testing system-containerized kube and friends

A month or so ago I jotted down some notes on using ansible to set up a kubernetes cluster on atomic hosts with kubernetes running in regular docker containers and flannel and etcd running in system containers.

I’ve been working on turning my kube containers into system containers. Three reasons jump to mind:

  • I want to run my kube containers via systemd, and system containers come with systemd unit files rolled in and deployed automatically when you run atomic install --system foo, as opposed to storing them somewhere separate from the containers, and copying them into place.
  • I’m using flannel and etcd system containers, in part because flannel needs to modify docker’s configs to do its thing, and etcd needs to be running for flannel to run, so there’s a bit of a chicken-and-egg situation that we avoid by running flannel and etcd outside of docker. I can save on a bit of storage by having flannel, etcd and kubernetes all share the same image in the ostree-based storage that system containers use.
  • I’ve been wanting to learn more about system containers for a little while now, and Yu Qi (Jerry) Zhang just wrote this system container howto.

I’ve been testing on a trio of fedora atomic hosts like this:

$ git clone https://github.com/jasonbrooks/contrib.git
$ cd contrib
$ git checkout system-containers
$ cd ansible
$ vi inventory/inventory

[masters]
kube-master-test.example.com

[etcd:children]
masters

[nodes]
kube-minion-test-[1:2].example.com

$ cd scripts
$ ./deploy-cluster.sh

Substitute those hostnames above with ones that match your own test machines. Alternatively, you should be able to use the Vagrantfile in the vagrant directory of that repo, though I haven’t tested that yet.

This involves a bunch of changes to run commands like atomic install --system --name etcd {{ container_registry }}/{{ container_namespace }}/etcd:{{ container_label }} to install flannel, etcd and kubernetes master and node components if desired and specified in the inventory/group_vars/all.yml file.

In that same config file, I’ve temporarily turned off some of the newish encrypted flannel stuff, because I need to tweak the flannel container to make it work.

If you run the script as laid out above, you’ll get etcd, flannel and kube containers from my namespace in the docker hub, because the current upstream fedora containers, in the case of etcd and flannel, need a couple of changes, and in the case of kube, the upstream fedora containers (that I maintain) aren’t yet modified to run as system containers.

Speaking of which, another cool thing about system containers is that they can be run as regular docker containers. To test whether my new system containers would run as regular docker containers, I ran through the steps I mentioned in my previous post, with a different branch of ansible modded to run kube in regular docker containers, but in the all.yml conf file, I set container_registry: docker.io and container_namespace: jasonbrooks and container_label: fc25 to grab the system container versions of everything that I’ve been talking about in this post. It worked.

So, yay. I have a couple items to work through still. There’s the flannel bit I mentioned above (I think I just need to mount another dir in the flannel system container’s config.json.template). Also, I’ve been needing to restart the kubelet service again in my nodes before the kubedns pod would work, so I need to track down where in the ansible that needs to happen to make it automatic.

Installing Kubernetes on CentOS Atomic Host with kubeadm

Version 1.4 of Kubernetes, the open-source system for automating deployment, scaling, and management of containerized applications, included an awesome new tool for bootstrapping clusters: kubeadm.

Using kubeadm is as simple as installing the tool on a set of servers, running kubeadm init to initialize a master for the cluster, and running kubeadm join on some nodes to join them to the cluster. With kubeadm, the kubelet is installed as a regular software package, and the rest of the components run as docker containers.

The tool is available in packaged form for CentOS and for Ubuntu hosts, so I figured I’d avail myself of the package-layering capabilities of CentOS Atomic Host Continuous to install the kubeadm rpm on a few of these hosts to get up and running with an up-to-date and mostly-containerized kubernetes cluster.

However, I hit an issue trying to install one of the dependencies for kubeadm, kubernetes-cni:

# rpm-ostree pkg-add kubelet kubeadm kubectl kubernetes-cni
Checking out tree 060b08b... done

Downloading metadata: [=================================================] 100%
Resolving dependencies... done
Will download: 5 packages (41.1 MB)

Downloading from base: [==============================================] 100%

Downloading from kubernetes: [========================================] 100%

Importing: [============================================================] 100%
Overlaying... error: Unpacking kubernetes-cni-0.3.0.1-0.07a8a2.x86_64: openat: No such file or directory

It turns out that kubernetes-cni installs files to /opt, and rpm-ostree, the hybrid image/package system that underpins atomic hosts, doesn’t allow for this. I managed to work around the issue by rolling my own copy of the kubeadm packages that included a kubernetes-cni package that installed its binaries to /usr/lib/opt, but I found that not only do kubernetes’ network plugins expect to find the cni binaries in /opt, but they place their own binaries in there as needed, too. In an rpm-ostree system, /usr is read-only, so even if I modified the plugins to use /usr/lib/opt, they wouldn’t be able to write to that location.

I worked around this second issue by further modding my kubernetes-cni package to use tmpfiles.d, a service for managing temporary files and runtime directories for daemons, to create symlinks from each of the cni binaries stored in /usr/lib/opt/cni/bin to locations in in /opt/cni/bin. You can see the changes I made to the spec file here and find a package based on these changes in this copr.

I’m not positive that this is the best way to work around the problem, but it allowed me to get up and running with kubeadm on CentOS Atomic Host Continuous. Here’s how to do that:

This first step may or may not be crucial, I added it to my mix on the suggestion of this kubeadm doc page while I was puzzling over why the weave network plugin wasn’t working.

# cat <<EOF > /etc/sysctl.d/k8s.conf
net.bridge.bridge-nf-call-ip6tables = 1
net.bridge.bridge-nf-call-iptables = 1
EOF

This set of steps adds my copr repo, overlays the needed packages, and kicks off a reboot for the overlay to take effect.

# cat <<EOF > /etc/yum.repos.d/jasonbrooks-kube-release-epel-7.repo
[jasonbrooks-kube-release]
name=Copr repo for kube-release owned by jasonbrooks
baseurl=https://copr-be.cloud.fedoraproject.org/results/jasonbrooks/kube-release/epel-7-x86_64/
type=rpm-md
skip_if_unavailable=True
gpgcheck=1
gpgkey=https://copr-be.cloud.fedoraproject.org/results/jasonbrooks/kube-release/pubkey.gpg
repo_gpgcheck=0
enabled=1
enabled_metadata=1
EOF

# rpm-ostree pkg-add --reboot kubelet kubeadm kubectl kubernetes-cni

These steps start the kubelet service, put selinux into permissive mode, which, according to this doc page should soon not be necessary, and initializes the cluster.

# systemctl enable kubelet.service --now

# setenforce 0

# kubeadm init --use-kubernetes-version "v1.4.3"

This step assigns the master node to also serve as a worker, and then deploys the weave network plugin on the cluster. To add additional workers, use the kubeadm join command provided when the cluster init operation completed.

# kubectl taint nodes --all dedicated-

# kubectl apply -f https://git.io/weave-kube

When the command kubectl get pods --all-namespaces shows that all of your pods are up and running, the cluster is ready for action.

The kubeadm tool is considered an “alpha” right now, but moving forward, this looks like it could be a great way to come up with an up-to-date kube cluster on atomic hosts. I’ll need to figure out whether my workaround to get kubernetes-cni working is sane enough before building a more official centos or fedora package for this, and I want to figure out how to swap out the project-built, debian-based kubernetes component containers with containers provided by centos or fedora, a topic I’ve written a bit about recently.

update: While the hyperkube containers that I’ve written about in the past were based on debian, the containers that kubeadm downloads appear to be built on busybox.

New CentOS Atomic Host with Package Layering Support

Last week, the CentOS Atomic SIG released an updated version of CentOS Atomic Host (tree version 7.20160818), featuring support for rpm-ostree package layering.

CentOS Atomic Host is available as a VirtualBox or libvirt-formatted Vagrant box, or as an installable ISO, qcow2 or Amazon Machine image. Check out the CentOS wiki for download links and installation instructions, or read on to learn more about what’s new in this release.

http://www.projectatomic.io/blog/2016/08/new-centos-atomic-host-with-package-layering-support/

running kubernetes in containers on atomic

The atomic hosts from CentOS and Fedora earn their “atomic” namesake by providing for atomic, image-based system updates via rpm-ostree, and atomic, image-based application updates via docker containers.

This “system” vs “application” division isn’t set in stone, however. There’s room for system components to move across from the somewhat rigid world of ostree commits to the freer-flowing container side.

In particular, the key atomic host components involved in orchestrating containers across multiple hosts, such as flannel, etcd and kubernetes, could run instead in containers, making life simpler for those looking to test out newer or different versions of these components, or to swap them out for alternatives.

Suraj Deshmukh wrote a post recently about running kubernetes in containers. He wanted to test kubernetes 1.3, for which Fedora packages aren’t yet available, so he turned to the upstream kubernetes-on-docker.

Suraj ran into trouble with flannel and etcd, so he ran those from installed rpms. Flannel can be tricky to run as a docker container, because docker’s own configs must be modified to use flannel, so there’s a bit of a chicken-and-egg situation.

One solution is system containers for atomic, which can be run independently from the docker daemon. Giuseppe Scrivano has built example containers for flannel and for etcd, and in this post, I’m describing how to use these system containers alongside a containerized kubernetes on an atomic host.

setting up flannel and etcd

You need a very recent version of the atomic command. I used a pair of CentOS Atomic Hosts running the “continuous” stream.

The master host needs etcd and flannel:

# atomic pull gscrivano/etcd

# atomic pull gscrivano/flannel

# atomic install --system gscrivano/etcd

With etcd running, we can use it to configure flannel:

# export MASTER_IP=YOUR-MASTER-IP

# runc exec gscrivano-etcd etcdctl set /atomic.io/network/config '{"Network":"172.17.0.0/16"}'

# atomic install --name=flannel --set FLANNELD_ETCD_ENDPOINTS=http://$MASTER_IP:2379 --system gscrivano/flannel

The worker node needs flannel as well:

# export MASTER_IP=YOUR-MASTER-IP

# atomic pull gscrivano/flannel

# atomic install --name=flannel --set ETCD_ENDPOINTS=http://$MASTER_IP:2379 --system gscrivano/flannel

On both the master and the worker, we need to make docker use flannel:

# echo "/usr/libexec/flannel/mk-docker-opts.sh -k DOCKER_NETWORK_OPTIONS -d /run/flannel/docker" | runc exec flannel bash

Also on both hosts, we need this docker tweak (because of this):

# cp /usr/lib/systemd/system/docker.service /etc/systemd/system/

# sed -i s/MountFlags=slave/MountFlags=/g /etc/systemd/system/docker.service

# systemctl daemon-reload

# systemctl restart docker

On both hosts, some context tweaks to make SELinux happy:

# mkdir -p /var/lib/kubelet/

# chcon -R -t svirt_sandbox_file_t /var/lib/kubelet/

# chcon -R -t svirt_sandbox_file_t /var/lib/docker/

setting up kube

With flannel and etcd running in system containers, and with docker configured properly, we can start up kubernetes in containers. I’ve pulled the following docker run commands from the docker-multinode scripts in the kubernetes project’s kube-deploy repository.

On the master:

# docker run -d \
--net=host \
--pid=host \
--privileged \
--restart="unless-stopped" \
--name kube_kubelet_$(date | md5sum | cut -c-5) \
-v /sys:/sys:rw \
-v /var/run:/var/run:rw \
-v /run:/run:rw \
-v /var/lib/docker:/var/lib/docker:rw \
-v /var/lib/kubelet:/var/lib/kubelet:shared \
-v /var/log/containers:/var/log/containers:rw \
gcr.io/google_containers/hyperkube-amd64:$(curl -sSL "https://storage.googleapis.com/kubernetes-release/release/stable.txt") \
/hyperkube kubelet \
--allow-privileged \
--api-servers=http://localhost:8080 \
--config=/etc/kubernetes/manifests-multi \
--cluster-dns=10.0.0.10 \
--cluster-domain=cluster.local \
--hostname-override=${MASTER_IP} \
--v=2

On the worker:

# export WORKER_IP=YOUR-WORKER-IP

# docker run -d \
--net=host \
--pid=host \
--privileged \
--restart="unless-stopped" \
--name kube_kubelet_$(date | md5sum | cut -c-5) \
-v /sys:/sys:rw \
-v /var/run:/var/run:rw \
-v /run:/run:rw \
-v /var/lib/docker:/var/lib/docker:rw \
-v /var/lib/kubelet:/var/lib/kubelet:shared \
-v /var/log/containers:/var/log/containers:rw \
gcr.io/google_containers/hyperkube-amd64:$(curl -sSL "https://storage.googleapis.com/kubernetes-release/release/stable.txt") \
/hyperkube kubelet \
--allow-privileged \
--api-servers=http://${MASTER_IP}:8080 \
--cluster-dns=10.0.0.10 \
--cluster-domain=cluster.local \
--hostname-override=${WORKER_IP} \
--v=2

# docker run -d \
--net=host \
--privileged \
--name kube_proxy_$(date | md5sum | cut -c-5) \
--restart="unless-stopped" \
gcr.io/google_containers/hyperkube-amd64:$(curl -sSL "https://storage.googleapis.com/kubernetes-release/release/stable.txt") \
/hyperkube proxy \
--master=http://${MASTER_IP}:8080 \
--v=2

get current kubectl

I usually test things out from the master node, so I’ll download the newest stable kubectl binary to there:

# curl -sSL https://storage.googleapis.com/kubernetes-release/release/$(curl -sSL "https://storage.googleapis.com/kubernetes-release/release/stable.txt")/bin/linux/amd64/kubectl > /usr/local/bin/kubectl

# chmod +x /usr/local/bin/kubectl

test it

It takes a few minutes for all the containers to get up and running. Once they are, you can start running kubernetes apps. I typically test with the guestbookgo atomicapp:

# atomic run projectatomic/guestbookgo-atomicapp

Wait a few minutes, until kubectl get pods tells you that your guestbook and redis pods are running, and then:

# kubectl describe service guestbook | grep NodePort

Visiting the NodePort returned above at either my master or worker IP (these kube scripts configure both to serve as workers) gives me this: