The Topology That Cannot Be Bridged: A Proxmox VM's PCIe Architecture Reveals the Fundamental Limits of GPU P2P

Introduction

In the pursuit of high-performance inference for large language models, few bottlenecks are as frustrating as those imposed by virtualization. When eight NVIDIA RTX PRO 6000 Blackwell GPUs are passed through to a Proxmox virtual machine, the promise of near-native performance collides with the unforgiving reality of hardware topology. Message 329 in this coding session represents a pivotal moment of revelation: the user, having been asked to investigate the Proxmox host's GPU configuration, pastes the raw output of diagnostic commands that collectively paint a picture of a hardware architecture that fundamentally prevents peer-to-peer (P2P) DMA between GPUs. This message is not merely a data dump—it is the moment when a hypothesis about software-configurable P2P enablement collides with the immutable constraints of physical hardware design.

The message arrives at a critical juncture. The assistant had been pursuing a multi-pronged strategy to improve inference throughput for the GLM-5-NVFP4 model, which was achieving approximately 485 total tokens per second at 64 concurrent requests—well short of the 1,000+ tok/s target. Earlier investigations had identified that cross-GPU communication was bottlenecked by a 13.7-microsecond latency floor per transfer, caused by the absence of P2P DMA between GPUs in the VM. The assistant's working hypothesis was that enabling IOMMU passthrough on the Proxmox host and potentially applying ACS (Access Control Services) override patches could merge IOMMU groups and allow direct GPU-to-GPU communication. Message 329 contains the data that would either validate or shatter that hypothesis.

The Context: A Session Built on Iterative Debugging

To understand the significance of message 329, one must appreciate the journey that led to it. The broader coding session (spanning segments 0 through 3) had been a marathon of environment setup, driver installation, build troubleshooting, and performance debugging. The team had successfully deployed the GLM-5-NVFP4 model on eight RTX PRO 6000 GPUs using SGLang with tensor parallelism of 8, only to discover that throughput was severely limited by cross-GPU communication latency.

The assistant had systematically worked through the problem. Initial NCCL tuning had yielded modest improvements. The investigation had then shifted to the virtualization layer, where the assistant hypothesized that the VM's chipset configuration (i440FX vs Q35) and PCIe topology might be contributing to the P2P limitation. The VM had been migrated from i440FX to Q35 with PCIe passthrough enabled, and a BAR allocation failure had been resolved with pci=realloc. Yet P2P remained stubbornly disabled.

In message 321, the assistant had explicitly asked the user about Proxmox host access, outlining the potential for IOMMU configuration and ACS override to enable P2P. The user confirmed access in message 322, providing initial host information including the kernel cmdline (which lacked IOMMU enablement) and evidence of eight AMD IOMMU units. The assistant then formulated a plan to investigate the GPU topology, IOMMU groups, VM configuration, and VFIO modules—and asked the user to run specific diagnostic commands on the host.

Message 329 is the user's response: a raw paste of command outputs, unadorned by interpretation or commentary. It is the raw material from which the assistant must diagnose the feasibility of P2P enablement.

What the Message Contains: A Detailed Examination

The message begins with the output of uname -a, confirming the Proxmox host runs kernel 6.8.12-9-pve on an x86_64 architecture. This is significant because the Proxmox kernel includes specific patches and configurations for virtualization, and the kernel version determines what IOMMU and VFIO features are available.

The lspci -nn | grep -i nvidia output reveals the eight GPUs at bus addresses:

• 01:00.0 — NVIDIA Device 2bb5 (RTX PRO 6000 Blackwell)
• 11:00.0
• 61:00.0
• 71:00.0
• 81:00.0
• 91:00.0
• e1:00.0
• f1:00.0 The device ID 10de:2bb5 confirms these are all the same GPU model. The bus addresses are scattered across different PCIe domains (0000:00 through 0000:f0), which is the first clue that these GPUs are not connected through a shared PCIe switch but rather each resides on its own root complex. The IOMMU group enumeration is the most critical piece of data. Each GPU is in a separate IOMMU group:
• Group 10: GPU at 71:00.0
• Group 28: GPU at 61:00.0
• Group 42: GPU at 01:00.0
• Group 61: GPU at 11:00.0
• Group 72: GPU at f1:00.0
• Group 90: GPU at e1:00.0
• Group 101: GPU at 81:00.0
• Group 117: GPU at 91:00.0 The group numbers are non-sequential and widely spaced (10, 28, 42, 61, 72, 90, 101, 117), which reflects the fact that each GPU is behind a distinct PCIe root complex on the AMD EPYC platform. In AMD's architecture, each root complex has its own IOMMU unit (as confirmed by the eight IOMMU units detected in message 322), and devices behind different root complexes are placed in separate IOMMU groups by default. The PCIe topology output from lspci -tv confirms this interpretation with devastating clarity. Each GPU is shown as:

+-01.1-[01]----00.0  NVIDIA Corporation Device 2bb5

under a different root complex: [0000:00], [0000:20], [0000:70], etc. The pattern is consistent: each root complex contains a "Turin PCIe Dummy Host Bridge" at 01.0, a "Turin RCEC" at 00.3, and a single PCIe slot at 01.1 that connects directly to one GPU. There are no PCIe switches anywhere in the topology—each GPU has a dedicated lane to its own root complex.

The VM configuration (qm config 128) shows the VM named "llm-one" with 450 GB of memory, 60 cores across 2 sockets, and crucially, eight hostpci entries all using mapping=pro6000. This means the GPUs are assigned via Proxmox's PCI mapping system, which abstracts the physical device assignment. The VM uses the Q35 chipset (implied by pcie=1 not being explicitly shown but known from earlier configuration), with NUMA enabled and host CPU type.

The VFIO module listing shows that vfio_pci, vfio_iommu_type1, vfio_pci_core, and iommufd are all loaded. The vfio_iommu_type1 module is particularly important—it's the module that manages the IOMMU groups for VFIO passthrough. Its presence confirms that the host is using VFIO for GPU passthrough, which is the standard approach for Proxmox.

The module configuration files show a clean setup: only vhost_net is loaded at boot, nvidiafb is blacklisted, and ZFS ARC is limited to 16 GB. There are no custom VFIO options or ACS override parameters.

The Revelation: Why P2P Is Fundamentally Impossible

This message is devastating to the assistant's P2P enablement hypothesis. The data reveals a hardware topology that no software configuration can overcome. Each GPU sits on its own PCIe root complex of the AMD EPYC Turin processor, with no shared PCIe switch connecting them. In this architecture:

1. Each GPU is in its own IOMMU group because the AMD IOMMU assigns groups based on PCIe topology. Devices behind different root complexes are inherently isolated.
2. ACS override cannot merge these groups because ACS (Access Control Services) is a feature of PCIe switches, not root complexes. ACS override patches modify the behavior of PCIe switches to allow transactions between different downstream ports. Since there are no switches in this topology—each GPU connects directly to a root complex port—there is no ACS setting to override.
3. VFIO cannot grant P2P across root complexes because the IOMMU translation tables are per-root-complex. The VFIO framework can only map DMA transactions within the same IOMMU domain. Cross-root-complex DMA requires the host system's IOMMU to coordinate, which introduces the very latency the team was trying to eliminate.
4. The hardware was designed for maximum per-GPU bandwidth, not for inter-GPU communication. Each GPU gets a dedicated PCIe Gen5 x16 link to its own root complex, which is optimal for workloads where GPUs work independently. For tightly-coupled tensor parallelism, this topology is suboptimal without NVLink or a shared PCIe switch. The message also reveals a subtle operational issue: the user's command shell had some parsing problems. The line -bash: 2.: command not found and -bash: syntax error near unexpected token newline'` suggest that the user may have copied commands imperfectly or that the shell interpreted some characters unexpectedly. This doesn't affect the diagnostic value of the output but indicates the user was working under some friction.

Assumptions Challenged and Knowledge Created

Before message 329, the assistant operated under several assumptions that this message fundamentally challenges:

Assumption 1: IOMMU groups could be merged with ACS override. This was based on common Proxmox configurations where ACS override patches enable grouping of devices behind a PCIe switch. The message reveals that ACS override is irrelevant here because there are no switches.

Assumption 2: Enabling IOMMU passthrough (amd_iommu=on, iommu=pt) would be sufficient. While these settings are necessary for VFIO passthrough, they cannot create P2P capability where the hardware topology doesn't support it. The IOMMU is already active (as shown by the IOMMU group enumeration), but it enforces isolation rather than enabling cooperation.

Assumption 3: The GPUs might share a PCIe bridge or switch. The earlier investigation had noted that GPUs 4-7 appeared to share a PIX topology, but the full host topology reveals that all eight GPUs are on separate root complexes. The PIX observation was likely a misinterpretation of the VM-level PCIe topology, which can differ from the physical host topology.

The message creates several important pieces of output knowledge:

1. A definitive topology map of the Proxmox host's PCIe hierarchy, showing eight separate root complexes each hosting one GPU. This is the foundational knowledge for all subsequent decisions about P2P workarounds.
2. Confirmation that VFIO is properly configured with the correct modules loaded and no missing dependencies. The passthrough setup is correct—it's the hardware that's the limitation.
3. The VM configuration details showing how GPUs are mapped via Proxmox's PCI mapping system, which will be relevant for any reconfiguration attempts.
4. The IOMMU group assignments with their specific group numbers, which will be needed if the team decides to attempt any kernel-level workarounds or if they need to update the PCI mapping file.

The Thinking Process: What This Message Enables

For the assistant receiving this message, the thinking process shifts from "how do we enable P2P" to "how do we work around the impossibility of P2P." The message forces a fundamental re-evaluation of the approach.

The assistant's previous strategy had been layered: first try NCCL tuning (quick, no restart needed), then try TP4+PP2 configuration (moderate effort), then investigate host-side Proxmox changes (high impact if feasible). The host-side changes were seen as the most promising path to transformative improvement. Message 329 closes that path, or at least transforms it from "enable P2P" to "find alternative workarounds."

The assistant must now consider:

• Can we use NVLink? The RTX PRO 6000 Blackwell GPUs may support NVLink, but NVLink bridges are physical hardware that must be installed. If the GPUs aren't physically connected via NVLink bridges, no software configuration can enable NVLink P2P.
• Can we reduce tensor parallelism? With TP4 instead of TP8, only 4 GPUs participate in each all-reduce, which halves the communication overhead. But the model must fit in 4 GPUs' memory.
• Can we use expert parallelism? For MoE models like GLM-5, expert parallelism distributes experts across GPUs differently than tensor parallelism, potentially reducing cross-GPU communication.
• Are there hacky kernel workarounds? The vfio_iommu_type1.allow_unsafe_interrupts parameter or the nv_peer_mem module might forcibly enable cross-group P2P, but these are insecure and may not work with the specific hardware topology. The message also enables the assistant to provide accurate, specific advice to the user. Instead of generic suggestions about "enabling IOMMU," the assistant can now say: "Your GPUs are on separate root complexes. ACS override won't help. Here are the options that remain."

The Broader Implications for ML Infrastructure

Beyond the immediate context of this coding session, message 329 illustrates a broader truth about GPU-accelerated virtualization: the hardware topology of the host machine is the single most important factor determining whether GPU passthrough can achieve near-native performance for tightly-coupled workloads.

For ML practitioners deploying large models across multiple GPUs, the choice between bare metal and virtualization is not just about convenience or resource sharing—it's a fundamental architectural decision. A Proxmox host with GPUs on separate root complexes (common in AMD EPYC platforms where each root complex serves a single PCIe slot) can provide excellent per-GPU performance for independent workloads but will bottleneck any workload requiring frequent cross-GPU communication.

This has practical implications for infrastructure design:

• For inference serving with tensor parallelism, bare metal or NVLink-connected GPUs are strongly preferred.
• For training with data parallelism, the communication pattern is less frequent (gradient sync every N steps), so virtualization overhead may be acceptable.
• For batch inference where each request can be processed independently, virtualization overhead is minimal. The message also highlights the importance of understanding the difference between PCIe topology at the host level versus what the VM sees. The VM may present a simplified PCIe topology that obscures the underlying root complex separation, leading to incorrect assumptions about P2P feasibility.

Conclusion: The Moment of Clarity

Message 329 is the moment in the coding session when ambiguity gives way to certainty. The assistant's hypothesis about P2P enablement through IOMMU configuration and ACS override is conclusively refuted by the hardware reality revealed in the diagnostic output. Each GPU on its own root complex, each in its own IOMMU group, with no PCIe switch in sight—this is a topology that software alone cannot bridge.

The message is remarkable for its raw, uninterpreted nature. The user simply pasted the output of the requested commands, letting the data speak for itself. There is no commentary, no analysis, no "I think this means X." The topology is what it is, and the numbers tell the story: eight GPUs, eight IOMMU groups, eight root complexes, zero possibility of P2P DMA through conventional means.

For the assistant, this message transforms the problem space. The search for a P2P solution through host-side configuration is over. New avenues must be explored: alternative parallelism strategies, kernel-level workarounds, or acceptance of the virtualization overhead and optimization within those constraints. The message doesn't provide answers—it provides the hard boundaries within which answers must be found.

In the broader narrative of the coding session, message 329 represents the point where the team's understanding of their infrastructure achieves maturity. They now know exactly what they're working with: a powerful but fundamentally limited virtualization setup that prioritizes per-GPU bandwidth over inter-GPU connectivity. Whether they can achieve their throughput targets within these constraints remains to be seen, but at least they now know the true shape of the problem they face.