Dual Boot: Proxmox & Rocky Linux

Creating an ultra-low latency baremetal proving ground on NVMe drives while preserving Proxmox ZFS RAID1 redundancy.

Published August 31, 2026

Dual Boot: Proxmox & Rocky Linux

This runbook outlines the exact sequence to carve out dedicated baremetal hardware access on the primary homelab machine.

The goal is to create an ultra-low latency proving ground using Rocky Linux to benchmark workloads without the 10–30ms penalty introduced by VMs, while retaining the Proxmox host's ZFS RAID1 redundancy.

The Architectural Constraint

The host runs two 2TB NVMe drives in a ZFS RAID1 mirror for the root filesystem.

ZFS pools cannot be shrunk in-place. There is no way to non-destructively shrink the Proxmox partition to make room for Rocky Linux. The only architecturally sound way to share these ultra-fast drives between a ZFS hypervisor and another OS is a clean reinstall of Proxmox that explicitly caps its storage allocation at install time.

Target Hardware Shape

  • nvme0n1 and nvme1n1 (2TB each):
    • Majority (~1800GB): Proxmox ZFS RAID1 (Mirrored)
    • Remaining ~50GB: Rocky Linux Software RAID1 (Mirrored)
  • sdd (SATA SSD): pbspool containing Proxmox Backup Server data. (Completely untouched during this process).

Phase 1: Pre-Flight and Backups

This process is destructive to the host OS. The backup tier is what makes this safe.

  1. Verify Backups: Ensure all critical VMs and LXCs (TrueNAS, Pi-Hole, OpenWebUI) have a current, successful backup run to pbspool on sdd.
  2. Export Host Configs: SCP or copy the /etc/pve and /etc/network/interfaces directories to a safe offline location for reference.
  3. Prepare Media:
    • Flash Proxmox VE 9.2 ISO (pve-manager/9.2.3, kernel 7.0) to a USB drive.
    • Flash Rocky Linux 10.2 LTS ISO to a separate USB drive.

Phase 2: Proxmox Reinstallation (Reserving Space)

Reinstall Proxmox, but intentionally reserve ~50GB at the end of the NVMe drives.

  1. Boot the server from the Proxmox USB installer.
  2. In the target hard disk configuration, select zfs (RAID1).
  3. Select both nvme0n1 and nvme1n1 as the target disks.
  4. Click Options (Advanced Options).
  5. Set the hdsize parameter to 1800 (reserving space on a 2TB drive).
    • Why: A 2TB drive has ~1863GB of usable space. Setting this to 1800 instructs the installer to only use the first 1800GB of the drives, leaving roughly 60GB completely unallocated for Rocky Linux.
  6. Complete the installation and verify Proxmox boots successfully.
  7. Import your backup pool: zpool import pbspool.

Phase 2.5: The PBS Chicken-and-Egg Recovery

Because your Proxmox Backup Server (PBS) runs as a container (CT 301) on the NVMe drives you just wiped, you are now in a "chicken-and-egg" scenario: you need PBS running to restore your VMs, but your PBS container is inside the backups.

To break the loop, install PBS temporarily on the baremetal Proxmox host:

  1. Install PBS on the host temporarily: 
    apt update
apt install -y proxmox-backup-server
  2. Mount the datastore: The pbspool should be mounted at /pbspool or /mnt/pbs-backups. Add it as a datastore in the temporary host PBS: 
    proxmox-backup-manager datastore create temp-restore /pbspool/backups
  3. Add to Proxmox: In the Proxmox UI, go to Datacenter -> Storage -> Add -> Proxmox Backup Server.
    • ID: temp-pbs
    • Server: 127.0.0.1
    • Username: root@pam (and your Proxmox root password)
    • Datastore: temp-restore
  4. Restore CT 301 (The real PBS): Go to the temp-pbs storage, find the latest backup of CT 301, and restore it to your local-zfs storage.
  5. Restore the rest of the lab: Start CT 301. In Proxmox, re-add your normal pbs-backups storage pointing to CT 301's IP (192.168.50.191). Restore TrueNAS, Pi-hole, and OpenWebUI.
  6. Cleanup: Remove temp-pbs from Datacenter Storage, and apt remove proxmox-backup-server from the host.

Phase 3: Hardware Isolation Warning

The Rocky Linux installer may attempt to install its EFI bootloader onto the existing Proxmox EFI System Partition (ESP). Because we need both drives active to create a Software RAID1 for Rocky Linux, do not disable any drives in the BIOS. Instead, we will manage this carefully in the Rocky Linux installer.

Phase 4: Rocky Linux Installation (Software RAID1)

  1. Boot from the Rocky Linux 10.2 LTS USB installer.
  2. In the storage configuration, select BOTH nvme0n1 and nvme1n1.
  3. Choose Custom Storage Configuration (do not let it automatically partition).
  4. In the manual partitioning screen, target the unallocated space (~60GB we left free in Phase 2).
  5. Create the following layout carefully:
    • /boot/efi: Standard Partition, ~600MB. (Restrict this to just one of the NVMe drives using the 'Modify storage devices' gear icon so it doesn't try to span or use the Proxmox ESP).
    • /boot: Device Type: RAID, RAID Level: RAID1, ~1GB.
    • /: Device Type: RAID, RAID Level: RAID1, taking the remainder of the free space.
  6. Complete the installation and verify the system boots directly into Rocky Linux.

Phase 5: Post-Install Configuration

Rely on the motherboard's built-in UEFI boot manager instead of trying to chainload bootloaders. This ensures Proxmox kernel updates never accidentally break the Rocky Linux bootloader, and vice versa.

  1. Re-verify Boot Order: Reboot and enter the MSI X570 BIOS.
  2. Default Boot Priority: Ensure the Proxmox UEFI boot entry is set as the default #1 boot device. This ensures the server always boots into the homelab normally after a power loss or unattended reboot.
  3. OS Selection: When you need to test ultra-low latency workloads, reboot the server, press F11 to access the MSI boot menu, and select the Rocky Linux EFI bootloader.

Verification

When booted into Rocky Linux, verify native hardware access:

# Verify both RTX 3090s are fully available without virtualization overhead
nvidia-smi
 
# Verify all 16 cores (32 threads) of the 5950X are exposed natively
lscpu

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