CPU limits and aggressive throttling in Kubernetes

Fayiz Musthafa
Feb 17, 2020 · 8 min read

Have you seen your application get stuck or fail to respond to health check requests, and you can’t find any explanation? It might be because of the CPU quota limit. We will explain more here.

TL;DR:
We would highly recommend removing CPU Limits in Kubernetes (or Disable CFS quota in Kublet) if you are using a kernel version with CFS quota bug unpatched. There is a serious, known CFS bug in the kernel that causes un-necessary throttling and stalls.

At Omio, we are 100% Kubernetes. All our stateful and stateless workloads run completely on Kubernetes (hosted using Google’s Kubernetes Engine). Since the last 6 months, we’ve been seeing random stalls. Applications stuck or failing to respond to health checks, broken network connections and so on. This sent us down a deep rabbit hole.

This article covers the following topics.

  • A primer on containers & kubernetes
  • How CPU request and limit is implemented
  • How CPU limit works in multi-core environments
  • How do you monitor CPU throttling
  • How do you recover

A primer on Containers & Kubernetes

Kubernetes (abbreviated as k8s) is pretty much a de-facto standard in the infrastructure world now. It is a container orchestrator.

Containers

In the past, we used to create artifacts such as Java JARs/WARs or Python Eggs or Executables, and throw them across the wall for someone to run them on servers. But to run them, there is more work — application runtime (Java/Python) has to be installed, appropriate files inappropriate places, specific OSes and so on. It takes a lot of configuration management, and is a frequent source of pain between developers and sysadmins. Containers change that. Here, the artifact is a Container image. Imagine it as a fat executable with not only your program, but also the complete runtime (Java/Python/…), necessary files and packages pre-installed & ready to run. This can be shipped and run on a variety of servers without any further customized installations needed.

Containers also run in their own sandboxed environment. They have their own virtual network adapter, their own restricted filesystem, their own process hierarchy, their own CPU and memory limits, etc. This is a kernel feature called namespaces.

Kubernetes

Kubernetes is a Container orchestrator. You give it a pool of machines. Then you tell it: “Hey kubernetes — run 10 instances of my container image with 2 cpus and 3GB RAM each, and keep it running!”. Kubernetes orchestrates the rest. It will run them wherever it finds free CPU capacity, restart them if they are unhealthy, do a rolling update if we change the versions, and so on.

Essentially, Kubernetes abstracts away the concept of machines, and makes all of them a single deployment target.

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Layman’s representation of Kubernetes

Understanding Kubernetes request and limit

OK, we understand what Containers and Kubernetes are. We also see that, multiple containers can fit inside the same machine.

This is like flat sharing. You take some big flats (machines/nodes) and share it with multiple, diverse tenants (containers). Kubernetes is our rental broker. But how does it keep all those tenants from squabbling with each other? What if one of them takes over the bathroom for half a day? ;)

This is where request and limit come into picture. CPU “Request” is just for scheduling purposes. It’s like the container’s wishlist, used mainly to find the best node suitable for it. Whereas CPU “Limit” is the rental contract. Once we find a node for the container, it absolutely cannot go over the limit.

And here is where the problem arises…

How Kubernetes request & limit is implemented

Kubernetes uses kernel throttling to implement CPU limit. If an application goes above the limit, it gets throttled (aka fewer CPU cycles). Memory requests and limits, on the other hand, are implemented differently, and it’s easier to detect. You only need to check if your pod’s last restart status is OOMKilled. But CPU throttling is not easy to identify, because k8s only exposes usage metrics and not cgroup related metrics.

CPU Request

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How CPU request is implemented

For the sake of simplicity, let’s discuss how it organized in a four-core machine.

The k8s uses a cgroup to control the resource allocation(for both memory and CPU ). It has a hierarchy model and can only use the resource allocated to the parent. The details are stored in a virtual filesystem (/sys/fs/cgroup). In the case of CPU it’s /sys/fs/cgroup/cpu,cpuacct/*.

The k8s uses cpu.share file to allocate the CPU resources. In this case, the root cgroup inherits 4096 CPU shares, which are 100% of available CPU power(1 core = 1024; this is fixed value). The root cgroup allocate its share proportionally based on children’s cpu.share and they do the same with their children and so on. In typical Kubernetes nodes, there are three cgroup under the root cgroup, namely system.slice, user.slice, and kubepods. The first two are used to allocate the resource for critical system workloads and non-k8s user space programs. The last one, kubepods is created by k8s to allocate the resource to pods.

If you look at the above graph, you can see that first and second cgroups have 1024 share each, and the kubepod has 4096. Now, you may be thinking that there is only 4096 CPU share available in the root, but the total of children’s shares exceeds that value (6144). The answer to this question is, this value is logical, and the Linux scheduler (CFS) uses this value to allocate the CPU proportionally. In this case, the first two cgroups get 680 (16.6% of 4096) each, and kubepod gets the remaining 2736. But in idle case, the first two cgroup would not be using all allocated resources. The scheduler has a mechanism to avoid the wastage of unused CPU shares. Scheduler releases the unused CPU to the global pool so that it can allocate to the cgroups that are demanding for more CPU power(it does in batches to avoid the accounting penalty). The same workflow will be applied to all grandchildren as well.

This mechanism will make sure that CPU power is shared fairly, and no one can steal the CPU from others.

CPU Limit

Even though the k8s config for Limit and Requests looks similar, the implementation is entirely different; this is the most misguiding and less documented part.

The k8s uses CFS’s quota mechanism to implement the limit. The config for the limit is configured in two files cfs_period_us and cfs_quota_us(next to cpu.share) under the cgroup directory.

Unlike cpu.share, the quota is based on time period and not based on available CPU power. cfs_period_us is used to define the time period, it’s always 100000us (100ms). k8s has an option to allow to change this value but still alpha and feature gated. The scheduler uses this time period to reset the used quota. The second file, cfs_quota_us is used to denote the allowed quota in the quota period.

Please note that it also configured in us unit. Quota can exceed the quota period. Which means you can configure quota more than 100ms.

Let’s discuss two scenarios on 16 core machines (Omio’s most common machine type).

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Scenario 1: 2 thread and 200ms limit. No throttling
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Scenario 2: 10 thread and 200ms limit. throttling starts after 20ms and only receive cpu power after 80ms.

Let’s say you have configured 2 core as CPU limit; the k8s will translate this to 200ms. That means the container can use a maximum of 200ms CPU time without getting throttled.

And here starts all misunderstanding. As I said above, the allowed quota is 200ms, which means if you are running ten parallel threads on 12 core machine (see the second figure) where all other pods are idle, your quota will exceed the limit in 20ms (i.e. 10 * 20ms = 200ms), and all threads running under that pod will get throttled for next 80ms (stop the world). To make the situation worse, the scheduler has a bug that is causing unnecessary throttling and prevents the container from reaching the allowed quota.

Checking the throttling rate of your pods

Just login to the pod and run cat /sys/fs/cgroup/cpu/cpu.stat.

  • nr_periods — Total schedule period
  • nr_throttled — Total throttled period out of nr_periods
  • throttled_time — Total throttled time in ns
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So what really happens?

We end up with a high throttle rate on multiple applications — up to 50% more than what we assumed the limits were set for!

This cascades as various errors — Readiness probe failures, Container stalls, Network disconnections and timeouts within service calls — all in all leading to reduced latency and increased error rates.

Fix and Impact

Simple. We disabled CPU limits until the latest kernel with bugfix was deployed across all our clusters.

Immediately, we found a huge reduction in error rates (HTTP 5xx) of our services:

HTTP Error Rates (5xx)

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HTTP 5xx rates of a critical service

p95 Response time

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p95 request latency of a critical service

Utilization costs

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Number of instance hours utilized

What’s the catch?

We said at the beginning of this article:

This is like flat sharing. Kubernetes is our rental broker. But how does it keep all those tenants from squabbling with each other? What if one of them takes over the bathroom for half a day? ;)

This is the catch. We risk some containers hogging up all CPUs in a machine. If you have a good application stack in place (e.g. proper JVM tuning, Go tuning, Node VM tuning) — then this is not a problem, you can live with this for a long time. But if you have applications that are either poorly optimized, or simply not optimized (FROM java:latest) — then results can backfire. At Omio we have automated base Dockerfiles with sane defaults for our primary language stacks, so this was not an issue for us.

Please do monitor USE (Utilization, Saturation and Errors) metrics, API latencies and error rates, and make sure your results match expectations.

Did you encounter similar issues or want to share your experiences with throttling in containerized production environments? Let us know in the Comments below!

If you liked this article and want to work on similar challenges at scale, why not consider joining forces :)

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