log/memory-usage.log

Troubleshooting Tips

If Swap Creation Fails

Check available disk space:

df -h

Ensure you have at least 2-3GB free space for the swap file.

If Compilation Still Fails

1. Increase swap size: Try 4GB instead of 2GB
2. Check for other memory-consuming processes: ps aux --sort=-%mem | head -10
3. Temporary process suspension: Stop non-essential services during compilation

Monitoring Compilation Progress

# Watch DKMS build progress
sudo tail -f /var/lib/dkms/zfs/*/build/make.log

Best Practices for Small VPS ZFS Management

1. Always configure swap before major updates
2. Schedule updates during low-traffic periods
3. Monitor memory usage regularly
4. Keep backups before major system changes
5. Consider upgrading VPS if you frequently hit memory limits

Conclusion

Memory-related compilation failures are common on small VPS instances, especially when building complex kernel modules like ZFS. The solution is straightforward: ensure adequate virtual memory through swap configuration before attempting large compilation tasks.

This temporary swap approach allows you to maintain your cost-effective small VPS while handling occasional memory-intensive operations. Remember to monitor your system’s memory usage patterns to determine if permanent swap configuration or VPS upgrades are warranted for your specific use case.

Struggling with ZFS deployment, DKMS compilation issues, or other Linux infrastructure challenges? As a Linux systems consultant, I specialize in ZFS implementations, storage solutions, and server optimization on constrained environments. Whether you’re facing complex ZFS configuration problems, dealing with memory-limited VPS deployments, or need expert guidance on storage architecture and system administration, I’m here to help. Contact me for professional consultation and customized solutions tailored to your infrastructure requirements.