No more CPU fights: how we build truly isolated cloud compute

by Peter Bangert, Senior Platform Engineer, Stelia

At Stelia AI, we have our own cloud infrastructure for self-hosting and self-delivery. Among our products — ranging from managed Kubernetes to Slurm — we provide an isolated GPU/compute instance comparable to EC2.

Our goal is simple: deliver compute instances (read: virtual machines with strict CPU ownership, NUMA locality, and zero cross-tenant contention — all inside Kubernetes.)

To accomplish this, we run virtual machines inside pods and pass host file descriptors into the hypervisor to attach paravirtualised (virtio) networking and storage devices. This gives us the operational flexibility of Kubernetes while maintaining VM-level isolation.

But doing this correctly requires careful control of CPU, memory, NUMA topology, and thread placement.

Let’s walk through how we built it.

Overview

This article is meant to be a technical guide providing an introduction to the tech stack, namely, Virtual Machines running on Kubernetes, and the motivation behind these choices, particularly pertaining to how we, at Stelia AI, perceive the future of the AI Infrastructure industry. Then we will be providing an introduction to the Kubernetes Topology Manager and the basics you need to set up your own NUMA-aware pod scheduling. Lastly, we will go a step further and discuss our highly technical approach to ensuring vCPU thread isolation for our Virtual Machines.

Motivation: focusing on duty, self-mastery, and trust in divine order

Why Kubernetes

There is a prevailing trend that AI/ML workloads are migrating to Kubernetes; CNCF reports that as of early 2026, 66% of organisations use Kubernetes for inferencing.

While we at Stelia AI have experience working with other infrastructure stacks, i.e., OpenStack, or simply bare metal, we chose Kubernetes because it has evolved beyond a container orchestrator into a universal control plane. By leveraging Custom Resource Definitions (CRDs), we treat our isolated VMs as first-class objects, benefiting from K8s’ robust object serialisation, RBAC, and API versioning out of the box. Also, by using the “Reconciler” controller pattern, you move away from “fire-and-forget” imperative scripts/IAC to more fine-grained state control.

Why Virtual Machines

By running virtual machines inside pods, we are using Kubernetes as the management plane (scheduling, networking, and storage) and the VM as the execution boundary. This also provides security hardening as opposed to providing pod/container access via mitigating the escape risk of a syscall exploit, and near hardware native performance via PCIe passthrough or SR-IOV.

NUMA Locality in Kubernetes

Reference: Topology Aware Scheduling in Kubernetes

Given our requirements to build an AI inferencing/training suitable infrastructure, we need to take lessons from classic HPC.

Not all memory is created equal. Non-Uniform Memory Access (NUMA) means that a specific group of CPU cores has “local” access to a specific bank of RAM.

The current gold standard for everyday AI workloads is the AMD EPYC dual socket processor, a very flexible workhorse that plays a pivotal role in creating balance by delivering high-performance, efficiency, and security. Below is a diagram of a Dual Socket system. Ideally, for HPC/AI workloads, you want your processes and threads running in a single socket, or NUMA node, as this eliminates the NUMA Hop by requesting memory across the interconnect, which results in a 15–30% drop in performance.

GPU Locality: In addition, GPUs are connected via the PCIe bus, so if your workload is running on the wrong socket, the data path between the CPU and GPU becomes a congested highway resulting in jitter or tail-latency.

To add another dimension, the amount of NUMA Nodes per Socket is configurable on most systems via the UEFI/BIOS. There exist typically NPS levels of 1,2, and 4, meaning on a Dual Socket system, you can configure up to 8 NUMA nodes. For our use case, we configure our systems with a single NUMA node per socket, so 2 in total.

But Dual Socket Systems aren’t that complex, is this overkill?

Following SuperMicros announcement in May 2023, unveiling an 8 Socket Server based on Intel CPUs…

It seems Dual Sockets are only the beginning. The sooner we adapt our Kubernetes topology management in the fast-growing world of bigger servers and larger workloads, the more prepared we will be moving forward.

Solving Resource Contention

When building and operating GPU compute resources, it's imperative that when a customer requests 20 CPUs for their virtual instance, they get 20 CPUs. In order to dedicate CPUs to instances, we’ll need to make the other stuff running on the system avoid them.

The traditional approach for that was the isolcpus kernel argument, but that’s deprecated, and cpusets in cgroups are the way to go.

Previously, when running our infrastructure on OpenStack or Bare-Metal, we had a tedious approach involving:

• Creating specific cgroups for different process types (system, instances, user)

• Manual CPU pinning (taskset)

• cpuset manipulation

Because we now operate inside Kubernetes, we can instead leverage three core components:

1. CPU Manager
2. Memory Manager
3. Device Manager
4. Coordinated by the Topology Manager

Kubernetes Topology Manager Deep Dive

Reference: Control Topology Management Policies on a node

The Topology Manager coordinates CPU, memory, and device allocation to ensure NUMA alignment. It acts as a central coordinator that polls three specific sub-managers to see what they have available:

1. CPU Manager: Decides which specific cores to assign (for Guaranteed QoS pods).
2. Memory Manager: Handles pinning memory pages to specific NUMA nodes.
3. Device Manager: Manages high-speed peripherals like GPUs or SR-IOV NICs.

Each manager sends back a Topology Hint, which is a bitmask saying, “I can satisfy this request using NUMA node 0 or node 1.”

The Topology Manager then merges these hints according to a configured policy.

Topology Manager Policies

The Topology Manager's responsibility is to coordinate how resources are allocated across NUMA nodes. Its goal is to align CPUs, memory, and devices so workloads avoid costly cross-socket communication, but there is a tunable policy to dictate its strictness.

The Topology Manager supports several policies:

none: No NUMA alignment is attempted. This is the default behavior and resources may come from any NUMA node.

best-effort: Attempts to align resources on the same NUMA node, but does not strictly enforce it. If alignment is not possible, the pod is still admitted.

restricted: Requires NUMA alignment when possible. If alignment cannot be achieved, the pod is rejected.

single-numa-node: The strictest policy. All requested resources must come from a single NUMA node, or the pod will not be scheduled.

Our Policy

Our goal is to provide performance-optimised resource allocation whenever possible, but ultimately we need to be flexible enough to account for instance requests which span well beyond a single NUMA node, therefore we chose to use the best-effort policy.

This is the configuration we are currently using in our kubelet configuration, please consult the kubernetes documents linked in this article to understand the purpose of the reserved memory/CPU requirements.

cpuManagerPolicy: static
memoryManagerPolicy: Static
topologyManagerPolicy: best-effort
topologyManagerScope: pod
reservedSystemCPUs: "0,64"
kubeReserved:
  cpu: "3"
  memory: "2Gi"
systemReserved:
  cpu: "1"
  memory: "1Gi"
evictionHard:
  memory.available: "1Gi"
  nodefs.available: "10%"
  imagefs.available: "15%"
reservedMemory:
- numaNode: 0
  limits:
    memory: "2Gi"
- numaNode: 1
  limits:
    memory: "2Gi"

Important: guaranteed QoS requirement

Reference: Kubernetes Pod Quality of Service Classes

Topology Manager alignment only works reliably for pods in the Guaranteed QoS class.

This requires that CPU and memory requests exactly match their limits, for example:

resources:
  requests:
    cpu: "4"
    memory: "8Gi"
  limits:
    cpu: "4"
    memory: "8Gi"

When a pod is in the Guaranteed class:

• the CPU Manager assigns exclusive CPU cores
• the Memory Manager can enforce NUMA-local allocations
• the Topology Manager can coordinate resource placement across subsystems

Pods in the Burstable or BestEffort QoS classes do not receive these guarantees, and their resources may be spread across NUMA nodes even when a topology policy is enabled.

The hidden problem: not all processes belong to the customer

If we look at all the running processes within the container that manages the hypervisor responsible for running the customer's virtual machine, we see something like this:

gpu-instance:/# ps
PID   USER     TIME  COMMAND
    1 root      0:00 instance-runner
   24 dnsmasq   0:00 dnsmasq 
   30 root      5:08 qemu-system-x86_64 
   35 root      5:08 virtiofsd
   37 root      0:00 bash
   43 root      0:00 ps
gpu-instance:/#

Even though Kubernetes gave the pod exclusive CPUs, all processes inside the pod share those CPUs.

That includes:

• vCPU threads (customer workload)
• I/O threads
• QEMU management threads
• Runtime threads from our controller
• virtiofsd (shared filesystem)
• dnsmasq (DHCP server) We needed isolation inside the container. Ideally, we would like everything besides the QEMU vCPU threads to be running on other cores elsewhere, meaning we need to move them to another cgroup.

About Control Group v2

As we discussed previously regarding the Pod Quality of Services classes, these classes are realised logically as different Cgroups by kubelet. Cgroups are a Linux Kernel feature that allows processes to be organised into hierarchical groups to limit, account for, and isolate resource usage.
Let's take a look at the Cgroups currently present on our worker node:

/sys/fs/cgroup/kubepods.slice
|   |-- kubepods-besteffort.slice
|   |   |-- kubepods-besteffort-pod0233c9aa_e18f_4614_97ba_94606228ec2f.slice
|   |   |   |-- cri-containerd-56b896a784d2bcb4c4a1877bc9350e0c412d9af98ec185ad3989aad78da0fead.scope
|   |   |   `-- cri-containerd-f486e076c03e5d720e7cf05abafd4456bff78d250ee896014ce79d65fd631d7b.scope
|   |   |-- kubepods-besteffort-pod232fe706_7428_4502_b880_19f28aa8ca3d.slice
|   |   |   |-- cri-containerd-4623cf1d300610228d5926a1f0c532dc9dd61db027d1d89a47a188e04871a73c.scope
|   |   |   |-- cri-containerd-72a8fb24580415a79e1b1b1142e6235ef61ca8ec2c2e7fec08da9574aea21810.scope
|   |-- kubepods-burstable.slice
|   |   |-- kubepods-burstable-pod332102fa_8018_4db4_9acc_50dd2f3a3460.slice
|   |   |   |-- cri-containerd-4fde7a33f9dc03c0d52d582266597e8f89d4d2bed6fd27232709eeb2dd34be0c.scope
|   |   |   |-- cri-containerd-7aca7509f4d290a8bcb7280c929cc85411fc803302dccf768aad3d937a169e95.scope
|   |-- kubepods-pod3ceda12c_3ee9_40fa_9f42_61428fe654a6.slice
|   |   |-- cri-containerd-0e16c65fb6a8d15dbd90aa3f1e07f6ba709d1adb47eee0af5aa6d1f92ffd4d04.scope
|   |   |-- cri-containerd-b02c37e654f2f8356cf2641f75a94194ecf3b8dbdb38d61de3644a67e49045a2.scope
|   |   `-- cri-containerd-eb6218013c1ba67fc5288216059150c3d8946da7ad6dd8cfdc7516621d80c260.scope

Here we see the three different QoS classes we previously described existing as different cgroup slices (unit of cgroups managed by systemd). Within each cgroup slice, we see pods, and within those pods, the individual containers.

For burstable and best-effort pod cgroups, you won't see much in terms of resource definitions, since kubelet and the topology manager don't provide any guarantees on resource isolation; however, you will see limits in place, such as memory.max.

root@worker1:/sys/fs/cgroup# cat kubepods.slice/kubepods-burstable.slice/kubepods-burstable-pod332102fa_8018_4db4_9acc_50dd2f3a3460.slice/cri-containerd-4fde7a33f9dc03c0d52d582266597e8f89d4d2bed6fd27232709eeb2dd34be0c.scope/memory.max
1073741824

However, for our guaranteed pods, you will see something more interesting: you will see cpuset.cpus defining the specific CPUs kubelet is reserving for the instance (in this case 4 cpus, 14–17)

root@worker1:/sys/fs/cgroup# cat kubepods.slice/kubepods-pod416de7c2_21de_472d_817c_fa9d4306cb7d.slice/cri-containerd-5baab67f1daf9297c60974e50ad9f94f288077161a7c41376478e79aae671e07.scope/cpuset.cpus
14-17

When a guaranteed pod is created, kubelet refers to its list of all currently guaranteed CPUs in its /var/lib/kubelet/cpu_manager_state, subtracts however many CPUs are being requested from its defaultCpuSet, allocates this for the requested pod, and then subtracts these CPUs from every burstable and best-effort pods' cgroup.
Let's take a look.

1. Currently our kubelet’s cpu_manager_state show us we have CPUs 2–11 on this 20 core system for shared use and the rest are reserved for instances.

{
  "policyName": "static",
  "defaultCpuSet": "2-11",
  "entries": {
    "3ceda12c-3ee9-40fa-9f42-61428fe654a6": {
      "instance": "0-1,12-13"
    },
    "416de7c2-21de-472d-817c-fa9d4306cb7d": {
      "instance": "14-17"
    },
    "b41f38d8-2c21-4168-af77-6d0cc5482dcb": {
      "instance": "18-19"
    }
  },
  "checksum": 3944432841
}

1. If we look at the cpusets allocated to the burstable and best-effort cgroups, they should coincide with the default cpuset:

root@worker1:/sys/fs/cgroup# cat kubepods.slice/kubepods-besteffort.slice/kubepods-besteffort-pod0233c9aa_e18f_4614_97ba_94606228ec2f.slice/cri-containerd-f486e076c03e5d720e7cf05abafd4456bff78d250ee896014ce79d65fd631d7b.scope/cpuset.cpus
2-11
root@worker1:/sys/fs/cgroup# cat kubepods.slice/kubepods-burstable.slice/kubepods-burstable-pod332102fa_8018_4db4_9acc_50dd2f3a3460.slice/cri-containerd-4fde7a33f9dc03c0d52d582266597e8f89d4d2bed6fd27232709eeb2dd34be0c.scope/cpuset.cpus
2-11

So how can we isolate the threads within our cgroup from one another?

Use threaded cgroups?

A simple solution to isolate our worker threads from all the other processes running within our Pod would be to simply create two children cgroups of the current cgroup our Pod belongs to, make them threaded cgroups, and split the threads between them.

However, there exists a limitation within Control Groups v2, in that when certain domain controllers are enabled, children cgroups cannot be threaded due to a lack of supporting control over sub-resources.

Currently, the following controllers are threaded and can be enabled in a threaded cgroup:

• cpu
• cpuset
• perf_event
• pids

What this means is that, since we have the memory manager enabled, this is not an option (it requires hugetlb and memory controllers).

root@worker1:/sys/fs/cgroup# cat kubepods.slice/kubepods-pod416de7c2_21de_472d_817c_fa9d4306cb7d.slice/cgroup.subtree_control
cpuset cpu io memory hugetlb pids rdma misc

As a result of these limitations, in order to accomplish our goal, we must develop our own solution.

Instance Cgroup Controller

To outline the overall approach, first we will define the goals and criteria for what we want to accomplish.

1. Create an Instance Cgroup controller, which we will deploy as a Daemonset on all worker nodes
2. The Instance Cgroup controller will manage a float cgroup and will allow for Instances to register new cgroups.
3. New cgroup registration will take parameters read from the current instance's cgroup (cpuset)
4. Develop our Instance Runner to then move all processes to the newly registered cgroup
5. All non-QEMU worker pids/threads should be placed within the float cgroup, and all vCPU threads should be placed in the registered cgroup
6. Deregistration and placing pids back in the original place during teardown

An architecture of this approach can be seen below:

Step 1: Set up Instance Cgroup Controller

The Instance Cgroup Controller is responsible for managing CPU topology and cgroup placement for all virtual machine instances running on a node. Conceptually, it acts as a local resource coordinator that sits between the instance lifecycle manager and the Linux kernel’s cgroup interfaces.

The primary goals of the controller are:

• Create and maintain cgroup heirarchy for float processes and instances
• Registration and deregistration API for Instance Runner
• Reconcile cpusets and cgroups statelessly, and manage cleanup

Establishing the Cgroup Hierarchy

The controller manages a dedicated subtree under the system cgroup hierarchy. The structure looks like:

steliа/
 ├─ instance-<pod-uuid>/
 ├─ float/

• stelia/ is the root cgroup managed by our runtime.
• instance-<pod-uuid>/ represents the cgroup assigned to a specific VM instance.
• float/ is a shared execution pool where processes temporarily run before they are pinned to dedicated CPUs.

The next step will be to enable the required domain controllers for this cgroup hierarchy and then make these sub-cgroups (float, instances) threaded cgroup types.

It is important to note that we will only be enabling the cpuset domain controller in our cgroup hierarchy, as we are allocating hugepages to our virtual machine. Hugepage allocation is taken from kubelets allocation and will remain static as it's bound to the process at start time, so this should not be affected when the pid is moved, and the stelia cgroup does not have a hugetlb controller enabled (doesn't exist for threaded cgroups), so the kernel should not touch these resources.

Setting this up in Rust will appear as follows:

use std::fs;
use std::io::Result;
use std::path::Path;

/// Ensure the stelia cgroup topology exists and is configured correctly.
fn ensure_topology(
    stelia_cgroup: &Path, // e.g. /sys/fs/cgroup/stelia
    float_cgroup: &Path, // e.g. /sys/fs/cgroup/stelia/float
    total_cpus: &str, // e.g. "0-19 (from cpu_manager_state)"
    mems: &str, // e.g. "0,1" number of memory domains (from memory_manager_state)"
) -> Result<()> {

    // Create the root stelia cgroup
    fs::create_dir_all(stelia_cgroup)?;

    // Configure cpuset settings for the root cgroup
    fs::write(stelia_cgroup.join("cpuset.mems"), mems)?;
    fs::write(stelia_cgroup.join("cpuset.cpus"), total_cpus)?;

    // Enable cpuset controller for children
    fs::write(stelia_cgroup.join("cgroup.subtree_control"), "+cpuset")?;

    // Create the shared "float" cgroup
    fs::create_dir_all(float_cgroup)?;

    // Configure the float cgroup
    fs::write(float_cgroup.join("cgroup.type"), "threaded")?;
    fs::write(float_cgroup.join("cpuset.mems"), mems)?;
    fs::write(float_cgroup.join("cpuset.cpus"), total_cpus)?;

    Ok(())
}

Registration and Deregistration endpoints

Using JSON-RPC over a Unix domain socket is a good fit for communication between the Instance Runner and the Instance Cgroup Controller because it provides a lightweight RPC mechanism without introducing unnecessary networking overhead. Since both components run on the same node, there is no need to traverse the full IP or HTTP networking stack and they can instead communicate through a Unix filesystem socket.

A simplified JSON-RPC request used by the Instance Runner might look like, where the Instance Runner will provide its pod uuid and cpuset:

{
  "jsonrpc": "2.0",
  "method": "registerCgroup",
  "params": {
    "uuid": "123",
    "cpuset": "4-7"
  },
  "id": 123
}

The controller responds with the newly registered instance group path:

{
  "jsonrpc": "2.0",
  "result": {
    "cgroup_path": "/sys/fs/cgroup/stelia/instance-123"
  },
  "id": 123
}

Reconciliation loop and cleanup

Every time an event occurs (such as an instance registering or deregistering), the controller performs a reconciliation pass. The reconciliation process does two main things:

1. Recalculate Float CPUs

The float cgroup is updated using the current defaultCpuSet value from kubelet /var/lib/kubelet/cpu_manager_state. If the defaultCpuSet differs from the current cpuset which is assigned to the float cgroup, it is updated.

This is done by updating the /sys/fs/cgroup/stelia/float/cpuset.cpus

{
  "policyName": "static",
  "defaultCpuSet": "2-11",
  "entries": {
    "3ceda12c-3ee9-40fa-9f42-61428fe654a6": {
      "instance": "0-1,12-13"
    },
    "416de7c2-21de-472d-817c-fa9d4306cb7d": {
      "instance": "14-17"
    },
    "b41f38d8-2c21-4168-af77-6d0cc5482dcb": {
      "instance": "18-19"
    }
  },
  "checksum": 3944432841
}

1. Cleanup: remove stale cgroups

Stale instance cgroups are cleaned up if:

• They do not appear in the kubelet CPU manager state
• They contain no processes

This prevents resource leaks if an instance crashes or kubelet restarts. If the cgroups.procs and cgroups.threads is empty, it can be considered stale and can be safely removed.

Step 2: manage processes from Instance Runner

Once the cgroup hierarchy and CPU topology are established, the Instance Runner becomes responsible for placing VM processes into the correct cgroups and assigning them CPUs.

The process typically involves the following steps:

1. Register with the Instance Cgroup controller
2. Move all PIDs to the float cgroup
3. Discover QEMU worker threads
4. Move QEMU worker threads to the instance cgroup
5. Pin QEMU worker threads to specific CPUs

Registering with the controller

The instance runner is able to discover its pod-uuid and the cpuset allocated to this container/pod by reading from /proc/self as shown below:

gpu-instance:/# cat /proc/self/cpuset
/kubepods.slice/kubepods-podb9e4f71c_64a5_4f8d_8574_41363cbaf8e5.slice/cri-containerd-506962bc49f80b0ae7461edb1dbefdd626c4ece2b4bf103747a402982e91bf39.scope
gpu-instance:/# cat /sys/fs/cgroup/kubepods.slice/kubepods-podb9e4f71c_64a5_4f8d_8574_41363cbaf8e5.slice/cri-containerd-506962bc49f80b0ae7461edb1dbefdd626c4ece2b4bf103747a402982e91bf39.scope/cpuset.cpus
18-19

With this information, the Instance Runner can construct a registration request over a JSON-RPC Unix domain socket, which is provided as a volume mount to the Instance Runner pod. This provides a lightweight control plane without requiring shared state between components.

A typical registration request looks like:

{
  "jsonrpc": "2.0",
  "method": "registerCgroup",
  "params": {
    "uuid": "123"
    "cpuset": "4-7"
  },
  "id": 1
}

The response returns the assigned instance cgroup and CPU allocation.

Moving processes into the float cgroup

Having received our newly registered cgroup, we want to first move all the processes within the container to the float cgroup (runs on shared CPUs), with the goal of later moving the vCPU threads to the CPU-isolated cgroup.

Let's take a look back at our process namespace from before. This is a list of all running processes in our container.

gpu-instance:/# ps
PID   USER     TIME  COMMAND
    1 root      0:00 instance-runner
   24 dnsmasq   0:00 dnsmasq 
   30 root      5:08 qemu-system-x86_64 
   35 root      5:08 virtiofsd
   37 root      0:00 bash
   43 root      0:00 ps
gpu-instance:/#

The simplest way to manage moving all processes to another cgroup is to move pid 1 (main process) before spawning any subprocesses; this way, all spawned processes will inherit the parent cgroup.

So to move the main process to the float cgroup, this is as simple as writing the pid to the float cgroup's cgroup.procs file.

Example:

echo 1 > /sys/fs/cgroup/stelia/float/cgroup.procs

Caveat: preventing Kubernetes cgroup cleanup

Because instances are launched inside Kubernetes pods, we must account for Kubelet’s cgroup reconciliation logic. Kubelet periodically cleans up cgroups that it believes are unused. If all processes are moved out of a container cgroup, the kubelet will delete it.

To prevent this, we keep a placeholder process inside the original Kubernetes cgroup. For this, the Instance Runner will spawn an infinite sleep process within the container:

use std::process::Command;

fn spawn_placeholder() -> std::io::Result<()> {
    Command::new("sleep")
        .arg("infinity")
        .spawn()?;
    Ok(())
}

This process never participates in the instance runtime but acts as a cgroup anchor.

Discovering vCPU Threads via QMP

Now that all processes are moved into the float cgroup and are now able to utilise all CPUs on the node, we need to isolate our vCPU ‘worker’ threads. How do we discover these threads?

QEMU exposes runtime information through the QEMU Machine Protocol (QMP). We use this interface to discover the thread IDs for each virtual CPU. Specifically, we call the QMP command:

query-cpus-fast

This returns information about all vCPU threads. In Rust, this might look like:

async fn try_get_vcpu_threads() -> Result<Vec<i32>> {
    let mut qmp = QmpClient::connect().await?;
    let response = qmp
        .execute("query-cpus-fast", None)
        .await
        .context("query-cpus-fast failed")?;

    let vcpus: Vec<QmpCpuInfo> = serde_json::from_value(response)?;

    debug!("Found {} QEMU vCPU threads", vcpus.len());

    Ok(vcpus.into_iter().map(|v| v.thread_id).collect())
}

Each returned thread_id corresponds to a Linux thread representing a QEMU vCPU.

Moving vCPU Threads to the instance cgroup

Once the vCPU thread IDs are known, they are moved into the instance cgroup, similar to how we moved processes before, however instead to cgroup.threads :

echo <tid> > /sys/fs/cgroup/stelia/sgcinstance-xxx/cgroup.threads

Pinning threads to specific CPUs

After the threads are placed in the correct cgroup, the final step is to assign each thread a CPU affinity. This ensures:

• minimal scheduling contention
• NUMA locality (as provided by kubelet allocation)

Example Rust implementation:

use nix::sched::{sched_setaffinity, CpuSet};
use nix::unistd::Pid;

fn pin_thread(tid: i32, cpu: usize) -> nix::Result<()> {
    let mut set = CpuSet::new();
    set.set(cpu)?;
    sched_setaffinity(Pid::from_raw(tid), &set)
}

Each vCPU thread is pinned to one CPU from the instance’s allocated CPU set.

Resulting process layout

After initialisation, the respective cgroups end up with a structure similar to this:

stelia/
├─ float/
│   └─ qemu
│   ├─ virtiofsd
│   ├─ dnsmasq
│   └─ instance runner
│
├─ instance-123/
│   └─ vcpu threads (pinned)

While the original Kubernetes pod still contains:

kubepods/
└─ pod-abc123/
    └─ placeholder (sleep infinity)

This approach allows us to combine Kubernetes lifecycle management with low-level CPU isolation without fighting kubelet’s cgroup garbage-collection logic.

Running on a Dual Socket system

So, after all this work, what do the results look like on an actual Dual Socket system? After configuring the kubelet with the aforementioned configuration on our AMD Epyc with 128 cpus and 256 GiB of memory, let's first observe the NUMA domains of each CPU on the system. We have ~5.5k 2MB hugepages configured on each NUMA node (~113 GiB).

NUMA:
  NUMA node(s):              2
  NUMA node0 CPU(s):         0-31,64-95
  NUMA node1 CPU(s):         32-63,96-127

root@gpu-node:~# cat /sys/devices/system/node/node*/hugepages/hugepages-2048kB/nr_hugepages
55552
55296

We will start by creating an instance with 40 CPUs and 80 GiB of hugepages. If we look at the CPU and hugepage allocation from kubelet in our containers cgroup, we see that the instances' CPUs and hugepages are localised to NUMA node 0:

root@gpu3:~# cat /sys/fs/cgroup/kubepods.slice/kubepods-podce32ebd2_f905_449e_b74b_4231a84b88e1.slice/cri-containerd-8a7496cc1fc043b490ebf3c3ec51d939cbeb988febb88a7c96b1dc871ae6a4e4.scope/cpuset.cpus
1-20,65-84
root@gpu-node:~# cat /sys/fs/cgroup/kubepods.slice/kubepods-podce32ebd2_f905_449e_b74b_4231a84b88e1.slice/cri-containerd-8a7496cc1fc043b490ebf3c3ec51d939cbeb988febb88a7c96b1dc871ae6a4e4.scope/hugetlb.2MB.numa_stat
total=8589934592 N0=8589934592 N1=0

After our controllers then complete their cgroup registration and process migrations, we can observe the following when running a script that checks for which cpuset a process may run on and which cpu they are currently running on. As we can see, every process is running on the defaultCpuSet (everything besides the allocated cpus for the instance), and there are exactly 40 QEMU threads which are pinned to a dedicated CPU:

root@gpu3:~# ./pid_affinity.sh

######################################################################
Inspecting: dnsmasq
######################################################################

======================================================================
==== dnsmasq PID: 3794608 ====
======================================================================

==== dnsmasq cgroup ====
0::/stelia-io/float

==== dnsmasq main thread affinity ====
pid 3794608's current affinity list: 0,21-64,85-127

==== Listing dnsmasq threads ====

TID        THREAD_NAME               ALLOWED_CPUS         RUNNING_ON
---------- ------------------------- -------------------  ----------
3794608    dnsmasq                   0,21-64,85-127       39


######################################################################
Inspecting: QEMU
######################################################################

======================================================================
==== QEMU PID: 3794651 ====
======================================================================

==== QEMU cgroup ====
0::/stelia-io/float

==== QEMU main thread affinity ====
pid 3794651's current affinity list: 0,21-64,85-127

==== Listing QEMU threads ====

TID        THREAD_NAME               ALLOWED_CPUS         RUNNING_ON
---------- ------------------------- -------------------  ----------
3794651    qemu-system-x86           0,21-64,85-127       62
3794652    qemu-system-x86           0,21-64,85-127       124
3794654    qemu-system-x86           0,21-64,85-127       61
3794656    qemu-system-x86           1                    1
3794657    qemu-system-x86           2                    2
3794658    qemu-system-x86           3                    3
3794659    qemu-system-x86           4                    4
3794660    qemu-system-x86           5                    5
3794661    qemu-system-x86           6                    6
3794663    qemu-system-x86           7                    7
3794664    qemu-system-x86           8                    8
3794665    qemu-system-x86           9                    9
3794666    qemu-system-x86           10                   10
3794667    qemu-system-x86           11                   11
3794668    qemu-system-x86           12                   12
3794669    qemu-system-x86           13                   13
3794670    qemu-system-x86           14                   14
3794671    qemu-system-x86           15                   15
3794672    qemu-system-x86           16                   16
3794673    qemu-system-x86           17                   17
3794674    qemu-system-x86           18                   18
3794675    qemu-system-x86           19                   19
3794676    qemu-system-x86           20                   20
3794677    qemu-system-x86           65                   65
3794678    qemu-system-x86           66                   66
3794679    qemu-system-x86           67                   67
3794680    qemu-system-x86           68                   68
3794681    qemu-system-x86           69                   69
3794682    qemu-system-x86           70                   70
3794683    qemu-system-x86           71                   71
3794684    qemu-system-x86           72                   72
3794685    qemu-system-x86           73                   73
3794686    qemu-system-x86           74                   74
3794687    qemu-system-x86           75                   75
3794688    qemu-system-x86           76                   76
3794689    qemu-system-x86           77                   77
3794690    qemu-system-x86           78                   78
3794691    qemu-system-x86           79                   79
3794692    qemu-system-x86           80                   80
3794693    qemu-system-x86           81                   81
3794694    qemu-system-x86           82                   82
3794695    qemu-system-x86           83                   83
3794696    qemu-system-x86           84                   84
3794737    kvm-nx-lpage-re           0,21-64,85-127       52


######################################################################
Inspecting: Instance Runner
######################################################################

======================================================================
==== Instance Runner PID: 3794442 ====
======================================================================

==== Instance Runner cgroup ====
0::/stelia-io/float

==== Instance Runner main thread affinity ====
pid 3794442's current affinity list: 0,21-64,85-127

==== Listing Instance Runner threads ====

TID        THREAD_NAME               ALLOWED_CPUS         RUNNING_ON
---------- ------------------------- -------------------  ----------
3794442    instance-runner           0,21-64,85-127       85
3794456    tokio-runtime-w           0,21-64,85-127       40
3794457    tokio-runtime-w           0,21-64,85-127       10
3794458    tokio-runtime-w           0,21-64,85-127       83
3794459    tokio-runtime-w           0,21-64,85-127       12
3794460    tokio-runtime-w           0,21-64,85-127       10
3794461    tokio-runtime-w           0,21-64,85-127       82

==== Done ====

Conclusion

In this article, we showed how to run NUMA-localised, thread-isolated virtual machines in Kubernetes for AI and HPC workloads. By leveraging Kubernetes’ CPU, Memory, and Topology Managers, we preserve exclusive CPU ownership and NUMA locality. Our Instance Cgroup Controller and Instance Runner isolate vCPU threads from runtime processes, pinning them to the allocated CPUs. The result is deterministic performance, low latency, and strong tenant isolation, all while fully operating inside Kubernetes.

Limitations and future work

NUMA localisation is critical for HPC and AI workloads. However, there is a known architectural limitation in Kubernetes:

Topology Manager complexity

The Topology Manager merges NUMA hints using bitmask intersections. In worst-case scenarios, the merging algorithm has exponential characteristics:

O(2^n)

Where n = number of NUMA nodes.

Today, this is manageable as most production systems are dual-socket (2 NUMA nodes), and AMD EPYC commonly presents 2 NUMA domains per socket configuration

But future systems are changing:

• 4-socket systems
• 8-socket high-density compute nodes
• CXL memory expansion

If Kubernetes runs on 8-socket NUMA systems, the current merging algorithm may become computationally expensive during scheduling.

And currently, this is a known issue as the bitmask affinity suggestions, as well, don't seem to filter out non-preferential affinity assignments.

Production-Grade Container Scheduling and Management - kubernetes

When we create a 1-GPU pod on a machine with 8 NUMA nodes (AMD CPU + NVIDIA 4090D), the hint providers for CPU, memory, hugepages, and GPU each generate approximately 255 hints. During the hint merging phase, the topology manager needs to evaluate 255⁴ (over 4.2 billion) possible hint combinations. In our testing, this process took nearly 21 minutes.