Troubleshooting I/O errors and read-only file systems on Dedibox Pro-2 servers

Problem

On machines built on the Dedibox Pro-2 line, you are encountering one or more of the following issues when running recent Linux kernels:

• Disks experience I/O packet loss
• The file system (e.g., EXT4) immediately switches to read‑only mode to protect the data
• System logs show DMA errors related to the IOMMU subsystem
• SATA link degradation (from 6.0 Gbps to 1.5 Gbps)

Typical log messages

ata2: SATA link up 1.5 Gbps (SStatus 113 SControl 310)
EXT4-fs (md1): Remounting filesystem read-only
DMAR: ERROR: DMA PTE for vPFN ... already set

This page explains the incompatibility causing the problem, lists the affected machines and operating systems, and provides a workaround.

Affected machines and operating systems

The following Dedibox Pro-2 servers are affected by the incompatibility issue (all based on the HP ProLiant DL320e Gen8 v2 chassis):

The following operating systems and kernel versions are affected:

• Debian (kernels ≥ 6.17.13, e.g., Debian 13 "Trixie" and later versions)
• Ubuntu (kernels 7.x.x, e.g., Ubuntu 26.04 and later versions)
• Proxmox VE (kernels ≥ 6.17.13, based on Debian)

Cause

A default change in the handling of Intel IOMMU in recent Linux kernels (Debian/Ubuntu) degrades the SATA link (drops to 1.5 Gbps, AHCI link resets) and generates I/O errors on the disk controller via the IOMMU subsystem (DMAR: ERROR: DMA PTE …).

Workaround

To resolve the issue without completely disabling IOMMU virtualization (VT‑d), configure the IOMMU in passthrough mode (iommu=pt).

1. Open a root terminal and create a dedicated GRUB configuration file:

   echo 'GRUB_CMDLINE_LINUX_DEFAULT="$GRUB_CMDLINE_LINUX_DEFAULT intel_iommu=on iommu=pt"' | sudo tee /etc/default/grub.d/iommu.cfg

2. Update the GRUB configuration:

   sudo update-grub

3. Reboot the server to apply the change:

   sudo reboot